1
|
Deng X, Yu YV, Jin YN. Non-canonical translation in cancer: significance and therapeutic potential of non-canonical ORFs, m 6A-modification, and circular RNAs. Cell Death Discov 2024; 10:412. [PMID: 39333489 PMCID: PMC11437038 DOI: 10.1038/s41420-024-02185-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 09/13/2024] [Accepted: 09/18/2024] [Indexed: 09/29/2024] Open
Abstract
Translation is a decoding process that synthesizes proteins from RNA, typically mRNA. The conventional translation process consists of four stages: initiation, elongation, termination, and ribosome recycling. Precise control over the translation mechanism is crucial, as dysregulation in this process is often linked to human diseases such as cancer. Recent discoveries have unveiled translation mechanisms that extend beyond typical well-characterized components like the m7G cap, poly(A)-tail, or translation factors like eIFs. These mechanisms instead utilize atypical elements, such as non-canonical ORF, m6A-modification, and circular RNA, as key components for protein synthesis. Collectively, these mechanisms are classified as non-canonical translations. It is increasingly clear that non-canonical translation mechanisms significantly impact the various regulatory pathways of cancer, including proliferation, tumorigenicity, and the behavior of cancer stem cells. This review explores the involvement of a variety of non-canonical translation mechanisms in cancer biology and provides insights into potential therapeutic strategies for cancer treatment.
Collapse
Affiliation(s)
- Xiaoyi Deng
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
| | - Yanxun V Yu
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, Hubei, China
| | - Youngnam N Jin
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China.
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, Hubei, China.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Kubickova A, De Sanctis JB, Hajduch M. Isoform-Directed Control of c-Myc Functions: Understanding the Balance from Proliferation to Growth Arrest. Int J Mol Sci 2023; 24:17524. [PMID: 38139353 PMCID: PMC10743581 DOI: 10.3390/ijms242417524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
The transcription factor c-Myc, a key regulator of cellular processes, has long been associated with roles in cell proliferation and apoptosis. This review analyses the multiple functions of c-Myc by examining the different c-Myc isoforms in detail. The impact of different c-Myc isoforms, in particular p64 and p67, on fundamental biological processes remains controversial. It is necessary to investigate the different isoforms in the context of proto-oncogenesis. The current knowledge base suggests that neoplastic lesions may possess the means for self-destruction via increased c-Myc activity. This review presents the most relevant information on the c-Myc locus and focuses on a number of isoforms, including p64 and p67. This compilation provides a basis for the development of therapeutic approaches that target the potent growth arresting and pro-apoptotic functions of c-Myc. This information can then be used to develop targeted interventions against specific isoforms with the aim of shifting the oncogenic effects of c-Myc from pro-proliferative to pro-apoptotic. The research summarised in this review can deepen our understanding of how c-Myc activity contributes to different cellular responses, which will be crucial in developing effective therapeutic strategies; for example, isoform-specific approaches may allow for precise modulation of c-Myc function.
Collapse
Affiliation(s)
- Agata Kubickova
- Institute of Molecular and Translational Medicine, Palacky University and University Hospital Olomouc, Hnevotinska 1333/5, 77900 Olomouc, Czech Republic; (A.K.); (J.B.D.S.)
- Institute of Molecular and Translational Medicine, Czech Advanced Technology and Research Institute, Palacky University in Olomouc, Hnevotinska 1333/5, 77900 Olomouc, Czech Republic
| | - Juan Bautista De Sanctis
- Institute of Molecular and Translational Medicine, Palacky University and University Hospital Olomouc, Hnevotinska 1333/5, 77900 Olomouc, Czech Republic; (A.K.); (J.B.D.S.)
- Institute of Molecular and Translational Medicine, Czech Advanced Technology and Research Institute, Palacky University in Olomouc, Hnevotinska 1333/5, 77900 Olomouc, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Palacky University and University Hospital Olomouc, Hnevotinska 1333/5, 77900 Olomouc, Czech Republic; (A.K.); (J.B.D.S.)
- Institute of Molecular and Translational Medicine, Czech Advanced Technology and Research Institute, Palacky University in Olomouc, Hnevotinska 1333/5, 77900 Olomouc, Czech Republic
| |
Collapse
|
4
|
Jang C, Blume SW, Choi HS. Novel protein products encoded by upstream open reading frames of the MYCN gene in pediatric embryonal tumors. J Cell Biochem 2023; 124:1615-1627. [PMID: 37682868 DOI: 10.1002/jcb.30470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 08/12/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
The MYCC and MYCN loci are each associated with two upstream open reading frames (uORFs) potentially encoding small proteins (9-21 kDa). We previously demonstrated that uORFs mrtl and MYCHEX1 of MYCC are translated, and their protein products may function to regulate the expression of the "parent" oncogene. We hypothesized that a similar relationship might exist between MYCN and its two uORFs: MYCNOT and MNOP, and investigated the uORF-encoded proteins associated with MYCN to confirm their expression and intracellular location in neuroblastoma and medulloblastoma cells and tissues. MNOP, MYCNOT, mrtl, and MYCHEX1 were readily detected via reverse transcription polymerase chain reaction and Western blot analysis in tumor cell lines. In tumor tissue, MNOP protein expression was confirmed; however, MCYNOT generated from alternative splicing MYCNΔ1b mRNA was not detected. Immunofluorescence staining of MYCNOT displayed multiple bright foci in the nucleus and diffuse staining in the cytoplasm, suggesting that this small protein may function in both the nucleus and cytoplasm. Upon JQ1 treatment, MYCN, MYCNOT, and mrtl decreased substantially or disappeared completely in three different tumor cell lines. Significant levels of apoptosis were observed in each pediatric embryonal tumor cell line but not T47D breast carcinoma cells, suggesting that response to JQ1 transcriptional inhibition is greatest in tumor cells, which depend on MYC to maintain an undifferentiated phenotype. In conclusion, both MYCN uORF-encoded proteins MNOP and MYCNOT, together with the two MYCC uORF-encoded proteins mrtl and MYCHEX1 were detected simultaneously in tumor cell lines and tumor tissues. These four distinct proteins are translated from the "5'-untranslated region" of MYCN or MYCC mRNA and display consistent distribution patterns within the cell. Additional studies to further elucidate the physiological and pathological roles of these uORF-encoded proteins are warranted, as insights gained could inform new strategies for modulating MYC-family oncogenes by targeting their uORFs.
Collapse
Affiliation(s)
- Chorong Jang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Scott W Blume
- Department of Medicine and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hyoung Soo Choi
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| |
Collapse
|
5
|
Internal Ribosome Entry Site (IRES)-Mediated Translation and Its Potential for Novel mRNA-Based Therapy Development. Biomedicines 2022; 10:biomedicines10081865. [PMID: 36009412 PMCID: PMC9405587 DOI: 10.3390/biomedicines10081865] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
Many conditions can benefit from RNA-based therapies, namely, those targeting internal ribosome entry sites (IRESs) and their regulatory proteins, the IRES trans-acting factors (ITAFs). IRES-mediated translation is an alternative mechanism of translation initiation, known for maintaining protein synthesis when canonical translation is impaired. During a stress response, it contributes to cell reprogramming and adaptation to the new environment. The relationship between IRESs and ITAFs with tumorigenesis and resistance to therapy has been studied in recent years, proposing new therapeutic targets and treatments. In addition, IRES-dependent translation initiation dysregulation is also related to neurological and cardiovascular diseases, muscular atrophies, or other syndromes. The participation of these structures in the development of such pathologies has been studied, yet to a far lesser extent than in cancer. Strategies involving the disruption of IRES–ITAF interactions or the modification of ITAF expression levels may be used with great impact in the development of new therapeutics. In this review, we aim to comprehend the current data on groups of human pathologies associated with IRES and/or ITAF dysregulation and their application in the designing of new therapeutic approaches using them as targets or tools. Thus, we wish to summarise the evidence in the field hoping to open new promising lines of investigation toward personalised treatments.
Collapse
|
6
|
Baisden JT, Childs-Disney JL, Ryan LS, Disney MD. Affecting RNA biology genome-wide by binding small molecules and chemically induced proximity. Curr Opin Chem Biol 2021; 62:119-129. [PMID: 34118759 PMCID: PMC9264282 DOI: 10.1016/j.cbpa.2021.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/08/2023]
Abstract
The ENCODE and genome-wide association projects have shown that much of the genome is transcribed into RNA and much less is translated into protein. These and other functional studies suggest that the druggable transcriptome is much larger than the druggable proteome. This review highlights approaches to define druggable RNA targets and structure-activity relationships across genomic RNA. Binding compounds can be identified and optimized into structure-specific ligands by using sequence-based design with various modes of action, for example, inhibiting translation or directing pre-mRNA splicing outcomes. In addition, strategies to direct protein activity against an RNA of interest via chemically induced proximity is a burgeoning area that has been validated both in cells and in preclinical animal models, and we describe that it may allow rapid access to new avenues to affect RNA biology. These approaches and the unique modes of action suggest that more RNAs are potentially amenable to targeting than proteins.
Collapse
Affiliation(s)
- Jared T Baisden
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Lucas S Ryan
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA.
| |
Collapse
|
7
|
van den Akker GGH, Zacchini F, Housmans BAC, van der Vloet L, Caron MMJ, Montanaro L, Welting TJM. Current Practice in Bicistronic IRES Reporter Use: A Systematic Review. Int J Mol Sci 2021; 22:5193. [PMID: 34068921 PMCID: PMC8156625 DOI: 10.3390/ijms22105193] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022] Open
Abstract
Bicistronic reporter assays have been instrumental for transgene expression, understanding of internal ribosomal entry site (IRES) translation, and identification of novel cap-independent translational elements (CITE). We observed a large methodological variability in the use of bicistronic reporter assays and data presentation or normalization procedures. Therefore, we systematically searched the literature for bicistronic IRES reporter studies and analyzed methodological details, data visualization, and normalization procedures. Two hundred fifty-seven publications were identified using our search strategy (published 1994-2020). Experimental studies on eukaryotic adherent cell systems and the cell-free translation assay were included for further analysis. We evaluated the following methodological details for 176 full text articles: the bicistronic reporter design, the cell line or type, transfection methods, and time point of analyses post-transfection. For the cell-free translation assay, we focused on methods of in vitro transcription, type of translation lysate, and incubation times and assay temperature. Data can be presented in multiple ways: raw data from individual cistrons, a ratio of the two, or fold changes thereof. In addition, many different control experiments have been suggested when studying IRES-mediated translation. In addition, many different normalization and control experiments have been suggested when studying IRES-mediated translation. Therefore, we also categorized and summarized their use. Our unbiased analyses provide a representative overview of bicistronic IRES reporter use. We identified parameters that were reported inconsistently or incompletely, which could hamper data reproduction and interpretation. On the basis of our analyses, we encourage adhering to a number of practices that should improve transparency of bicistronic reporter data presentation and improve methodological descriptions to facilitate data replication.
Collapse
Affiliation(s)
- Guus Gijsbertus Hubert van den Akker
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Federico Zacchini
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, I-40138 Bologna, Italy; (F.Z.); (L.M.)
- Centro di Ricerca Biomedica Applicata—CRBA, Bologna University, Policlinico di Sant’Orsola, I-40138 Bologna, Italy
| | - Bas Adrianus Catharina Housmans
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Laura van der Vloet
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Marjolein Maria Johanna Caron
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, I-40138 Bologna, Italy; (F.Z.); (L.M.)
- Centro di Ricerca Biomedica Applicata—CRBA, Bologna University, Policlinico di Sant’Orsola, I-40138 Bologna, Italy
- Programma Dipartimentale in Medicina di Laboratorio, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Tim Johannes Maria Welting
- Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands; (G.G.H.v.d.A.); (B.A.C.H.); (L.v.d.V.); (M.M.J.C.)
| |
Collapse
|
8
|
Reprogramming translation for gene therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:439-476. [PMID: 34175050 DOI: 10.1016/bs.pmbts.2021.01.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Translational control plays a fundamental role in the regulation of gene expression in eukaryotes. Modulating translational efficiency allows the cell to fine-tune the expression of genes, spatially control protein localization, and trigger fast responses to environmental stresses. Translational regulation involves mechanisms acting on multiple steps of the protein synthesis pathway: initiation, elongation, and termination. Many cis-acting elements present in the 5' UTR of transcripts can influence translation at the initiation step. Among them, the Kozak sequence impacts translational efficiency by regulating the recognition of the start codon; upstream open reading frames (uORFs) are associated with inhibition of translation of the downstream protein; internal ribosomal entry sites (IRESs) can promote cap-independent translation. CRISPR-Cas technology is a revolutionary gene-editing tool that has also been applied to the regulation of gene expression. In this chapter, we focus on the genome editing approaches developed to modulate the translational efficiency with the aim to find novel therapeutic approaches, in particular acting on the cis-elements, that regulate the initiation of protein synthesis.
Collapse
|
9
|
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: 5.3] [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.
Collapse
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
| |
Collapse
|
10
|
Péladeau C, Jasmin BJ. Targeting IRES-dependent translation as a novel approach for treating Duchenne muscular dystrophy. RNA Biol 2020; 18:1238-1251. [PMID: 33164678 DOI: 10.1080/15476286.2020.1847894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Internal-ribosomal entry sites (IRES) are translational elements that allow the initiation machinery to start protein synthesis via internal initiation. IRESs promote tissue-specific translation in stress conditions when conventional cap-dependent translation is inhibited. Since many IRES-containing mRNAs are relevant to diseases, this cellular mechanism is emerging as an attractive therapeutic target for pharmacological and genetic modulations. Indeed, there has been growing interest over the past years in determining the therapeutic potential of IRESs for several disease conditions such as cancer, neurodegeneration and neuromuscular diseases including Duchenne muscular dystrophy (DMD). IRESs relevant for DMD have been identified in several transcripts whose protein product results in functional improvements in dystrophic muscles. Together, these converging lines of evidence indicate that activation of IRES-mediated translation of relevant transcripts in DMD muscle represents a novel and appropriate therapeutic strategy for DMD that warrants further investigation, particularly to identify agents that can modulate their activity.
Collapse
Affiliation(s)
- Christine Péladeau
- Department of Cellular and Molecular Medicine, and the Eric Poulin Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Bernard J Jasmin
- Department of Cellular and Molecular Medicine, and the Eric Poulin Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
11
|
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: 1.4] [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.
Collapse
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
| |
Collapse
|
12
|
Benavides-Serrato A, Saunders JT, Holmes B, Nishimura RN, Lichtenstein A, Gera J. Repurposing Potential of Riluzole as an ITAF Inhibitor in mTOR Therapy Resistant Glioblastoma. Int J Mol Sci 2020; 21:ijms21010344. [PMID: 31948038 PMCID: PMC6981868 DOI: 10.3390/ijms21010344] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/27/2019] [Accepted: 12/31/2019] [Indexed: 12/17/2022] Open
Abstract
Internal ribosome entry site (IRES)-mediated protein synthesis has been demonstrated to play an important role in resistance to mechanistic target of rapamycin (mTOR) targeted therapies. Previously, we have demonstrated that the IRES trans-acting factor (ITAF), hnRNP A1 is required to promote IRES activity and small molecule inhibitors which bind specifically to this ITAF and curtail IRES activity, leading to mTOR inhibitor sensitivity. Here we report the identification of riluzole (Rilutek®), an FDA-approved drug for amyotrophic lateral sclerosis (ALS), via an in silico docking analysis of FDA-approved compounds, as an inhibitor of hnRNP A1. In a riluzole-bead coupled binding assay and in surface plasmon resonance imaging analyses, riluzole was found to directly bind to hnRNP A1 and inhibited IRES activity via effects on ITAF/RNA-binding. Riluzole also demonstrated synergistic anti-glioblastoma (GBM) affects with mTOR inhibitors in vitro and in GBM xenografts in mice. These data suggest that repurposing riluzole, used in conjunction with mTOR inhibitors, may serve as an effective therapeutic option in glioblastoma.
Collapse
Affiliation(s)
- Angelica Benavides-Serrato
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA 91343, USA
| | - Jacquelyn T. Saunders
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA 91343, USA
| | - Brent Holmes
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA 91343, USA
| | - Robert N. Nishimura
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA 91343, USA
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Alan Lichtenstein
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA 91343, USA
- Jonnson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA 90095, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Joseph Gera
- Department of Research & Development, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, CA 91343, USA
- Jonnson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA 90095, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA 90095, USA
- Correspondence: ; Tel.: +00-1-818-895-9416
| |
Collapse
|
13
|
Vaklavas C, Blume SW, Grizzle WE. Hallmarks and Determinants of Oncogenic Translation Revealed by Ribosome Profiling in Models of Breast Cancer. Transl Oncol 2020; 13:452-470. [PMID: 31911279 PMCID: PMC6948383 DOI: 10.1016/j.tranon.2019.12.002] [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: 08/28/2019] [Revised: 11/28/2019] [Accepted: 12/01/2019] [Indexed: 12/21/2022] Open
Abstract
Gene expression is extensively and dynamically modulated at the level of translation. How cancer cells prioritize the translation of certain mRNAs over others from a pool of competing mRNAs remains an open question. Here, we analyze translation in cell line models of breast cancer and normal mammary tissue by ribosome profiling. We identify key recurrent themes of oncogenic translation: higher ribosome occupancy, greater variance of translational efficiencies, and preferential translation of transcriptional regulators and signaling proteins in malignant cells as compared with their nonmalignant counterpart. We survey for candidate RNA interacting proteins that could associate with the 5′untranslated regions of the transcripts preferentially translated in breast tumour cells. We identify SRSF1, a prototypic splicing factor, to have a pervasive direct and indirect impact on translation. In a representative estrogen receptor–positive and estrogen receptor–negative cell line, we find that protein synthesis relies heavily on SRSF1. SRSF1 is predominantly intranuclear. Under certain conditions, SRSF1 translocates from the nucleus to the cytoplasm where it associates with MYC and CDK1 mRNAs and upregulates their internal ribosome entry site–mediated translation. Our results point to a synergy between splicing and translation and unveil how certain RNA-binding proteins modulate the translational landscape in breast cancer.
Collapse
Affiliation(s)
- Christos Vaklavas
- Department of Medicine, Division of Hematology / Oncology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Scott W Blume
- Department of Medicine, Division of Hematology / Oncology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - William E Grizzle
- Department of Pathology, O'Neal Comprehensive Cancer Centre, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| |
Collapse
|
14
|
Spiniello M, Steinbrink MI, Cesnik AJ, Miller RM, Scalf M, Shortreed MR, Smith LM. Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. RNA (NEW YORK, N.Y.) 2019; 25:1337-1352. [PMID: 31296583 PMCID: PMC6800478 DOI: 10.1261/rna.072157.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 06/27/2019] [Indexed: 05/10/2023]
Abstract
Proteins bind mRNA through their entire life cycle from transcription to degradation. We analyzed c-Myc mRNA protein interactors in vivo using the HyPR-MS method to capture the crosslinked mRNA by hybridization and then analyzed the bound proteins using mass spectrometry proteomics. Using HyPR-MS, 229 c-Myc mRNA-binding proteins were identified, confirming previously proposed interactors, suggesting new interactors, and providing information related to the roles and pathways known to involve c-Myc. We performed structural and functional analysis of these proteins and validated our findings with a combination of RIP-qPCR experiments, in vitro results released in past studies, publicly available RIP- and eCLIP-seq data, and results from software tools for predicting RNA-protein interactions.
Collapse
Affiliation(s)
- Michele Spiniello
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Medicine of Precision, University of Studi della Campania Luigi Vanvitelli, Naples 80138, Italy
- Division of Immuno-Hematology and Transfusion Medicine, Cardarelli Hospital, Naples 80131, Italy
| | - Maisie I Steinbrink
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| |
Collapse
|
15
|
Esteves P, Dard L, Brillac A, Hubert C, Sarlak S, Rousseau B, Dumon E, Izotte J, Bonneu M, Lacombe D, Dupuy JW, Amoedo N, Rossignol R. Nuclear control of lung cancer cells migration, invasion and bioenergetics by eukaryotic translation initiation factor 3F. Oncogene 2019; 39:617-636. [PMID: 31527668 PMCID: PMC6962096 DOI: 10.1038/s41388-019-1009-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 08/07/2019] [Accepted: 08/20/2019] [Indexed: 02/07/2023]
Abstract
The basic understanding of the biological effects of eukaryotic translation initiation factors (EIFs) remains incomplete, notably for their roles independent of protein translation. Different EIFs exhibit nuclear localization and DNA-related functions have been proposed, but the understanding of EIFs novel functions beyond protein translation lacks of integrative analyses between the genomic and the proteomic levels. Here, the noncanonical function of EIF3F was studied in human lung adenocarcinoma by combining methods that revealed both the protein-protein and the protein-DNA interactions of this factor. We discovered that EIF3F promotes cell metastasis in vivo. The underpinning molecular mechanisms involved the regulation of a cluster of 34 metastasis-promoting genes including Snail2, as revealed by proteomics combined with immuno-affinity purification of EIF3F and ChIP-seq/Q-PCR analyses. The interaction between EIF3F and signal transducer and activator of transcription 3 (STAT3) controlled the EIF3F-mediated increase in Snail2 expression and cellular invasion, which were specifically abrogated using the STAT3 inhibitor Nifuroxazide or knockdown approaches. Furthermore, EIF3F overexpression reprogrammed energy metabolism through the activation of AMP-activated protein kinase and the stimulation of oxidative phosphorylation. Our findings demonstrate the role of EIF3F in the molecular control of cell migration, invasion, bioenergetics, and metastasis. The discovery of a role for EIF3F-STAT3 interaction in the genetic control of cell migration and metastasis in human lung adenocarcinoma could lead to the development of diagnosis and therapeutic strategies.
Collapse
Affiliation(s)
- Pauline Esteves
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Laetitia Dard
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Aurélia Brillac
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Christophe Hubert
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Saharnaz Sarlak
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Benoît Rousseau
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,Transgenic Animal Facility A2, University of Bordeaux, 33000, Bordeaux, France
| | - Elodie Dumon
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Julien Izotte
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,Transgenic Animal Facility A2, University of Bordeaux, 33000, Bordeaux, France
| | - Marc Bonneu
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,Functional Genomics Center (CGFB), Proteomics Facility, 146 Rue Léo Saignat, 33076, Bordeaux, France.,Bordeaux-INP, Avenue des Facultés, 33405, Talence Cedex, France
| | - Didier Lacombe
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,INSERM U1211, 33000, Bordeaux, France
| | - Jean-William Dupuy
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France.,Functional Genomics Center (CGFB), Proteomics Facility, 146 Rue Léo Saignat, 33076, Bordeaux, France
| | - Nivea Amoedo
- CELLOMET, Functional Genomics Center (CGFB), 146 rue Léo Saignat, 33000, Bordeaux, France
| | - Rodrigue Rossignol
- Bordeaux University, 146 rue Léo Saignat, 33000, Bordeaux, France. .,INSERM U1211, 33000, Bordeaux, France. .,CELLOMET, Functional Genomics Center (CGFB), 146 rue Léo Saignat, 33000, Bordeaux, France.
| |
Collapse
|
16
|
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: 65] [Impact Index Per Article: 9.3] [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.
Collapse
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
| |
Collapse
|
17
|
Vaklavas C, Zinn KR, Samuel SL, Meng Z, Grizzle WE, Choi H, Blume SW. Translational control of the undifferentiated phenotype in ER‑positive breast tumor cells: Cytoplasmic localization of ERα and impact of IRES inhibition. Oncol Rep 2018; 39:2482-2498. [PMID: 29620220 PMCID: PMC5983923 DOI: 10.3892/or.2018.6332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/12/2018] [Indexed: 01/07/2023] Open
Abstract
Using a series of potential biomarkers relevant to mechanisms of protein synthesis, we observed that estrogen receptor (ER)-positive breast tumor cells exist in two distinct yet interconvertible phenotypic states (of roughly equal proportion) which differ in the degree of differentiation and use of IRES-mediated translation. Nascently translated IGF1R in the cytoplasm positively correlated with IRES activity and the undifferentiated phenotype, while epitope accessibility of RACK1, an integral component of the 40S ribosomal subunit, aligned with the more differentiated IRES-off state. When deprived of soluble growth factors, the entire tumor cell population shifted to the undifferentiated phenotype in which IRES-mediated translation was active, facilitating survival under these adverse microenvironmental conditions. However, if IRES-mediated translation was inhibited, the cells instead were forced to transition uniformly to the more differentiated state. Notably, cytoplasmic localization of estrogen receptor α (ERα/ESR1) precisely mirrored the pattern observed with nascent IGF1R, correlating with the undifferentiated IRES-active phenotype. Inhibition of IRES-mediated translation resulted in both a shift in ERα to the nucleus (consistent with differentiation) and a marked decrease in ERα abundance (consistent with the inhibition of ERα synthesis via its IRES). Although breast tumor cells tolerated forced differentiation without extensive loss of their viability, their reproductive capacity was severely compromised. In addition, CDK1 was decreased, connexin 43 eliminated and Myc translation altered as a consequence of IRES inhibition. Isolated or low-density ER-positive breast tumor cells were particularly vulnerable to IRES inhibition, losing the ability to generate viable cohesive colonies, or undergoing massive cell death. Collectively, these results provide further evidence for the integral relationship between IRES-mediated translation and the undifferentiated phenotype and demonstrate how therapeutic manipulation of this specialized mode of protein synthesis may be used to limit the phenotypic plasticity and incapacitate or eliminate these otherwise highly resilient breast tumor cells.
Collapse
Affiliation(s)
- Christos Vaklavas
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kurt R Zinn
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Sharon L Samuel
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zheng Meng
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - William E Grizzle
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hyoungsoo Choi
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Scott W Blume
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| |
Collapse
|
18
|
Lampe S, Kunze M, Scholz A, Brauß TF, Winslow S, Simm S, Keller M, Heidler J, Wittig I, Brüne B, Schmid T. Identification of the TXNIP IRES and characterization of the impact of regulatory IRES trans-acting factors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:147-157. [PMID: 29378331 DOI: 10.1016/j.bbagrm.2018.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Sebastian Lampe
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Michael Kunze
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Anica Scholz
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Thilo F Brauß
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Sofia Winslow
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Stefan Simm
- Department of Molecular Cell Biology of Plants, Faculty of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Mario Keller
- Department of Molecular Cell Biology of Plants, Faculty of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Juliana Heidler
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Ilka Wittig
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany.
| |
Collapse
|
19
|
circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations. Sci Rep 2016; 6:34985. [PMID: 27725737 PMCID: PMC5057092 DOI: 10.1038/srep34985] [Citation(s) in RCA: 333] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/21/2016] [Indexed: 11/09/2022] Open
Abstract
It has been known that circular RNAs are widely expressed in human tissues and cells, and play important regulatory roles in physiological or pathological processes. However, there is lack of comprehensively annotated human circular RNAs database. In this study we established a circRNA database, named as circRNADb, containing 32,914 human exonic circRNAs carefully selected from diversified sources. The detailed information of the circRNA, including genomic information, exon splicing, genome sequence, internal ribosome entry site (IRES), open reading frame (ORF) and references were provided in circRNADb. In addition, circRNAs were found to be able to encode proteins, which have not been reported in any species. 16328 circRNAs were annotated to have ORF longer than 100 amino acids, of which 7170 have IRES elements. 46 circRNAs from 37 genes were found to have their corresponding proteins expressed according mass spectrometry. The database provides the function of data search, browse, download, submit and feedback for the user to study particular circular RNA of interest and update the database continually. circRNADb will be built to be a biological information platform for circRNA molecules and related biological functions in the future. The database can be freely available through the web server at http://reprod.njmu.edu.cn/circrnadb.
Collapse
|
20
|
D'Amico D, Canettieri G. Translating Hedgehog in Cancer: Controlling Protein Synthesis. Trends Mol Med 2016; 22:851-862. [PMID: 27591077 DOI: 10.1016/j.molmed.2016.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 11/17/2022]
Abstract
Developmental Hedgehog (Hh) signaling is found deregulated in a broad spectrum of human malignancies and, thus, is an attractive target for cancer therapy. Currently available Hh inhibitors have shown the rapid occurrence of drug resistance, due to altered signaling in collateral pathways. Emerging observations suggest that Hh signaling regulates protein translation in pathways that depend both on Cap- and IRES-mediated translation. In addition, translational regulators have been shown to modulate Hh function. In this opinion, we describe this novel Hh/translation crosstalk and argue that it plays a relevant role in Hh-mediated tumorigenesis and drug resistance. As such, we suggest that drugs targeting translation might be introduced in novel protocols aimed at treating malignancies driven by aberrant Hh signaling.
Collapse
Affiliation(s)
- Davide D'Amico
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | |
Collapse
|
21
|
Vaklavas C, Grizzle WE, Choi H, Meng Z, Zinn KR, Shrestha K, Blume SW. IRES inhibition induces terminal differentiation and synchronized death in triple-negative breast cancer and glioblastoma cells. Tumour Biol 2016; 37:13247-13264. [PMID: 27460074 PMCID: PMC5097113 DOI: 10.1007/s13277-016-5161-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/12/2016] [Indexed: 01/07/2023] Open
Abstract
Internal ribosome entry site (IRES)-mediated translation is a specialized mode of protein synthesis which malignant cells depend on to survive adverse microenvironmental conditions. Our lab recently reported the identification of a group of compounds which selectively interfere with IRES-mediated translation, completely blocking de novo IGF1R synthesis, and differentially modulating synthesis of the two c-Myc isoforms. Here, we examine the phenotypic consequences of sustained IRES inhibition in human triple-negative breast carcinoma and glioblastoma cells. A sudden loss of viability affects the entire tumor cell population after ∼72-h continuous exposure to the lead compound. The extraordinarily steep dose-response relationship (Hill-Slope coefficients −15 to −35) and extensive physical connections established between the cells indicate that the cells respond to IRES inhibition collectively as a population rather than as individual cells. Prior to death, the treated cells exhibit prominent features of terminal differentiation, with marked gains in cytoskeletal organization, planar polarity, and formation of tight junctions or neuronal processes. In addition to IGF1R and Myc, specific changes in connexin 43, BiP, CHOP, p21, and p27 also correlate with phenotypic outcome. This unusual mode of tumor cell death is absolutely dependent on exceeding a critical threshold in cell density, suggesting that a quorum-sensing mechanism may be operative. Death of putative tumor stem cells visualized in situ helps to explain the inability of tumor cells to recover and repopulate once the compound is removed. Together, these findings support the concept that IRES-mediated translation is of fundamental importance to maintenance of the undifferentiated phenotype and survival of undifferentiated malignant cells.
Collapse
Affiliation(s)
- Christos Vaklavas
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - William E Grizzle
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Hyoungsoo Choi
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Pediatrics, Seoul National University Bundang Hospital, Gyeonggi-do, 463-707, South Korea
| | - Zheng Meng
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Bevill Biomedical Research Bldg Room 765, 845 19th Street S, Birmingham, AL, 35294, USA.,Analytical Development Division, Novavax Inc., Rockville, MD, 20850, USA
| | - Kurt R Zinn
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Kedar Shrestha
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Scott W Blume
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA. .,Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA. .,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Bevill Biomedical Research Bldg Room 765, 845 19th Street S, Birmingham, AL, 35294, USA.
| |
Collapse
|
22
|
sST2 translation is regulated by FGF2 via an hnRNP A1-mediated IRES-dependent mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:848-59. [PMID: 27168114 DOI: 10.1016/j.bbagrm.2016.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 04/15/2016] [Accepted: 05/05/2016] [Indexed: 11/23/2022]
Abstract
Translation is an energy-intensive process and tightly regulated. Generally, translation is initiated in a cap-dependent manner. Under stress conditions, typically found within the tumor microenvironment in association with e.g. nutrient deprivation or hypoxia, cap-dependent translation decreases, and alternative modes of translation initiation become more important. Specifically, internal ribosome entry sites (IRES) facilitate translation of specific mRNAs under otherwise translation-inhibitory conditions. This mechanism is controlled by IRES trans-acting factors (ITAF), i.e. by RNA-binding proteins, which interact with and determine the activity of selected IRESs. We aimed at characterizing the translational regulation of the IL-33 decoy receptor sST2, which was enhanced by fibroblast growth factor 2 (FGF2). We identified and verified an IRES within the 5'UTR of sST2. Furthermore, we found that MEK/ERK signaling contributes to FGF2-induced, sST2-IRES activation and translation. Determination of the sST2-5'UTR structure by in-line probing followed by deletion analyses identified 23 nucleotides within the sST2-5'UTR to be required for optimal IRES activity. Finally, we show that the RNA-binding protein heterogeneous ribonucleoprotein A1 (hnRNP A1) binds to the sST2-5'UTR, acts as an ITAF, and thus controls the activity of the sST2-IRES and consequently sST2 translation. Specifically, FGF2 enhances nuclear-cytoplasmic translocation of hnRNP A1, which requires intact MEK/ERK activity. In summary, we provide evidence that the sST2-5'UTR contains an IRES element, which is activated by a MEK/ERK-dependent increase in cytoplasmic localization of hnRNP A1 in response to FGF2, enhancing the translation of sST2.
Collapse
|