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Mars JC, Culjkovic-Kraljacic B, Borden KLB. eIF4E orchestrates mRNA processing, RNA export and translation to modify specific protein production. Nucleus 2024; 15:2360196. [PMID: 38880976 DOI: 10.1080/19491034.2024.2360196] [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: 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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Wang Z, Ding J, Xiao Y, Xiao K, Su P, Dong Z, Zhang Y. Serum extracellular vesicles with NSD1 and FBXO7 mRNA as novel biomarkers for gastric cancer. Clin Biochem 2023; 120:110653. [PMID: 37742869 DOI: 10.1016/j.clinbiochem.2023.110653] [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: 07/14/2023] [Revised: 09/05/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Messenger RNAs (mRNAs) in serum extracellular vesicles (EVs) are effective non-invasive biomarkers for various types of cancer, however, their role as biomarkers for gastric cancer is yet to be investigated. Therefore, the current study was designed to explore their potential as novel biomarkers for gastric cancer. METHODS The mRNAs in serum EVs from four patients with gastric cancer and four healthy controls were investigated. mRNAs in serum EVs were extracted for high-throughput RNA sequencing (RNA-seq). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to predict cancer-related genes. Candidate mRNAs were validated using reverse transcription-quantitative polymerase chain reaction. The diagnostic and prognostic values of mRNAs for gastric cancer were evaluated by receiver operating characteristic (ROC) curves and Kaplan-Meier analysis, respectively. RESULTS RNA-seq revealed 13,229 upregulated and 7,079 downregulated mRNAs in serum EVs. GO and KEGG analyses showed that certain mRNAs were associated with tumorigenesis and progression. From these, 10 were selected according to our criteria (|Fold Change| > 10, P < 0.05). NSD1 was upregulated and FBXO7 was downregulated in patients with gastric cancer compared with the healthy controls. The area under the ROC curves of these two mRNAs combined was 0.84, with a sensitivity of 78 % and a specificity of 92 %. NSD1 and FBXO7 were also associated with tumor size, distal metastasis, and TNM stage. Furthermore, NSD1 expression was strongly associated with prognosis, as revealed from our follow-up studies and online database analysis. However, FBXO7 was only significantly associated with prognosis in our follow-up data. CONCLUSIONS NSD1 and FBXO7 in serum EVs have important roles in gastric cancer and may be useful biomarkers for its diagnosis and prognosis.
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Affiliation(s)
- Zhen Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China; Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, 107 Wenhuaxi Road, Jinan 250012, Shandong, China
| | - Juan Ding
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China; Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, 107 Wenhuaxi Road, Jinan 250012, Shandong, China
| | - Yilei Xiao
- Department of Neurosurgery, Liaocheng People's Hospital, 67 Dongchangxi Road, Liaocheng 252000, Shandong, China
| | - Ke Xiao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China; Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, 107 Wenhuaxi Road, Jinan 250012, Shandong, China
| | - Ping Su
- National Administration of Health Data, Jinan 250000, Shandong, China
| | - Zhaogang Dong
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China; Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, 107 Wenhuaxi Road, Jinan 250012, Shandong, China.
| | - Yi Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China; Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, 107 Wenhuaxi Road, Jinan 250012, Shandong, China.
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3
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Guo J, Zhu Y, Ma X, Shang G, Liu B, Zhang K. Virus Infection and mRNA Nuclear Export. Int J Mol Sci 2023; 24:12593. [PMID: 37628773 PMCID: PMC10454920 DOI: 10.3390/ijms241612593] [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: 04/21/2023] [Revised: 07/29/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Gene expression in eukaryotes begins with transcription in the nucleus, followed by the synthesis of messenger RNA (mRNA), which is then exported to the cytoplasm for its translation into proteins. Along with transcription and translation, mRNA export through the nuclear pore complex (NPC) is an essential regulatory step in eukaryotic gene expression. Multiple factors regulate mRNA export and hence gene expression. Interestingly, proteins from certain types of viruses interact with these factors in infected cells, and such an interaction interferes with the mRNA export of the host cell in favor of viral RNA export. Thus, these viruses hijack the host mRNA nuclear export mechanism, leading to a reduction in host gene expression and the downregulation of immune/antiviral responses. On the other hand, the viral mRNAs successfully evade the host surveillance system and are efficiently exported from the nucleus to the cytoplasm for translation, which enables the continuation of the virus life cycle. Here, we present this review to summarize the mechanisms by which viruses suppress host mRNA nuclear export during infection, as well as the key strategies that viruses use to facilitate their mRNA nuclear export. These studies have revealed new potential antivirals that may be used to inhibit viral mRNA transport and enhance host mRNA nuclear export, thereby promoting host gene expression and immune responses.
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Affiliation(s)
- Jiayin Guo
- University of Chinese Academy of Sciences, Beijing 100049, China; (J.G.); (Y.Z.); (X.M.)
| | - Yaru Zhu
- University of Chinese Academy of Sciences, Beijing 100049, China; (J.G.); (Y.Z.); (X.M.)
| | - Xiaoya Ma
- University of Chinese Academy of Sciences, Beijing 100049, China; (J.G.); (Y.Z.); (X.M.)
| | - Guijun Shang
- Shanxi Provincial Key Laboratory of Protein Structure Determination, Shanxi Academy of Advanced Research and Innovation, Taiyuan 030012, China;
| | - Bo Liu
- Key Laboratory of Molecular Virology and Immunology, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Huashen Institute of Microbes and Infections, Shanghai 200052, China
| | - Ke Zhang
- Key Laboratory of Molecular Virology and Immunology, Chinese Academy of Sciences, Shanghai 200031, China
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4
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Rossi S, Di Salvio M, Balì M, De Simone A, Apolloni S, D’Ambrosi N, Arisi I, Cipressa F, Cozzolino M, Cestra G. C9orf72 Toxic Species Affect ArfGAP-1 Function. Cells 2023; 12:2007. [PMID: 37566088 PMCID: PMC10416972 DOI: 10.3390/cells12152007] [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: 07/15/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/12/2023] Open
Abstract
Compelling evidence indicates that defects in nucleocytoplasmic transport contribute to the pathogenesis of amyotrophic lateral sclerosis (ALS). In particular, hexanucleotide (G4C2) repeat expansions in C9orf72, the most common cause of genetic ALS, have a widespread impact on the transport machinery that regulates the nucleocytoplasmic distribution of proteins and RNAs. We previously reported that the expression of G4C2 hexanucleotide repeats in cultured human and mouse cells caused a marked accumulation of poly(A) mRNAs in the cell nuclei. To further characterize the process, we set out to systematically identify the specific mRNAs that are altered in their nucleocytoplasmic distribution in the presence of C9orf72-ALS RNA repeats. Interestingly, pathway analysis showed that the mRNAs involved in membrane trafficking are particularly enriched among the identified mRNAs. Most importantly, functional studies in cultured cells and Drosophila indicated that C9orf72 toxic species affect the membrane trafficking route regulated by ADP-Ribosylation Factor 1 GTPase Activating Protein (ArfGAP-1), which exerts its GTPase-activating function on the small GTPase ADP-ribosylation factor 1 to dissociate coat proteins from Golgi-derived vesicles. We demonstrate that the function of ArfGAP-1 is specifically affected by expanded C9orf72 RNA repeats, as well as by C9orf72-related dipeptide repeat proteins (C9-DPRs), indicating the retrograde Golgi-to-ER vesicle-mediated transport as a target of C9orf72 toxicity.
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Affiliation(s)
- Simona Rossi
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), 00133 Rome, Italy; (S.R.); (I.A.)
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy;
| | - Michela Di Salvio
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), 00185 Rome, Italy;
| | - Marilisa Balì
- Department of Biology and Biotechnology, University of Rome “La Sapienza”, 00185 Rome, Italy; (M.B.); (A.D.S.)
| | - Assia De Simone
- Department of Biology and Biotechnology, University of Rome “La Sapienza”, 00185 Rome, Italy; (M.B.); (A.D.S.)
| | - Savina Apolloni
- Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy;
| | - Nadia D’Ambrosi
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy;
- Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy;
| | - Ivan Arisi
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), 00133 Rome, Italy; (S.R.); (I.A.)
- European Brain Research Institute “Rita Levi-Montalcini”, 00161 Rome, Italy
| | - Francesca Cipressa
- Department of Ecological and Biological Science, University of Tuscia, 01100 Viterbo, Italy;
| | - Mauro Cozzolino
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), 00133 Rome, Italy; (S.R.); (I.A.)
| | - Gianluca Cestra
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy;
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), 00185 Rome, Italy;
- Department of Biology and Biotechnology, University of Rome “La Sapienza”, 00185 Rome, Italy; (M.B.); (A.D.S.)
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Chou YJ, Lin CC, Hsu YC, Syu JL, Tseng LM, Chiu JH, Lo JF, Lin CH, Fu SL. Andrographolide suppresses the malignancy of triple-negative breast cancer by reducing THOC1-promoted cancer stem cell characteristics. Biochem Pharmacol 2022; 206:115327. [PMID: 36330949 DOI: 10.1016/j.bcp.2022.115327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 12/14/2022]
Abstract
Triple-negative breast cancers (TNBCs) are difficult to cure and currently lack of effective treatment strategies. Cancer stem cells (CSCs) are highly associated with the poor clinical outcome of TNBCs. Thoc1 is a core component of the THO complex (THOC) that regulates the elongation, processing and nuclear export of mRNA. The function of thoc1 in TNBC and whether Thoc1 serves as a drug target are poorly understood. In this study, we demonstrated that thoc1 expression is elevated in TNBC cell lines and human TNBC patient tissues. Knockdown of thoc1 decreased cancer stem cell populations, reduced mammosphere formation, impaired THOC function, and downregulated the expression of stemness-related proteins. Moreover, the thoc1-knockdown 4T1 cells showed less lung metastasis in an orthotopic breast cancer mouse model. Overexpression of Thoc1 promoted TNBC malignancy and the mRNA export of stemness-related genes. Furthermore, treatment of TNBC cells with the natural compound andrographolide reduced the expression of Thoc1 expression, impaired homeostasis of THOC, suppressed CSC properties, and delayed tumor growth in a 4T1-implanted orthotopic mouse model. Andrographolide also reduced the activity of NF-κB, an upstream transcriptional regulator of Thoc1. Notably, thoc1 overexpression attenuates andrographolide-suppressed cellular proliferation. Altogether, our results demonstrate that THOC1 promotes cancer stem cell characteristics of TNBC, and andrographolide is a potential natural compound for eliminating CSCs of TNBCs by downregulating the NF-κB-thoc1 axis.
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Affiliation(s)
- Yi-Ju Chou
- Program in Molecular Medicine, School of Life Sciences, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 11221, Taiwan
| | - Ching-Cheng Lin
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Ya-Chi Hsu
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Jia-Ling Syu
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jen-Hwey Chiu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jeng-Fan Lo
- Institute of Oral Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Chao-Hsiung Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Shu-Ling Fu
- Program in Molecular Medicine, School of Life Sciences, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 11221, Taiwan; Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.
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6
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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] [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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7
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Muñoz-Ayala A, Chimal-Vega B, García-González V. Translation initiation and its relationship with metabolic mechanisms in cancer development, progression and chemoresistance. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:111-141. [PMID: 36088073 DOI: 10.1016/bs.apcsb.2022.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pathways that regulate protein homeostasis (proteostasis) in cells range from mRNA processing to protein degradation; perturbations in regulatory mechanisms of these pathways can lead to oncogenic cellular processes. Protein synthesis modulation failures are common phenomena in cancer cells, wherein specific conditions that promote the translation of protein factors promoting carcinogenesis are present. These specific conditions may be favored by metabolic lipid alterations like those found in metabolic syndrome and obesity. Protein translation modifications have been described in obesity, favoring the translation of protein targets that benefit lipid accumulation; a determining factor is the activity of the cap-binding eukaryotic translation initiation factor 4E (eIF4E), a crosstalk in protein translation and lipogenesis. Besides, alterations of protein translation initiation steps are critical participants for the development of both pathogenic conditions, cancer, and obesity. This chapter is focused on the regulation of recognition and processing of carcinogenic-mRNA and the connections among lipid metabolism and cell signaling pathways that promote oncogenesis, tumoral microenvironment generation and potentially the development of chemoresistance. We performed an in-depth analysis of events, such as those occurring in obesity and dyslipidemias, that may influence protein translation, driving the recognition of certain mRNAs and favoring cancer development and chemoresistance.
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Affiliation(s)
- Andrea Muñoz-Ayala
- Departamento de Bioquímica, Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali, México; Laboratorio Multidisciplinario de Estudios Metabólicos y Cáncer, Universidad Autónoma de Baja California, Mexicali, México
| | - Brenda Chimal-Vega
- Departamento de Bioquímica, Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali, México; Laboratorio Multidisciplinario de Estudios Metabólicos y Cáncer, Universidad Autónoma de Baja California, Mexicali, México
| | - Victor García-González
- Departamento de Bioquímica, Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali, México; Laboratorio Multidisciplinario de Estudios Metabólicos y Cáncer, Universidad Autónoma de Baja California, Mexicali, México.
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8
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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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Chen BR, Wei TW, Tang CP, Sun JT, Shan TK, Fan Y, Yang TT, Li YF, Ma Y, Wang SB, Wang ZM, Wang H, Shi JZ, Liu L, Chen JW, Zhou LH, Du C, Sun R, Wang QM, Wang LS. MNK2-eIF4E axis promotes cardiac repair in the infarcted mouse heart by activating cyclin D1. J Mol Cell Cardiol 2022; 166:91-106. [DOI: 10.1016/j.yjmcc.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 10/19/2022]
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10
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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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Control of the eIF4E activity: structural insights and pharmacological implications. Cell Mol Life Sci 2021; 78:6869-6885. [PMID: 34541613 PMCID: PMC8558276 DOI: 10.1007/s00018-021-03938-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/28/2021] [Accepted: 09/08/2021] [Indexed: 12/17/2022]
Abstract
The central role of eukaryotic translation initiation factor 4E (eIF4E) in controlling mRNA translation has been clearly assessed in the last decades. eIF4E function is essential for numerous physiological processes, such as protein synthesis, cellular growth and differentiation; dysregulation of its activity has been linked to ageing, cancer onset and progression and neurodevelopmental disorders, such as autism spectrum disorder (ASD) and Fragile X Syndrome (FXS). The interaction between eIF4E and the eukaryotic initiation factor 4G (eIF4G) is crucial for the assembly of the translational machinery, the initial step of mRNA translation. A well-characterized group of proteins, named 4E-binding proteins (4E-BPs), inhibits the eIF4E–eIF4G interaction by competing for the same binding site on the eIF4E surface. 4E-BPs and eIF4G share a single canonical motif for the interaction with a conserved hydrophobic patch of eIF4E. However, a second non-canonical and not conserved binding motif was recently detected for eIF4G and several 4E-BPs. Here, we review the structural features of the interaction between eIF4E and its molecular partners eIF4G and 4E-BPs, focusing on the implications of the recent structural and biochemical evidence for the development of new therapeutic strategies. The design of novel eIF4E-targeting molecules that inhibit translation might provide new avenues for the treatment of several conditions.
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12
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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: 10] [Impact Index Per Article: 3.3] [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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The Mammalian Ecdysoneless Protein Interacts with RNA Helicase DDX39A To Regulate Nuclear mRNA Export. Mol Cell Biol 2021; 41:e0010321. [PMID: 33941617 PMCID: PMC8224239 DOI: 10.1128/mcb.00103-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The mammalian orthologue of ecdysoneless (ECD) protein is required for embryogenesis, cell cycle progression, and mitigation of endoplasmic reticulum stress. Here, we identified key components of the mRNA export complexes as binding partners of ECD and characterized the functional interaction of ECD with key mRNA export-related DEAD BOX protein helicase DDX39A. We find that ECD is involved in RNA export through its interaction with DDX39A. ECD knockdown (KD) blocks mRNA export from the nucleus to the cytoplasm, which is rescued by expression of full-length ECD but not an ECD mutant that is defective in interaction with DDX39A. We have previously shown that ECD protein is overexpressed in ErbB2+ breast cancers (BC). In this study, we extended the analyses to two publicly available BC mRNA The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) data sets. In both data sets, ECD mRNA overexpression correlated with short patient survival, specifically ErbB2+ BC. In the METABRIC data set, ECD overexpression also correlated with poor patient survival in triple-negative breast cancer (TNBC). Furthermore, ECD KD in ErbB2+ BC cells led to a decrease in ErbB2 mRNA level due to a block in its nuclear export and was associated with impairment of oncogenic traits. These findings provide novel mechanistic insight into the physiological and pathological functions of ECD.
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Wang Y, Zhang W, Liu W, Huang L, Wang Y, Li D, Wang G, Zhao Z, Chi X, Xue Y, Song Y, Liu X, Zhan Q. Long Noncoding RNA VESTAR Regulates Lymphangiogenesis and Lymph Node Metastasis of Esophageal Squamous Cell Carcinoma by Enhancing VEGFC mRNA Stability. Cancer Res 2021; 81:3187-3199. [PMID: 33771898 DOI: 10.1158/0008-5472.can-20-1713] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 01/04/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022]
Abstract
Lymph node metastasis is one of the most malignant clinical features in patients with esophageal squamous cell carcinoma (ESCC). Understanding the mechanism of lymph node metastasis will provide treatment strategies for patients with ESCC. Long noncoding RNAs (lncRNA) play a critical role in the development and progression of human cancers. However, the role and mechanism of lncRNAs in lymph node metastasis remain largely unknown. Here we show that VEGFC mRNA stability-associated long noncoding RNA (VESTAR) is involved in lymph node metastasis of ESCC. VESTAR was overexpressed in ESCC tissues and was predictive of poor prognosis in patients with ESCC. In ESCC, NXF1 and SRSF3 facilitated nuclear export of VESTAR to the cytoplasm, which was associated with lymph node metastasis. Depletion of VESTAR inhibited ESCC-associated lymphangiogenesis and lymphatic metastasis. Mechanistically, VESTAR directly bound and stabilized VEGFC mRNA. VESTAR also interacted with HuR, a positive regulator of VEGFC mRNA stability, and increased HuR binding to VEGFC mRNA. Our study reveals a novel lncRNA-guided mechanism of lymph node metastasis in ESCC and may provide a potential target for treatment of ESCC lymphatic metastasis. SIGNIFICANCE: These findings illustrate the lncRNA-guided regulation of VEGFC mRNA stability via direct RNA-RNA interactions, highlighting a therapeutic target for patients with ESCC with lymphatic metastasis.
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Affiliation(s)
- Yali Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weimin Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Wenzhong Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Lijie Huang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Dan Li
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guangchao Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zitong Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinming Chi
- Liaoning Key Laboratory of Proteomics, Dalian Medical University, Dalian, China
| | - Yu Xue
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yongmei Song
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuefeng Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China. .,Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Peking University Shenzhen Hospital, Shenzhen, China
| | - Qimin Zhan
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. .,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China.,Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China.,Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences
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15
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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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Bong SM, Bae SH, Song B, Gwak H, Yang SW, Kim S, Nam S, Rajalingam K, Oh SJ, Kim TW, Park S, Jang H, Lee BI. Regulation of mRNA export through API5 and nuclear FGF2 interaction. Nucleic Acids Res 2020; 48:6340-6352. [PMID: 32383752 PMCID: PMC7293033 DOI: 10.1093/nar/gkaa335] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 04/19/2020] [Accepted: 04/22/2020] [Indexed: 01/13/2023] Open
Abstract
API5 (APoptosis Inhibitor 5) and nuclear FGF2 (Fibroblast Growth Factor 2) are upregulated in various human cancers and are correlated with poor prognosis. Although their physical interaction has been identified, the function related to the resulting complex is unknown. Here, we determined the crystal structure of the API5–FGF2 complex and identified critical residues driving the protein interaction. These findings provided a structural basis for the nuclear localization of the FGF2 isoform lacking a canonical nuclear localization signal and identified a cryptic nuclear localization sequence in FGF2. The interaction between API5 and FGF2 was important for mRNA nuclear export through both the TREX and eIF4E/LRPPRC mRNA export complexes, thus regulating the export of bulk mRNA and specific mRNAs containing eIF4E sensitivity elements, such as c-MYC and cyclin D1. These data show the newly identified molecular function of API5 and nuclear FGF2, and provide a clue to understanding the dynamic regulation of mRNA export.
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Affiliation(s)
- Seoung Min Bong
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi 10408, Republic of Korea
| | - Seung-Hyun Bae
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi 10408, Republic of Korea.,Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang-si, Gyeonggi 10408, Republic of Korea
| | - Bomin Song
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi 10408, Republic of Korea
| | - HyeRan Gwak
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi 10408, Republic of Korea
| | - Seung-Won Yang
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi 10408, Republic of Korea
| | - Sunshin Kim
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi 10408, Republic of Korea
| | - Seungyoon Nam
- Department of Life Sciences, College of BioNano Technology and Department of Genome Medicine and Science, Graduate School of Medicine, Gachon University, Incheon 21565, Republic of Korea
| | | | - Se Jin Oh
- Department of Biomedical Sciences, Graduate School of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Tae Woo Kim
- Department of Biomedical Sciences, Graduate School of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - SangYoun Park
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Hyonchol Jang
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi 10408, Republic of Korea.,Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang-si, Gyeonggi 10408, Republic of Korea
| | - Byung Il Lee
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi 10408, Republic of Korea.,Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang-si, Gyeonggi 10408, Republic of Korea
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17
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Sakai Y, Phimsen S, Okada S, Kuwahara K. The critical role of germinal center-associated nuclear protein in cell biology, immunohematology, and hematolymphoid oncogenesis. Exp Hematol 2020; 90:30-38. [PMID: 32827560 DOI: 10.1016/j.exphem.2020.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/14/2020] [Accepted: 08/16/2020] [Indexed: 11/16/2022]
Abstract
Germinal center-associated nuclear protein (GANP) is a unique and multifunctional protein that plays a critical role in cell biology, neurodegenerative disorders, immunohematology, and oncogenesis. GANP is an orthologue of Saccharomyces Sac3, one of the components of the transcription export 2 (TREX-2) complex and a messenger RNA (mRNA) nuclear export factor. GANP is widely conserved in all mammals, including humans. Although GANP was originally discovered as a molecule upregulated in the germinal centers of secondary lymphoid follicles in peripheral lymphoid organs, it is expressed ubiquitously in many tissues. It serves numerous functions, including making up part of the mammalian TREX-2 complex; mRNA nuclear export via nuclear pores; prevention of R-loop formation, genomic instability, and hyper-recombination; and B-cell affinity maturation. In this review, we first overview the extensive analyses that have revealed the basic functions of GANP and its ancestor molecule Sac3, including mRNA nuclear export and regulation of R-loop formation. We then describe how aberrant expression of GANP is significantly associated with cancer development. Moreover, we discuss a crucial role for GANP in B-cell development, especially affinity maturation in germinal centers. Finally, we illustrate that overexpression of GANP in B cells leads to lymphomagenesis resembling Hodgkin lymphoma derived from germinal center B cells, and that GANP may be involved in transdifferentiation of B cells to macrophages, which strongly affects Hodgkin lymphomagenesis.
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Affiliation(s)
- Yasuhiro Sakai
- Department of Diagnostic Pathology, Fujita Health University School of Medicine, Toyoake, Japan.
| | - Suchada Phimsen
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Seiji Okada
- Division of Hematopoiesis, Joint Research Center for Retroviral Infection, Kumamoto University, Kumamoto, Japan
| | - Kazuhiko Kuwahara
- Department of Diagnostic Pathology, Fujita Health University School of Medicine, Toyoake, Japan.
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18
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Davis MR, Delaleau M, Borden KLB. Nuclear eIF4E Stimulates 3'-End Cleavage of Target RNAs. Cell Rep 2020; 27:1397-1408.e4. [PMID: 31042468 PMCID: PMC6661904 DOI: 10.1016/j.celrep.2019.04.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 02/16/2019] [Accepted: 03/29/2019] [Indexed: 11/27/2022] Open
Abstract
The eukaryotic translation initiation factor eIF4E is nuclear and cytoplasmic where it plays roles in export and translation of specific transcripts, respectively. When we were studying its mRNA export activity, we unexpectedly discovered that eIF4E drives the protein expression of elements of the 3′-end core cleavage complex involved in cleavage and polyadenylation (CPA), including CPSF3, the enzyme responsible for cleavage, as well as its co-factors CPSF1, CPSF2, CPSF4, Symplekin, WDR33, and FIP1L1. Using multiple strategies, we demonstrate that eIF4E stimulates 3′-end cleavage of selected RNAs. eIF4E physically interacts with CPSF3, CPSF1, and uncleaved target RNA, suggesting it acts directly and indirectly on the pathway. Through these effects, eIF4E can generate better substrates for its mRNA export and translation activities. Thus, we identified an unanticipated function for eIF4E in 3′-end processing of specific target RNAs, and this function could potentially affect the expression of a broad range of oncoproteins. Davis et al. demonstrate that the eukaryotic translation initiation factor eIF4E, which is usually associated with nuclear export and translation of specific transcripts, also acts in 3′-end processing of selected RNAs. Through these effects, eIF4E can generate better substrates for its export and translation activities and, thus, modulate the proteome.
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Affiliation(s)
- Margaret Rose Davis
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal, Pavillon Marcelle-Coutu, 2950 Chemin de Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Mildred Delaleau
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal, Pavillon Marcelle-Coutu, 2950 Chemin de Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Katherine L B Borden
- Institute of Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal, Pavillon Marcelle-Coutu, 2950 Chemin de Polytechnique, Montreal, QC H3T 1J4, Canada.
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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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20
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Okazaki R, Yamazoe K, Inoue YH. Nuclear Export of Cyclin B Mediated by the Nup62 Complex Is Required for Meiotic Initiation in Drosophila Males. Cells 2020; 9:E270. [PMID: 31979075 PMCID: PMC7072204 DOI: 10.3390/cells9020270] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The central channel of the nuclear pore complex plays an important role in the selective transport of proteins between the nucleus and cytoplasm. Previous studies have demonstrated that the depletion of the Nup62 complex, constructing the nuclear pore channel in premeiotic Drosophila cells, resulted in the absence of meiotic cells. We attempted to understand the mechanism underlying the cell cycle arrest before meiosis. METHODS We induced dsRNAs against the nucleoporin mRNAs using the Gal4/UAS system in Drosophila. RESULTS The cell cycle of the Nup62-depleted cells was arrested before meiosis without CDK1 activation. The ectopic over-expression of CycB, but not constitutively active CDK1, resulted in partial rescue from the arrest. CycB continued to exist in the nuclei of Nup62-depleted cells and cells depleted of exportin encoded by emb. Protein complexes containing CycB, Emb, and Nup62 were observed in premeiotic spermatocytes. CycB, which had temporally entered the nucleus, was associated with Emb, and the complex was transported back to the cytoplasm through the central channel, interacting with the Nup62 complex. Conclusion: We proposed that CycB is exported with Emb through the channel interacting with the Nup62 complex before the onset of meiosis. The nuclear export ensures the modification and formation of sufficient CycB-CDK1 in the cytoplasm.
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Affiliation(s)
| | | | - Yoshihiro H. Inoue
- Department of Insect Biomedical Research, Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Kyoto, Japan; (R.O.); (K.Y.)
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21
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Structural studies of the eIF4E-VPg complex reveal a direct competition for capped RNA: Implications for translation. Proc Natl Acad Sci U S A 2019; 116:24056-24065. [PMID: 31712417 DOI: 10.1073/pnas.1904752116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Viruses have transformed our understanding of mammalian RNA processing, including facilitating the discovery of the methyl-7-guanosine (m7G) cap on the 5' end of RNAs. The m7G cap is required for RNAs to bind the eukaryotic translation initiation factor eIF4E and associate with the translation machinery across plant and animal kingdoms. The potyvirus-derived viral genome-linked protein (VPg) is covalently bound to the 5' end of viral genomic RNA (gRNA) and associates with host eIF4E for successful infection. Divergent models to explain these observations proposed either an unknown mode of eIF4E engagement or a competition of VPg for the m7G cap-binding site. To dissect these possibilities, we resolved the structure of VPg, revealing a previously unknown 3-dimensional (3D) fold, and characterized the VPg-eIF4E complex using NMR and biophysical techniques. VPg directly bound the cap-binding site of eIF4E and competed for m7G cap analog binding. In human cells, VPg inhibited eIF4E-dependent RNA export, translation, and oncogenic transformation. Moreover, VPg formed trimeric complexes with eIF4E-eIF4G, eIF4E bound VPg-luciferase RNA conjugates, and these VPg-RNA conjugates were templates for translation. Informatic analyses revealed structural similarities between VPg and the human kinesin EG5. Consistently, EG5 directly bound eIF4E in a similar manner to VPg, demonstrating that this form of engagement is relevant beyond potyviruses. In all, we revealed an unprecedented modality for control and engagement of eIF4E and show that VPg-RNA conjugates functionally engage eIF4E. As such, potyvirus VPg provides a unique model system to interrogate eIF4E.
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22
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Hernández-Lemus E, Reyes-Gopar H, Espinal-Enríquez J, Ochoa S. The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook. Genes (Basel) 2019; 10:E865. [PMID: 31671657 PMCID: PMC6896122 DOI: 10.3390/genes10110865] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 12/16/2022] Open
Abstract
Cancer is a complex disease at many different levels. The molecular phenomenology of cancer is also quite rich. The mutational and genomic origins of cancer and their downstream effects on processes such as the reprogramming of the gene regulatory control and the molecular pathways depending on such control have been recognized as central to the characterization of the disease. More important though is the understanding of their causes, prognosis, and therapeutics. There is a multitude of factors associated with anomalous control of gene expression in cancer. Many of these factors are now amenable to be studied comprehensively by means of experiments based on diverse omic technologies. However, characterizing each dimension of the phenomenon individually has proven to fall short in presenting a clear picture of expression regulation as a whole. In this review article, we discuss some of the more relevant factors affecting gene expression control both, under normal conditions and in tumor settings. We describe the different omic approaches that we can use as well as the computational genomic analysis needed to track down these factors. Then we present theoretical and computational frameworks developed to integrate the amount of diverse information provided by such single-omic analyses. We contextualize this within a systems biology-based multi-omic regulation setting, aimed at better understanding the complex interplay of gene expression deregulation in cancer.
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Affiliation(s)
- Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Helena Reyes-Gopar
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
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Reduction of mRNA export unmasks different tissue sensitivities to low mRNA levels during Caenorhabditis elegans development. PLoS Genet 2019; 15:e1008338. [PMID: 31525188 PMCID: PMC6762213 DOI: 10.1371/journal.pgen.1008338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 09/26/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022] Open
Abstract
Animal development requires the execution of specific transcriptional programs in different sets of cells to build tissues and functional organs. Transcripts are exported from the nucleus to the cytoplasm where they are translated into proteins that, ultimately, carry out the cellular functions. Here we show that in Caenorhabditis elegans, reduction of mRNA export strongly affects epithelial morphogenesis and germline proliferation while other tissues remain relatively unaffected. Epithelialization and gamete formation demand a large number of transcripts in the cytoplasm for the duration of these processes. In addition, our findings highlight the existence of a regulatory feedback mechanism that activates gene expression in response to low levels of cytoplasmic mRNA. We expand the genetic characterization of nuclear export factor NXF-1 to other members of the mRNA export pathway to model mRNA export and recycling of NXF-1 back to the nucleus. Our model explains how mutations in genes involved in general processes, such as mRNA export, may result in tissue-specific developmental phenotypes. The Central Dogma of Biology schematically highlights the transmission of genetic information stored in DNA, through RNA, to the formation of proteins. This general flow implicates RNA export from the nucleus to the cytoplasm and proper protein localization within the eukaryotic cell. Ultimately, proteins are the cell’s structural and catalytic functional units. As a result, cells differentiate into one cell type or another (such as epithelial, muscle, neuron…) and exhibit specific shape and functionality. Here we describe, in a C. elegans model, how mutations in genes involved in a general and ubiquitous mechanism, such as mRNA export, may result in tissue-specific developmental phenotypes that show up in processes that are highly demanding of cytoplasmic transcripts like epithelialization and gamete formation. A deep understanding of the mechanisms underlying the "connectors" shown in the Central Dogma of Biology is key both to unravel the general genetic control of an organism’s development and, at the same time, contribute to a better understanding of tissue-specific diseases.
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24
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Xie Y, Ren Y. Mechanisms of nuclear mRNA export: A structural perspective. Traffic 2019; 20:829-840. [PMID: 31513326 DOI: 10.1111/tra.12691] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 08/26/2019] [Indexed: 12/28/2022]
Abstract
Export of mRNA from the nucleus to the cytoplasm is a critical process for all eukaryotic gene expression. As mRNA is synthesized, it is packaged with a myriad of RNA-binding proteins to form ribonucleoprotein particles (mRNPs). For each step in the processes of maturation and export, mRNPs must have the correct complement of proteins. Much of the mRNA export pathway revolves around the heterodimeric export receptor yeast Mex67•Mtr2/human NXF1•NXT1, which is recruited to signal the completion of nuclear mRNP assembly, mediates mRNP targeting/translocation through the nuclear pore complex (NPC), and is displaced at the cytoplasmic side of the NPC to release the mRNP into the cytoplasm. Directionality of the transport is governed by at least two DEAD-box ATPases, yeast Sub2/human UAP56 in the nucleus and yeast Dbp5/human DDX19 at the cytoplasmic side of the NPC, which respectively mediate the association and dissociation of Mex67•Mtr2/NXF1•NXT1 onto the mRNP. Here we review recent progress from structural studies of key constituents in different steps of nuclear mRNA export. These findings have laid the foundation for further studies to obtain a comprehensive mechanistic view of the mRNA export pathway.
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Affiliation(s)
- Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
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25
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Tian Q, Zhao G, Sun Y, Yuan D, Guo Q, Zhang Y, Liu J, Zhang S. Exportin-1 is required for the maintenance of the planarian epidermal lineage. Int J Biol Macromol 2019; 126:1050-1055. [PMID: 30615964 DOI: 10.1016/j.ijbiomac.2019.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 01/27/2023]
Abstract
Nucleocytoplasmic transport is essential for normal cellular function that mediates cargo transport from the cytoplasm to the nucleus. However, the mechanisms of nucleocytoplasmic transport that integrate stem cell development remain largely unknown. Since it has a large population of stem cells, the planarian flatworm is an ideal system for the study of adult stem cell lineage development in vivo. Here, we focus on exportin-1, which is the most conserved nuclear export receptor. Homologs of exportin-1 have no currently known role in stem cell biology. RNA interference targeting exportin-1 caused a failure in anterior and posterior regeneration, and resulted in curly and lysis phenotypes in both intact and regenerating flatworms. During the course of exportin-1 RNAi phenotype, cell division was significantly decreased, and the expression of the epidermal cell markers (vimentin and laminB) were lost from the intact body. Additionally, the expression levels of the neoblast marker piwiA decreased. By contrast, the expression levels of the epidermal progenitor markers NB21.11e and AGAT1 increased. These results suggest that exportin-1 is required for the maintenance of the epidermal lineage in planarians. Inhibition of exportin-1 could promote the premature differentiation of neoblasts to the epidermal lineages, disrupting the proper epidermal maturation.
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Affiliation(s)
- Qingnan Tian
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Guixia Zhao
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yujia Sun
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Dandan Yuan
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Qi Guo
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yizhe Zhang
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiaqian Liu
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China.
| | - Shoutao Zhang
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China; Henan Key Laboratory of Bioactive Macromolecules, Zhengzhou, Henan, China.
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Oh JH, Lee JY, Yu S, Cho Y, Hur S, Nam KT, Kim MH. RAE1 mediated ZEB1 expression promotes epithelial-mesenchymal transition in breast cancer. Sci Rep 2019; 9:2977. [PMID: 30814639 PMCID: PMC6393568 DOI: 10.1038/s41598-019-39574-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/24/2019] [Indexed: 12/21/2022] Open
Abstract
Breast cancer metastasis accounts for most of the deaths from breast cancer. Since epithelial-mesenchymal transition (EMT) plays an important role in promoting metastasis of cancer, many mechanisms regarding EMT have been studied. We previously showed that Ribonucleic acid export 1 (RAE1) is dysregulated in breast cancer and its overexpression leads to aggressive breast cancer phenotypes by inducing EMT. Here, we evaluated the functional capacity of RAE1 in breast cancer metastasis by using a three-dimensional (3D) culture system and xenograft models. Furthermore, to investigate the mechanisms of RAE1-driven EMT, in vitro studies were carried out. The induction of EMT with RAE1-overexpression was confirmed under the 3D culture system and in vivo system. Importantly, RAE1 mediates upregulation of an EMT marker ZEB1, by binding to the promoter region of ZEB1. Knockdown of ZEB1 in RAE1-overexpressing cells suppressed invasive and migratory behaviors, accompanied by an increase in epithelial and a decrease in mesenchymal markers. Taken together, these data demonstrate that RAE1 contributes to breast cancer metastasis by regulating a key EMT-inducing factor ZEB1 expression, suggesting its potential as a therapeutic target.
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Affiliation(s)
- Ji Hoon Oh
- Department of Anatomy, Embryology Laboratory, Yonsei University College of Medicine, Seoul, 03722, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Ji-Yeon Lee
- Department of Anatomy, Embryology Laboratory, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Sungsook Yu
- Severance Biomedical Science Institute and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Yejin Cho
- Severance Biomedical Science Institute and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Sumin Hur
- Severance Biomedical Science Institute and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Ki Taek Nam
- Severance Biomedical Science Institute and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Korea.
| | - Myoung Hee Kim
- Department of Anatomy, Embryology Laboratory, Yonsei University College of Medicine, Seoul, 03722, Korea. .,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Korea.
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Culjkovic-Kraljacic B, Borden KLB. The Impact of Post-transcriptional Control: Better Living Through RNA Regulons. Front Genet 2018; 9:512. [PMID: 30455716 PMCID: PMC6230556 DOI: 10.3389/fgene.2018.00512] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 10/12/2018] [Indexed: 12/26/2022] Open
Abstract
Traditionally, cancer is viewed as a disease driven by genetic mutations and/or epigenetic and transcriptional dysregulation. While these are undoubtedly important drivers, many recent studies highlight the disconnect between the proteome and the genome or transcriptome. At least in part, this disconnect arises as a result of dysregulated RNA metabolism which underpins the altered proteomic landscape observed. Thus, it is important to understand the basic mechanisms governing post-transcriptional control and how these processes can be co-opted to drive cancer cell phenotypes. In some cases, groups of mRNAs that encode protein involved in specific oncogenic processes can be co-regulated at multiple processing levels in order to turn on entire biochemical pathways. Indeed, the RNA regulon model was postulated as a means to understand how cells coordinately regulate transcripts encoding proteins in the same biochemical pathways. In this review, we describe some of the basic mRNA processes that are dysregulated in cancer and the biological impact this has on the cell. This dysregulation can affect networks of RNAs simultaneously thereby underpinning the oncogenic phenotypes observed.
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Affiliation(s)
- Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
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Schneider-Poetsch T, Yoshida M. Along the Central Dogma-Controlling Gene Expression with Small Molecules. Annu Rev Biochem 2018; 87:391-420. [PMID: 29727582 DOI: 10.1146/annurev-biochem-060614-033923] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The central dogma of molecular biology, that DNA is transcribed into RNA and RNA translated into protein, was coined in the early days of modern biology. Back in the 1950s and 1960s, bacterial genetics first opened the way toward understanding life as the genetically encoded interaction of macromolecules. As molecular biology progressed and our knowledge of gene control deepened, it became increasingly clear that expression relied on many more levels of regulation. In the process of dissecting mechanisms of gene expression, specific small-molecule inhibitors played an important role and became valuable tools of investigation. Small molecules offer significant advantages over genetic tools, as they allow inhibiting a process at any desired time point, whereas mutating or altering the gene of an important regulator would likely result in a dead organism. With the advent of modern sequencing technology, it has become possible to monitor global cellular effects of small-molecule treatment and thereby overcome the limitations of classical biochemistry, which usually looks at a biological system in isolation. This review focuses on several molecules, especially natural products, that have played an important role in dissecting gene expression and have opened up new fields of investigation as well as clinical venues for disease treatment.
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Affiliation(s)
- Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan;
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan; .,Department of Biotechnology, University of Tokyo, Tokyo 113-8657, Japan
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Hautbergue GM. RNA Nuclear Export: From Neurological Disorders to Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1007:89-109. [PMID: 28840554 DOI: 10.1007/978-3-319-60733-7_6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The presence of a nuclear envelope, also known as nuclear membrane, defines the structural framework of all eukaryotic cells by separating the nucleus, which contains the genetic material, from the cytoplasm where the synthesis of proteins takes place. Translation of proteins in Eukaryotes is thus dependent on the active transport of DNA-encoded RNA molecules through pores embedded within the nuclear membrane. Several mechanisms are involved in this process generally referred to as RNA nuclear export or nucleocytoplasmic transport of RNA. The regulated expression of genes requires the nuclear export of protein-coding messenger RNA molecules (mRNAs) as well as non-coding RNAs (ncRNAs) together with proteins and pre-assembled ribosomal subunits. The nuclear export of mRNAs is intrinsically linked to the co-transcriptional processing of nascent transcripts synthesized by the RNA polymerase II. This functional coupling is essential for the survival of cells allowing for timely nuclear export of fully processed transcripts, which could otherwise cause the translation of abnormal proteins such as the polymeric repeat proteins produced in some neurodegenerative diseases. Alterations of the mRNA nuclear export pathways can also lead to genome instability and to various forms of cancer. This chapter will describe the molecular mechanisms driving the nuclear export of RNAs with a particular emphasis on mRNAs. It will also review their known alterations in neurological disorders and cancer, and the recent opportunities they offer for the potential development of novel therapeutic strategies.
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Affiliation(s)
- Guillaume M Hautbergue
- RNA Biology Laboratory, Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield, S10 2HQ, UK.
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31
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Piserà A, Campo A, Campo S. Structure and functions of the translation initiation factor eIF4E and its role in cancer development and treatment. J Genet Genomics 2018; 45:13-24. [DOI: 10.1016/j.jgg.2018.01.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 12/22/2022]
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Zahreddine HA, Culjkovic-Kraljacic B, Emond A, Pettersson F, Midura R, Lauer M, Del Rincon S, Cali V, Assouline S, Miller WH, Hascall V, Borden KL. The eukaryotic translation initiation factor eIF4E harnesses hyaluronan production to drive its malignant activity. eLife 2017; 6:29830. [PMID: 29111978 PMCID: PMC5705209 DOI: 10.7554/elife.29830] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 11/03/2017] [Indexed: 01/03/2023] Open
Abstract
The microenvironment provides a functional substratum supporting tumour growth. Hyaluronan (HA) is a major component of this structure. While the role of HA in malignancy is well-defined, the mechanisms driving its biosynthesis in cancer are poorly understood. We show that the eukaryotic translation initiation factor eIF4E, an oncoprotein, drives HA biosynthesis. eIF4E stimulates production of enzymes that synthesize the building blocks of HA, UDP-Glucuronic acid and UDP-N-Acetyl-Glucosamine, as well as hyaluronic acid synthase which forms the disaccharide chain. Strikingly, eIF4E inhibition alone repressed HA levels as effectively as directly targeting HA with hyaluronidase. Unusually, HA was retained on the surface of high-eIF4E cells, rather than being extruded into the extracellular space. Surface-associated HA was required for eIF4E’s oncogenic activities suggesting that eIF4E potentiates an oncogenic HA program. These studies provide unique insights into the mechanisms driving HA production and demonstrate that an oncoprotein can co-opt HA biosynthesis to drive malignancy.
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Affiliation(s)
- Hiba Ahmad Zahreddine
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, Université de Montréal, Québec, Canada
| | - Biljana Culjkovic-Kraljacic
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, Université de Montréal, Québec, Canada
| | - Audrey Emond
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Québec, Canada
| | - Filippa Pettersson
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Québec, Canada
| | - Ronald Midura
- Orthopaedic Research Center, The Cleveland Clinic Foundation, Cleveland, United States.,Department of Biomedical Engineering, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, United States
| | - Mark Lauer
- Orthopaedic Research Center, The Cleveland Clinic Foundation, Cleveland, United States.,Department of Biomedical Engineering, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, United States
| | - Sonia Del Rincon
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Québec, Canada
| | - Valbona Cali
- Orthopaedic Research Center, The Cleveland Clinic Foundation, Cleveland, United States.,Department of Biomedical Engineering, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, United States
| | - Sarit Assouline
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Québec, Canada
| | - Wilson H Miller
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Québec, Canada
| | - Vincent Hascall
- Orthopaedic Research Center, The Cleveland Clinic Foundation, Cleveland, United States.,Department of Biomedical Engineering, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, United States
| | - Katherine Lb Borden
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, Université de Montréal, Québec, Canada
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Martins RP, Fåhraeus R. A matter of maturity: The impact of pre-mRNA processing in gene expression and antigen presentation. Int J Biochem Cell Biol 2017; 91:203-211. [PMID: 28549625 DOI: 10.1016/j.biocel.2017.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/15/2017] [Accepted: 05/18/2017] [Indexed: 12/28/2022]
Abstract
RNA processing plays a pivotal role in the diversification of high eukaryotes transcriptome and proteome. The expression of gene products controlling a variety of cellular and physiological processes depends largely on a complex maturation process undergone by pre-mRNAs to become translation-competent mRNAs. Here we review the different mechanisms involved in the pre-mRNA processing and disclose their impact in the gene regulation process in eukaryotic cells. We describe some viral strategies targeting pre-mRNA processing to control gene expression and host immune response and discuss their relevance as tools for a better understanding of cell biology. Finally, we highlight accumulating evidences toward the occurrence of a translation event coupled to mRNA biogenesis in the nuclear compartment and argue how this is relevant for the production of antigenic peptide substrates for the major histocompatibility complex class I pathway.
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Affiliation(s)
- Rodrigo Prado Martins
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 rue Juliette Dodu, 75010 Paris, France.
| | - Robin Fåhraeus
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, 27 rue Juliette Dodu, 75010 Paris, France; Department of Medical Biosciences, Umeå University, Umeå, Sweden; RECAMO, Masaryk Memorial Cancer Institute, Brno, Czech Republic
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Björk P, Wieslander L. Integration of mRNP formation and export. Cell Mol Life Sci 2017; 74:2875-2897. [PMID: 28314893 PMCID: PMC5501912 DOI: 10.1007/s00018-017-2503-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 12/13/2022]
Abstract
Expression of protein-coding genes in eukaryotes relies on the coordinated action of many sophisticated molecular machineries. Transcription produces precursor mRNAs (pre-mRNAs) and the active gene provides an environment in which the pre-mRNAs are processed, folded, and assembled into RNA–protein (RNP) complexes. The dynamic pre-mRNPs incorporate the growing transcript, proteins, and the processing machineries, as well as the specific protein marks left after processing that are essential for export and the cytoplasmic fate of the mRNPs. After release from the gene, the mRNPs move by diffusion within the interchromatin compartment, making up pools of mRNPs. Here, splicing and polyadenylation can be completed and the mRNPs recruit the major export receptor NXF1. Export competent mRNPs interact with the nuclear pore complex, leading to export, concomitant with compositional and conformational changes of the mRNPs. We summarize the integrated nuclear processes involved in the formation and export of mRNPs.
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Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
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Cai W, Xiong Chen Z, Rane G, Satendra Singh S, Choo Z, Wang C, Yuan Y, Zea Tan T, Arfuso F, Yap CT, Pongor LS, Yang H, Lee MB, Cher Goh B, Sethi G, Benoukraf T, Tergaonkar V, Prem Kumar A. Wanted DEAD/H or Alive: Helicases Winding Up in Cancers. J Natl Cancer Inst 2017; 109:2957323. [PMID: 28122908 DOI: 10.1093/jnci/djw278] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/08/2016] [Accepted: 10/20/2016] [Indexed: 12/23/2022] Open
Abstract
Cancer is one of the most studied areas of human biology over the past century. Despite having attracted much attention, hype, and investments, the search to find a cure for cancer remains an uphill battle. Recent discoveries that challenged the central dogma of molecular biology not only further increase the complexity but also demonstrate how various types of noncoding RNAs such as microRNA and long noncoding RNA, as well as their related processes such as RNA editing, are important in regulating gene expression. Parallel to this aspect, an increasing number of reports have focused on a family of proteins known as DEAD/H-box helicases involved in RNA metabolism, regulation of long and short noncoding RNAs, and novel roles as "editing helicases" and their association with cancers. This review summarizes recent findings on the roles of RNA helicases in various cancers, which are broadly classified into adult solid tumors, childhood solid tumors, leukemia, and cancer stem cells. The potential small molecule inhibitors of helicases and their therapeutic value are also discussed. In addition, analyzing next-generation sequencing data obtained from public portals and reviewing existing literature, we provide new insights on the potential of DEAD/H-box helicases to act as pharmacological drug targets in cancers.
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Affiliation(s)
- Wanpei Cai
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Zhi Xiong Chen
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Grishma Rane
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Shikha Satendra Singh
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Zhang'e Choo
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Chao Wang
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Yi Yuan
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Tuan Zea Tan
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Frank Arfuso
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Celestial T Yap
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Lorinc S Pongor
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Henry Yang
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Martin B Lee
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Boon Cher Goh
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Gautam Sethi
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Touati Benoukraf
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Vinay Tergaonkar
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Alan Prem Kumar
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
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Schunter AJ, Yue X, Hummon AB. Phosphoproteomics of colon cancer metastasis: comparative mass spectrometric analysis of the isogenic primary and metastatic cell lines SW480 and SW620. Anal Bioanal Chem 2016; 409:1749-1763. [PMID: 27987026 DOI: 10.1007/s00216-016-0125-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 11/28/2016] [Indexed: 12/25/2022]
Abstract
The contributions of phosphorylation-mediated signaling networks to colon cancer metastasis are poorly defined. To interrogate constitutive signaling alterations in cancer progression, the global phosphoproteomes of patient-matched SW480 (primary colon tumor origin) and SW620 (lymph node metastasis) cell lines were compared with TiO2 and immobilized metal affinity chromatography phosphopeptide enrichment followed by liquid chromatography-tandem mass spectrometry. Network analysis of the significantly altered phosphosites revealed differential regulation in cellular adhesion, mitosis, and messenger RNA translational machinery. Messenger RNA biogenesis and splicing, transport through the nuclear pores, initiation of translation, and stability and degradation were also affected. Although alterations in these processes have been associated with oncogenic transformation, control of messenger RNA stability has typically not been associated with cancer progression. Notably, the single phosphosite with the greatest relative change in SW620 cells was Ser2 on eukaryotic translation initiation factor 2 subunit 2, suggesting that SW620 cells translate faster or with greater efficiency than SW480 cells. These broad changes in the regulation of translation also occur without overexpression of eukaryotic translation initiation factor 4E. The findings suggest that metastatic cells exhibit constitutive changes to the phosphoproteome, and that messenger RNA stability and translational efficiency may be important targets of deregulation during cancer progression.
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Affiliation(s)
- Alissa J Schunter
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556, USA
| | - Xiaoshan Yue
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556, USA
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556, USA.
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Li Y, Zhang X, Ge J, Liu X, Xu S, Zhu Z, Fang G, Liu J, Zhang H, Sun X. Can Nup88 expression be associated with atypical endometrial hyperplasia and endometrial cancer? A preliminary study. Pathol Res Pract 2016; 212:274-8. [DOI: 10.1016/j.prp.2016.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 12/30/2015] [Accepted: 01/09/2016] [Indexed: 11/26/2022]
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Li P, Noegel AA. Inner nuclear envelope protein SUN1 plays a prominent role in mammalian mRNA export. Nucleic Acids Res 2015; 43:9874-88. [PMID: 26476453 PMCID: PMC4787764 DOI: 10.1093/nar/gkv1058] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 10/01/2015] [Indexed: 11/12/2022] Open
Abstract
Nuclear export of messenger ribonucleoproteins (mRNPs) through the nuclear pore complex (NPC) can be roughly classified into two forms: bulk and specific export, involving an nuclear RNA export factor 1 (NXF1)-dependent pathway and chromosome region maintenance 1 (CRM1)-dependent pathway, respectively. SUN proteins constitute the inner nuclear envelope component of the linker of nucleoskeleton and cytoskeleton (LINC) complex. Here, we show that mammalian cells require SUN1 for efficient nuclear mRNP export. The results indicate that both SUN1 and SUN2 interact with heterogeneous nuclear ribonucleoprotein (hnRNP) F/H and hnRNP K/J. SUN1 depletion inhibits the mRNP export, with accumulations of both hnRNPs and poly(A)+RNA in the nucleus. Leptomycin B treatment indicates that SUN1 functions in mammalian mRNA export involving the NXF1-dependent pathway. SUN1 mediates mRNA export through its association with mRNP complexes via a direct interaction with NXF1. Additionally, SUN1 associates with the NPC through a direct interaction with Nup153, a nuclear pore component involved in mRNA export. Taken together, our results reveal that the inner nuclear envelope protein SUN1 has additional functions aside from being a central component of the LINC complex and that it is an integral component of the mammalian mRNA export pathway suggesting a model whereby SUN1 recruits NXF1-containing mRNP onto the nuclear envelope and hands it over to Nup153.
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Affiliation(s)
- Ping Li
- Institute of Biochemistry I, Medical Faculty, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Cologne, Germany
| | - Angelika A Noegel
- Institute of Biochemistry I, Medical Faculty, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Cologne, Germany
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39
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Dickmanns A, Monecke T, Ficner R. Structural Basis of Targeting the Exportin CRM1 in Cancer. Cells 2015; 4:538-68. [PMID: 26402707 PMCID: PMC4588050 DOI: 10.3390/cells4030538] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/07/2015] [Accepted: 09/11/2015] [Indexed: 12/19/2022] Open
Abstract
Recent studies have demonstrated the interference of nucleocytoplasmic trafficking with the establishment and maintenance of various cancers. Nucleocytoplasmic transport is highly regulated and coordinated, involving different nuclear transport factors or receptors, importins and exportins, that mediate cargo transport from the cytoplasm into the nucleus or the other way round, respectively. The exportin CRM1 (Chromosome region maintenance 1) exports a plethora of different protein cargoes and ribonucleoprotein complexes. Structural and biochemical analyses have enabled the deduction of individual steps of the CRM1 transport cycle. In addition, CRM1 turned out to be a valid target for anticancer drugs as it exports numerous proto-oncoproteins and tumor suppressors. Clearly, detailed understanding of the flexibility, regulatory features and cooperative binding properties of CRM1 for Ran and cargo is a prerequisite for the design of highly effective drugs. The first compound found to inhibit CRM1-dependent nuclear export was the natural drug Leptomycin B (LMB), which blocks export by competitively interacting with a highly conserved cleft on CRM1 required for nuclear export signal recognition. Clinical studies revealed serious side effects of LMB, leading to a search for alternative natural and synthetic drugs and hence a multitude of novel therapeutics. The present review examines recent progress in understanding the binding mode of natural and synthetic compounds and their inhibitory effects.
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Affiliation(s)
- Achim Dickmanns
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, Göttingen 37077, Germany.
| | - Thomas Monecke
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, Göttingen 37077, Germany.
| | - Ralf Ficner
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, Göttingen 37077, Germany.
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40
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Delaleau M, Borden KLB. Multiple Export Mechanisms for mRNAs. Cells 2015; 4:452-73. [PMID: 26343730 PMCID: PMC4588045 DOI: 10.3390/cells4030452] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 12/20/2022] Open
Abstract
Nuclear mRNA export plays an important role in gene expression. We describe the mechanisms of mRNA export including the importance of mRNP assembly, docking with the nuclear basket of the nuclear pore complex (NPC), transit through the central channel of the NPC and cytoplasmic release. We describe multiple mechanisms of mRNA export including NXF1 and CRM1 mediated pathways. Selective groups of mRNAs can be preferentially transported in order to respond to cellular stimuli. RNAs can be selected based on the presence of specific cis-acting RNA elements and binding of specific adaptor proteins. The role that dysregulation of this process plays in human disease is also discussed.
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Affiliation(s)
- Mildred Delaleau
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3C 3J7, Canada.
| | - Katherine L B Borden
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3C 3J7, Canada.
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41
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Dickmanns A, Kehlenbach RH, Fahrenkrog B. Nuclear Pore Complexes and Nucleocytoplasmic Transport: From Structure to Function to Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 320:171-233. [PMID: 26614874 DOI: 10.1016/bs.ircmb.2015.07.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nucleocytoplasmic transport is an essential cellular activity and occurs via nuclear pore complexes (NPCs) that reside in the double membrane of the nuclear envelope. Significant progress has been made during the past few years in unravelling the ultrastructural organization of NPCs and their constituents, the nucleoporins, by cryo-electron tomography and X-ray crystallography. Mass spectrometry and genomic approaches have provided deeper insight into the specific regulation and fine tuning of individual nuclear transport pathways. Recent research has also focused on the roles nucleoporins play in health and disease, some of which go beyond nucleocytoplasmic transport. Here we review emerging results aimed at understanding NPC architecture and nucleocytoplasmic transport at the atomic level, elucidating the specific function individual nucleoporins play in nuclear trafficking, and finally lighting up the contribution of nucleoporins and nuclear transport receptors in human diseases, such as cancer and certain genetic disorders.
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Affiliation(s)
- Achim Dickmanns
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Ralph H Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Göttingen, Göttingen, Germany
| | - Birthe Fahrenkrog
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, Charleroi, Belgium
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42
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Osborne MJ, Borden KLB. The eukaryotic translation initiation factor eIF4E in the nucleus: taking the road less traveled. Immunol Rev 2015; 263:210-23. [PMID: 25510279 DOI: 10.1111/imr.12240] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The eukaryotic translation initiation factor eIF4E is a potent oncogene. Although eIF4E has traditional roles in translation initiation in the cytoplasm, it is also found in the nucleus, suggesting that it has activities beyond its role in protein synthesis. The road less traveled has been taken to study these nuclear activities and to understand their contribution to the oncogenic potential of eIF4E. The molecular features and biological pathways underpinning eIF4E's nuclear mRNA export are described. New classes of eIF4E regulators have been identified and their relevance to cancer shown. The studies presented here reveal the molecular, biophysical, and structural bases for eIF4E regulation. Finally, recent clinical work targeting eIF4E in acute myeloid leukemia patients with ribavirin is discussed. In summary, these findings provide a novel paradigm for eIF4E function and the molecular basis for targeting it in leukemia patients.
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Affiliation(s)
- Michael J Osborne
- Institute for Research in Immunology and Cancer & Dept. of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
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43
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Xu L, Pan L, Li J, Huang B, Feng J, Li C, Wang S, The E, Liu Y, Yuan T, Zhen L, Liang D, Liu Y, Li L, Cui Y, Jiang X, Peng L, Chen YH. Nucleoporin 35 regulates cardiomyocyte pH homeostasis by controlling Na+-H+ exchanger-1 expression. J Mol Cell Biol 2015; 7:476-85. [PMID: 26260029 DOI: 10.1093/jmcb/mjv054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 06/08/2015] [Indexed: 12/23/2022] Open
Abstract
The mammalian nuclear pore complex is comprised of ∼ 30 different nucleoporins (Nups). It governs the nuclear import of gene expression modulators and the export of mRNAs. In cardiomyocytes, Na(+)-H(+) exchanger-1 (NHE1) is an integral membrane protein that exclusively regulates intracellular pH (pHi) by exchanging one intracellular H(+) for one extracellular Na(+). However, the role of Nups in cardiac NHE1 expression remains unknown. We herein report that Nup35 regulates cardiomyocyte NHE1 expression by controlling the nucleo-cytoplasmic trafficking of nhe1 mRNA. The N-terminal domain of Nup35 determines nhe1 mRNA nuclear export by targeting the 5'-UTR (-412 to -213 nt) of nhe1 mRNA. Nup35 ablation weakens the resistance of cardiomyocytes to an acid challenge by depressing NHE1 expression. Moreover, we identify that Nup35 and NHE1 are simultaneously downregulated in ischemic cardiomyocytes both in vivo and in vitro. Enforced expression of Nup35 effectively counteracts the anoxia-induced intracellular acidification. We conclude that Nup35 selectively regulates cardiomyocyte pHi homeostasis by posttranscriptionally controlling NHE1 expression. This finding reveals a novel regulatory mechanism of cardiomyocyte pHi, and may provide insight into the therapeutic strategy for ischemic cardiac diseases.
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Affiliation(s)
- Liang Xu
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Lei Pan
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jun Li
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Bijun Huang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jing Feng
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Changming Li
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Shiyi Wang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Erlinda The
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yuan Liu
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Tianyou Yuan
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Lixiao Zhen
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Dandan Liang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Yi Liu
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Li Li
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Yingyu Cui
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Xiaoyan Jiang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Luying Peng
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Yi-Han Chen
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
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Wickramasinghe VO, Laskey RA. Control of mammalian gene expression by selective mRNA export. Nat Rev Mol Cell Biol 2015; 16:431-42. [PMID: 26081607 DOI: 10.1038/nrm4010] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nuclear export of mRNAs is a crucial step in the regulation of gene expression, linking transcription in the nucleus to translation in the cytoplasm. Although important components of the mRNA export machinery are well characterized, such as transcription-export complexes TREX and TREX-2, recent work has shown that, in some instances, mammalian mRNA export can be selective and can regulate crucial biological processes such as DNA repair, gene expression, maintenance of pluripotency, haematopoiesis, proliferation and cell survival. Such findings show that mRNA export is an unexpected, yet potentially important, mechanism for the control of gene expression and of the mammalian transcriptome.
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Affiliation(s)
- Vihandha O Wickramasinghe
- Medical Research Centre (MRC) Cancer Unit, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Ronald A Laskey
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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Abstract
Cancer cells rapidly evolve a multitude of defense mechanisms to evade the effects of the oncologist's drug arsenal. Unfortunately, clinical strategies to overcome these lag far behind. This mismatch likely underlies our inability to implement new durable treatment strategies. Here, a new form of multidrug resistance, inducible drug glucuronidation, is discussed. This form was discovered while developing means to target a specific oncogene, the eukaryotic translation initiation factor 4E (eIF4E), with its inhibitor ribavirin. In two clinical studies, ribavirin treatment led to substantial clinical responses, but all responding patients eventually relapsed. In most cases, this was due to the overexpression of the sonic hedgehog transcription factor Gli1, which elevated the UDP glucuronsyltransferase UGT1A enzymes. UGT1As add glucuronic acid to many drugs. Indeed, these cells are resistant to not only ribavirin, but also Ara-C, and likely other drugs. Inhibition of Gli1 reduced UGT1As, eliminated drug glucuronides, and renewed sensitivity to ribavirin and Ara-C. These studies highlight that cancer cells and their resistant counterparts metabolize drugs differently from each other as well as from normal cells. Likely, these inducible modifications go beyond glucuronidation. Understanding the extent of inducible drug modifications and the pathways that drive expression of the corresponding enzymatic machinery will better position us to finally make resistance futile.
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Affiliation(s)
- Katherine L B Borden
- Department of Pathology and Cell Biology, Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada.
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46
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Quan B, Qi X, Yu Z, Jiang Y, Liao M, Wang G, Feng R, Zhang L, Chen Z, Jiang Q, Liu G. Pathway analysis of genome-wide association study and transcriptome data highlights new biological pathways in colorectal cancer. Mol Genet Genomics 2014; 290:603-10. [PMID: 25362561 DOI: 10.1007/s00438-014-0945-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 10/17/2014] [Indexed: 12/11/2022]
Abstract
Colorectal cancer (CRC) is a common malignancy that meets the definition of a complex disease. Genome-wide association study (GWAS) has identified several loci of weak predictive value in CRC, however, these do not fully explain the occurrence risk. Recently, gene set analysis has allowed enhanced interpretation of GWAS data in CRC, identifying a number of metabolic pathways as important for disease pathogenesis. Whether there are other important pathways involved in CRC, however, remains unclear. We present a systems analysis of KEGG pathways in CRC using (1) a human CRC GWAS dataset and (2) a human whole transcriptome CRC case-control expression dataset. Analysis of the GWAS dataset revealed significantly enriched KEGG pathways related to metabolism, immune system and diseases, cellular processes, environmental information processing, genetic information processing, and neurodegenerative diseases. Altered gene expression was confirmed in these pathways using the transcriptome dataset. Taken together, these findings not only confirm previous work in this area, but also highlight new biological pathways whose deregulation is critical for CRC. These results contribute to our understanding of disease-causing mechanisms and will prove useful for future genetic and functional studies in CRC.
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Affiliation(s)
- Baoku Quan
- Department of General Surgery, The First Hospital of Harbin, Harbin, China
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47
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Giulietti M, Milantoni SA, Armeni T, Principato G, Piva F. ExportAid: database of RNA elements regulating nuclear RNA export in mammals. Bioinformatics 2014; 31:246-51. [PMID: 25273107 DOI: 10.1093/bioinformatics/btu620] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION Regulation of nuclear mRNA export or retention is carried out by RNA elements but the mechanism is not yet well understood. To understand the mRNA export process, it is important to collect all the involved RNA elements and their trans-acting factors. RESULTS By hand-curated literature screening we collected, in ExportAid database, experimentally assessed data about RNA elements regulating nuclear export or retention of endogenous, heterologous or artificial RNAs in mammalian cells. This database could help to understand the RNA export language and to study the possible export efficiency alterations owing to mutations or polymorphisms. Currently, ExportAid stores 235 and 96 RNA elements, respectively, increasing and decreasing export efficiency, and 98 neutral assessed sequences. AVAILABILITY AND IMPLEMENTATION Freely accessible without registration at http://www.introni.it/ExportAid/ExportAid.html. Database and web interface are implemented in Perl, MySQL, Apache and JavaScript with all major browsers supported.
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Affiliation(s)
- Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona 60131, Italy
| | - Sara Armida Milantoni
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona 60131, Italy
| | - Tatiana Armeni
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona 60131, Italy
| | - Giovanni Principato
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona 60131, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Ancona 60131, Italy
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48
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Bonnet A, Palancade B. Regulation of mRNA trafficking by nuclear pore complexes. Genes (Basel) 2014; 5:767-91. [PMID: 25184662 PMCID: PMC4198930 DOI: 10.3390/genes5030767] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 08/25/2014] [Accepted: 08/26/2014] [Indexed: 11/17/2022] Open
Abstract
Over the last two decades, multiple studies have explored the mechanisms governing mRNA export out of the nucleus, a crucial step in eukaryotic gene expression. During transcription and processing, mRNAs are assembled into messenger ribonucleoparticles (mRNPs). mRNPs are then exported through nuclear pore complexes (NPCs), which are large multiprotein assemblies made of several copies of a limited number of nucleoporins. A considerable effort has been put into the dissection of mRNA export through NPCs at both cellular and molecular levels, revealing the conserved contributions of a subset of nucleoporins in this process, from yeast to vertebrates. Several reports have also demonstrated the ability of NPCs to sort out properly-processed mRNPs for entry into the nuclear export pathway. Importantly, changes in mRNA export have been associated with post-translational modifications of nucleoporins or changes in NPC composition, depending on cell cycle progression, development or exposure to stress. How NPC modifications also impact on cellular mRNA export in disease situations, notably upon viral infection, is discussed.
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Affiliation(s)
- Amandine Bonnet
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité, Paris F-75205, France.
| | - Benoit Palancade
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité, Paris F-75205, France.
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49
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Wang L, Miao YL, Zheng X, Lackford B, Zhou B, Han L, Yao C, Ward JM, Burkholder A, Lipchina I, Fargo DC, Hochedlinger K, Shi Y, Williams CJ, Hu G. The THO complex regulates pluripotency gene mRNA export and controls embryonic stem cell self-renewal and somatic cell reprogramming. Cell Stem Cell 2014; 13:676-90. [PMID: 24315442 DOI: 10.1016/j.stem.2013.10.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/14/2013] [Accepted: 10/16/2013] [Indexed: 12/20/2022]
Abstract
Embryonic stem cell (ESC) self-renewal and differentiation are governed by a broad-ranging regulatory network. Although the transcriptional regulatory mechanisms involved have been investigated extensively, posttranscriptional regulation is still poorly understood. Here we describe a critical role of the THO complex in ESC self-renewal and differentiation. We show that THO preferentially interacts with pluripotency gene transcripts through Thoc5 and is required for self-renewal at least in part by regulating their export and expression. During differentiation, THO loses its interaction with those transcripts due to reduced Thoc5 expression, leading to decreased expression of pluripotency proteins that facilitates exit from self-renewal. THO is also important for the establishment of pluripotency, because its depletion inhibits somatic cell reprogramming and blastocyst development. Together, our data indicate that THO regulates pluripotency gene mRNA export to control ESC self-renewal and differentiation, and therefore uncover a role for this aspect of posttranscriptional regulation in stem cell fate specification.
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Affiliation(s)
- Li Wang
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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50
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Jackson BR, Noerenberg M, Whitehouse A. A novel mechanism inducing genome instability in Kaposi's sarcoma-associated herpesvirus infected cells. PLoS Pathog 2014; 10:e1004098. [PMID: 24788796 PMCID: PMC4006916 DOI: 10.1371/journal.ppat.1004098] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 03/13/2014] [Indexed: 01/05/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic herpesvirus associated with multiple AIDS-related malignancies. Like other herpesviruses, KSHV has a biphasic life cycle and both the lytic and latent phases are required for tumorigenesis. Evidence suggests that KSHV lytic replication can cause genome instability in KSHV-infected cells, although no mechanism has thus far been described. A surprising link has recently been suggested between mRNA export, genome instability and cancer development. Notably, aberrations in the cellular transcription and export complex (hTREX) proteins have been identified in high-grade tumours and these defects contribute to genome instability. We have previously shown that the lytically expressed KSHV ORF57 protein interacts with the complete hTREX complex; therefore, we investigated the possible intriguing link between ORF57, hTREX and KSHV-induced genome instability. Herein, we show that lytically active KSHV infected cells induce a DNA damage response and, importantly, we demonstrate directly that this is due to DNA strand breaks. Furthermore, we show that sequestration of the hTREX complex by the KSHV ORF57 protein leads to this double strand break response and significant DNA damage. Moreover, we describe a novel mechanism showing that the genetic instability observed is a consequence of R-loop formation. Importantly, the link between hTREX sequestration and DNA damage may be a common feature in herpesvirus infection, as a similar phenotype was observed with the herpes simplex virus 1 (HSV-1) ICP27 protein. Our data provide a model of R-loop induced DNA damage in KSHV infected cells and describes a novel system for studying genome instability caused by aberrant hTREX. The hallmarks of cancer comprise the essential elements that permit the formation and development of human tumours. Genome instability is an enabling characteristic that allows the progression of tumorigenesis through genetic mutation and therefore, understanding the molecular causes of genome instability in all cancers is essential for development of therapeutics. The Kaposi's sarcoma-associated herpesvirus (KSHV) is an important human pathogen that causes multiple AIDS-related cancers. Recent studies have shown that during KSHV infection, cells show an increase in a double-strand DNA break marker, signifying a severe form of genome instability. Herein, we show that KSHV infection does cause DNA strand breaks. Moreover, we describe a novel molecular mechanism for genome instability involving the KSHV ORF57 protein interacting with the mRNA export complex, hTREX. We demonstrate that over-expression of ORF57 results in the formation of RNA:DNA hybrids, or R-loops, that lead to an increase in genome instability. DNA strand breaks have been previously reported in herpes simplex, cytomegalovirus and Epstein-Barr virus infected cells. Therefore, as this work describes for the first time the mechanism of R-loop induced genome instability involving a conserved herpesvirus protein, it may have far-reaching implications for other viral RNA export factors.
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Affiliation(s)
- Brian R Jackson
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Marko Noerenberg
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
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