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Dasgupta A, Prensner JR. Upstream open reading frames: new players in the landscape of cancer gene regulation. NAR Cancer 2024; 6:zcae023. [PMID: 38774471 PMCID: PMC11106035 DOI: 10.1093/narcan/zcae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/24/2024] Open
Abstract
The translation of RNA by ribosomes represents a central biological process and one of the most dysregulated processes in cancer. While translation is traditionally thought to occur exclusively in the protein-coding regions of messenger RNAs (mRNAs), recent transcriptome-wide approaches have shown abundant ribosome activity across diverse stretches of RNA transcripts. The most common type of this kind of ribosome activity occurs in gene leader sequences, also known as 5' untranslated regions (UTRs) of the mRNA, that precede the main coding sequence. Translation of these upstream open reading frames (uORFs) is now known to occur in upwards of 25% of all protein-coding genes. With diverse functions from RNA regulation to microprotein generation, uORFs are rapidly igniting a new arena of cancer biology, where they are linked to cancer genetics, cancer signaling, and tumor-immune interactions. This review focuses on the contributions of uORFs and their associated 5'UTR sequences to cancer biology.
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Affiliation(s)
- Anwesha Dasgupta
- Chad Carr Pediatric Brain Tumor Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John R Prensner
- Chad Carr Pediatric Brain Tumor Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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2
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Ruggiero V, Fagioli C, de Pretis S, Di Carlo V, Landsberger N, Zacchetti D. Complex CDKL5 translational regulation and its potential role in CDKL5 deficiency disorder. Front Cell Neurosci 2023; 17:1231493. [PMID: 37964795 PMCID: PMC10642286 DOI: 10.3389/fncel.2023.1231493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/10/2023] [Indexed: 11/16/2023] Open
Abstract
CDKL5 is a kinase with relevant functions in correct neuronal development and in the shaping of synapses. A decrease in its expression or activity leads to a severe neurodevelopmental condition known as CDKL5 deficiency disorder (CDD). CDD arises from CDKL5 mutations that lie in the coding region of the gene. However, the identification of a SNP in the CDKL5 5'UTR in a patient with symptoms consistent with CDD, together with the complexity of the CDKL5 transcript leader, points toward a relevant translational regulation of CDKL5 expression with important consequences in physiological processes as well as in the pathogenesis of CDD. We performed a bioinformatics and molecular analysis of the 5'UTR of CDKL5 to identify translational regulatory features. We propose an important role for structural cis-acting elements, with the involvement of the eukaryotic translational initiation factor eIF4B. By evaluating both cap-dependent and cap-independent translation initiation, we suggest the presence of an IRES supporting the translation of CDKL5 mRNA and propose a pathogenic effect of the C>T -189 SNP in decreasing the translation of the downstream protein.
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Affiliation(s)
- Valeria Ruggiero
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Claudio Fagioli
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefano de Pretis
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valerio Di Carlo
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | - Nicoletta Landsberger
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | - Daniele Zacchetti
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
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3
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Fabo T, Khavari P. Functional characterization of human genomic variation linked to polygenic diseases. Trends Genet 2023; 39:462-490. [PMID: 36997428 PMCID: PMC11025698 DOI: 10.1016/j.tig.2023.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023]
Abstract
The burden of human disease lies predominantly in polygenic diseases. Since the early 2000s, genome-wide association studies (GWAS) have identified genetic variants and loci associated with complex traits. These have ranged from variants in coding sequences to mutations in regulatory regions, such as promoters and enhancers, as well as mutations affecting mediators of mRNA stability and other downstream regulators, such as 5' and 3'-untranslated regions (UTRs), long noncoding RNA (lncRNA), and miRNA. Recent research advances in genetics have utilized a combination of computational techniques, high-throughput in vitro and in vivo screening modalities, and precise genome editing to impute the function of diverse classes of genetic variants identified through GWAS. In this review, we highlight the vastness of genomic variants associated with polygenic disease risk and address recent advances in how genetic tools can be used to functionally characterize them.
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Affiliation(s)
- Tania Fabo
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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4
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Ryczek N, Łyś A, Makałowska I. The Functional Meaning of 5'UTR in Protein-Coding Genes. Int J Mol Sci 2023; 24:ijms24032976. [PMID: 36769304 PMCID: PMC9917990 DOI: 10.3390/ijms24032976] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
As it is well known, messenger RNA has many regulatory regions along its sequence length. One of them is the 5' untranslated region (5'UTR), which itself contains many regulatory elements such as upstream ORFs (uORFs), internal ribosome entry sites (IRESs), microRNA binding sites, and structural components involved in the regulation of mRNA stability, pre-mRNA splicing, and translation initiation. Activation of the alternative, more upstream transcription start site leads to an extension of 5'UTR. One of the consequences of 5'UTRs extension may be head-to-head gene overlap. This review describes elements in 5'UTR of protein-coding transcripts and the functional significance of protein-coding genes 5' overlap with implications for transcription, translation, and disease.
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5
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Fan X, Zhao Z, Ma L, Huang X, Zhan Q, Song Y. PTBP1 promotes IRES-mediated translation of cyclin B1 in cancer. Acta Biochim Biophys Sin (Shanghai) 2022; 54:696-707. [PMID: 35643957 PMCID: PMC9828304 DOI: 10.3724/abbs.2022046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022] Open
Abstract
Cyclin B1 is an essential cyclin-dependent protein that involves in the G2/M transition. Multiple studies report that cyclin B1 is upregulated in cancers and promotes cancer progression. However, the mechanism of cyclin B1 upregulation remains unclear. Here we report that the 5'UTR of cyclin B1 mRNA contains an internal ribosome entry site (IRES) by using a bicistronic fluorescent reporter. We show that IRES can initiate the translation of cyclin B1, and the IRES-mediated translation is further activated under cell stress. Interacting trans-acting factors (ITAFs) are required by most IRES to initiate the translation. We find that PTBP1 promotes the IRES-mediated translation of cyclin B1 by binding to the 5'UTR of cyclin B1. On top of that, PTBP1 promotes the malignancy of ESCC cells. Our data suggest that the IRES-mediated translation of cyclin B1 plays an essential role in the cyclin B1 upregulation in cancers.
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Affiliation(s)
- Xinyi Fan
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021 China
- Department of Radiation OncologyWeill Cornell Medical CollegeNew YorkNY10065USA
| | - Zitong Zhao
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021 China
| | - Liying Ma
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021 China
| | | | - Qimin Zhan
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021 China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Laboratory of Molecular OncologyPeking University Cancer Hospital & InstituteBeijing100142China
| | - Yongmei Song
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021 China
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6
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RNA-Binding Proteins as Regulators of Internal Initiation of Viral mRNA Translation. Viruses 2022; 14:v14020188. [PMID: 35215780 PMCID: PMC8879377 DOI: 10.3390/v14020188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/03/2022] [Accepted: 01/14/2022] [Indexed: 12/17/2022] Open
Abstract
Viruses are obligate intracellular parasites that depend on the host’s protein synthesis machinery for translating their mRNAs. The viral mRNA (vRNA) competes with the host mRNA to recruit the translational machinery, including ribosomes, tRNAs, and the limited eukaryotic translation initiation factor (eIFs) pool. Many viruses utilize non-canonical strategies such as targeting host eIFs and RNA elements known as internal ribosome entry sites (IRESs) to reprogram cellular gene expression, ensuring preferential translation of vRNAs. In this review, we discuss vRNA IRES-mediated translation initiation, highlighting the role of RNA-binding proteins (RBPs), other than the canonical translation initiation factors, in regulating their activity.
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7
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Effects of MicroRNA-195-5p on Biological Behaviors and Radiosensitivity of Lung Adenocarcinoma Cells via Targeting HOXA10. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:4522210. [PMID: 34925694 PMCID: PMC8672108 DOI: 10.1155/2021/4522210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 10/19/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022]
Abstract
Objective To explore the effects of miR-195-5p and its target gene HOXA10 on the biological behaviors and radiosensitivity of lung adenocarcinoma (LUAD) cells. Methods The effects of miR-195-5p on LUAD cell proliferation, migration, invasion, cycle arrest, apoptosis, and radiosensitivity were investigated by in vitro experiments. The bioinformatics analysis was used to assess its clinical value and predict target genes. Double-luciferase experiments were used to verify whether the miR-195-5p directly targeted HOXA10. A xenograft tumor-bearing mouse model was used to examine its effects on the radiosensitivity of LUAD in vivo. Results Both gain- and loss-of-function assays demonstrated that miR-195-5p inhibited LUAD cell proliferation, invasion, and migration, induced G1 phase arrest and apoptosis, and enhanced radiosensitivity. Double-luciferase experiments confirmed that miR-195-5p directly targeted HOXA10. Downregulation of HOXA10 also inhibited LUAD cell proliferation, migration, and invasion, induced G1 phase arrest and apoptosis, and enhanced radiosensitivity. The protein levels of β-catenin, c-myc, and Wnt1 were decreased by miR-195-5p and increased by its inhibitor. Moreover, the effects of the miR-195-5p inhibitor could be eliminated by HOXA10-siRNA. Furthermore, miR-195-5p improved radiosensitivity of LUAD cells in vivo. Conclusion miR-195-5p has excellent antitumor effects via inhibiting cancer cell growth, invasion, and migration, arresting the cell cycle, promoting apoptosis, and sensitizing LUAD cells to X-ray irradiation by targeting HOXA10. Thus, miR-195-5p may serve as a potential candidate for the treatment of LUAD.
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Mariggiò MA, Palumbi R, Vinella A, Laterza R, Petruzzelli MG, Peschechera A, Gabellone A, Gentile O, Vincenti A, Margari L. DRD1 and DRD2 Receptor Polymorphisms: Genetic Neuromodulation of the Dopaminergic System as a Risk Factor for ASD, ADHD and ASD/ADHD Overlap. Front Neurosci 2021; 15:705890. [PMID: 34658761 PMCID: PMC8511701 DOI: 10.3389/fnins.2021.705890] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/07/2021] [Indexed: 01/18/2023] Open
Abstract
The dopaminergic system (DS) is one of the most important neuromodulator systems involved in complex functions that are compromised in both autism spectrum disorder (ASD) and attention deficit/hyperactivity disorder (ADHD), conditions that frequently occur in overlap. This evidence suggests that both disorders might have common neurobiological pathways involving the DS. Therefore, the aim of this study was to examine the DRD1 and DRD2 dopamine receptor single nucleotide polymorphisms (SNPs) as potential risk factors for ASD, ADHD, and ASD/ADHD overlap. Genetic data were obtained from four groups: 75 ASD patients, 75 ADHD patients, 30 patients with ASD/ADHD overlap, and 75 healthy controls. All participants were between 2 and 17 years old. We compared the genotypic and allelic frequency of 18 SNPs among all of the study groups. Moreover, in the case of statistically significant differences, odds ratios (OR) were obtained to evaluate if the presence of SNPs might be a risk factor of developing a specific clinical phenotype. This study found that DRD1 and DRD2 receptors SNPs might be considered as potential risk factors for ASD and ADHD. However, only DRD2-12 (rs7131465) was significantly associated with a higher risk for the ASD/ADHD overlap. These data support the hypothesis of the genetic neuromodulation of the DS in the neurobiology of these conditions.
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Affiliation(s)
| | - Roberto Palumbi
- Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Angela Vinella
- Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Riccardo Laterza
- Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | | | - Antonia Peschechera
- Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Alessandra Gabellone
- Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Ottavio Gentile
- Pediatric Surgery Unit, Giovanni XXIII Hospital, Bari, Italy
| | - Alessandra Vincenti
- Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Lucia Margari
- Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
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9
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Strand E, Hollås H, Sakya SA, Romanyuk S, Saraste MEV, Grindheim AK, Patil SS, Vedeler A. Annexin A2 binds the internal ribosomal entry site of c- myc mRNA and regulates its translation. RNA Biol 2021; 18:337-354. [PMID: 34346292 PMCID: PMC8677036 DOI: 10.1080/15476286.2021.1947648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The expression and localization of the oncoprotein c-Myc is highly regulated at the level of transcription, mRNA transport, translation, as well as stability of the protein. We previously showed that Annexin A2 (AnxA2) binds to a specific localization element in the 3'untranslated region (UTR) of c-myc mRNA and is involved in its localization to the perinuclear region. In the present study, we demonstrate that AnxA2 binds in a Ca2+-dependent manner to the internal ribosomal entry site (IRES) containing two pseudo-knots in the 5´UTR of the c-myc mRNA. Here, we employ an in vitro rabbit reticulocyte lysate system with chimeric c-myc reporter mRNAs to demonstrate that binding of AnxA2 to the c-myc IRES modulates the expression of c-Myc. Notably, we show that low levels of AnxA2 appear to increase, while high levels of AnxA2 inhibits translation of the chimeric mRNA. However, when both the AnxA2-binding site and the ribosomal docking site in the c-myc IRES are deleted, AnxA2 has no effect on the translation of the reporter mRNA. Forskolin-treatment of PC12 cells results in upregulation of Ser25 phosphorylated AnxA2 expression while c-Myc expression is down-regulated. The effect of forskolin on c-Myc expression and the level of Ser25 phosphorylated AnxA2 was abolished in the presence of EGTA. These findings indicate that AnxA2 regulates both the transport and subsequent translation of the c-myc mRNA, possibly by silencing the mRNA during its transport. They also suggest that AnxA2 act as a switch to turn off the c-myc IRES activity in the presence of calcium.Abbreviations: AnxA2, Annexin A2; β2--µglob, β2-microglobulin; cpm, counts per minute; hnRNP, heterogenous nuclear ribonucleoprotein; IRES, internal ribosomal entry site; ITAF, IRES trans-acting factor; MM, multiple myeloma; PABP, poly(A)-binding protein; PCBP, poly(rC) binding protein; PSF, PTB-associated splicing factor; PTB, polypyrimidine tract binding protein; RRL, rabbit reticulocyte lysate; UTR, untranslated region; YB, Y-box binding protein.
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Affiliation(s)
- Elin Strand
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Immunology and Transfusion Medicine, Haukeland University Hospital, Bergen, Norway
| | - Hanne Hollås
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Siri Aastedatter Sakya
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Pharmacology, Institute of Clinical Medicine, University of Oslo, Norway
| | - Sofya Romanyuk
- Department of Biomedicine, University of Bergen, Bergen, Norway.,City Hospital №40, St. Petersburg, Russia
| | - Mikko E V Saraste
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Quality Control Unit, Thermo Fisher Scientific - Life Technologies, Lillestrøm, Norway
| | | | | | - Anni Vedeler
- Department of Biomedicine, University of Bergen, Bergen, Norway
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10
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Malaney P, Velasco-Estevez M, Aguilar-Garrido P, Aitken MJL, Chan LE, Zhang X, Post SM, Gallardo M. The Eµ-hnRNP K Murine Model of Lymphoma: Novel Insights into the Role of hnRNP K in B-Cell Malignancies. Front Immunol 2021; 12:634584. [PMID: 33912162 PMCID: PMC8072109 DOI: 10.3389/fimmu.2021.634584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/23/2021] [Indexed: 01/18/2023] Open
Abstract
B-cell lymphomas are one of the most biologically and molecularly heterogeneous group of malignancies. The inherent complexity of this cancer subtype necessitates the development of appropriate animal model systems to characterize the disease with the ultimate objective of identifying effective therapies. In this article, we discuss a new driver of B-cell lymphomas - hnRNP K (heterogenous nuclear ribonucleoprotein K)-an RNA-binding protein. We introduce the Eµ-Hnrnpk mouse model, a murine model characterized by hnRNP K overexpression in B cells, which develops B-cell lymphomas with high penetrance. Molecular analysis of the disease developed in this model reveals an upregulation of the c-Myc oncogene via post-transcriptional and translational mechanisms underscoring the impact of non-genomic MYC activation in B-cell lymphomas. Finally, the transplantability of the disease developed in Eµ-Hnrnpk mice makes it a valuable pre-clinical platform for the assessment of novel therapeutics.
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MESH Headings
- Animals
- Animals, Genetically Modified
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Disease Models, Animal
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Heterogeneous-Nuclear Ribonucleoprotein K/genetics
- Heterogeneous-Nuclear Ribonucleoprotein K/metabolism
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Phenotype
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- Up-Regulation
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Affiliation(s)
- Prerna Malaney
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | | | | | - Marisa J. L. Aitken
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Lauren E. Chan
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Xiaorui Zhang
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Sean M. Post
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, United States
| | - Miguel Gallardo
- H12O–CNIO Haematological Malignancies Clinical Research Unit, CNIO, Madrid, Spain
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11
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Smith RCL, Kanellos G, Vlahov N, Alexandrou C, Willis AE, Knight JRP, Sansom OJ. Translation initiation in cancer at a glance. J Cell Sci 2021; 134:jcs248476. [PMID: 33441326 DOI: 10.1242/jcs.248476] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cell division, differentiation and function are largely dependent on accurate proteome composition and regulated gene expression. To control this, protein synthesis is an intricate process governed by upstream signalling pathways. Eukaryotic translation is a multistep process and can be separated into four distinct phases: initiation, elongation, termination and recycling of ribosomal subunits. Translation initiation, the focus of this article, is highly regulated to control the activity and/or function of eukaryotic initiation factors (eIFs) and permit recruitment of mRNAs to the ribosomes. In this Cell Science at a Glance and accompanying poster, we outline the mechanisms by which tumour cells alter the process of translation initiation and discuss how this benefits tumour formation, proliferation and metastasis.
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Affiliation(s)
- Rachael C L Smith
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, G61 1QH, UK
| | - Georgios Kanellos
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Nikola Vlahov
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | | | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Cambridge CB2 1QW, UK
| | - John R P Knight
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Owen J Sansom
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, G61 1QH, UK
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12
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Li L, Peng G, Liu X, Zhang Y, Han H, Liu ZR. Pyruvate Kinase M2 Coordinates Metabolism Switch between Glycolysis and Glutaminolysis in Cancer Cells. iScience 2020; 23:101684. [PMID: 33196019 PMCID: PMC7644948 DOI: 10.1016/j.isci.2020.101684] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/03/2020] [Accepted: 10/12/2020] [Indexed: 12/21/2022] Open
Abstract
Cancer cells alter their nutrition metabolism to cope the stressful environment. One important metabolism adjustment is that cancer cells activate glutaminolysis in response to the reduced carbon from glucose entering into the TCA cycle due to inactivation of several enzymes in glycolysis. An important question is how the cancer cells coordinate the changes of glycolysis and glutaminolysis. In this report, we demonstrate that the pyruvate kinase inactive dimer PKM2 facilitates activation of glutaminolysis. Our experiments show that growth stimulations promote PKM2 dimer. The dimer PKM2 plays a role in regulation of glutaminolysis by upregulation of mitochondrial glutaminase I (GLS-1). PKM2 dimer regulates the GLS-1 expression by controlling internal ribosome entry site (IRES)-dependent c-myc translation. Growth stimulations promote PKM2 interacting with c-myc IRES-RNA, thus facilitating c-myc IRES-dependent translation. Our study reveals an important linker that coordinates the metabolism adjustment in cancer cells.
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Affiliation(s)
- Liangwei Li
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA 30303, USA
| | - Guangda Peng
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA 30303, USA
| | - Xiaowei Liu
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA 30303, USA
| | - Yinwei Zhang
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA 30303, USA
| | - Hongwei Han
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA 30303, USA
| | - Zhi-Ren Liu
- Department of Biology, Georgia State University, 145 Piedmont Ave SE, Atlanta, GA 30303, USA
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13
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Barrera A, Olguín V, Vera-Otarola J, López-Lastra M. Cap-independent translation initiation of the unspliced RNA of retroviruses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194583. [PMID: 32450258 DOI: 10.1016/j.bbagrm.2020.194583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/12/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Retroviruses are a unique family of RNA viruses that utilize a virally encoded reverse transcriptase (RT) to replicate their genomic RNA (gRNA) through a proviral DNA intermediate. The provirus is permanently integrated into the host cell chromosome and is expressed by the host cell transcription, RNA processing, and translation machinery. Retroviral messenger RNAs (mRNAs) entirely resemble a cellular mRNA as they have a 5'cap structure, 5'untranslated region (UTR), an open reading frame (ORF), 3'UTR, and a 3'poly(A) tail. The primary transcription product interacts with the cellular RNA processing machinery and is spliced, exported to the cytoplasm, and translated. However, a proportion of the pre-mRNA subverts typical RNA processing giving rise to the full-length RNA. In the cytoplasm, the full-length retroviral RNA fulfills a dual role acting as mRNA and as the gRNA. Simple retroviruses generate two pools of full-length RNA, one for each purpose. However, complex retroviruses have a single pool of full-length RNA, which is destined for translation or encapsidation. As for eukaryotic mRNAs, translational control of retroviral protein synthesis is mostly exerted at the step of initiation. Interestingly, some retroviral mRNAs, both simple and complex, use a dual mechanism to initiate protein synthesis, a cap-dependent initiation mechanism, or via internal initiation using an internal ribosome entry site (IRES). In this review, we describe and discuss data regarding the molecular mechanism driving the canonical cap-dependent and IRES-mediated translation initiation for retroviral mRNA, focusing the discussion mainly on the most studied retroviral mRNA, the HIV-1 mRNA.
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Affiliation(s)
- Aldo Barrera
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Valeria Olguín
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Jorge Vera-Otarola
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Marcelo López-Lastra
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile.
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14
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Jaud M, Philippe C, Di Bella D, Tang W, Pyronnet S, Laurell H, Mazzolini L, Rouault-Pierre K, Touriol C. Translational Regulations in Response to Endoplasmic Reticulum Stress in Cancers. Cells 2020; 9:cells9030540. [PMID: 32111004 PMCID: PMC7140484 DOI: 10.3390/cells9030540] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 12/20/2022] Open
Abstract
During carcinogenesis, almost all the biological processes are modified in one way or another. Among these biological processes affected, anomalies in protein synthesis are common in cancers. Indeed, cancer cells are subjected to a wide range of stresses, which include physical injuries, hypoxia, nutrient starvation, as well as mitotic, oxidative or genotoxic stresses. All of these stresses will cause the accumulation of unfolded proteins in the Endoplasmic Reticulum (ER), which is a major organelle that is involved in protein synthesis, preservation of cellular homeostasis, and adaptation to unfavourable environment. The accumulation of unfolded proteins in the endoplasmic reticulum causes stress triggering an unfolded protein response in order to promote cell survival or to induce apoptosis in case of chronic stress. Transcription and also translational reprogramming are tightly controlled during the unfolded protein response to ensure selective gene expression. The majority of stresses, including ER stress, induce firstly a decrease in global protein synthesis accompanied by the induction of alternative mechanisms for initiating the translation of mRNA, later followed by a translational recovery. After a presentation of ER stress and the UPR response, we will briefly present the different modes of translation initiation, then address the specific translational regulatory mechanisms acting during reticulum stress in cancers and highlight the importance of translational control by ER stress in tumours.
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Affiliation(s)
- Manon Jaud
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
| | - Céline Philippe
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Doriana Di Bella
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Weiwei Tang
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Stéphane Pyronnet
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
| | - Henrik Laurell
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
- Inserm UMR1048, I2MC (Institut des Maladies Métaboliques et Cardiovasculaires), BP 84225, CEDEX 04, 31 432 Toulouse, France
| | - Laurent Mazzolini
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- CNRS ERL5294, CRCT, F-31037 Toulouse, France
| | - Kevin Rouault-Pierre
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Christian Touriol
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
- Correspondence:
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15
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Godet AC, David F, Hantelys F, Tatin F, Lacazette E, Garmy-Susini B, Prats AC. IRES Trans-Acting Factors, Key Actors of the Stress Response. Int J Mol Sci 2019; 20:ijms20040924. [PMID: 30791615 PMCID: PMC6412753 DOI: 10.3390/ijms20040924] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 12/16/2022] Open
Abstract
The cellular stress response corresponds to the molecular changes that a cell undergoes in response to various environmental stimuli. It induces drastic changes in the regulation of gene expression at transcriptional and posttranscriptional levels. Actually, translation is strongly affected with a blockade of the classical cap-dependent mechanism, whereas alternative mechanisms are activated to support the translation of specific mRNAs. A major mechanism involved in stress-activated translation is the internal ribosome entry site (IRES)-driven initiation. IRESs, first discovered in viral mRNAs, are present in cellular mRNAs coding for master regulators of cell responses, whose expression must be tightly controlled. IRESs allow the translation of these mRNAs in response to different stresses, including DNA damage, amino-acid starvation, hypoxia or endoplasmic reticulum stress, as well as to physiological stimuli such as cell differentiation or synapse network formation. Most IRESs are regulated by IRES trans-acting factor (ITAFs), exerting their action by at least nine different mechanisms. This review presents the history of viral and cellular IRES discovery as well as an update of the reported ITAFs regulating cellular mRNA translation and of their different mechanisms of action. The impact of ITAFs on the coordinated expression of mRNA families and consequences in cell physiology and diseases are also highlighted.
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Affiliation(s)
- Anne-Claire Godet
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florian David
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Fransky Hantelys
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Florence Tatin
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Eric Lacazette
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Barbara Garmy-Susini
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
| | - Anne-Catherine Prats
- UMR 1048-I2MC, Inserm, Université de Toulouse, UT3, 31432 Toulouse cedex 4, France.
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16
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Seo JY, Jung Y, Kim DY, Ryu HG, Lee J, Kim SW, Kim KT. DAP5 increases axonal outgrowth of hippocampal neurons by enhancing the cap-independent translation of DSCR1.4 mRNA. Cell Death Dis 2019; 10:49. [PMID: 30718468 PMCID: PMC6362140 DOI: 10.1038/s41419-018-1299-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/30/2018] [Accepted: 12/19/2018] [Indexed: 12/18/2022]
Abstract
Proper wiring between neurons is indispensable for proper brain function. From the early developmental stage, axons grow and navigate to connect to targets according to specific guidance cues. The accuracy of axonal outgrowth and navigation are controlled by a variety of genes, and mutations and/or deficiencies in these genes are closely related to several brain disorders, such as autism. DSCR1 is one of these genes and regulates actin filament formation in axons. Thus, identifying the detailed regulatory mechanisms of DSCR1 expression is crucial for the understanding of the axon development of neurons; however, these regulatory mechanisms of DSCR1 remain unknown. Here, we discovered that mRNA encoding the DSCR1 isoform DSCR1.4 is present and mainly translated by the cap-independent initiation mechanisms in both the soma and axons of hippocampal neurons. We found that translation of DSCR1.4 mRNA is enhanced by death-associated protein 5 (DAP5), which can bind to DSCR1.4 5'UTR. BDNF-stimulus induced an increase in DAP5 expression and the cap-independent translation efficiency of DSCR1.4 mRNA in axon as well as soma. Furthermore, we showed the importance of the cap-independent translation of DSCR1.4 on enhancement of DSCR1.4 expression by BDNF-stimulus and axonal outgrowth of hippocampal neurons. Our findings suggest a new translational regulatory mechanism for DSCR1.4 expressions and a novel function of DAP5 as a positive regulator of DSCR1.4 mRNA translation induced in soma and axon of hippocampal neurons.
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Affiliation(s)
- Ji-Young Seo
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Youngseob Jung
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University (KNU), Daegu, Republic of Korea
| | - Hye Guk Ryu
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Juhyun Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Sung Wook Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Kyong-Tai Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea. .,Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea.
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17
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Robert F, Pelletier J. Exploring the Impact of Single-Nucleotide Polymorphisms on Translation. Front Genet 2018; 9:507. [PMID: 30425729 PMCID: PMC6218417 DOI: 10.3389/fgene.2018.00507] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/10/2018] [Indexed: 01/08/2023] Open
Abstract
Over the past 15 years, sequencing of the human genome and The Cancer Genome Atlas (TCGA) project have led to comprehensive lists of single-nucleotide polymorphisms (SNPs) and gene mutations across a large number of human samples. However, our ability to predict the functional impact of SNPs and mutations on gene expression is still in its infancy. Here, we provide key examples to help understand how mutations present in genes can affect translational output.
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Affiliation(s)
- Francis Robert
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, QC, Canada.,Department of Oncology, McGill University, Montreal, QC, Canada.,Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
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18
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Sriram A, Bohlen J, Teleman AA. Translation acrobatics: how cancer cells exploit alternate modes of translational initiation. EMBO Rep 2018; 19:embr.201845947. [PMID: 30224410 DOI: 10.15252/embr.201845947] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/09/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
Recent work has brought to light many different mechanisms of translation initiation that function in cells in parallel to canonical cap-dependent initiation. This has important implications for cancer. Canonical cap-dependent translation initiation is inhibited by many stresses such as hypoxia, nutrient limitation, proteotoxic stress, or genotoxic stress. Since cancer cells are often exposed to these stresses, they rely on alternate modes of translation initiation for protein synthesis and cell growth. Cancer mutations are now being identified in components of the translation machinery and in cis-regulatory elements of mRNAs, which both control translation of cancer-relevant genes. In this review, we provide an overview on the various modes of non-canonical translation initiation, such as leaky scanning, translation re-initiation, ribosome shunting, IRES-dependent translation, and m6A-dependent translation, and then discuss the influence of stress on these different modes of translation. Finally, we present examples of how these modes of translation are dysregulated in cancer cells, allowing them to grow, to proliferate, and to survive, thereby highlighting the importance of translational control in cancer.
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Affiliation(s)
- Ashwin Sriram
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Jonathan Bohlen
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg University, Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Germany .,Heidelberg University, Heidelberg, Germany
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19
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Human rhinovirus internal ribosome entry site element enhances transgene expression in transfected CHO-S cells. Sci Rep 2018; 8:6661. [PMID: 29703950 PMCID: PMC5923211 DOI: 10.1038/s41598-018-25049-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/13/2018] [Indexed: 01/27/2023] Open
Abstract
Chinese hamster ovary (CHO) cells are mainly used for recombinant protein production. However, the unstable transgene expression and lower transgene copy numbers are the major issues need to be resolved. Here, eleven internal ribosome entry site (IRES) elements from viral and cellular IRES were evaluated for foreign gene expression in CHO-S cells. We constructed eleven fusing plasmids containing different IRES sequences downstream of the enhanced green fluorescent protein (EGFP) gene. EGFP expression was detected by flow cytometry and the transgene copy number was evaluated by quantitative PCR. The erythropoietin (EPO) protein was also used to assess the stronger IRES. The results showed that IRES from human rhinovirus (HRV) exhibited the highest EGFP expression level under transient and stable transfections. The EGFP expression level of vector with IRES from HRV was related to the gene copy number in stably transfected CHO-S cells. Moreover, IRES from HRV induced higher expression level of EPO compared with one mutant IRES from EMCV in transfected cells. In conclusion, IRES from HRV can function as a strong IRES element for stable expression in CHO-S cells, which could potentially guide more effective foreign gene expression in CHO-S cells.
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20
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Leppek K, Das R, Barna M. Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat Rev Mol Cell Biol 2018; 19:158-174. [PMID: 29165424 PMCID: PMC5820134 DOI: 10.1038/nrm.2017.103] [Citation(s) in RCA: 471] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5' untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5' UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms.
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Affiliation(s)
- Kathrin Leppek
- Department of Developmental Biology, Stanford University, Stanford, California 94305, USA
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Rhiju Das
- Departments of Biochemistry and Physics, Stanford University, Stanford, California 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, California 94305, USA
- Department of Genetics, Stanford University, Stanford, California 94305, USA
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21
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Deng N, Zhou H, Fan H, Yuan Y. Single nucleotide polymorphisms and cancer susceptibility. Oncotarget 2017; 8:110635-110649. [PMID: 29299175 PMCID: PMC5746410 DOI: 10.18632/oncotarget.22372] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/03/2017] [Indexed: 12/12/2022] Open
Abstract
A large number of genes associated with various cancer types contain single nucleotide polymorphisms (SNPs). SNPs are located in gene promoters, exons, introns as well as 5'- and 3'- untranslated regions (UTRs) and affect gene expression by different mechanisms. These mechanisms depend on the role of the genetic elements in which the individual SNPs are located. Moreover, alterations in epigenetic regulation due to gene polymorphisms add to the complexity underlying cancer susceptibility related to SNPs. In this systematic review, we discuss the various genetic and epigenetic mechanisms involved in determining cancer susceptibility related to various SNPs located in different genetic elements. We also discuss the diagnostic potential of these SNPs and the focus for future studies.
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Affiliation(s)
- Na Deng
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China.,Department of Hematology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Heng Zhou
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Hua Fan
- Department of Hematology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China.,National Clinical Research Center for Digestive Diseases, Xi'an 110001, China
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22
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Tang YS, Khan RA, Xiao S, Hansen DK, Stabler SP, Kusumanchi P, Jayaram HN, Antony AC. Evidence Favoring a Positive Feedback Loop for Physiologic Auto Upregulation of hnRNP-E1 during Prolonged Folate Deficiency in Human Placental Cells. J Nutr 2017; 147:482-498. [PMID: 28250194 PMCID: PMC5368577 DOI: 10.3945/jn.116.241364] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/07/2016] [Accepted: 01/11/2017] [Indexed: 12/27/2022] Open
Abstract
Background: Previously, we determined that heterogeneous nuclear ribonucleoprotein E1 (hnRNP-E1) functions as an intracellular physiologic sensor of folate deficiency. In this model, l-homocysteine, which accumulates intracellularly in proportion to the extent of folate deficiency, covalently binds to and thereby activates homocysteinylated hnRNP-E1 to interact with folate receptor-α mRNA; this high-affinity interaction triggers the translational upregulation of cell surface folate receptors, which enables cells to optimize folate uptake from the external milieu. However, integral to this model is the need for ongoing generation of hnRNP-E1 to replenish homocysteinylated hnRNP-E1 that is degraded.Objective: We searched for an interrelated physiologic mechanism that could also maintain the steady-state concentration of hnRNP-E1 during prolonged folate deficiency.Methods: A novel RNA-protein interaction was functionally characterized by using molecular and biochemical approaches in vitro and in vivo.Results: l-homocysteine triggered a dose-dependent high-affinity interaction between hnRNP-E1 and a 25-nucleotide cis element within the 5'-untranslated region of hnRNP-E1 mRNA; this led to a proportionate increase in these RNA-protein complexes, and translation of hnRNP-E1 both in vitro and within placental cells. Targeted perturbation of this RNA-protein interaction either by specific 25-nucleotide antisense oligonucleotides or mutation within this cis element or by small interfering RNA to hnRNP-E1 mRNA significantly reduced cellular biosynthesis of hnRNP-E1. Conversely, transfection of hnRNP-E1 mutant proteins that mimicked homocysteinylated hnRNP-E1 stimulated both cellular hnRNP-E1 and folate receptor biosynthesis. In addition, ferrous sulfate heptahydrate [iron(II)], which also binds hnRNP-E1, significantly perturbed this l-homocysteine-triggered RNA-protein interaction in a dose-dependent manner. Finally, folate deficiency induced dual upregulation of hnRNP-E1 and folate receptors in cultured human cells and tumor xenografts, and more selectively in various fetal tissues of folate-deficient dams.Conclusions: This novel positive feedback loop amplifies hnRNP-E1 during prolonged folate deficiency and thereby maximizes upregulation of folate receptors in order to restore folate homeostasis toward normalcy in placental cells. It will also functionally impact several other mRNAs of the nutrition-sensitive, folate-responsive posttranscriptional RNA operon that is orchestrated by homocysteinylated hnRNP-E1.
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Affiliation(s)
- Ying-Sheng Tang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Rehana A Khan
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Suhong Xiao
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | | | - Sally P Stabler
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO; and
| | - Praveen Kusumanchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | | | - Aśok C Antony
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN; .,Richard L Roudebush Veterans Affairs Medical Center, Indianapolis, IN
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23
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Carvajal F, Vallejos M, Walters B, Contreras N, Hertz MI, Olivares E, Cáceres CJ, Pino K, Letelier A, Thompson SR, López-Lastra M. Structural domains within the HIV-1 mRNA and the ribosomal protein S25 influence cap-independent translation initiation. FEBS J 2016; 283:2508-27. [PMID: 27191820 DOI: 10.1111/febs.13756] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 04/28/2016] [Accepted: 05/13/2016] [Indexed: 12/14/2022]
Abstract
The 5' leader of the HIV-1 genomic RNA is a multifunctional region that folds into secondary/tertiary structures that regulate multiple processes during viral replication including translation initiation. In this work, we examine the internal ribosome entry site (IRES) located in the 5' leader that drives translation initiation of the viral Gag protein under conditions that hinder cap-dependent translation initiation. We show that activity of the HIV-1 IRES relies on ribosomal protein S25 (eS25). Additionally, a mechanistic and mutational analysis revealed that the HIV-1 IRES is modular in nature and that once the 40S ribosomal subunit is recruited to the IRES, translation initiates without the need of ribosome scanning. These findings elucidate a mechanism of initiation by the HIV-1 IRES whereby a number of highly structured sites present within the HIV-1 5' leader leads to the recruitment of the 40S subunit directly at the site of initiation of protein synthesis.
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Affiliation(s)
- Felipe Carvajal
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Maricarmen Vallejos
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Beth Walters
- Department of Microbiology, University of Alabama at Birmingham, AL, USA
| | - Nataly Contreras
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marla I Hertz
- Department of Microbiology, University of Alabama at Birmingham, AL, USA
| | - Eduardo Olivares
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos J Cáceres
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Karla Pino
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro Letelier
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sunnie R Thompson
- Department of Microbiology, University of Alabama at Birmingham, AL, USA
| | - Marcelo López-Lastra
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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24
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Diederichs S, Bartsch L, Berkmann JC, Fröse K, Heitmann J, Hoppe C, Iggena D, Jazmati D, Karschnia P, Linsenmeier M, Maulhardt T, Möhrmann L, Morstein J, Paffenholz SV, Röpenack P, Rückert T, Sandig L, Schell M, Steinmann A, Voss G, Wasmuth J, Weinberger ME, Wullenkord R. The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non-coding RNA and synonymous mutations. EMBO Mol Med 2016; 8:442-57. [PMID: 26992833 PMCID: PMC5126213 DOI: 10.15252/emmm.201506055] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cancer is a disease of the genome caused by oncogene activation and tumor suppressor gene inhibition. Deep sequencing studies including large consortia such as TCGA and ICGC identified numerous tumor‐specific mutations not only in protein‐coding sequences but also in non‐coding sequences. Although 98% of the genome is not translated into proteins, most studies have neglected the information hidden in this “dark matter” of the genome. Malignancy‐driving mutations can occur in all genetic elements outside the coding region, namely in enhancer, silencer, insulator, and promoter as well as in 5′‐UTR and 3′‐UTR. Intron or splice site mutations can alter the splicing pattern. Moreover, cancer genomes contain mutations within non‐coding RNA, such as microRNA, lncRNA, and lincRNA. A synonymous mutation changes the coding region in the DNA and RNA but not the protein sequence. Importantly, oncogenes such as TERT or miR‐21 as well as tumor suppressor genes such as TP53/p53,APC,BRCA1, or RB1 can be affected by these alterations. In summary, coding‐independent mutations can affect gene regulation from transcription, splicing, mRNA stability to translation, and hence, this largely neglected area needs functional studies to elucidate the mechanisms underlying tumorigenesis. This review will focus on the important role and novel mechanisms of these non‐coding or allegedly silent mutations in tumorigenesis.
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Affiliation(s)
- Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany Division of RNA Biology & Cancer (B150), German Cancer Research Center (DKFZ), Heidelberg, Germany German Cancer Consortium (DKTK), Freiburg, Germany
| | - Lorenz Bartsch
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Julia C Berkmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Karin Fröse
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Jana Heitmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Caroline Hoppe
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Deetje Iggena
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Danny Jazmati
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Philipp Karschnia
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Miriam Linsenmeier
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Thomas Maulhardt
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Lino Möhrmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Johannes Morstein
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Stella V Paffenholz
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Paula Röpenack
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Timo Rückert
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Ludger Sandig
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Maximilian Schell
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Anna Steinmann
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Gjendine Voss
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Jacqueline Wasmuth
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Maria E Weinberger
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
| | - Ramona Wullenkord
- German Academic Scholarship Foundation - Studienstiftung des deutschen Volkes, Bonn, Germany
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25
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Hong MN, Nam KY, Kim KK, Kim SY, Kim I. The small molecule '1-(4-biphenylylcarbonyl)-4-(5-bromo-2-methoxybenzyl) piperazine oxalate' and its derivatives regulate global protein synthesis by inactivating eukaryotic translation initiation factor 2-alpha. Cell Stress Chaperones 2016; 21:485-97. [PMID: 26873011 PMCID: PMC4837177 DOI: 10.1007/s12192-016-0677-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 01/29/2016] [Accepted: 01/30/2016] [Indexed: 10/22/2022] Open
Abstract
By environmental stresses, cells can initiate a signaling pathway in which eukaryotic translation initiation factor 2-alpha (eIF2-α) is involved to regulate the response. Phosphorylation of eIF2-α results in the reduction of overall protein neogenesis, which allows cells to conserve resources and to reprogram energy usage for effective stress control. To investigate the role of eIF2-α in cell stress responses, we conducted a viability-based compound screen under endoplasmic reticulum (ER) stress condition, and identified 1-(4-biphenylylcarbonyl)-4-(5-bromo-2-methoxybenzyl) piperazine oxalate (AMC-01) and its derivatives as eIF2-α-inactivating chemical. Molecular characterization of this signaling pathway revealed that AMC-01 induced inactivation of eIF2-α by phosphorylating serine residue 51 in a dose- and time-dependent manner, while the negative control compounds did not affect eIF2-α phosphorylation. In contrast with ER stress induction by thapsigargin, phosphorylation of eIF2-α persisted for the duration of incubation with AMC-01. By pathway analysis, AMC-01 clearly induced the activation of protein kinase RNA-activated (PKR) kinase and nuclear factor-κB (NF-κB), whereas it did not modulate the activity of PERK or heme-regulated inhibitor (HRI). Finally, we could detect a lower protein translation rate in cells incubated with AMC-01, establishing AMC-01 as a potent chemical probe that can regulate eIF2-α activity. We suggest from these data that AMC-01 and its derivative compounds can be used as chemical probes in future studies of the role of eIF2-α in protein synthesis-related cell physiology.
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Affiliation(s)
- Mi-Na Hong
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, Convergence Medicine Research Building, 43 gil Olympicro, Pungnapdong, Songpagu, Seoul, 138-736, Republic of Korea
| | - Ky-Youb Nam
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, Convergence Medicine Research Building, 43 gil Olympicro, Pungnapdong, Songpagu, Seoul, 138-736, Republic of Korea
| | - Kyung Kon Kim
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, Convergence Medicine Research Building, 43 gil Olympicro, Pungnapdong, Songpagu, Seoul, 138-736, Republic of Korea
- Department of Convergence Medicine, College of Medicine, University of Ulsan, Seoul, Republic of Korea
| | - So-Young Kim
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, Convergence Medicine Research Building, 43 gil Olympicro, Pungnapdong, Songpagu, Seoul, 138-736, Republic of Korea
| | - InKi Kim
- Department of Convergence Medicine, Asan Institute for Life Sciences, Asan Medical Center, Convergence Medicine Research Building, 43 gil Olympicro, Pungnapdong, Songpagu, Seoul, 138-736, Republic of Korea.
- Department of Convergence Medicine, College of Medicine, University of Ulsan, Seoul, Republic of Korea.
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26
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Jing H, Hu J, He B, Negrón Abril YL, Stupinski J, Weiser K, Carbonaro M, Chiang YL, Southard T, Giannakakou P, Weiss RS, Lin H. A SIRT2-Selective Inhibitor Promotes c-Myc Oncoprotein Degradation and Exhibits Broad Anticancer Activity. Cancer Cell 2016; 29:297-310. [PMID: 26977881 PMCID: PMC4811675 DOI: 10.1016/j.ccell.2016.02.007] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 07/03/2015] [Accepted: 02/08/2016] [Indexed: 12/23/2022]
Abstract
Targeting sirtuins for cancer treatment has been a topic of debate due to conflicting reports and lack of potent and specific inhibitors. We have developed a thiomyristoyl lysine compound, TM, as a potent SIRT2-specific inhibitor with a broad anticancer effect in various human cancer cells and mouse models of breast cancer. Mechanistically, SIRT2 inhibition promotes c-Myc ubiquitination and degradation. The anticancer effect of TM correlates with its ability to decrease c-Myc level. TM had limited effects on non-cancerous cells and tumor-free mice, suggesting that cancer cells have an increased dependency on SIRT2 that can be exploited for therapeutic benefit. Our studies demonstrate that SIRT2-selective inhibitors are promising anticancer agents and may represent a general strategy to target certain c-Myc-driven cancers.
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Affiliation(s)
- Hui Jing
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jing Hu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Bin He
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Jack Stupinski
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Keren Weiser
- Division of Hematology & Medical Oncology, Weill Medical College of Cornell University, 1300 York Avenue, C610C, New York, NY 10065-4896, USA
| | - Marisa Carbonaro
- Division of Hematology & Medical Oncology, Weill Medical College of Cornell University, 1300 York Avenue, C610C, New York, NY 10065-4896, USA
| | - Ying-Ling Chiang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Teresa Southard
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Paraskevi Giannakakou
- Division of Hematology & Medical Oncology, Weill Medical College of Cornell University, 1300 York Avenue, C610C, New York, NY 10065-4896, USA
| | - Robert S Weiss
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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27
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Xu-Monette ZY, Deng Q, Manyam GC, Tzankov A, Li L, Xia Y, Wang XX, Zou D, Visco C, Dybkær K, Li J, Zhang L, Liang H, Montes-Moreno S, Chiu A, Orazi A, Zu Y, Bhagat G, Richards KL, Hsi ED, Choi WWL, van Krieken JH, Huh J, Ponzoni M, Ferreri AJM, Parsons BM, Møller MB, Wang SA, Miranda RN, Piris MA, Winter JN, Medeiros LJ, Li Y, Young KH. Clinical and Biologic Significance of MYC Genetic Mutations in De Novo Diffuse Large B-cell Lymphoma. Clin Cancer Res 2016; 22:3593-605. [PMID: 26927665 DOI: 10.1158/1078-0432.ccr-15-2296] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/09/2016] [Indexed: 12/21/2022]
Abstract
PURPOSE MYC is a critical driver oncogene in many cancers, and its deregulation in the forms of translocation and overexpression has been implicated in lymphomagenesis and progression of diffuse large B-cell lymphoma (DLBCL). The MYC mutational profile and its roles in DLBCL are unknown. This study aims to determine the spectrum of MYC mutations in a large group of patients with DLBCL, and to evaluate the clinical significance of MYC mutations in patients with DLBCL treated with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) immunochemotherapy. EXPERIMENTAL DESIGN We identified MYC mutations in 750 patients with DLBCL using Sanger sequencing and evaluated the prognostic significance in 602 R-CHOP-treated patients. RESULTS The frequency of MYC mutations was 33.3% at the DNA level (mutations in either the coding sequence or the untranslated regions) and 16.1% at the protein level (nonsynonymous mutations). Most of the nonsynonymous mutations correlated with better survival outcomes; in contrast, T58 and F138 mutations (which were associated with MYC rearrangements), as well as several mutations occurred at the 3' untranslated region, correlated with significantly worse survival outcomes. However, these mutations occurred infrequently (only in approximately 2% of DLBCL). A germline SNP encoding the Myc-N11S variant (observed in 6.5% of the study cohort) was associated with significantly better patient survival, and resulted in reduced tumorigenecity in mouse xenografts. CONCLUSIONS Various types of MYC gene mutations are present in DLBCL and show different impact on Myc function and clinical outcomes. Unlike MYC gene translocations and overexpression, most MYC gene mutations may not have a role in driving lymphomagenesis. Clin Cancer Res; 22(14); 3593-605. ©2016 AACR.
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Affiliation(s)
- Zijun Y Xu-Monette
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qipan Deng
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio
| | - Ganiraju C Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Ling Li
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yi Xia
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiao-Xiao Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dehui Zou
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Li Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - April Chiu
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Attilio Orazi
- Weill Medical College of Cornell University, New York, New York
| | - Youli Zu
- The Methodist Hospital, Houston, Texas
| | - Govind Bhagat
- Columbia University Medical Center and New York Presbyterian Hospital, New York, New York
| | - Kristy L Richards
- University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | | | - William W L Choi
- University of Hong Kong Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - J Han van Krieken
- Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Jooryung Huh
- Asan Medical Center, Ulsan University College of Medicine, Seoul, Korea
| | | | | | - Ben M Parsons
- Gundersen Lutheran Health System, La Crosse, Wisconsin
| | | | - Sa A Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roberto N Miranda
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Miguel A Piris
- Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Jane N Winter
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yong Li
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio.
| | - Ken H Young
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas. The University of Texas School of Medicine, Graduate School of Biomedical Sciences, Houston, Texas.
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28
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Horvilleur E, Wilson LA, Bastide A, Piñeiro D, Pöyry TAA, Willis AE. Cap-Independent Translation in Hematological Malignancies. Front Oncol 2015; 5:293. [PMID: 26734574 PMCID: PMC4685420 DOI: 10.3389/fonc.2015.00293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/08/2015] [Indexed: 12/25/2022] Open
Abstract
Hematological malignancies are a heterogeneous group of diseases deriving from blood cells progenitors. Although many genes involved in blood cancers contain internal ribosome entry sites (IRESes), there has been only few studies focusing on the role of cap-independent translation in leukemia and lymphomas. Expression of IRES trans-acting factors can also be altered, and interestingly, BCL-ABL1 fusion protein expressed from “Philadelphia” chromosome, found in some types of leukemia, regulates several of them. A mechanism involving c-Myc IRES and cap-independent translation and leading to resistance to chemotherapy in multiple myeloma emphasize the contribution of cap-independent translation in blood cancers and the need for more work to be done to clarify the roles of known IRESes in pathology and response to chemotherapeutics.
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Affiliation(s)
| | | | | | - David Piñeiro
- Medical Research Council Toxicology Unit , Leicester , UK
| | | | - Anne E Willis
- Medical Research Council Toxicology Unit , Leicester , UK
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29
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Vaklavas C, Meng Z, Choi H, Grizzle WE, Zinn KR, Blume SW. Small molecule inhibitors of IRES-mediated translation. Cancer Biol Ther 2015; 16:1471-85. [PMID: 26177060 PMCID: PMC4846101 DOI: 10.1080/15384047.2015.1071729] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Many genes controlling cell proliferation and survival (those most important to cancer biology) are now known to be regulated specifically at the translational (RNA to protein) level. The internal ribosome entry site (IRES) provides a mechanism by which the translational efficiency of an individual or group of mRNAs can be regulated independently of the global controls on general protein synthesis. IRES-mediated translation has been implicated as a significant contributor to the malignant phenotype and chemoresistance, however there has been no effective means by which to interfere with this specialized mode of protein synthesis. A cell-based empirical high-throughput screen was performed in attempt to identify compounds capable of selectively inhibiting translation mediated through the IGF1R IRES. Results obtained using the bicistronic reporter system demonstrate selective inhibition of second cistron translation (IRES-dependent). The lead compound and its structural analogs completely block de novo IGF1R protein synthesis in genetically-unmodified cells, confirming activity against the endogenous IRES. Spectrum of activity extends beyond IGF1R to include the c-myc IRES. The small molecule IRES inhibitor differentially modulates synthesis of the oncogenic (p64) and growth-inhibitory (p67) isoforms of Myc, suggesting that the IRES controls not only translational efficiency, but also choice of initiation codon. Sustained IRES inhibition has profound, detrimental effects on human tumor cells, inducing massive (>99%) cell death and complete loss of clonogenic survival in models of triple-negative breast cancer. The results begin to reveal new insights into the inherent complexity of gene-specific translational regulation, and the importance of IRES-mediated translation to tumor cell biology.
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Affiliation(s)
- Christos Vaklavas
- a Comprehensive Cancer Center; University of Alabama at Birmingham ; Birmingham , AL USA.,b Department of Medicine , Division of Hematology / Oncology; University of Alabama at Birmingham ; Birmingham , AL USA
| | - Zheng Meng
- c Department of Biochemistry and Molecular Genetics; University of Alabama at Birmingham ; Birmingham , AL USA.,d Current address: Analytical Development Department; Novavax Inc. ; Gaithersburg , MD USA
| | - Hyoungsoo Choi
- a Comprehensive Cancer Center; University of Alabama at Birmingham ; Birmingham , AL USA.,b Department of Medicine , Division of Hematology / Oncology; University of Alabama at Birmingham ; Birmingham , AL USA.,e Current address: Department of Pediatrics; Seoul National University Bundang Hospital; Gyeonggi-do , Korea
| | - William E Grizzle
- a Comprehensive Cancer Center; University of Alabama at Birmingham ; Birmingham , AL USA.,f Department of Pathology; University of Alabama at Birmingham ; Birmingham , AL USA
| | - Kurt R Zinn
- a Comprehensive Cancer Center; University of Alabama at Birmingham ; Birmingham , AL USA.,b Department of Medicine , Division of Hematology / Oncology; University of Alabama at Birmingham ; Birmingham , AL USA.,f Department of Pathology; University of Alabama at Birmingham ; Birmingham , AL USA
| | - Scott W Blume
- a Comprehensive Cancer Center; University of Alabama at Birmingham ; Birmingham , AL USA.,b Department of Medicine , Division of Hematology / Oncology; University of Alabama at Birmingham ; Birmingham , AL USA.,c Department of Biochemistry and Molecular Genetics; University of Alabama at Birmingham ; Birmingham , AL USA
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30
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Alenina N, Böhme I, Bader M, Walther T. Multiple non-coding exons and alternative splicing in the mouse Mas protooncogene. Gene 2015; 568:155-64. [PMID: 26003294 DOI: 10.1016/j.gene.2015.05.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/23/2015] [Accepted: 05/16/2015] [Indexed: 10/23/2022]
Abstract
The Mas protooncogene encodes a G protein-coupled receptor with the common seven transmembrane domains, expressed mainly in the testis and brain. We provided evidence that Mas is a functional angiotensin-(1-7) receptor and can interact with the angiotensin II type 1 (AT1) receptor. The gene is transcriptionally regulated during development in the brain and testis, but its structure was unresolved. In this study we used 5'- and 3'-RACE, RT-PCR, and RNase-protection assays to elucidate the complete Mas gene structure and organization. We identified 12 exons in the mouse Mas gene with 11 in the 5' untranslated mRNA, which can be alternatively spliced. We also showed that Mas transcription can start from 4 tissue-specific promoters, whereby testis-specific Mas mRNA is transcribed from two upstream promoters, and the expression of Mas in the brain starts from two downstream promoters. Alternative splicing and multiple promoter usage result in at least 12 Mas transcripts in which different 5' untranslated regions are fused to a common coding sequence. Moreover, termination of Mas mRNA is regulated by two different polyadenylation signals. The gene spans approximately 27 kb, and the longest detected mRNA contains 2,451 bp. Thus, our results characterize the Mas protooncogene as the gene with the most complex gene structure of all described members of the gene family coding for G protein-coupled receptors.
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Affiliation(s)
- Natalia Alenina
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13092 Berlin-Buch, Germany; Federal University of Minas Gerais (UFMG), ICB, 6627 Belo Horizonte, MG, Brasil
| | - Ilka Böhme
- Centre for Perinatal Medicine, University Medical Centre Leipzig, Liebigstraße 20a, 04103 Leipzig, Germany
| | - Michael Bader
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13092 Berlin-Buch, Germany; Federal University of Minas Gerais (UFMG), ICB, 6627 Belo Horizonte, MG, Brasil; Charité University Medicine Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Thomas Walther
- Centre for Perinatal Medicine, University Medical Centre Leipzig, Liebigstraße 20a, 04103 Leipzig, Germany; Department of Pharmacology and Therapeutics, 2nd Floor, Western Road, University College Cork, Cork, Ireland.
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31
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Jackstadt R, Hermeking H. MicroRNAs as regulators and mediators of c-MYC function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:544-53. [DOI: 10.1016/j.bbagrm.2014.04.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 03/27/2014] [Accepted: 04/04/2014] [Indexed: 12/19/2022]
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32
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Fu Q, Chen Z, Gong X, Cai Y, Chen Y, Ma X, Zhu R, Jin J. β-Catenin expression is regulated by an IRES-dependent mechanism and stimulated by paclitaxel in human ovarian cancer cells. Biochem Biophys Res Commun 2015; 461:21-7. [PMID: 25849888 DOI: 10.1016/j.bbrc.2015.03.161] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 03/27/2015] [Indexed: 11/29/2022]
Abstract
Paclitaxel (PTX) is commonly used in the chemotherapy of ovarian cancer, but resistance occurs in most cases, allowing cancer progression. The Wnt/β-catenin pathway has been associated with this resistance, but there are no reports on the regulation of β-catenin expression at the translational level. In the present study, we found that PTX induced different transcription and translation levels of β-catenin in the human ovarian cancer cell lines A2780 and SKOV3. We also demonstrated that β-catenin mRNA contained an internal ribosome entry segment (IRES) that regulated its translation. Using gene transfection and reporter assays, we revealed that the entire CTNNB1 5'-untranslated region (UTR) contributed to IRES activity. Interestingly, we found that c-myc and cyclin D1 increased significantly in transfected cells with increasing PTX concentration, and cell-survival rates remained at 60% while the PTX concentration increased. Suppressing β-catenin resulted in decreased expression of c-myc and cyclin D1 and made these cells less resistant. These results indicate that β-catenin translation is initiated via the IRES and this is regulated by PTX, suggesting that regulation of the IRES-dependent translation of β-catenin may be involved in the cancer cell response to PTX treatment.
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Affiliation(s)
- Qianyun Fu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Zhen Chen
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Xiaohai Gong
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Yanfei Cai
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Yun Chen
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Xin Ma
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Ruiyu Zhu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China.
| | - Jian Jin
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China.
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33
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Faye MD, Holcik M. The role of IRES trans-acting factors in carcinogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:887-97. [PMID: 25257759 DOI: 10.1016/j.bbagrm.2014.09.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/09/2014] [Accepted: 09/14/2014] [Indexed: 02/06/2023]
Abstract
Regulation of protein expression through RNA metabolism is a key aspect of cellular homeostasis. Upon specific cellular stresses, distinct transcripts are selectively controlled to modify protein output in order to quickly and appropriately respond to stress. Reprogramming of the translation machinery is one node of this strict control that typically consists of an attenuation of the global, cap-dependent translation and accompanying switch to alternative mechanisms of translation initiation, such as internal ribosome entry site (IRES)-mediated initiation. In cancer, many aspects of the RNA metabolism are frequently misregulated to provide cancer cells with a growth and survival advantage. This includes changes in the expression and function of RNA binding proteins termed IRES trans-acting factors (ITAFs) that are central to IRES translation. In this review, we will examine select emerging, as well as established, ITAFs with important roles in cancer initiation and progression, and in particular their role in IRES-mediated translation. This article is part of a Special Issue entitled: Translation and Cancer.
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Affiliation(s)
- Mame Daro Faye
- Apoptosis Research Centre, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa K1H 8M5, Canada
| | - Martin Holcik
- Apoptosis Research Centre, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa K1H 8M5, Canada; Department of Pediatrics, University of Ottawa, 451 Smyth Road, Ottawa K1H 8M5, Canada.
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Jiménez-González AS, Fernández N, Martínez-Salas E, Sánchez de Jiménez E. Functional and structural analysis of maize hsp101 IRES. PLoS One 2014; 9:e107459. [PMID: 25222534 PMCID: PMC4164631 DOI: 10.1371/journal.pone.0107459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/17/2014] [Indexed: 11/18/2022] Open
Abstract
Maize heat shock protein of 101 KDa (HSP101) is essential for thermotolerance induction in this plant. The mRNA encoding this protein harbors an IRES element in the 5'UTR that mediates cap-independent translation initiation. In the current work it is demonstrated that hsp101 IRES comprises the entire 5'UTR sequence (150 nts), since deletion of 17 nucleotides from the 5' end decreased translation efficiency by 87% compared to the control sequence. RNA structure analysis of maize hsp101 IRES revealed the presence of three stem-loops toward its 5' end, whereas the remainder sequence contains a great proportion of unpaired nucleotides. Furthermore, HSP90 protein was identified by mass spectrometry as the protein preferentially associated with the maize hsp101 IRES. In addition, it has been found that eIFiso4G rather than eIF4G initiation factor mediates translation of the maize hsp101 mRNA.
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Affiliation(s)
| | - Noemí Fernández
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas –Universidad Autónoma de Madrid, Madrid, Spain
| | - Encarnación Martínez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas –Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail: (ESDJ); (EMS)
| | - Estela Sánchez de Jiménez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México DF, México
- * E-mail: (ESDJ); (EMS)
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Lee KM, Yang SJ, Choi JH, Park CS. Functional effects of a pathogenic mutation in Cereblon (CRBN) on the regulation of protein synthesis via the AMPK-mTOR cascade. J Biol Chem 2014; 289:23343-52. [PMID: 24993823 PMCID: PMC4156075 DOI: 10.1074/jbc.m113.523423] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 06/29/2014] [Indexed: 11/06/2022] Open
Abstract
Initially identified as a protein implicated in human mental deficit, cereblon (CRBN) was recently recognized as a negative regulator of adenosine monophosphate-activated protein kinase (AMPK) in vivo and in vitro. Here, we present results showing that CRBN can effectively regulate new protein synthesis through the mammalian target of rapamycin (mTOR) signaling pathway, a downstream target of AMPK. Whereas deficiency of Crbn repressed protein translation via activation of the AMPK-mTOR cascade in Crbn-knock-out mice, ectopic expression of the wild-type CRBN increased protein synthesis by inhibiting endogenous AMPK. Unlike the wild-type CRBN, a mutant CRBN found in human patients, which lacks the last 24 amino acids, failed to rescue mTOR-dependent repression of protein synthesis in Crbn-deficient mouse fibroblasts. These results provide the first evidence that Crbn can activate the protein synthesis machinery through the mTOR signaling pathway by inhibiting AMPK. In light of the fact that protein synthesis regulated by mTOR is essential for various forms of synaptic plasticity that underlie the cognitive functions of the brain, the results of this study suggest a plausible mechanism for CRBN involvement in higher brain function in humans, and they may help explain how a specific mutation in CRBN can affect the cognitive ability of patients.
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Affiliation(s)
- Kwang Min Lee
- From the School of Life Sciences, Cell Dynamics Research Center and National Leading Research Laboratory, Gwangju Institute Science and Technology (GIST), Gwangju, 500-712, The Republic of Korea
| | - Seung-Joo Yang
- From the School of Life Sciences, Cell Dynamics Research Center and National Leading Research Laboratory, Gwangju Institute Science and Technology (GIST), Gwangju, 500-712, The Republic of Korea
| | - Ja-Hyun Choi
- From the School of Life Sciences, Cell Dynamics Research Center and National Leading Research Laboratory, Gwangju Institute Science and Technology (GIST), Gwangju, 500-712, The Republic of Korea
| | - Chul-Seung Park
- From the School of Life Sciences, Cell Dynamics Research Center and National Leading Research Laboratory, Gwangju Institute Science and Technology (GIST), Gwangju, 500-712, The Republic of Korea
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Sharathchandra A, Katoch A, Das S. IRES mediated translational regulation of p53 isoforms. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:131-9. [PMID: 24343861 DOI: 10.1002/wrna.1202] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 09/14/2013] [Accepted: 09/21/2013] [Indexed: 01/08/2023]
Abstract
p53 is a well known tumor suppressor protein that plays a critical role in cell cycle arrest and apoptosis. It has several isoforms which are produced by transcriptional and posttranscriptional regulatory mechanisms. p53 mRNA has been demonstrated to be translated into two isoforms, full-length p53 (FL-p53) and a truncated isoform ΔN-p53 by the use of alternative translation initiation sites. The mechanism of translation regulation of these two isoforms was further elucidated by the discovery of IRES elements in the p53 mRNA. These two IRESs were shown to regulate the translation of p53 and ΔN-p53 in a distinct cell-cycle phase-dependent manner. This review focuses on the current understanding of the regulation of p53 IRES mediated translation and the role of cis and trans acting factors that influence expression of p53 isoforms.
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Chen J, Yang JT, Doctor DL, Rawlins BA, Shields BC, Vaughn JC. 5'-UTR mediated translational control of splicing assembly factor RNP-4F expression during development of the Drosophila central nervous system. Gene 2013; 528:154-62. [PMID: 23892091 DOI: 10.1016/j.gene.2013.07.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 07/17/2013] [Indexed: 11/24/2022]
Abstract
Drosophila RNP-4F is a highly conserved protein from yeast to human and functions as a spliceosome assembly factor during pre-mRNA splicing. Two major developmentally regulated rnp-4f mRNA isoforms have been described during fly development, designated "long" and "short," differing by a 177-nt tract in the 5'-UTR. This region potentially folds into a single long stable stem-loop by pairing of intron 0 and part of exon 2. Since the coding potential for the two isoforms is identical, the interesting question arises as to the functional significance of this evolutionarily-conserved 5'-UTR feature. Here we describe the effects of wild-type and mutated stem-loop on modulation of rnp-4f gene expression in embryos using a GFP reporter assay. In this work, a new GFP expression vector designated pUAS-Neostinger was constructed. The UAS-GAL4 system was utilized to trigger GFP expression using tissue-specific promoter driver fly lines. Fluorescence microscopy visualization, Western blotting and real-time qRT-PÇR were used to study and quantify GFP reporter protein and mRNA levels. A significant increase in GFP reporter protein expression due to presence of the wild-type stem-loop sequence/structure was unexpectedly observed with no concomitant increase in GFP reporter mRNA levels, showing that the 177-nt region enhancement acts posttranscriptionally. The effects of potential cis-acting elements within the stem-loop were evaluated using the reporter assay in two mutant constructs. Results of GFP reporter over-expression show that RNP-4F translational regulation is highly sensitive in the developing fly central nervous system. The potential molecular mechanism behind the observed translational enhancement is discussed.
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Affiliation(s)
- Jing Chen
- Department of Biology, Cell Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
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Pichon X, Wilson LA, Stoneley M, Bastide A, King HA, Somers J, Willis AEE. RNA binding protein/RNA element interactions and the control of translation. Curr Protein Pept Sci 2013; 13:294-304. [PMID: 22708490 PMCID: PMC3431537 DOI: 10.2174/138920312801619475] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/10/2012] [Accepted: 01/20/2012] [Indexed: 01/18/2023]
Abstract
A growing body of work demonstrates the importance of post-transcriptional control, in particular translation
initiation, in the overall regulation of gene expression. Here we focus on the contribution of regulatory elements within the
5’ and 3’ untranslated regions of mRNA to gene expression in eukaryotic cells including terminal oligopyrimidine tracts,
internal ribosome entry segments, upstream open reading frames and cytoplasmic polyadenylation elements. These
mRNA regulatory elements may adopt complex secondary structures and/or contain sequence motifs that allow their interaction
with a variety of regulatory proteins, RNAs and RNA binding proteins, particularly hnRNPs. The resulting interactions
are context-sensitive, and provide cells with a sensitive and fast response to cellular signals such as hormone exposure
or cytotoxic stress. Importantly, an increasing number of diseases have been identified, particularly cancers and
those associated with neurodegeneration, which originate either from mutation of these regulatory motifs, or from deregulation
of their cognate binding partners.
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Affiliation(s)
- Xavier Pichon
- Medical Research Council Toxicology Unit, Leicester, UK
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Shi Y, Frost P, Hoang B, Yang Y, Fukunaga R, Gera J, Lichtenstein A. MNK kinases facilitate c-myc IRES activity in rapamycin-treated multiple myeloma cells. Oncogene 2013; 32:190-7. [PMID: 22370634 PMCID: PMC3401333 DOI: 10.1038/onc.2012.43] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 01/13/2012] [Accepted: 01/15/2012] [Indexed: 12/20/2022]
Abstract
When mTOR inhibitor rapalogs prevent cap-dependent translation of cell-cycle proteins like c-myc, continuing tumor cell growth depends on cap-independent translation, which is mediated by internal ribosome entry sites (IRESes) located in the 5'-UTR (untranslated region) of transcripts. To investigate if rapalog-induced activation of MNK kinases had a role in such IRES activity, we studied multiple myeloma (MM) cells. Rapamycin (RAP)-activated MNK1 kinase activity in MM cell lines and primary specimens by a mitogen-activated protein kinase-dependent mechanism. Pharmacological inhibition of MNK activity or genetic silencing of MNK1 prevented a rapalog-induced upregulation of c-myc IRES activity. Although RAP, used alone, had little effect on myc protein expression, when combined with a MNK inhibitor, myc protein expression was abrogated. In contrast, there was no inhibition of myc RNA, consistent with an effect on myc translation. In a RAP-resistant MM cell lines as well as a resistant primary MM specimen, co-exposure to a MNK inhibitor or MNK1 knockdown significantly sensitized cells for RAP-induced cytoreduction. Studies in MNK-null murine embryonic fibroblasts additionally supported a role for MNK kinases in RAP-induced myc IRES stimulation. These results indicate that MNK kinase activity has a critical role in the fail-safe mechanism of IRES-dependent translation when mTOR is inhibited. As kinase activity also regulated sensitivity to RAP, the data also provide a rationale for therapeutically targeting MNK kinases for combined treatment with mTOR inhibitors.
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Affiliation(s)
- Y Shi
- Department of Medicine, Greater Los Angeles VA Healthcare Center and Jonsson Comprehensive Cancer Center of the UCLA Medical Center, Los Angeles, CA, USA
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40
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Genome-wide analysis of c-MYC-regulated mRNAs and miRNAs, and c-MYC DNA binding by next-generation sequencing. Methods Mol Biol 2013; 1012:145-85. [PMID: 24006064 DOI: 10.1007/978-1-62703-429-6_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The c-MYC oncogene is activated in ~50 % of all tumors, and its product, the c-MYC transcription factor, regulates numerous processes, which contribute to tumor initiation and progression. Therefore, the genome-wide characterization of c-MYC targets and their role in different tumor entities is a recurrent theme in cancer research. Recently, next-generation sequencing (NGS) has become a powerful tool to analyze mRNA and miRNA expression, as well as DNA binding of proteins in a genome-wide manner with an extremely high resolution and coverage. Since the c-MYC transcription factor regulates mRNA and miRNA expression by binding to specific DNA elements in the vicinity of promoters, NGS can be used to generate integrated representations of c-MYC-mediated regulations of gene transcription and chromatin modifications. Here, we provide protocols and examples of NGS-based analyses of c-MYC-regulated mRNA and miRNA expression, as well as of DNA binding by c-MYC. Furthermore, the validation of single c-MYC targets identified by NGS is described. Taken together, these approaches allow an accelerated and comprehensive analysis of c-MYC function in numerous cellular contexts which will further illuminate the role of this important oncogene.
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Didiot MC, Hewett J, Varin T, Freuler F, Selinger D, Nick H, Reinhardt J, Buckler A, Myer V, Schuffenhauer A, Guy CT, Parker CN. Identification of cardiac glycoside molecules as inhibitors of c-Myc IRES-mediated translation. ACTA ACUST UNITED AC 2012; 18:407-19. [PMID: 23150017 DOI: 10.1177/1087057112466698] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Translation initiation is a fine-tuned process that plays a critical role in tumorigenesis. The use of small molecules that modulate mRNA translation provides tool compounds to explore the mechanism of translational initiation and to further validate protein synthesis as a potential pharmaceutical target for cancer therapeutics. This report describes the development and use of a click beetle, dual luciferase cell-based assay multiplexed with a measure of compound toxicity using resazurin to evaluate the differential effect of natural products on cap-dependent or internal ribosome entry site (IRES)-mediated translation initiation and cell viability. This screen identified a series of cardiac glycosides as inhibitors of IRES-mediated translation using, in particular, the oncogene mRNA c-Myc IRES. Treatment of c-Myc-dependent cancer cells with these compounds showed a decrease in c-Myc protein associated with a significant modulation of cell viability. These findings suggest that inhibition of IRES-mediated translation initiation may be a strategy to inhibit c-Myc-driven tumorigenesis.
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Grzmil M, Hemmings BA. Translation Regulation as a Therapeutic Target in Cancer: Figure 1. Cancer Res 2012; 72:3891-900. [DOI: 10.1158/0008-5472.can-12-0026] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Bommert KS, Effenberger M, Leich E, Küspert M, Murphy D, Langer C, Moll R, Janz S, Mottok A, Weissbach S, Rosenwald A, Bargou R, Bommert K. The feed-forward loop between YB-1 and MYC is essential for multiple myeloma cell survival. Leukemia 2012; 27:441-50. [PMID: 22772059 DOI: 10.1038/leu.2012.185] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Y-box binding protein 1 (YB-1) functions as a translational regulator and has been suggested to elevate MYC mRNA translation via an internal ribosome entry segment (IRES) point mutation in multiple myeloma (MM). We show that YB-1-mediated translation of MYC mRNA occurs independently of the reported IRES mutation, as 87 MM patients (n=88) and all tested human MM cell lines (HMCLs) were negative for the mutation. We show for the first time that positive MYC staining predicts YB-1 co-expression in malignant plasma cells and YB-1/MYC co-expression increases from 30% in medullary to 70% in extramedullary MM. YB-1 knockdown in HMCLs reduced both MYC protein levels and MYC mRNA in the polysomal fraction, providing a mechanism by which YB-1 controls MYC translation. MYC transcription of YB-1 is demonstrated in HMCLs as MYC knockdown resulted in reduced YB-1 protein and mRNA levels. Furthermore, MYC activation in non-malignant mouse embryonic fibroblasts (MEFs) increased YB-1 mRNA, clearly indicating that MYC drives YB-1 transcription. Importantly, perturbation of the MYC/YB-1 oncogenic circuit leads to apoptosis in HMCLs. Here, we demonstrate that these two proteins co-regulate each other via combined transcriptional/translational activity establishing their pivotal role in MM cell survival. We therefore suggest that targeting the YB-1/mRNA interaction provides a new strategy for MM drug development.
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Affiliation(s)
- K S Bommert
- Division of Haematology and Medical Oncology, Department of Internal Medicine II, Comprehensive Cancer Centre Mainfranken, University Hospital Würzburg, Würzburg, Germany.
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Jiang H, Schwertz H, Schmid DI, Jones BB, Kriesel J, Martinez ML, Weyrich AS, Zimmerman GA, Kraiss LW. Different mechanisms preserve translation of programmed cell death 8 and JunB in virus-infected endothelial cells. Arterioscler Thromb Vasc Biol 2012; 32:997-1004. [PMID: 22328780 DOI: 10.1161/atvbaha.112.245324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
OBJECTIVE Translation initiation of eukaryotic mRNAs typically occurs by cap-dependent ribosome scanning mechanism. However, certain mRNAs are translated by ribosome assembly at internal ribosome entry sites (IRESs). Whether IRES-mediated translation occurs in stressed primary human endothelial cells (ECs) is unknown. METHODS AND RESULTS We performed microarray analysis of polyribosomal mRNA from ECs to identify IRES-containing mRNAs. Cap-dependent translation was disabled by poliovirus (PV) infection and confirmed by loss of polysome peaks, detection of eukaryotic initiation factor (eIF) 4G cleavage, and decreased protein synthesis. We found that 87.4% of mRNAs were dissociated from polysomes in virus-infected ECs. Twelve percent of mRNAs remained associated with polysomes, and 0.6% were enriched ≥2-fold in polysome fractions from infected ECs. Quantitative reverse transcription-polymerase chain reaction confirmed the microarray findings for 31 selected mRNAs. We found that enriched polysome associations of programmed cell death 8 (PDCD8) and JunB mRNA resulted in increased protein expression in PV-infected ECs. The presence of IRESs in the 5' untranslated region of PDCD8 mRNA, but not of JunB mRNA, was confirmed by dicistronic analysis. CONCLUSIONS We show that microarray profiling of polyribosomal mRNA transcripts from PV-infected ECs successfully identifies mRNAs whose translation is preserved in the face of stress-induced, near complete cessation of cap-dependent initiation. Nevertheless, internal ribosome entry is not the only mechanism responsible for this privileged translation.
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Affiliation(s)
- Huimiao Jiang
- Division of Vascular Surgery, University of Utah, Salt Lake City, USA
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Adeli K. Translational control mechanisms in metabolic regulation: critical role of RNA binding proteins, microRNAs, and cytoplasmic RNA granules. Am J Physiol Endocrinol Metab 2011; 301:E1051-64. [PMID: 21971522 DOI: 10.1152/ajpendo.00399.2011] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Regulated cell metabolism involves acute and chronic regulation of gene expression by various nutritional and endocrine stimuli. To respond effectively to endogenous and exogenous signals, cells require rapid response mechanisms to modulate transcript expression and protein synthesis and cannot, in most cases, rely on control of transcriptional initiation that requires hours to take effect. Thus, co- and posttranslational mechanisms have been increasingly recognized as key modulators of metabolic function. This review highlights the critical role of mRNA translational control in modulation of global protein synthesis as well as specific protein factors that regulate metabolic function. First, the complex lifecycle of eukaryotic mRNAs will be reviewed, including our current understanding of translational control mechanisms, regulation by RNA binding proteins and microRNAs, and the role of RNA granules, including processing bodies and stress granules. Second, the current evidence linking regulation of mRNA translation with normal physiological and metabolic pathways and the associated disease states are reviewed. A growing body of evidence supports a key role of translational control in metabolic regulation and implicates translational mechanisms in the pathogenesis of metabolic disorders such as type 2 diabetes. The review also highlights translational control of apolipoprotein B (apoB) mRNA by insulin as a clear example of endocrine modulation of mRNA translation to bring about changes in specific metabolic pathways. Recent findings made on the role of 5'-untranslated regions (5'-UTR), 3'-UTR, RNA binding proteins, and RNA granules in mediating insulin regulation of apoB mRNA translation, apoB protein synthesis, and hepatic lipoprotein production are discussed.
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Affiliation(s)
- Khosrow Adeli
- Program in Molecular Structure & Function, Research Institute, The Hospital for Sick Children, Atrium 3653, 555 University Ave., Toronto, ON, M5G 1X8 Canada.
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Tang YS, Khan RA, Zhang Y, Xiao S, Wang M, Hansen DK, Jayaram HN, Antony AC. Incrimination of heterogeneous nuclear ribonucleoprotein E1 (hnRNP-E1) as a candidate sensor of physiological folate deficiency. J Biol Chem 2011; 286:39100-15. [PMID: 21930702 DOI: 10.1074/jbc.m111.230938] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mechanism underlying the sensing of varying degrees of physiological folate deficiency, prior to adaptive optimization of cellular folate uptake through the translational up-regulation of folate receptors (FR) is unclear. Because homocysteine, which accumulates intracellularly during folate deficiency, stimulated interactions between heterogeneous nuclear ribonucleoprotein E1 (hnRNP-E1) and an 18-base FR-α mRNA cis-element that led to increased FR biosynthesis and net up-regulation of FR at cell surfaces, hnRNP-E1 was a plausible candidate sensor of folate deficiency. Accordingly, using purified components, we evaluated the physiological basis whereby L-homocysteine triggered these RNA-protein interactions to stimulate FR biosynthesis. L-homocysteine induced a concentration-dependent increase in RNA-protein binding affinity throughout the range of physiological folate deficiency, which correlated with a proportionate increase in translation of FR in vitro and in cultured human cells. Targeted reduction of newly synthesized hnRNP-E1 proteins by siRNA to hnRNP-E1 mRNA reduced both constitutive and L-homocysteine-induced rates of FR biosynthesis. Furthermore, L-homocysteine covalently bound hnRNP-E1 via multiple protein-cysteine-S-S-homocysteine mixed disulfide bonds within K-homology domains known to interact with mRNA. These data suggest that a concentration-dependent, sequential disruption of critical cysteine-S-S-cysteine bonds by covalently bound L-homocysteine progressively unmasks an underlying RNA-binding pocket in hnRNP-E1 to optimize interaction with FR-α mRNA cis-element preparatory to FR up-regulation. Collectively, such data incriminate hnRNP-E1 as a physiologically relevant, sensitive, cellular sensor of folate deficiency. Because diverse mammalian and viral mRNAs also interact with this RNA-binding domain with functional consequences to their protein expression, homocysteinylated hnRNP-E1 also appears well positioned to orchestrate a novel, nutrition-sensitive (homocysteine-responsive), posttranscriptional RNA operon in folate-deficient cells.
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Affiliation(s)
- Ying-Sheng Tang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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Liu X, Xiao N, Guo W, Wu Y, Cai Z, He Q, Zhang L, Chen X, Sun C, Wang J, Zhu C, Jin H, Wang Y. The hOGG1 gene 5′-UTR variant c.−53G>C contributes to the risk of gastric cancer but not colorectal cancer in the Chinese population. J Cancer Res Clin Oncol 2011; 137:1477-85. [DOI: 10.1007/s00432-011-1022-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 07/21/2011] [Indexed: 02/05/2023]
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49
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Shi Y, Frost P, Hoang B, Benavides A, Gera J, Lichtenstein A. IL-6-induced enhancement of c-Myc translation in multiple myeloma cells: critical role of cytoplasmic localization of the rna-binding protein hnRNP A1. J Biol Chem 2010; 286:67-78. [PMID: 20974848 DOI: 10.1074/jbc.m110.153221] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prior work indicates that IL-6 can stimulate c-Myc expression in multiple myeloma (MM) cells, which is independent of effects on transcription and due to enhanced translation mediated by an internal ribosome entry site in the 5'-UTR of the c-Myc RNA. The RNA-binding protein hnRNP A1 (A1) was also critical to IL-6-stimulated translation. Because A1 shuttles between nucleus and cytoplasm, we investigated whether the ability of IL-6 to enhance Myc translation was mediated by stimulation of A1 shuttling. In MM cell lines and primary specimens, IL-6 increased A1 cytoplasmic localization. In contrast, there was no effect on the total cellular levels of A1. Use of a dominant negative A1 construct, which prevents endogenous A1 from nucleus-to-cytoplasm transit, prevented the ability of IL-6 to enhance Myc internal ribosome entry site activity, Myc protein expression, and MM cell growth. IL-6-stimulated cytoplasmic localization was mediated by alterations in the C-terminal M9 peptide of A1, and this correlated with the ability of IL-6 to induce serine phosphorylation of this domain. A p38 kinase inhibitor prevented IL-6-induced A1 phosphorylation. Thus, IL-6 activates c-Myc translation in MM cells by inducing A1 phosphorylation and cytoplasmic localization in a p38-dependent fashion. These data suggest A1 as a potential therapeutic target in MM.
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Affiliation(s)
- Yijiang Shi
- Division of Hematology Oncology, University of California at Los Angeles-Greater Los Angeles Veterans Affairs Healthcare Center, Jonnsson Comprehensive Cancer Center, Los Angeles, California 90073, USA
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Gendron K, Ferbeyre G, Heveker N, Brakier-Gingras L. The activity of the HIV-1 IRES is stimulated by oxidative stress and controlled by a negative regulatory element. Nucleic Acids Res 2010; 39:902-12. [PMID: 20935056 PMCID: PMC3035469 DOI: 10.1093/nar/gkq885] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Initiation of translation of the full-length messenger RNA of HIV-1, which generates the viral structural proteins and enzymes, is cap-dependent but can also use an internal ribosome entry site (IRES) located in the 5′ untranslated region. Our aim was to define, through a mutational analysis, regions of HIV-1 IRES that are important for its activity. A dual-luciferase reporter construct where the Renilla luciferase (Rluc) translation is cap-dependent while the firefly luciferase (Fluc) translation depends on HIV-1 IRES was used. The Fluc/Rluc ratio was measured in lysates of Jurkat T cells transfected with the dual-luciferase plasmid bearing either the wild-type or a mutated IRES. Deletions or mutations in three regions decreased the IRES activity but deletion or mutations of a stem-loop preceding the primer binding site increased the IRES activity. The wild-type IRES activity, but not that of an IRES with a mutated stem-loop, was increased when cells were treated with agents that induce oxidative stress. Such stress is known to be caused by HIV-1 infection and we propose that this stem-loop is involved in a switch that stimulates the IRES activity in cells infected with HIV-1, supporting the suggestion that the IRES activity is up-regulated in the course of HIV-1 replication cycle.
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Affiliation(s)
- Karine Gendron
- Département de biochimie, Université de Montréal, Montréal, Québec H3T 1J4, Canada
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