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Boyer JA, Sharma M, Dorso MA, Mai N, Amor C, Reiter JM, Kannan R, Gadal S, Xu J, Miele M, Li Z, Chen X, Chang Q, Pareja F, Worland S, Warner D, Sperry S, Chiang GG, Thompson PA, Yang G, Ouerfelli O, de Stanchina E, Wendel HG, Rosen EY, Chandarlapaty S, Rosen N. eIF4A controls translation of estrogen receptor alpha and is a therapeutic target in advanced breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593195. [PMID: 38766126 PMCID: PMC11100762 DOI: 10.1101/2024.05.08.593195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The majority of human breast cancers are dependent on hormone-stimulated estrogen receptor alpha (ER) and are sensitive to its inhibition. Treatment resistance arises in most advanced cancers due to genetic alterations that promote ligand independent activation of ER itself or ER target genes. Whereas re-targeting of the ER ligand binding domain (LBD) with newer ER antagonists can work in some cases, these drugs are largely ineffective in many genetic backgrounds including ER fusions that lose the LBD or in cancers that hyperactivate ER targets. By identifying the mechanism of ER translation, we herein present an alternative strategy to target ER and difficult to treat ER variants. We find that ER translation is cap-independent and mTOR inhibitor insensitive, but dependent on 5' UTR elements and sensitive to pharmacologic inhibition of the translation initiation factor eIF4A, an mRNA helicase. EIF4A inhibition rapidly reduces expression of ER and short-lived targets of ER such as cyclin D1 and other components of the cyclin D-CDK complex in breast cancer cells. These effects translate into suppression of growth of a variety of ligand-independent breast cancer models including those driven by ER fusion proteins that lack the ligand binding site. The efficacy of eIF4A inhibition is enhanced when it is combined with fulvestrant-an ER degrader. Concomitant inhibition of ER synthesis and induction of its degradation causes synergistic and durable inhibition of ER expression and tumor growth. The clinical importance of these findings is confirmed by results of an early clinical trial (NCT04092673) of the selective eIF4A inhibitor zotatifin in patients with estrogen receptor positive metastatic breast cancer. Multiple clinical responses have been observed on combination therapy including durable regressions. These data suggest that eIF4A inhibition could be a useful new strategy for treating advanced ER+ breast cancer.
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Affiliation(s)
- Jacob A. Boyer
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ, USA
| | - Malvika Sharma
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Madeline A. Dorso
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicholas Mai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Corina Amor
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason M. Reiter
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Ram Kannan
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sunyana Gadal
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Jianing Xu
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
| | - Matthew Miele
- Microchemistry and Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhuoning Li
- Microchemistry and Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaoping Chen
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 11065, USA
| | - Qing Chang
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 11065, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephan Worland
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Douglas Warner
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Sam Sperry
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Gary G. Chiang
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Peggy A. Thompson
- Department of Cancer Biology, eFFECTOR Therapeutics, Inc., San Diego, CA, United States
| | - Guangli Yang
- The Organic Synthesis Core Facility, MSK, New York, NY, USA
| | | | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 11065, USA
| | - Hans-Guido Wendel
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ezra Y. Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Neal Rosen
- Program in Molecular Pharmacology, Department of Medicine, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY, USA
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Marallano VJ, Ughetta ME, Tejero R, Nanda S, Ramalingam R, Stalbow L, Sattiraju A, Huang Y, Ramakrishnan A, Shen L, Wojcinski A, Kesari S, Zou H, Tsankov AM, Friedel RH. Hypoxia drives shared and distinct transcriptomic changes in two invasive glioma stem cell lines. Sci Rep 2024; 14:7246. [PMID: 38538643 PMCID: PMC10973515 DOI: 10.1038/s41598-024-56102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/01/2024] [Indexed: 07/12/2024] Open
Abstract
Glioblastoma (GBM) is the most common primary malignant cancer of the central nervous system. Insufficient oxygenation (hypoxia) has been linked to GBM invasion and aggression, leading to poor patient outcomes. Hypoxia induces gene expression for cellular adaptations. However, GBM is characterized by high intertumoral (molecular subtypes) and intratumoral heterogeneity (cell states), and it is not well understood to what extent hypoxia triggers patient-specific gene responses and cellular diversity in GBM. Here, we surveyed eight patient-derived GBM stem cell lines for invasion phenotypes in 3D culture, which identified two GBM lines showing increased invasiveness in response to hypoxia. RNA-seq analysis of the two patient GBM lines revealed a set of shared hypoxia response genes concerning glucose metabolism, angiogenesis, and autophagy, but also a large set of patient-specific hypoxia-induced genes featuring cell migration and anti-inflammation, highlighting intertumoral diversity of hypoxia responses in GBM. We further applied the Shared GBM Hypoxia gene signature to single cell RNA-seq datasets of glioma patients, which showed that hypoxic cells displayed a shift towards mesenchymal-like (MES) and astrocyte-like (AC) states. Interestingly, in response to hypoxia, tumor cells in IDH-mutant gliomas displayed a strong shift to the AC state, whereas tumor cells in IDH-wildtype gliomas mainly shifted to the MES state. This distinct hypoxia response of IDH-mutant gliomas may contribute to its more favorable prognosis. Our transcriptomic studies provide a basis for future approaches to better understand the diversity of hypoxic niches in gliomas.
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Affiliation(s)
- Valerie J Marallano
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mary E Ughetta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rut Tejero
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sidhanta Nanda
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rohana Ramalingam
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lauren Stalbow
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Anirudh Sattiraju
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yong Huang
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexandre Wojcinski
- Pacific Neuroscience Institute and Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - Santosh Kesari
- Pacific Neuroscience Institute and Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - Hongyan Zou
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Roland H Friedel
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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González-Sánchez AM, Castellanos-Silva EA, Díaz-Figueroa G, Cate JHD. JUN mRNA translation regulation is mediated by multiple 5' UTR and start codon features. PLoS One 2024; 19:e0299779. [PMID: 38483896 PMCID: PMC10939236 DOI: 10.1371/journal.pone.0299779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024] Open
Abstract
Regulation of mRNA translation by eukaryotic initiation factors (eIFs) is crucial for cell survival. In humans, eIF3 stimulates translation of the JUN mRNA which encodes the transcription factor JUN, an oncogenic transcription factor involved in cell cycle progression, apoptosis, and cell proliferation. Previous studies revealed that eIF3 activates translation of the JUN mRNA by interacting with a stem loop in the 5' untranslated region (5' UTR) and with the 5' -7-methylguanosine cap structure. In addition to its interaction site with eIF3, the JUN 5' UTR is nearly one kilobase in length, and has a high degree of secondary structure, high GC content, and an upstream start codon (uAUG). This motivated us to explore the complexity of JUN mRNA translation regulation in human cells. Here we find that JUN translation is regulated in a sequence and structure-dependent manner in regions adjacent to the eIF3-interacting site in the JUN 5' UTR. Furthermore, we identify contributions of an additional initiation factor, eIF4A, in JUN regulation. We show that enhancing the interaction of eIF4A with JUN by using the compound Rocaglamide A (RocA) represses JUN translation. We also find that both the upstream AUG (uAUG) and the main AUG (mAUG) contribute to JUN translation and that they are conserved throughout vertebrates. Our results reveal additional layers of regulation for JUN translation and show the potential of JUN as a model transcript for understanding multiple interacting modes of translation regulation.
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Affiliation(s)
- Angélica M. González-Sánchez
- Comparative Biochemistry Graduate Program, University of California, Berkeley, Berkeley, CA, United States of America
| | - Eimy A. Castellanos-Silva
- Department of Biochemistry and Molecular Biology, University of California, Davis, Davis, CA, United States of America
| | - Gabriela Díaz-Figueroa
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America
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Suresh BM, Tong Y, Abegg D, Adibekian A, Childs-Disney JL, Disney MD. Altering the Cleaving Effector in Chimeric Molecules that Target RNA Enhances Cellular Selectivity. ACS Chem Biol 2023; 18:2385-2393. [PMID: 37824291 PMCID: PMC10825929 DOI: 10.1021/acschembio.3c00363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Small molecules that target RNA and effect their cleavage are useful chemical probes and potential lead medicines. In this study, we investigate factors affecting degradation of two cancer-associated RNA targets, the mRNA that encodes the transcription factor JUN (c-Jun) and the hairpin precursor to microRNA-372 (pre-miR-372). The two RNA targets harbor the same small-molecule binding site juxtaposed with different neighboring structures. Specifically, pre-miR-372 has AU pairs and contiguous purines on one strand near the small-molecule binding site, making it an ideal substrate for oxidative cleavage via the direct degrader bleomycin A5. In contrast, while JUN mRNA has a similar number of AU pairs near the small-molecule binding site, it lacks contiguous purine nucleotides. Instead, it contains unpaired pyrimidine nucleotides, which are preferred substrates for RNase L, a ribonuclease that can be recruited to RNA with heterobifunctional ribonuclease targeting chimeras (RiboTACs). We hypothesized that structural features surrounding the binding site could be leveraged to program selective small-molecule degradation by alteration of the cleaving module. Indeed, the bleomycin degrader cleaves pre-miR-372 in gastric cancer cells but not JUN mRNA. Conversely, the RiboTAC cleaves JUN mRNA but not pre-miR-372. Thus, the selection of the appropriate cleaving effector moiety for an RNA-binding small molecule can be leveraged to cleave an RNA selectively in a predictable manner, which could have broad implications.
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Affiliation(s)
- Blessy M. Suresh
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology and The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Yuquan Tong
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology and The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Daniel Abegg
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology and The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Alexander Adibekian
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology and The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology and The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology and The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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González-Sánchez AM, Castellanos-Silva EA, Díaz-Figueroa G, Cate JHD. JUN mRNA Translation Regulation is Mediated by Multiple 5' UTR and Start Codon Features. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.17.567602. [PMID: 38014201 PMCID: PMC10680820 DOI: 10.1101/2023.11.17.567602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Regulation of mRNA translation by eukaryotic initiation factors (eIFs) is crucial for cell survival. In humans, eIF3 stimulates translation of the JUN mRNA which encodes the transcription factor JUN, an oncogenic transcription factor involved in cell cycle progression, apoptosis, and cell proliferation. Previous studies revealed that eIF3 activates translation of the JUN mRNA by interacting with a stem loop in the 5' untranslated region (5' UTR) and with the 5'-7-methylguanosine cap structure. In addition to its interaction site with eIF3, the JUN 5' UTR is nearly one kilobase in length, and has a high degree of secondary structure, high GC content, and an upstream start codon (uAUG). This motivated us to explore the complexity of JUN mRNA translation regulation in human cells. Here we find that JUN translation is regulated in a sequence and structure-dependent manner in regions adjacent to the eIF3-interacting site in the JUN 5' UTR. Furthermore, we identify contributions of an additional initiation factor, eIF4A, in JUN regulation. We show that enhancing the interaction of eIF4A with JUN by using the compound Rocaglamide A (RocA) represses JUN translation. We also find that both the upstream AUG (uAUG) and the main AUG (mAUG) contribute to JUN translation and that they are conserved throughout vertebrates. Our results reveal additional layers of regulation for JUN translation and show the potential of JUN as a model transcript for understanding multiple interacting modes of translation regulation.
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Affiliation(s)
| | - Eimy A Castellanos-Silva
- University of California, Davis, Department of Biochemistry and Molecular Biology, Davis, CA, USA
| | - Gabriela Díaz-Figueroa
- University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA, USA
| | - Jamie H D Cate
- University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA, USA
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Manuel MTA, Tayo LL. Navigating the Gene Co-Expression Network and Drug Repurposing Opportunities for Brain Disorders Associated with Neurocognitive Impairment. Brain Sci 2023; 13:1564. [PMID: 38002524 PMCID: PMC10669457 DOI: 10.3390/brainsci13111564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Neurocognitive impairment refers to a spectrum of disorders characterized by a decline in cognitive functions such as memory, attention, and problem-solving, which are often linked to structural or functional abnormalities in the brain. While its exact etiology remains elusive, genetic factors play a pivotal role in disease onset and progression. This study aimed to identify highly correlated gene clusters (modules) and key hub genes shared across neurocognition-impairing diseases, including Alzheimer's disease (AD), Parkinson's disease with dementia (PDD), HIV-associated neurocognitive disorders (HAND), and glioma. Herein, the microarray datasets AD (GSE5281), HAND (GSE35864), glioma (GSE15824), and PD (GSE7621) were used to perform Weighted Gene Co-expression Network Analysis (WGCNA) to identify highly preserved modules across the studied brain diseases. Through gene set enrichment analysis, the shared modules were found to point towards processes including neuronal transcriptional dysregulation, neuroinflammation, protein aggregation, and mitochondrial dysfunction, hallmarks of many neurocognitive disorders. These modules were used in constructing protein-protein interaction networks to identify hub genes shared across the diseases of interest. These hub genes were found to play pivotal roles in processes including protein homeostasis, cell cycle regulation, energy metabolism, and signaling, all associated with brain and CNS diseases, and were explored for their drug repurposing experiments. Drug repurposing based on gene signatures highlighted drugs including Dorzolamide and Oxybuprocaine, which were found to modulate the expression of the hub genes in play and may have therapeutic implications in neurocognitive disorders. While both drugs have traditionally been used for other medical purposes, our study underscores the potential of a combined WGCNA and drug repurposing strategy for searching for new avenues in the simultaneous treatment of different diseases that have similarities in gene co-expression networks.
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Affiliation(s)
- Mathew Timothy Artuz Manuel
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila City 1002, Philippines;
- School of Graduate Studies, Mapúa University, Manila City 1002, Philippines
| | - Lemmuel L. Tayo
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila City 1002, Philippines;
- School of Graduate Studies, Mapúa University, Manila City 1002, Philippines
- Department of Biology, School of Medicine and Health Sciences, Mapúa University, Makati City 1200, Philippines
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Arnold L, Gomez JP, Barry M, Yap M, Jackson L, Ly T, Standing D, Padhye SB, Biersack B, Anant S, Thomas SM. Acryl-3,5-bis(2,4-difluorobenzylidene)-4-piperidone targeting cellular JUN proto-oncogene, AP-1 transcription factor subunit inhibits head and neck squamous cell carcinoma progression. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:1104-1121. [PMID: 38023989 PMCID: PMC10651473 DOI: 10.37349/etat.2023.00184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/17/2023] [Indexed: 12/01/2023] Open
Abstract
Aim Head and neck squamous cell carcinoma (HNSCC) is the seventh most common cancer worldwide with a survival rate below fifty percent. Addressing meager therapeutic options, a series of small molecule inhibitors were screened for antitumor efficacy. The most potent analog, acryl-3,5-bis(2,4-difluorobenzylidene)-4-piperidone (DiFiD; A-DiFiD), demonstrated strong cellular JUN proto-oncogene, activator protein 1 (AP-1) transcription factor subunit (JUN, c-Jun) antagonism. c-Jun, an oncogenic transcription factor, promotes cancer progression, invasion, and adhesion; high (JUN) mRNA expression correlates with poorer HNSCC survival. Methods Four new small molecules were generated for cytotoxicity screening in HNSCC cell lines. A-DiFiD-treated HNSCC cells were assessed for cytotoxicity, colony formation, invasion, migration, and adhesion. Dot blot array was used to identify targets. Phospho-c-Jun (p-c-Jun) expression was analyzed using immunoblotting. The Cancer Genome Atlas (TCGA) head and neck cancer datasets were utilized to determine overall patient survival. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) datasets interfaced with University of Alabama at Birmingham Cancer Data Analysis Portal (UALCAN) were analyzed to determine protein levels of c-Jun in HNSCC patients and correlate levels with patient. Results Of the small molecules tested, A-DiFiD was the most potent in HNSCC lines, while demonstrating low half-maximal drug inhibitory concentration (IC50) in non-malignant Het-1A cells. Additionally, A-DiFiD abrogated cell invasion, migration, and colony formation. Phospho-kinase in vitro array demonstrated A-DiFiD reduced p-c-Jun. Likewise, a time dependent reduction in p-c-Jun was observed starting at 3 min post A-DiFiD treatment. TCGA Firehose Legacy vs. recurrent and metastatic head and neck cancer reveal a nearly 3% DNA amplification in recurrent/metastatic tumor compared to below 1% in primary tumors that had no lymph node metastasis. CPTAC analysis show higher tumor c-Jun levels compared to normal. Patients with high JUN expression had significantly reduced 3-year survival. Conclusions A-DiFiD targets c-Jun, a clinical HNSCC driver, with potent anti-tumor effects.
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Affiliation(s)
- Levi Arnold
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Juan Pineda Gomez
- Department of Otolaryngology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Michael Barry
- Department of Otolaryngology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Marrion Yap
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Laura Jackson
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Thuc Ly
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - David Standing
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Subhash B. Padhye
- Interdisciplinary Science and Technology Research Academy, University of Pune, Pune 411007, Maharashtra, India
| | - Bernhard Biersack
- Department of Biology, Chemistry, Earth Sciences, University of Bayreuth, 95440 Bayreuth, Germany
| | - Shrikant Anant
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Sufi Mary Thomas
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
- Department of Otolaryngology, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
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Luo YM, Yang SD, Wen MY, Wang B, Liu JH, Li ST, Li YY, Cheng H, Zhao LL, Li SM, Jiang JJ. Insights into the mechanisms of triptolide nephrotoxicity through network pharmacology-based analysis and RNA-seq. FRONTIERS IN PLANT SCIENCE 2023; 14:1144583. [PMID: 36959927 PMCID: PMC10027700 DOI: 10.3389/fpls.2023.1144583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Triptolide (TPL) is a promising plant-derived compound for clinical therapy of multiple human diseases; however, its application was limited considering its toxicity. METHODS To explore the underlying molecular mechanism of TPL nephrotoxicity, a network pharmacology based approach was utilized to predict candidate targets related with TPL toxicity, followed by deep RNA-seq analysis to characterize the features of three transcriptional elements include protein coding genes (PCGs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) as well as their associations with nephrotoxicity in rats with TPL treatment. RESULTS & DISCUSSION Although the deeper mechanisms of TPL nephrotoxcity remain further exploration, our results suggested that c-Jun is a potential target of TPL and Per1 related circadian rhythm signaling is involved in TPL induced renal toxicity.
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Affiliation(s)
- Yue-Ming Luo
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Shu-Dong Yang
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Miao-Yu Wen
- Department of Geriatrics, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Bing Wang
- Department of Nephrology, Shenzhen Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Jia-Hui Liu
- Department of Nephrology, Shenzhen Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Si-Ting Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yu-Yan Li
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Hong Cheng
- Department of Geriatrics, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Li-Li Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Graduate school of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Shun-Min Li
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Jian-Jun Jiang
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
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Srimongkol A, Laosillapacharoen N, Saengwimol D, Chaitankar V, Rojanaporn D, Thanomchard T, Borwornpinyo S, Hongeng S, Kaewkhaw R. Sunitinib efficacy with minimal toxicity in patient-derived retinoblastoma organoids. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2023; 42:39. [PMID: 36726110 PMCID: PMC9890748 DOI: 10.1186/s13046-023-02608-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/20/2023] [Indexed: 02/03/2023]
Abstract
BACKGROUND Recurrence of retinoblastoma (RB) following chemoreduction is common and is often managed with local (intra-arterial/intravitreal) chemotherapy. However, some tumors are resistant to even local administration of maximum feasible drug dosages, or effective tumor control and globe preservation may be achieved at the cost of vision loss due to drug-induced retinal toxicity. The aim of this study was to identify drugs with improved antitumor activity and more favorable retinal toxicity profiles via screening of potentially repurposable FDA-approved drugs in patient-derived tumor organoids. METHODS Genomic profiling of five RB organoids and the corresponding parental tissues was performed. RB organoids were screened with 133 FDA-approved drugs, and candidate drugs were selected based on cytotoxicity and potency. RNA sequencing was conducted to generate a drug signature from RB organoids, and the effects of drugs on cell cycle progression and proliferative tumor cone restriction were examined. Drug toxicity was assessed with human embryonic stem cell-derived normal retinal organoids. The efficacy/toxicity profiles of candidate drugs were compared with those of drugs in clinical use. RESULTS RB organoids maintained the genomic features of the parental tumors. Sunitinib was identified as highly cytotoxic against both classical RB1-deficient and novel MYCN-amplified RB organoids and inhibited proliferation while inducing differentiation in RB. Sunitinib was a more effective suppressor of proliferative tumor cones in RB organoids and had lower toxicity in normal retinal organoids than either melphalan or topotecan. CONCLUSION The efficacy and retinal toxicity profiles of sunitinib suggest that it could potentially be repurposed for local chemotherapy of RB.
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Affiliation(s)
- Atthapol Srimongkol
- grid.10223.320000 0004 1937 0490Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 10400 Bangkok, Thailand
| | - Natanan Laosillapacharoen
- grid.10223.320000 0004 1937 0490Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 10400 Bangkok, Thailand
| | - Duangporn Saengwimol
- grid.10223.320000 0004 1937 0490Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 10400 Bangkok, Thailand
| | - Vijender Chaitankar
- grid.94365.3d0000 0001 2297 5165Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD USA
| | - Duangnate Rojanaporn
- grid.10223.320000 0004 1937 0490Department of Ophthalmology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 10400 Bangkok, Thailand
| | - Thanastha Thanomchard
- grid.10223.320000 0004 1937 0490Ramathibodi Comprehensive Cancer Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 10400 Bangkok, Thailand
| | - Suparerk Borwornpinyo
- grid.10223.320000 0004 1937 0490Excellent Center for Drug Discovery, Faculty of Science, Mahidol University, 10400 Bangkok, Thailand ,grid.10223.320000 0004 1937 0490Department of Biotechnology, Faculty of Science, Mahidol University, 10400 Bangkok, Thailand
| | - Suradej Hongeng
- grid.10223.320000 0004 1937 0490Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 10400 Bangkok, Thailand
| | - Rossukon Kaewkhaw
- grid.10223.320000 0004 1937 0490Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 10400 Bangkok, Thailand ,grid.10223.320000 0004 1937 0490Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 10540 Samut Prakan, Thailand
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10
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Cuciniello R, Di Meo F, Sulli M, Demurtas OC, Tanori M, Mancuso M, Villano C, Aversano R, Carputo D, Baldi A, Diretto G, Filosa S, Crispi S. Aglianico Grape Seed Semi-Polar Extract Exerts Anticancer Effects by Modulating MDM2 Expression and Metabolic Pathways. Cells 2023; 12:cells12020210. [PMID: 36672146 PMCID: PMC9856309 DOI: 10.3390/cells12020210] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Grapevine (Vitis vinifera L.) seeds are rich in polyphenols including proanthocyanidins, molecules with a variety of biological effects including anticancer action. We have previously reported that the grape seed semi-polar extract of Aglianico cultivar (AGS) was able to induce apoptosis and decrease cancer properties in different mesothelioma cell lines. Concomitantly, this extract resulted in enriched oligomeric proanthocyanidins which might be involved in determining the anticancer activity. Through transcriptomic and metabolomic analyses, we investigated in detail the anticancer pathway induced by AGS. Transcriptomics analysis and functional annotation allowed the identification of the relevant causative genes involved in the apoptotic induction following AGS treatment. Subsequent biological validation strengthened the hypothesis that MDM2 could be the molecular target of AGS and that it could act in both a p53-dependent and independent manner. Finally, AGS significantly inhibited tumor progression in a xenograft mouse model of mesothelioma, confirming also in vivo that MDM2 could act as molecular player responsible for the AGS antitumor effect. Our findings indicated that AGS, exerting a pro-apoptotic effect by hindering MDM2 pathway, could represent a novel source of anticancer molecules.
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Affiliation(s)
- Rossana Cuciniello
- Institute of Biosciences and BioResources-UOS Naples CNR, Via P. Castellino 111, 80131 Naples, Italy
- IRCCS Neuromed, 86077 Pozzilli, Italy
| | - Francesco Di Meo
- Institute of Biosciences and BioResources-UOS Naples CNR, Via P. Castellino 111, 80131 Naples, Italy
- Department of Medicine, Indiana University School of Medicine, 975 W Walnut Street, Indianapolis, IN 46202, USA
| | - Maria Sulli
- Division of Biotechnology and Agroindustry, Biotechnology Laboratory, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
| | - Olivia Costantina Demurtas
- Division of Biotechnology and Agroindustry, Biotechnology Laboratory, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
| | - Mirella Tanori
- Division of Health Protection Technologies, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
| | - Mariateresa Mancuso
- Division of Health Protection Technologies, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
| | - Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Alfonso Baldi
- Institute of Biosciences and BioResources-UOS Naples CNR, Via P. Castellino 111, 80131 Naples, Italy
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “L. Vanvitelli”, 81055 Caserta, Italy
| | - Gianfranco Diretto
- Division of Biotechnology and Agroindustry, Biotechnology Laboratory, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
- Correspondence: (G.D.); (S.C.)
| | - Stefania Filosa
- Institute of Biosciences and BioResources-UOS Naples CNR, Via P. Castellino 111, 80131 Naples, Italy
- IRCCS Neuromed, 86077 Pozzilli, Italy
| | - Stefania Crispi
- Institute of Biosciences and BioResources-UOS Naples CNR, Via P. Castellino 111, 80131 Naples, Italy
- Correspondence: (G.D.); (S.C.)
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11
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Ervin EH, French R, Chang CH, Pauklin S. Inside the stemness engine: Mechanistic links between deregulated transcription factors and stemness in cancer. Semin Cancer Biol 2022; 87:48-83. [PMID: 36347438 DOI: 10.1016/j.semcancer.2022.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/07/2022]
Abstract
Cell identity is largely determined by its transcriptional profile. In tumour, deregulation of transcription factor expression and/or activity enables cancer cell to acquire a stem-like state characterised by capacity to self-renew, differentiate and form tumours in vivo. These stem-like cancer cells are highly metastatic and therapy resistant, thus warranting a more complete understanding of the molecular mechanisms downstream of the transcription factors that mediate the establishment of stemness state. Here, we review recent research findings that provide a mechanistic link between the commonly deregulated transcription factors and stemness in cancer. In particular, we describe the role of master transcription factors (SOX, OCT4, NANOG, KLF, BRACHYURY, SALL, HOX, FOX and RUNX), signalling-regulated transcription factors (SMAD, β-catenin, YAP, TAZ, AP-1, NOTCH, STAT, GLI, ETS and NF-κB) and unclassified transcription factors (c-MYC, HIF, EMT transcription factors and P53) across diverse tumour types, thereby yielding a comprehensive overview identifying shared downstream targets, highlighting unique mechanisms and discussing complexities.
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Affiliation(s)
- Egle-Helene Ervin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Rhiannon French
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Chao-Hui Chang
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, United Kingdom.
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12
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Wu G, Hao Q, Liu B, Zhou J, Fan C, Liu R. Network pharmacology-based screening of the active ingredients and mechanisms of evodiae fructus anti-glioblastoma multiforme. Medicine (Baltimore) 2022; 101:e30853. [PMID: 36181021 PMCID: PMC9524918 DOI: 10.1097/md.0000000000030853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Evodiae fructus has been shown to have anti-glioblastoma multiforme (GBM) effects. However, its anti-GBM active components and mechanism remain unclear. In this study, the active components of evodiae fructus were screened by network pharmacology to explore the possible molecular mechanism of resistance to GBM. MATERIALS AND METHODS The main active ingredients of evodiae fructus were derived from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and Batch-traditional Chinese medicine (TCM). TCMSP and Swiss absorption, distribution, metabolism and elimination (ADME) predict genetic targets for ingredients that meet pharmacological criteria. GBM-related targets were obtained from DisGeNet, GeneCards, Online Mendelian Inheritance in Man (OMIM), Therapeutic Target Database (TTD), and TCGA. A Venn diagram was used to obtain the common targets of evodiae fructus and GBM. Protein-protein interaction (PPI) networks and component-disease target networks were constructed using Cytoscape 3.8.1 software for visualization. GBM gene differential expression was visualized by VolcaNoseR, and potential targets were enriched by Gene Ontology (GO) function and annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway by SRplot. Molecular docking verification was conducted using AutoDock Vina software. RESULTS According to the screening conditions, 24 active components and 80 drug targets were obtained. The PPI network contains 80 proteins. The molecular docking verification showed the molecular docking affinity of the core active compounds in evodiae fructus with CASP3, JUN, EGFR, and AKT1. CONCLUSIONS This study preliminarily identified the various molecular targets and multiple pathways of evodiae fructus against GBM.
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Affiliation(s)
- Gang Wu
- Department of Neurosurgery, Peking University People’s Hospital, China
| | - Qingpei Hao
- Department of Neurosurgery, Peking University People’s Hospital, China
| | - Bo Liu
- Department of Neurosurgery, Peking University People’s Hospital, China
| | - Jingru Zhou
- Department of Neurosurgery, Peking University People’s Hospital, China
| | - Cungang Fan
- Department of Neurosurgery, Peking University People’s Hospital, China
| | - Ruen Liu
- Department of Neurosurgery, Peking University People’s Hospital, China
- *Correspondence: Ruen Liu, Department of Neurosurgery, Peking University People’s Hospital, No.11 Xizhimen South Street, Beijing 100044, China (e-mail: )
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13
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Umeda-Miyara K, Miyara M, Sanoh S, Kotake Y. Trehalose decreases mRNA and protein expressions of c-Jun and JunB in human cervical cancer HeLa cells. J Biochem 2022; 172:177-187. [PMID: 35748379 DOI: 10.1093/jb/mvac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 06/07/2022] [Indexed: 11/14/2022] Open
Abstract
Increasing evidence suggests that trehalose, a non-reducing disaccharide, ameliorates disease phenotypes by activating autophagy in animal models of various human diseases, including neurodegenerative diseases. Multiple in vitro studies suggest that activation of transcription factor EB, a master regulator of lysosomal biogenesis and autophagy genes, is a major contributor to trehalose-induced autophagy at later stages of exposure. However, underlying causes of trehalose-induced autophagy possibly occur at the early stage of the exposure period. In this study, we investigated the effects of short-term exposure of HeLa cells to trehalose on several signal transduction pathways to elucidate the initial events involved in its beneficial effects. Phospho-protein array analysis revealed that trehalose decreases levels of phosphorylated c-Jun, a component of the transcription factor activator protein-1, after 6 h. Trehalose also rapidly reduced mRNA expression levels of c-Jun and JunB, a member of the Jun family, within 1 h, resulting in a subsequent decrease in their protein levels. Future studies, exploring the interplay between decreased c-Jun and JunB protein levels and beneficial effects of trehalose may provide novel insights into the mechanisms of trehalose action.
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Affiliation(s)
- Kanae Umeda-Miyara
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Hiroshima 734-8553, Japan
| | - Masatsugu Miyara
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Hiroshima 734-8553, Japan.,Research Fellow of Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan.,Laboratory of Hygienic Chemistry and Molecular Toxicology, Gifu Pharmaceutical University, Gifu, Gifu 501-1196, Japan
| | - Seigo Sanoh
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Hiroshima 734-8553, Japan
| | - Yaichiro Kotake
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Hiroshima 734-8553, Japan
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14
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A Split NanoLuc Reporter Quantitatively Measures Circular RNA IRES Translation. Genes (Basel) 2022; 13:genes13020357. [PMID: 35205400 PMCID: PMC8871761 DOI: 10.3390/genes13020357] [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: 01/13/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 02/02/2023] Open
Abstract
Internal ribosomal entry sites (IRESs) are RNA secondary structures that mediate translation independent from the m7G RNA cap. The dicistronic luciferase assay is the most frequently used method to measure IRES-mediated translation. While this assay is quantitative, it requires numerous controls and can be time-consuming. Circular RNAs generated by splinted ligation have been shown to also accurately report on IRES-mediated translation, however suffer from low yield and other challenges. More recently, cellular sequences were shown to facilitate RNA circle formation through backsplicing. Here, we used a previously published backsplicing circular RNA split GFP reporter to create a highly sensitive and quantitative split nanoluciferase (NanoLuc) reporter. We show that NanoLuc expression requires backsplicing and correct orientation of a bona fide IRES. In response to cell stress, IRES-directed NanoLuc expression remained stable or increased while a capped control reporter decreased in translation. In addition, we detected NanoLuc expression from putative cellular IRESs and the Zika virus 5' untranslated region that is proposed to harbor IRES function. These data together show that our IRES reporter construct can be used to verify, identify and quantify the ability of sequences to mediate IRES-translation within a circular RNA.
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15
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Aznauryan E, Yermanos A, Kinzina E, Devaux A, Kapetanovic E, Milanova D, Church GM, Reddy ST. Discovery and validation of human genomic safe harbor sites for gene and cell therapies. CELL REPORTS METHODS 2022; 2:100154. [PMID: 35474867 PMCID: PMC9017210 DOI: 10.1016/j.crmeth.2021.100154] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 11/12/2021] [Accepted: 12/22/2021] [Indexed: 12/13/2022]
Abstract
Existing approaches to therapeutic gene transfer are marred by the transient nature of gene expression following non-integrative gene delivery and by safety concerns due to the random mechanism of viral-mediated genomic insertions. The disadvantages of these methods encourage future research in identifying human genomic sites that allow for durable and safe expression of genes of interest. We conducted a bioinformatic search followed by the experimental characterization of human genomic sites, identifying two that demonstrated the stable expression of integrated reporter and therapeutic genes without malignant changes to the cellular transcriptome. The cell-type agnostic criteria used in our bioinformatic search suggest widescale applicability of identified sites for engineering of a diverse range of tissues for clinical and research purposes, including modified T cells for cancer therapy and engineered skin to ameliorate inherited diseases and aging. In addition, the stable and robust levels of gene expression from identified sites allow for the industry-scale biomanufacturing of proteins in human cells.
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Affiliation(s)
- Erik Aznauryan
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Systems Biology Program, Life Science Zürich Graduate School, Zürich, Switzerland
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Elvira Kinzina
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anna Devaux
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Edo Kapetanovic
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Denitsa Milanova
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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16
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DNAzymes, Novel Therapeutic Agents in Cancer Therapy: A Review of Concepts to Applications. J Nucleic Acids 2021; 2021:9365081. [PMID: 34760318 PMCID: PMC8575636 DOI: 10.1155/2021/9365081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/06/2021] [Indexed: 11/17/2022] Open
Abstract
The past few decades have witnessed a rapid evolution in cancer drug research which is aimed at developing active biological interventions to regulate cancer-specific molecular targets. Nucleic acid-based therapeutics, including ribozymes, antisense oligonucleotides, small interference RNA (siRNA), aptamer, and DNAzymes, have emerged as promising candidates regulating cancer-specific genes at either the transcriptional or posttranscriptional level. Gene-specific catalytic DNA molecules, or DNAzymes, have shown promise as a therapeutic intervention against cancer in various in vitro and in vivo models, expediting towards clinical applications. DNAzymes are single-stranded catalytic DNA that has not been observed in nature, and they are synthesized through in vitro selection processes from a large pool of random DNA libraries. The intrinsic properties of DNAzymes like small molecular weight, higher stability, excellent programmability, diversity, and low cost have brought them to the forefront of the nucleic acid-based therapeutic arsenal available for cancers. In recent years, considerable efforts have been undertaken to assess a variety of DNAzymes against different cancers. However, their therapeutic application is constrained by the low delivery efficiency, cellular uptake, and target detection within the tumour microenvironment. Thus, there is a pursuit to identify efficient delivery methods in vivo before the full potential of DNAzymes in cancer therapy is realized. In this light, a review of the recent advances in the use of DNAzymes against cancers in preclinical and clinical settings is valuable to understand its potential as effective cancer therapy. We have thus sought to firstly provide a brief overview of construction and recent improvements in the design of DNAzymes. Secondly, this review stipulates the efficacy, safety, and tolerability of DNAzymes developed against major hallmarks of cancers tested in preclinical and clinical settings. Lastly, the recent advances in DNAzyme delivery systems along with the challenges and prospects for the clinical application of DNAzymes as cancer therapy are also discussed.
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17
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Combinatorial Effect of PLK1 Inhibition with Temozolomide and Radiation in Glioblastoma. Cancers (Basel) 2021; 13:cancers13205114. [PMID: 34680264 PMCID: PMC8533781 DOI: 10.3390/cancers13205114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary There is a critical need to identify readily translatable adjuncts to potentiate the dismal median survivals of only 15–20 months in glioblastoma (GBM) patients after standard of care, i.e., concurrent Temozolomide (TMZ) and radiation (XRT) therapy. Here we demonstrated that the Polo-like kinase 1 (PLK1) inhibitor volasertib, which has been employed in cancer clinical trials, has activity against GBM in the contexts of both as monotherapy and as an adjunct to standard of care (SOC). In addition to corroborating the known effects of volasertib, we found novel impacts of volasertib on mitochondrial membrane potential, ROS generation, persistent DNA damage and signaling pathways such as ERK/MAPK, AMPK and glucocorticoid receptor. Together these studies support the potential importance of PLK1 inhibitors as an adjunct to GBM SOC therapy that warrants further preclinical investigation. Abstract New strategies that improve median survivals of only ~15–20 months for glioblastoma (GBM) with the current standard of care (SOC) which is concurrent temozolomide (TMZ) and radiation (XRT) treatment are urgently needed. Inhibition of polo-like kinase 1 (PLK1), a multifunctional cell cycle regulator, overexpressed in GBM has shown therapeutic promise but has never been tested in the context of SOC. Therefore, we examined the mechanistic and therapeutic impact of PLK1 specific inhibitor (volasertib) alone and in combination with TMZ and/or XRT on GBM cells. We quantified the effects of volasertib alone and in combination with TMZ and/or XRT on GBM cell cytotoxicity/apoptosis, mitochondrial membrane potential (MtMP), reactive oxygen species (ROS), cell cycle, stemness, DNA damage, DNA repair genes, cellular signaling and in-vivo tumor growth. Volasertib alone and in combination with TMZ and/or XRT promoted apoptotic cell death, altered MtMP, increased ROS and G2/M cell cycle arrest. Combined volasertib and TMZ treatment reduced side population (SP) indicating activity against GBM stem-like cells. Volasertib combinatorial treatment also significantly increased DNA damage and reduced cell survival by inhibition of DNA repair gene expression and modulation of ERK/MAPK, AMPK and glucocorticoid receptor signaling. Finally, as observed in-vitro, combined volasertib and TMZ treatment resulted in synergistic inhibition of tumor growth in-vivo. Together these results identify new mechanisms of action for volasertib that provide a strong rationale for further investigation of PLK1 inhibition as an adjunct to current GBM SOC therapy.
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18
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Brennan A, Leech JT, Kad NM, Mason JM. Selective antagonism of cJun for cancer therapy. J Exp Clin Cancer Res 2020; 39:184. [PMID: 32917236 PMCID: PMC7488417 DOI: 10.1186/s13046-020-01686-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/20/2020] [Indexed: 01/10/2023] Open
Abstract
The activator protein-1 (AP-1) family of transcription factors modulate a diverse range of cellular signalling pathways into outputs which can be oncogenic or anti-oncogenic. The transcription of relevant genes is controlled by the cellular context, and in particular by the dimeric composition of AP-1. Here, we describe the evidence linking cJun in particular to a range of cancers. This includes correlative studies of protein levels in patient tumour samples and mechanistic understanding of the role of cJun in cancer cell models. This develops an understanding of cJun as a focal point of cancer-altered signalling which has the potential for therapeutic antagonism. Significant work has produced a range of small molecules and peptides which have been summarised here and categorised according to the binding surface they target within the cJun-DNA complex. We highlight the importance of selectively targeting a single AP-1 family member to antagonise known oncogenic function and avoid antagonism of anti-oncogenic function.
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Affiliation(s)
- Andrew Brennan
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - James T Leech
- School of Biosciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Neil M Kad
- School of Biosciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Jody M Mason
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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19
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Chang HH, Cheng YC, Tsai WC, Chen Y. PSMB8 inhibition decreases tumor angiogenesis in glioblastoma through vascular endothelial growth factor A reduction. Cancer Sci 2020; 111:4142-4153. [PMID: 32816328 PMCID: PMC7648028 DOI: 10.1111/cas.14625] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma, also known as glioblastoma multiforme (GBM), is a fast‐growing tumor and the most aggressive brain malignancy. Proteasome subunit beta type‐8 (PSMB8) is one of the 17 essential subunits for the complete assembly of the 20S proteasome complex. The aim of the present study was to evaluate the role of PSMB8 expression in GBM progression and angiogenesis. PSMB8 expression in glioblastoma LN229 and U87MG was knocked down by siRNA or inducible shRNA both in vitro and in vivo. After PSMB8 reduction, cell survival, migration, invasion, angiogenesis, and the related signaling cascades were evaluated. An orthotopic mouse tumor model was also provided to examine the angiogenesis within tumors. A GEO profile analysis indicated that high expression of PSMB8 mRNA in GBM patients was correlated with a low survival rate. In immunohistochemistry analysis, PSMB8 expression was higher in high‐grade than in low‐grade brain tumors. The proliferation, migration, and angiogenesis of human GBM cells were decreased by PSMB8 knockdown in vitro. Furthermore, phosphorylated focal adhesion kinase (p‐FAK), p‐paxillin, MMP2, MMP9, and cathepsin B were significantly reduced in LN229 cells. Integrin β1 and β3 were reduced in HUVEC after incubation with LN229‐conditioned medium. In an orthotopic mouse tumor model, inducible knockdown of PSMB8 reduced the expression of vascular endothelial growth factor (VEGF), VEGF receptor, and CD31 as well as the progression of human glioblastoma. In this article, we demonstrated the role of PSMB8 in glioblastoma progression, especially neovascularization in vitro and in vivo. These results may provide a target for the anti–angiogenic effect of PSMB8 in glioblastoma therapy in the future.
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Affiliation(s)
- Hsin-Han Chang
- Department of Biology and Anatomy, National Defense Medical Center, Taipei, Taiwan.,Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Chen Cheng
- Department of Biology and Anatomy, National Defense Medical Center, Taipei, Taiwan.,Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan
| | - Wen-Chiuan Tsai
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Ying Chen
- Department of Biology and Anatomy, National Defense Medical Center, Taipei, Taiwan.,Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan
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20
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Walker MJ, Shortridge MD, Albin DD, Cominsky LY, Varani G. Structure of the RNA Specialized Translation Initiation Element that Recruits eIF3 to the 5'-UTR of c-Jun. J Mol Biol 2020; 432:1841-1855. [PMID: 31953146 PMCID: PMC7225069 DOI: 10.1016/j.jmb.2020.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/10/2019] [Accepted: 01/02/2020] [Indexed: 02/05/2023]
Abstract
Specialized translation initiation is a novel form of regulation of protein synthesis, whereby RNA structures within the 5'-UTR regulate translation rates of specific mRNAs. Similar to internal ribosome entry sites (IRESs), specialized translation initiation requires the recruitment of eukaryotic initiation factor 3 (eIF3), but also requires cap recognition by eIF3d, a new 5'-m7GTP recognizing protein. How these RNA structures mediate eIF3 recruitment to affect translation of specific mRNAs remains unclear. Here, we report the nuclear magnetic resonance (NMR) structure of a stem-loop within the c-JUN 5' UTR recognized by eIF3 and essential for specialized translation initiation of this well-known oncogene. The structure exhibits similarity to eIF3 recognizing motifs found in hepatitis C virus (HCV)-like IRESs, suggesting mechanistic similarities. This work establishes the RNA structural features involved in c-JUN specialized translation initiation and provides a basis to search for small molecule inhibitors of aberrant expression of the proto-oncogenic c-JUN.
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Affiliation(s)
- Matthew J Walker
- Department of Chemistry, University of Washington, Seattle, WA, USA 98195
| | | | - Dreycey D Albin
- Department of Chemistry, University of Washington, Seattle, WA, USA 98195
| | - Lauren Y Cominsky
- Department of Chemistry, University of Washington, Seattle, WA, USA 98195
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA, USA 98195.
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21
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Wang L, Sun J, Wu Z, Lian X, Han S, Huang S, Yang C, Wang L, Song L. AP-1 regulates the expression of IL17-4 and IL17-5 in the pacific oyster Crassostrea gigas. FISH & SHELLFISH IMMUNOLOGY 2020; 97:554-563. [PMID: 31887409 DOI: 10.1016/j.fsi.2019.12.080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 06/10/2023]
Abstract
The activator protein-1 (AP-1) plays an important role in inducing the immune effector production in response to cellular stress and bacterial infection. In the present study, an AP-1 was identified from Pacific oyster Crassostrea gigas (designed as CgAP-1) and its function was investigated in response against lipopolysaccharide (LPS) stimulation. CgAP-1 was consisted of 290 amino acids including a Jun domain and a basic region leucine zipper (bZIP) domain. CgAP-1 shared 98.6% similarities with ChAP-1 from oyster C. hongkongensis, and assigned into the branch of invertebrates in the phylogenetic tree. The mRNA transcripts of CgAP-1 gene were detected in all tested tissues with highest expression level in hemocytes, especially in granulocytes. The mRNA expression level of CgAP-1 gene in hemocytes was significantly up-regulated (8.53-fold of that in PBS group, p < 0.01) at 6 h after LPS stimulation. CgAP-1 protein could be translocated into the nucleus of oyster hemocytes after LPS stimulation. The mRNA transcripts of interleukin17s (CgIL17-4 and CgIL17-5) in the hemocytes of CgAP-1-RNAi oysters decreased significantly at 24 h after LPS stimulation, which were 0.37-fold (p < 0.05) and 0.17-fold (p < 0.01) compared with that in EGFP-RNAi oysters, respectively. The results suggested that CgAP-1 played an important role in the immune response of oyster by regulating the expression of CgIL17s.
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Affiliation(s)
- Liyan Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Jiejie Sun
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China.
| | - Zhaojun Wu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Xingye Lian
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Shuo Han
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Shu Huang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Chuanyan Yang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China.
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22
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Marina D, Arnaud L, Paul Noel L, Felix S, Bernard R, Natacha C. Relevance of Translation Initiation in Diffuse Glioma Biology and its Therapeutic Potential. Cells 2019; 8:E1542. [PMID: 31795417 PMCID: PMC6953081 DOI: 10.3390/cells8121542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 02/06/2023] Open
Abstract
Cancer cells are continually exposed to environmental stressors forcing them to adapt their protein production to survive. The translational machinery can be recruited by malignant cells to synthesize proteins required to promote their survival, even in times of high physiological and pathological stress. This phenomenon has been described in several cancers including in gliomas. Abnormal regulation of translation has encouraged the development of new therapeutics targeting the protein synthesis pathway. This approach could be meaningful for glioma given the fact that the median survival following diagnosis of the highest grade of glioma remains short despite current therapy. The identification of new targets for the development of novel therapeutics is therefore needed in order to improve this devastating overall survival rate. This review discusses current literature on translation in gliomas with a focus on the initiation step covering both the cap-dependent and cap-independent modes of initiation. The different translation initiation protagonists will be described in normal conditions and then in gliomas. In addition, their gene expression in gliomas will systematically be examined using two freely available datasets. Finally, we will discuss different pathways regulating translation initiation and current drugs targeting the translational machinery and their potential for the treatment of gliomas.
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Affiliation(s)
- Digregorio Marina
- Laboratory of Nervous System Disorders and Therapy, GIGA-Neurosciences Research Centre, University of Liège, 4000 Liège, Belgium; (D.M.); (L.A.); (L.P.N.); (S.F.); (R.B.)
| | - Lombard Arnaud
- Laboratory of Nervous System Disorders and Therapy, GIGA-Neurosciences Research Centre, University of Liège, 4000 Liège, Belgium; (D.M.); (L.A.); (L.P.N.); (S.F.); (R.B.)
- Department of Neurosurgery, CHU of Liège, 4000 Liège, Belgium
| | - Lumapat Paul Noel
- Laboratory of Nervous System Disorders and Therapy, GIGA-Neurosciences Research Centre, University of Liège, 4000 Liège, Belgium; (D.M.); (L.A.); (L.P.N.); (S.F.); (R.B.)
| | - Scholtes Felix
- Laboratory of Nervous System Disorders and Therapy, GIGA-Neurosciences Research Centre, University of Liège, 4000 Liège, Belgium; (D.M.); (L.A.); (L.P.N.); (S.F.); (R.B.)
- Department of Neurosurgery, CHU of Liège, 4000 Liège, Belgium
| | - Rogister Bernard
- Laboratory of Nervous System Disorders and Therapy, GIGA-Neurosciences Research Centre, University of Liège, 4000 Liège, Belgium; (D.M.); (L.A.); (L.P.N.); (S.F.); (R.B.)
- Department of Neurology, CHU of Liège, 4000 Liège, Belgium
| | - Coppieters Natacha
- Laboratory of Nervous System Disorders and Therapy, GIGA-Neurosciences Research Centre, University of Liège, 4000 Liège, Belgium; (D.M.); (L.A.); (L.P.N.); (S.F.); (R.B.)
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23
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Rotondo JC, Borghi A, Selvatici R, Mazzoni E, Bononi I, Corazza M, Kussini J, Montinari E, Gafà R, Tognon M, Martini F. Association of Retinoic Acid Receptor β Gene With Onset and Progression of Lichen Sclerosus-Associated Vulvar Squamous Cell Carcinoma. JAMA Dermatol 2019; 154:819-823. [PMID: 29898214 PMCID: PMC6128494 DOI: 10.1001/jamadermatol.2018.1373] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Importance Molecular alterations in lichen sclerosus-associated vulvar squamous cell carcinoma (LS-VSCC) are largely unknown. Objective To determine whether the retinoic acid receptor β (RARβ) tumor-suppressor gene is involved in the onset and/or progression of LS-VSCC. Design, Setting, and Participants The case-control study, conducted at University-Hospital of Ferrara, Italy, included 20 LS-VSCC (mean [SD] age, 75 [3] years) and 20 cancer-associated vulvar LS (caVLS; mean [SD] age, 62 [11] years) formalin-fixed embedded tissue specimens, 20 cancer-free vulvar LS (cfVLS), and 20 normal skin fresh specimens from diagnostic biopsies and women surgically treated for nonmalignant skin lesions, respectively. RARβ gene expression and promoter methylation were investigated in LS-VSCC and caVLS adjacent to VSCC specimens, and in cfVLS and normal skin specimens, as controls, by RT-Q real-time polymerase chain reaction (PCR) analysis, and sequencing of PCR-amplified bisulfite-treated DNA. c-Jun expression, an RARβ pathway-related gene, was also investigated. Main Outcomes and Measures RARβ expression, correlation with its promoter methylation and c-Jun expression, and association with onset or progression of LS-VSCC. Results In LS-VSCC, RARβ messenger RNA was 3.4-, 3.6-, and 4.8-fold lower than in caVLS (P = .001), cfVLS (P = .005), and normal skin (P < .001), respectively. The RARβ mRNA levels were similar in caVLS, cfVLS, and normal skin. The RARβ promoter was hypermethylated in 18 (90%) of 20 LS-VSCC, 11 (55%) of 20 cfVLS, 10 (50%) of 20 caVLS, and 5 (25%) of 20 in the normal skin group. The degree of methylation of RARβ promoter was higher in LS-VSCC, ranging from 5 to 9 (full promoter methylation) CpGs methylated, than in caVLS (P = .02), cfVLS (P = .03), or normal skin (P < .001), which was up to 5 CpGs methylated. Importantly, 0 of 8 LS-VSCC with 5 to 6 CpGs methylated and 5 (63%) of 8 LS-VSCC with 7 to 8 CpGs methylated were from patients with lymph node metastasis at diagnosis, respectively, whereas there were 2 of 2 (100%) LS-VSCC samples with 9 CpG methylated from patients with lymph node metastasis at diagnosis and subsequent recurrence. In LS-VSCC c-Jun mRNA was 4.3-, 1.4-, and 2.6-fold higher than in caVLS (P < .001), cfVLS (P = .001), and normal skin (P < .001), respectively. The expression of c-Jun was similar in caVLS, cfVLS, and normal skin. Conclusions and Relevance Hypermethylation-induced RARβ down-expression was associated with LS-VSCC and correlates with the upregulation of c-Jun. The degree of methylation of RARβ promoter increased with the malignancy of LS-VSCC. Therefore, RARβ gene dysregulation may play a role in progression of LS-VSCC, and RARβ promoter methylation status may be used as a prognostic marker in clinical treatment of patients with LS-VSCC.
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Affiliation(s)
- John Charles Rotondo
- Section of Pathology, Oncology and Experimental Biology, Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, via Fossato di Mortara 64/B, 44121 Ferrara, Italy
| | - Alessandro Borghi
- Section of Dermatology and Infectious Diseases, Department of Medical Sciences, University of Ferrara, via Savonarola 9, 44121 Ferrara, Italy
| | - Rita Selvatici
- Department of Medical Sciences, University of Ferrara, via Fossato di Mortara 70, 44121 Ferrara, Italy
| | - Elisa Mazzoni
- Section of Pathology, Oncology and Experimental Biology, Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, via Fossato di Mortara 64/B, 44121 Ferrara, Italy
| | - Ilaria Bononi
- Section of Pathology, Oncology and Experimental Biology, Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, via Fossato di Mortara 64/B, 44121 Ferrara, Italy
| | - Monica Corazza
- Section of Dermatology and Infectious Diseases, Department of Medical Sciences, University of Ferrara, via Savonarola 9, 44121 Ferrara, Italy
| | - Jacqueline Kussini
- Section of Dermatology and Infectious Diseases, Department of Medical Sciences, University of Ferrara, via Savonarola 9, 44121 Ferrara, Italy
| | - Elena Montinari
- Section of Anatomic Pathology, Department of Morphology, Surgery and Experimental Medicine, University of Ferrara and S. Anna University Hospital Via Aldo Moro, 8, 44124 Cona, Ferrara, Italy
| | - Roberta Gafà
- Section of Anatomic Pathology, Department of Morphology, Surgery and Experimental Medicine, University of Ferrara and S. Anna University Hospital Via Aldo Moro, 8, 44124 Cona, Ferrara, Italy
| | - Mauro Tognon
- Section of Pathology, Oncology and Experimental Biology, Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, via Fossato di Mortara 64/B, 44121 Ferrara, Italy
| | - Fernanda Martini
- Section of Pathology, Oncology and Experimental Biology, Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, via Fossato di Mortara 64/B, 44121 Ferrara, Italy
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24
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Delaidelli A, Jan A, Herms J, Sorensen PH. Translational control in brain pathologies: biological significance and therapeutic opportunities. Acta Neuropathol 2019; 137:535-555. [PMID: 30739199 DOI: 10.1007/s00401-019-01971-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 01/30/2019] [Accepted: 02/04/2019] [Indexed: 12/13/2022]
Abstract
Messenger RNA (mRNA) translation is the terminal step in protein synthesis, providing a crucial regulatory checkpoint for this process. Translational control allows specific cell types to respond to rapid changes in the microenvironment or to serve specific functions. For example, neurons use mRNA transport to achieve local protein synthesis at significant distances from the nucleus, the site of RNA transcription. Altered expression or functions of the various components of the translational machinery have been linked to several pathologies in the central nervous system. In this review, we provide a brief overview of the basic principles of mRNA translation, and discuss alterations of this process relevant to CNS disease conditions, with a focus on brain tumors and chronic neurological conditions. Finally, synthesizing this knowledge, we discuss the opportunities to exploit the biology of altered mRNA translation for novel therapies in brain disorders, as well as how studying these alterations can shed new light on disease mechanisms.
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Affiliation(s)
- Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
| | - Asad Jan
- Department of Biomedicine, Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, 8000, Aarhus C, Denmark
| | - Jochen Herms
- Department for Translational Brain Research, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University, Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Ludwig-Maximilians-University Munich, Schillerstraße 44, 80336, Munich, Germany
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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25
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Kwan T, Thompson SR. Noncanonical Translation Initiation in Eukaryotes. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032672. [PMID: 29959190 DOI: 10.1101/cshperspect.a032672] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The vast majority of eukaryotic messenger RNAs (mRNAs) initiate translation through a canonical, cap-dependent mechanism requiring a free 5' end and 5' cap and several initiation factors to form a translationally active ribosome. Stresses such as hypoxia, apoptosis, starvation, and viral infection down-regulate cap-dependent translation during which alternative mechanisms of translation initiation prevail to express proteins required to cope with the stress, or to produce viral proteins. The diversity of noncanonical initiation mechanisms encompasses a broad range of strategies and cellular cofactors. Herein, we provide an overview and, whenever possible, a mechanistic understanding of the various noncanonical mechanisms of initiation used by cells and viruses. Despite many unanswered questions, recent advances have propelled our understanding of the scope, diversity, and mechanisms of alternative initiation.
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Affiliation(s)
- Thaddaeus Kwan
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Sunnie R Thompson
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
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26
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Gao Y, Liu B, Feng L, Sun B, He S, Yang Y, Wu G, E G, Liu C, Gao Y, Zhang E, Zhu B. Targeting JUN, CEBPB, and HDAC3: A Novel Strategy to Overcome Drug Resistance in Hypoxic Glioblastoma. Front Oncol 2019; 9:33. [PMID: 30775317 PMCID: PMC6367651 DOI: 10.3389/fonc.2019.00033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/14/2019] [Indexed: 11/23/2022] Open
Abstract
Hypoxia is a predominant feature in glioblastoma (GBM) and contributes greatly to its drug resistance. However, the molecular mechanisms which are responsible for the development of the resistant phenotype of GBM under hypoxic conditions remain unclear. To analyze the key pathways promoting therapy resistance in hypoxic GBM, we utilized the U87-MG cell line as a human GBM cell model and the human brain HEB cell line as a non-neoplastic brain cell model. These cell lines were cultured in the presence of 21, 5, and 1% O2 for 24 h. We detected the changes in transcriptional profiling and analyzed the biological processes and functional interactions for the genes with different expression levels under different hypoxia conditions. The results indicated that those alterations of U87-MG cells presented specific transcriptional signature in response to diverse hypoxia levels. Gene ontology analysis revealed that the genes related to the DNA replication and cell cycle were suppressed, while the genes involved in tissue and system development to promote cancer development were activated following hypoxia. Moreover, functional interaction analysis suggested that the epigenetic regulator HDAC3 and the transcriptional factors CEBPB and JUN played a central role in organ and system developmental process pathway. Previous studies reported the global alterations caused by activation of HDAC3, CEBPB, and JUN could form the molecular basis of the resistance to chemotherapy and radiation therapy of hypoxic GBM. In our study, the significant growth inhibitory effect of temozolomide on hypoxic GBM cells could be promoted under downregulation of these genes. The experiment suggested that HDAC3, CEBPB, and JUN were closely involved in the drug-resistance phenotype of hypoxic GBM. In summary, we profiled the hypoxia-dependent changes in the transcriptome of the U87-MG cell line and the human brain cell line HEB to identify the transcriptional signatures of U87-MG cells and elucidate the role of hypoxia in the drug-resistant phenotype of GBM. Furthermore, we identified three key genes and explored their important roles in the drug resistance of hypoxic GBM.
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Affiliation(s)
- Yixing Gao
- Department of Oncology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Bao Liu
- Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- Key Laboratory of High Altitude Medicine, People's Liberation Army, Chongqing, China
| | - Lan Feng
- Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- Key Laboratory of High Altitude Medicine, People's Liberation Army, Chongqing, China
| | - Binda Sun
- Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- Key Laboratory of High Altitude Medicine, People's Liberation Army, Chongqing, China
| | - Shu He
- Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- Key Laboratory of High Altitude Medicine, People's Liberation Army, Chongqing, China
| | - Yidong Yang
- Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- Key Laboratory of High Altitude Medicine, People's Liberation Army, Chongqing, China
| | - Gang Wu
- Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- Key Laboratory of High Altitude Medicine, People's Liberation Army, Chongqing, China
| | - Guoji E
- Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- Key Laboratory of High Altitude Medicine, People's Liberation Army, Chongqing, China
| | - Chang Liu
- Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- Key Laboratory of High Altitude Medicine, People's Liberation Army, Chongqing, China
| | - Yuqi Gao
- Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- Key Laboratory of High Altitude Medicine, People's Liberation Army, Chongqing, China
| | - Erlong Zhang
- Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University, Chongqing, China
- Key Laboratory of High Altitude Medicine, People's Liberation Army, Chongqing, China
| | - Bo Zhu
- Department of Oncology, Xinqiao Hospital, Army Medical University, Chongqing, China
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27
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Kielosto M, Eriksson J, Nummela P, Yin M, Hölttä E. Divergent roles of lysyl oxidase family members in ornithine decarboxylase- and RAS-transformed mouse fibroblasts and human melanoma cells. Oncotarget 2018; 9:37733-37752. [PMID: 30701028 PMCID: PMC6340875 DOI: 10.18632/oncotarget.26508] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 12/13/2018] [Indexed: 12/12/2022] Open
Abstract
We have previously shown that proto-oncoprotein c-Jun is activated in ornithine decarboxylase (ODC)- and RAS-transformed mouse fibroblasts, and that the transformed morphology of these cells can be reversed by expressing the transactivation domain deletion mutant of c-Jun (TAM67). Here, we found that lysyl oxidase (Lox), encoding an extracellular matrix-modifying enzyme, is downregulated in a c-Jun-dependent manner in ODC-transformed fibroblasts (Odc cells). In addition to Lox, the Lox family members Lox-like 1 and 3 (Loxl1 and Loxl3) were found to be downregulated in Odc as well as in RAS-transformed fibroblasts (E4), whereas Lox-like 4 (Loxl4) was upregulated in Odc and downregulated in E4 cells compared to normal N1 fibroblasts. Tetracycline-regulatable LOX re-expression in Odc cells led to inhibition of cell growth and invasion in three-dimensional Matrigel in an activity-independent manner. On the contrary, LOX and especially LOXL2, LOXL3, and LOXL4 were found to be upregulated in several human melanoma cell lines, and LOX inhibitor B-aminopropionitrile inhibited the invasive growth of these cells particularly when co-cultured with fibroblasts in Matrigel. Knocking down the expression of LOX and especially LOXL2 in melanoma cells almost completely abrogated the invasive growth capability. Further, LOXL2 was significantly upregulated in clinical human primary melanomas compared to benign nevi, and high expression of LOXL2 in primary melanomas was associated with formation of metastases and shorter survival of patients. Thus, our studies reveal that inactive pro-LOX (together with Lox propeptide) functions as a tumor suppressor in ODC- and RAS-transformed murine fibroblasts by inhibiting cell growth and invasion, and active LOX and LOXL2 as tumor promoters in human melanoma cells by promoting their invasive growth.
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Affiliation(s)
- Mari Kielosto
- Department of Pathology, University of Helsinki, Helsinki, Finland
| | - Johanna Eriksson
- Department of Pathology, University of Helsinki, Helsinki, Finland
| | - Pirjo Nummela
- Department of Pathology, University of Helsinki, Helsinki, Finland.,Current address: University of Helsinki, Genome-Scale Biology Research Program, Helsinki, Finland
| | - Miao Yin
- Department of Pathology, University of Helsinki, Helsinki, Finland
| | - Erkki Hölttä
- Department of Pathology, University of Helsinki, Helsinki, Finland
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28
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Belanova AA, Chmykhalo VK, Makarenko MS, Lyangasova OV, Belousova MM, Aleksandrova AA, Zolotukhin PV. Effects of JUN and NFE2L2 knockdown on oxidative status and NFE2L2/AP-1 targets expression in HeLa cells in basal conditions and upon sub-lethal hydrogen peroxide treatment. Mol Biol Rep 2018; 46:27-39. [DOI: 10.1007/s11033-018-4412-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 10/03/2018] [Indexed: 11/29/2022]
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29
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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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30
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González-Morales A, Zabaleta A, Guruceaga E, Alonso MM, García-Moure M, Fernández-Irigoyen J, Santamaría E. Spatial and temporal proteome dynamics of glioma cells during oncolytic adenovirus Delta-24-RGD infection. Oncotarget 2018; 9:31045-31065. [PMID: 30123426 PMCID: PMC6089549 DOI: 10.18632/oncotarget.25774] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/22/2018] [Indexed: 11/25/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common and aggressive type of malignant glioma. Oncolytic adenoviruses are being modified to exploit the aberrant expression of proteins in tumor cells to increase the antiglioma efficacy. E1A mutant adenovirus Delta-24-RGD (DNX-2401) has shown a favorable toxicity profile and remarkable efficacy in a first-in-human phase I clinical trial. However, the comprehensive modulation of glioma metabolism in response to Delta-24-RGD infection is poorly understood. Integrating mass spectrometry based-quantitative proteomics, physical and functional interaction data, and biochemical approaches, we conducted a cell-wide study of cytosolic, nuclear, and secreted glioma proteomes throughout the early time course of Delta-24-RGD infection. In addition to the severe proteostasis impairment detected during the first hours post-infection (hpi), Delta-24-RGD induces a transient inhibition of signal transducer and activator of transcription 3 (STAT3), and transcription factor AP-1 (c-JUN) between 3 and 10hpi, increasing the nuclear factor kappa B (NF-κB) activity at 6hpi. Furthermore, Delta-24-RGD specifically modulates the activation dynamics of protein kinase C (PKC), extracellular signal-regulated kinase 1/2 (ERK1/2), and p38 mitogen-activated protein kinase (p38 MAPK) pathways early in infection. At extracellular level, Delta-24-RGD triggers a time -dependent dynamic production of multitasking cytokines, and chemotactic factors, suggesting potential pleiotropic effects on the immune system reactivation. Taken together, these data help us to understand the mechanisms used by Delta-24-RGD to exploit glioma proteome organization. Further mining of this proteomic resource may enable design and engineering complementary adenoviral based-vectors to increase the specificity and potency against glioma.
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Affiliation(s)
- Andrea González-Morales
- Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea, Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea, Pamplona, Spain
| | - Aintzane Zabaleta
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Oncohematology Area, University Hospital of Navarra, Center for Applied Medical Research, CIBERONC, Pamplona, Spain
| | - Elizabeth Guruceaga
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Bioinformatics Unit, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Marta M Alonso
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Program in Solid Tumors and Biomarkers, Foundation for the Applied Medical Research, Pamplona, Spain.,Department of Pediatrics, University Hospital of Navarra, Pamplona, Spain
| | - Marc García-Moure
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Program in Solid Tumors and Biomarkers, Foundation for the Applied Medical Research, Pamplona, Spain.,Department of Pediatrics, University Hospital of Navarra, Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea, Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea, Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea, Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea, Pamplona, Spain
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31
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Dai J, Ma Y, Chu S, Le N, Cao J, Wang Y. Identification of key genes and pathways in meningioma by bioinformatics analysis. Oncol Lett 2018; 15:8245-8252. [PMID: 29805558 PMCID: PMC5950024 DOI: 10.3892/ol.2018.8376] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 11/23/2017] [Indexed: 12/12/2022] Open
Abstract
Meningioma is the most frequently occurring type of brain tumor. The present study aimed to conduct a comprehensive bioinformatics analysis of key genes and relevant pathways involved in meningioma, and acquire further insight into the underlying molecular mechanisms. Initially, differentially expressed genes (DEGs) in 47 meningioma samples as compared with 4 normal meninges were identified. Subsequently, these DEGs were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. In addition, a protein-protein interaction (PPI) network of the identified DEGs was constructed using the Search Tool for the Retrieval of Interacting Genes and visualized using Cytoscape. In total, 1,683 DEGs were identified, including 66 upregulated and 1,617 downregulated genes. The GO analysis results revealed that the DEGs were significantly associated with the ‘protein binding’, ‘cytoplasm’, ‘extracellular matrix (ECM) organization’ and ‘cell adhesion’ terms. The KEGG analysis results demonstrated the significant pathways included ‘AGE-RAGE signaling pathway in diabetic complications’, ‘PI3K-Akt signaling pathway’, ‘ECM-receptor interaction’ and ‘cell adhesion molecules’. The top five hub genes obtained from the PPI network were JUN, PIK3R1, FOS, AGT and MYC, and the most enriched KEGG pathways associated with the four obtained modules were ‘chemokine signaling pathway’, ‘cytokine-cytokine receptor interaction’, ‘allograft rejection’, and ‘complement and coagulation cascades’. In conclusion, bioinformatics analysis identified a number of potential biomarkers and relevant pathways that may represent key mechanisms involved in the development and progression of meningioma. However, these findings require verification in future experimental studies.
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Affiliation(s)
- Junxi Dai
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201900, P.R. China
| | - Yanbin Ma
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201900, P.R. China
| | - Shenghua Chu
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201900, P.R. China
| | - Nanyang Le
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201900, P.R. China
| | - Jun Cao
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201900, P.R. China
| | - Yang Wang
- Department of Emergency, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200082, P.R. China
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32
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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: 0.2] [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.
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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
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33
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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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34
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Heiland DH, Ferrarese R, Claus R, Dai F, Masilamani AP, Kling E, Weyerbrock A, Kling T, Nelander S, Carro MS. c-Jun-N-terminal phosphorylation regulates DNMT1 expression and genome wide methylation in gliomas. Oncotarget 2018; 8:6940-6954. [PMID: 28036297 PMCID: PMC5351681 DOI: 10.18632/oncotarget.14330] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 12/15/2016] [Indexed: 12/19/2022] Open
Abstract
High-grade gliomas (HGG) are the most common brain tumors, with an average survival time of 14 months. A glioma-CpG island methylator phenotype (G-CIMP), associated with better clinical outcome, has been described in low and high-grade gliomas. Mutation of IDH1 is known to drive the G-CIMP status. In some cases, however, the hypermethylation phenotype is independent of IDH1 mutation, suggesting the involvement of other mechanisms. Here, we demonstrate that DNMT1 expression is higher in low-grade gliomas compared to glioblastomas and correlates with phosphorylated c-Jun. We show that phospho-c-Jun binds to the DNMT1 promoter and causes DNA hypermethylation. Phospho-c-Jun activation by Anisomycin treatment in primary glioblastoma-derived cells attenuates the aggressive features of mesenchymal glioblastomas and leads to promoter methylation and downregulation of key mesenchymal genes (CD44, MMP9 and CHI3L1). Our findings suggest that phospho-c-Jun activates an important regulatory mechanism to control DNMT1 expression and regulate global DNA methylation in Glioblastoma.
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Affiliation(s)
- Dieter H Heiland
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Roberto Ferrarese
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rainer Claus
- Department of Hematology, Oncology, and Stem Cell Transplantation, University of Freiburg Medical Center, Freiburg, Germany
| | - Fangping Dai
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anie P Masilamani
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eva Kling
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Astrid Weyerbrock
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Teresia Kling
- Department of Immunology, Genetics and Pathology and Science for Life Laboratories, University of Uppsala, Uppsala, Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology and Science for Life Laboratories, University of Uppsala, Uppsala, Sweden
| | - Maria S Carro
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
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35
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Knirsh R, Ben-Dror I, Modai S, Shomron N, Vardimon L. MicroRNA 10b promotes abnormal expression of the proto-oncogene c-Jun in metastatic breast cancer cells. Oncotarget 2018; 7:59932-59944. [PMID: 27494896 PMCID: PMC5312359 DOI: 10.18632/oncotarget.11000] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/30/2016] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs have been shown to act as oncogenes or tumor suppressers via various cellular pathways. Specifically, in breast cancer, upregulation of miR-10b is positively associated with aggressiveness of tumors. However, the mechanism by which miR-10b contributes to cell malignancy is largely unknown. Here we show that at the receiving end of the miR-10b pathway is the proto-oncogene c-Jun, a transcription factor that plays a critical role in stimulation of cell proliferation and tumor progression. c-Jun is known to be translationally activated by loss of cell contacts or restructuring of the cytoskeleton. A comprehensive analysis of miRNA expression exhibited a significant increase in miR-10b expression. This was supported by analysis of breast cancer cells, which showed that loss of E-cadherin in metastatic cells is accompanied by elevation of miR-10b and interestingly, by a marked increase in accumulation of c-Jun. Silencing miR-10b in metastatic breast cancer cells leads to a decline in c-Jun expression, whereas overexpression of miR-10b in HaCaT cells is sufficient to elevate the accumulation of c-Jun. The increase in c-Jun protein accumulation in metastatic cells is not accompanied by an increase in c-Jun mRNA and is not dependent on MAPK activity. Knockdown and overexpression experiments revealed that the increase is mediated by NF1 and RhoC, downstream targets of miR-10b that affect cytoskeletal dynamics through the ROCK pathway. Overall, we show the ability of miR-10b to activate the expression of c-Jun through RhoC and NF1, which represents a novel pathway for promoting migration and invasion of human cancer cells.
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Affiliation(s)
- Revital Knirsh
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Iris Ben-Dror
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shira Modai
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lily Vardimon
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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36
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Cate JHD. Human eIF3: from 'blobology' to biological insight. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0176. [PMID: 28138064 PMCID: PMC5311922 DOI: 10.1098/rstb.2016.0176] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 02/06/2023] Open
Abstract
Translation in eukaryotes is highly regulated during initiation, a process impacted by numerous readouts of a cell's state. There are many cases in which cellular messenger RNAs likely do not follow the canonical ‘scanning’ mechanism of translation initiation, but the molecular mechanisms underlying these pathways are still being uncovered. Some RNA viruses such as the hepatitis C virus use highly structured RNA elements termed internal ribosome entry sites (IRESs) that commandeer eukaryotic translation initiation, by using specific interactions with the general eukaryotic translation initiation factor eIF3. Here, I present evidence that, in addition to its general role in translation, eIF3 in humans and likely in all multicellular eukaryotes also acts as a translational activator or repressor by binding RNA structures in the 5′-untranslated regions of specific mRNAs, analogous to the role of the mediator complex in transcription. Furthermore, eIF3 in multicellular eukaryotes also harbours a 5′ 7-methylguanosine cap-binding subunit—eIF3d—which replaces the general cap-binding initiation factor eIF4E in the translation of select mRNAs. Based on results from cell biological, biochemical and structural studies of eIF3, it is likely that human translation initiation proceeds through dozens of different molecular pathways, the vast majority of which remain to be explored. This article is part of the themed issue ‘Perspectives on the ribosome’.
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Affiliation(s)
- Jamie H D Cate
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220, USA .,Lawrence Berkeley National Laboratory, Division of Molecular Biophysics and Integrated Bioimaging, Berkeley, CA 94720, USA
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37
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Heerma van Voss MR, van Diest PJ, Raman V. Targeting RNA helicases in cancer: The translation trap. Biochim Biophys Acta Rev Cancer 2017; 1868:510-520. [PMID: 28965870 DOI: 10.1016/j.bbcan.2017.09.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 12/14/2022]
Abstract
Cancer cells are reliant on the cellular translational machinery for both global elevation of protein synthesis and the translation of specific mRNAs that promote tumor cell survival. Targeting translational control in cancer is therefore increasingly recognized as a promising therapeutic strategy. In this regard, DEAD/H box RNA helicases are a very interesting group of proteins, with several family members regulating mRNA translation in cancer cells. In this review, we delineate the mechanisms by which DEAD/H box proteins modulate oncogenic translation and how inhibition of these RNA helicases can be exploited for anti-cancer therapeutics.
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Affiliation(s)
- Marise R Heerma van Voss
- Department of Radiology and Radiological Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD, USA; Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paul J van Diest
- Department of Radiology and Radiological Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD, USA; Department of Oncology, Johns Hopkins University, School of Medicine, MD, USA
| | - Venu Raman
- Department of Radiology and Radiological Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD, USA; Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Oncology, Johns Hopkins University, School of Medicine, MD, USA.
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38
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Vaklavas C, Blume SW, Grizzle WE. Translational Dysregulation in Cancer: Molecular Insights and Potential Clinical Applications in Biomarker Development. Front Oncol 2017; 7:158. [PMID: 28798901 PMCID: PMC5526920 DOI: 10.3389/fonc.2017.00158] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 07/06/2017] [Indexed: 01/04/2023] Open
Abstract
Although transcript levels have been traditionally used as a surrogate measure of gene expression, it is increasingly recognized that the latter is extensively and dynamically modulated at the level of translation (messenger RNA to protein). Over the recent years, significant progress has been made in dissecting the complex posttranscriptional mechanisms that regulate gene expression. This advancement in knowledge came hand in hand with the progress made in the methodologies to study translation both at gene-specific as well as global genomic level. The majority of translational control is exerted at the level of initiation; nonetheless, protein synthesis can be modulated at the level of translation elongation, termination, and recycling. Sequence and structural elements and epitranscriptomic modifications of individual transcripts allow for dynamic gene-specific modulation of translation. Cancer cells usurp the regulatory mechanisms that govern translation to carry out translational programs that lead to the phenotypic hallmarks of cancer. Translation is a critical nexus in neoplastic transformation. Multiple oncogenes and signaling pathways that are activated, upregulated, or mutated in cancer converge on translation and their transformative impact "bottlenecks" at the level of translation. Moreover, this translational dysregulation allows cancer cells to adapt to a diverse array of stresses associated with a hostile microenviroment and antitumor therapies. All elements involved in the process of translation, from the transcriptional template, the components of the translational machinery, to the proteins that interact with the transcriptome, have been found to be qualitatively and/or quantitatively perturbed in cancer. This review discusses the regulatory mechanisms that govern translation in normal cells and how translation becomes dysregulated in cancer leading to the phenotypic hallmarks of malignancy. We also discuss how dysregulated mediators or components of translation can be utilized as biomarkers with potential diagnostic, prognostic, or predictive significance. Such biomarkers have the potential advantage of uniform applicability in the face of inherent tumor heterogeneity and deoxyribonucleic acid instability. As translation becomes increasingly recognized as a process gone awry in cancer and agents are developed to target it, the utility and significance of these potential biomarkers is expected to increase.
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Affiliation(s)
- Christos Vaklavas
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Scott W Blume
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - William E Grizzle
- Department of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, AL, United States
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39
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Terenin IM, Smirnova VV, Andreev DE, Dmitriev SE, Shatsky IN. A researcher's guide to the galaxy of IRESs. Cell Mol Life Sci 2017; 74:1431-1455. [PMID: 27853833 PMCID: PMC11107752 DOI: 10.1007/s00018-016-2409-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/01/2016] [Accepted: 11/02/2016] [Indexed: 12/25/2022]
Abstract
The idea of internal initiation is frequently exploited to explain the peculiar translation properties or unusual features of some eukaryotic mRNAs. In this review, we summarize the methods and arguments most commonly used to address cases of translation governed by internal ribosome entry sites (IRESs). Frequent mistakes are revealed. We explain why "cap-independent" does not readily mean "IRES-dependent" and why the presence of a long and highly structured 5' untranslated region (5'UTR) or translation under stress conditions cannot be regarded as an argument for appealing to internal initiation. We carefully describe the known pitfalls and limitations of the bicistronic assay and artefacts of some commercially available in vitro translation systems. We explain why plasmid DNA transfection should not be used in IRES studies and which control experiments are unavoidable if someone decides to use it anyway. Finally, we propose a workflow for the validation of IRES activity, including fast and simple experiments based on a single genetic construct with a sequence of interest.
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Affiliation(s)
- Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | - Victoria V Smirnova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Dmitri E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Department of Biochemistry, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
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40
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Xia Y, Yang C, Hu N, Yang Z, He X, Li T, Zhang L. Exploring the key genes and signaling transduction pathways related to the survival time of glioblastoma multiforme patients by a novel survival analysis model. BMC Genomics 2017; 18:950. [PMID: 28198665 PMCID: PMC5310279 DOI: 10.1186/s12864-016-3256-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND This study is to explore the key genes and signaling transduction pathways related to the survival time of glioblastoma multiforme (GBM) patients. RESULTS Our results not only showed that mutually explored GBM survival time related genes and signaling transduction pathways are closely related to the GBM, but also demonstrated that our innovated constrained optimization algorithm (CoxSisLasso strategy) are better than the classical methods (CoxLasso and CoxSis strategy). CONCLUSION We analyzed why the CoxSisLasso strategy can outperform the existing classical methods and discuss how to extend this research in the distant future.
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Affiliation(s)
- Yuan Xia
- College of Computer and Information Science, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Chuanwei Yang
- Systems Biology, the University of Texas MD Anderson Cancer Center, Houston, USA
- Breast Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, USA
| | - Nan Hu
- Cancer Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, 400042 People’s Republic of China
| | - Zhenzhou Yang
- Cancer Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, 400042 People’s Republic of China
| | - Xiaoyu He
- Chongqing Zhongdi Medical Information Technology Co., Ltd, Chongqing, 401320 People’s Republic of China
| | - Tingting Li
- College of Mathematics and Statistics, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Le Zhang
- College of Computer and Information Science, Southwest University, Chongqing, 400715 People’s Republic of China
- College of Mathematics and Statistics, Southwest University, Chongqing, 400715 People’s Republic of China
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41
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Kawashima F, Saito K, Kurata H, Maegaki Y, Mori T. c-jun is differentially expressed in embryonic and adult neural precursor cells. Histochem Cell Biol 2017; 147:721-731. [PMID: 28091742 DOI: 10.1007/s00418-016-1536-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/25/2016] [Indexed: 12/23/2022]
Abstract
c-jun, a major component of AP-1 transcription factor, has a wide variety of functions. In the embryonic brain, c-jun mRNA is abundantly expressed in germinal layers around the ventricles. Although the subventricular zone (SVZ) of the adult brain is a derivative of embryonic germinal layers and contains neural precursor cells (NPCs), the c-jun expression pattern is not clear. To study the function of c-jun in adult neurogenesis, we analyzed c-jun expression in the adult SVZ by immunohistochemistry and compared it with that of the embryonic brain. We found that almost all proliferating embryonic NPCs expressed c-jun, but the number of c-jun immunopositive cells among proliferating adult NPCs was about half. In addition, c-jun was hardly expressed in post-mitotic migrating neurons in the embryonic brain, but the majority of c-jun immunopositive cells were tangentially migrating neuroblasts heading toward the olfactory bulb in the adult brain. In addition, status epilepticus is known to enhance the transient proliferation of adult NPCs, but the c-jun expression pattern was not significantly affected. These expression patterns suggest that c-jun has a pivotal role in the proliferation of embryonic NPCs, but it has also other roles in adult neurogenesis.
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Affiliation(s)
- Fumiaki Kawashima
- Department of Biological Regulation, School of Health Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Kengo Saito
- Department of Biological Regulation, School of Health Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Hirofumi Kurata
- Department of Biological Regulation, School of Health Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan.,Division of Child Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, 36-1 Nishi-cho, Yonago, Tottori, 683-8504, Japan
| | - Yoshihiro Maegaki
- Division of Child Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, 36-1 Nishi-cho, Yonago, Tottori, 683-8504, Japan
| | - Tetsuji Mori
- Department of Biological Regulation, School of Health Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan.
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42
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Li Q, Gao WQ, Dai WY, Yu C, Zhu RY, Jin J. ATF2 translation is induced under chemotherapeutic drug-mediated cellular stress via an IRES-dependent mechanism in human hepatic cancer Bel7402 cells. Oncol Lett 2016; 12:4795-4802. [PMID: 28105187 DOI: 10.3892/ol.2016.5274] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/09/2016] [Indexed: 12/16/2022] Open
Abstract
Activating transcription factor (ATF) 2 is a member of the ATF/cyclic AMP-responsive element binding protein family, which exhibits both oncogenic and tumor-suppressor functions. In our preliminary experiments, it was observed that the expression of the ATF2 protein was induced following treatment with adriamycin (ADR) and paclitaxel (PTX), which may be regulated by internal ribosome entry segment (IRES)-mediated translation. By constructing a bicistronic vector containing the ATF2 5'-untranslated region (UTR), it was demonstrated that the ATF2 5'-UTR contains an IRES and maps a 30-nucleotide (nt) sequence (from nt 299 to nt ~269), which was essential for the IRES activity. The ATF2 IRES activity exhibited significant variation in different cell lines. In addition, it was observed that ADR and PTX also induced ATF2 IRES activity in Bel7402 cells. The present study has demonstrated that ATF2 translation is initiated via IRES, which is upregulated by ADR and PTX, thus suggesting that the regulation of the IRES-dependent translation of ATF2 may be involved in effecting the cancer cell response to chemotherapeutic drugs-mediated cellular stress.
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Affiliation(s)
- Qi Li
- Laboratory of Molecular Pharmacology, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Wen-Qing Gao
- Laboratory of Molecular Pharmacology, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Wen-Yan Dai
- Laboratory of Molecular Pharmacology, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Chuang Yu
- Laboratory of Molecular Pharmacology, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Rui-Yu Zhu
- Laboratory of Molecular Pharmacology, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Jian Jin
- Laboratory of Molecular Pharmacology, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
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43
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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: 1.6] [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.
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Affiliation(s)
- Davide D'Amico
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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44
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eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation. Nature 2016; 536:96-9. [PMID: 27462815 PMCID: PMC5003174 DOI: 10.1038/nature18954] [Citation(s) in RCA: 231] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 06/21/2016] [Indexed: 12/19/2022]
Abstract
Eukaryotic mRNAs contain a 5' cap structure critical for recruitment of the translation machinery and initiation of protein synthesis. mRNA recognition is thought to require direct interactions between eukaryotic initiation factor 4E (eIF4E) and the mRNA cap. However, translation of numerous capped mRNAs remains robust during cellular stress, early development, and cell cycle progression1 despite eIF4E inactivation. Here we describe a new cellular cap-dependent pathway of translation initiation that relies on a previously unknown cap-binding activity of eIF3d, a subunit of the 800-kilodalton eukaryotic initiation factor 3 (eIF3) complex. A 1.4 Å crystal structure of the eIF3d cap-binding domain reveals unexpected homology to endonucleases involved in RNA turnover, and allows modeling of cap recognition by eIF3d. eIF3d makes specific contacts to the cap, as exemplified by cap analog competition, and these interactions are essential for assembly of translation initiation complexes on eIF3-specialized mRNAs2 such as the cell proliferation regulator c-Jun. The c-Jun mRNA further encodes an inhibitory RNA element that blocks eIF4E recruitment, thus enforcing alternative cap recognition by eIF3d. Our results reveal a new mechanism of cap-dependent translation independent of eIF4E, and illustrate how modular RNA elements work in concert to direct specialized forms of translation initiation.
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45
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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: 1.3] [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.
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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.
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46
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Network Modeling Identifies Patient-specific Pathways in Glioblastoma. Sci Rep 2016; 6:28668. [PMID: 27354287 PMCID: PMC4926112 DOI: 10.1038/srep28668] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/08/2016] [Indexed: 12/26/2022] Open
Abstract
Glioblastoma is the most aggressive type of malignant human brain tumor. Molecular profiling experiments have revealed that these tumors are extremely heterogeneous. This heterogeneity is one of the principal challenges for developing targeted therapies. We hypothesize that despite the diverse molecular profiles, it might still be possible to identify common signaling changes that could be targeted in some or all tumors. Using a network modeling approach, we reconstruct the altered signaling pathways from tumor-specific phosphoproteomic data and known protein-protein interactions. We then develop a network-based strategy for identifying tumor specific proteins and pathways that were predicted by the models but not directly observed in the experiments. Among these hidden targets, we show that the ERK activator kinase1 (MEK1) displays increased phosphorylation in all tumors. By contrast, protein numb homolog (NUMB) is present only in the subset of the tumors that are the most invasive. Additionally, increased S100A4 is associated with only one of the tumors. Overall, our results demonstrate that despite the heterogeneity of the proteomic data, network models can identify common or tumor specific pathway-level changes. These results represent an important proof of principle that can improve the target selection process for tumor specific treatments.
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47
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Walters B, Thompson SR. Cap-Independent Translational Control of Carcinogenesis. Front Oncol 2016; 6:128. [PMID: 27252909 PMCID: PMC4879784 DOI: 10.3389/fonc.2016.00128] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/10/2016] [Indexed: 01/04/2023] Open
Abstract
Translational regulation has been shown to play an important role in cancer and tumor progression. Despite this fact, the role of translational control in cancer is an understudied and under appreciated field, most likely due to the technological hurdles and paucity of methods available to establish that changes in protein levels are due to translational regulation. Tumors are subjected to many adverse stress conditions such as hypoxia or starvation. Under stress conditions, translation is globally downregulated through several different pathways in order to conserve energy and nutrients. Many of the proteins that are synthesized during stress in order to cope with the stress use a non-canonical or cap-independent mechanism of initiation. Tumor cells have utilized these alternative mechanisms of translation initiation to promote survival during tumor progression. This review will specifically discuss the role of cap-independent translation initiation, which relies on an internal ribosome entry site (IRES) to recruit the ribosomal subunits internally to the messenger RNA. We will provide an overview of the role of IRES-mediated translation in cancer by discussing the types of genes that use IRESs and the conditions under which these mechanisms of initiation are used. We will specifically focus on three well-studied examples: Apaf-1, p53, and c-Jun, where IRES-mediated translation has been demonstrated to play an important role in tumorigenesis or tumor progression.
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Affiliation(s)
- Beth Walters
- Department of Microbiology, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Sunnie R Thompson
- Department of Microbiology, University of Alabama at Birmingham , Birmingham, AL , USA
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48
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Liu Y, Long Y, Xing Z, Zhang D. C-Jun recruits the NSL complex to regulate its target gene expression by modulating H4K16 acetylation and promoting the release of the repressive NuRD complex. Oncotarget 2016; 6:14497-506. [PMID: 25971333 PMCID: PMC4546482 DOI: 10.18632/oncotarget.3988] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/15/2015] [Indexed: 11/25/2022] Open
Abstract
The proto-oncogene c-Jun plays essential roles in various cellular processes, including cell proliferation, cell differentiation, and cellular apoptosis. Enormous efforts have been made to understand the mechanisms regulating c-Jun activation. The males absent on the first (MOF)-containing non-specific lethal (NSL) complex has been shown to positively regulate gene expression. However, the biological function of the NSL complex is largely unknown. Here we present evidence showing that c-Jun recruits the NSL complex to c-Jun target genes upon activation. The NSL complex catalyzes H4K16 acetylation at c-Jun target genes, thereby promoting c-Jun target gene transcription. More interestingly, we also found that the NSL complex promotes the release of the repressive NuRD complex from c-Jun target genes, thus activating c-Jun. Our findings not only reveal a new mechanism regulating c-Jun activation, but also identify the NSL complex as a c-Jun co-activator in c-Jun-regulated gene expression, expanding our knowledge of the function of the NSL complex in gene expression regulation.
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Affiliation(s)
- Yan Liu
- College of Life Sciences, Hebei United University, Tangshan, China
| | - Yuehong Long
- College of Life Sciences, Hebei United University, Tangshan, China
| | - Zhaobin Xing
- College of Life Sciences, Hebei United University, Tangshan, China
| | - Daoyong Zhang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
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49
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Pazos E, Portela C, Penas C, Vázquez ME, Mascareñas JL. Peptide-DNA conjugates as tailored bivalent binders of the oncoprotein c-Jun. Org Biomol Chem 2016; 13:5385-90. [PMID: 25778494 DOI: 10.1039/c5ob00318k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We describe a ds-oligonucleotide-peptide conjugate that is able to efficiently dismount preformed DNA complexes of the bZIP regions of oncoproteins c-Fos and c-Jun (AP-1), and therefore might be useful as disrupters of AP-1-mediated gene expression pathways.
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Affiliation(s)
- Elena Pazos
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, C/Jenaro de la Fuente s/n, Campus Vida, 15782 Santiago de Compostela, Spain.
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50
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Fogli A, Chautard E, Vaurs-Barrière C, Pereira B, Müller-Barthélémy M, Court F, Biau J, Pinto AA, Kémény JL, Khalil T, Karayan-Tapon L, Verrelle P, Costa BM, Arnaud P. The tumoral A genotype of the MGMT rs34180180 single-nucleotide polymorphism in aggressive gliomas is associated with shorter patients' survival. Carcinogenesis 2015; 37:169-176. [PMID: 26717998 DOI: 10.1093/carcin/bgv251] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/19/2015] [Indexed: 01/09/2023] Open
Abstract
Malignant gliomas are the most common primary brain tumors. Grade III and IV gliomas harboring wild-type IDH1/2 are the most aggressive. In addition to surgery and radiotherapy, concomitant and adjuvant chemotherapy with temozolomide (TMZ) significantly improves overall survival (OS). The methylation status of the O(6)-methylguanine-DNA methyltransferase (MGMT) promoter is predictive of TMZ response and a prognostic marker of cancer outcome. However, the promoter regions the methylation of which correlates best with survival in aggressive glioma and whether the promoter methylation status predictive value could be refined or improved by other MGMT-associated molecular markers are not precisely known. In a cohort of 87 malignant gliomas treated with radiotherapy and TMZ-based chemotherapy, we retrospectively determined the MGMT promoter methylation status, genotyped single nucleotide polymorphisms (SNPs) in the promoter region and quantified MGMT mRNA expression level. Each of these variables was correlated with each other and with the patients' OS. We found that methylation of the CpG sites within MGMT exon 1 best correlated with OS and MGMT expression levels, and confirmed MGMT methylation as a stronger independent prognostic factor compared to MGMT transcription levels. Our main finding is that the presence of only the A allele at the rs34180180 SNP in the tumor was significantly associated with shorter OS, independently of the MGMT methylation status. In conclusion, in the clinic, rs34180180 SNP genotyping could improve the prognostic value of the MGMT promoter methylation assay in patients with aggressive glioma treated with TMZ.
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Affiliation(s)
- Anne Fogli
- INSERM-U1103 and.,CNRS-UMR 6293, Clermont-Ferrand 63001, France.,GReD Laboratory, Clermont Auvergne University, Clermont-Ferrand 63000, France.,Biochemistry and Molecular Biology Department, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Emmanuel Chautard
- Clermont Auvergne University, EA 7283 CREaT, Clermont-Ferrand 63000, France.,Radiotherapy Department, Jean Perrin Center, Clermont-Ferrand 63011, France
| | - Catherine Vaurs-Barrière
- INSERM-U1103 and.,CNRS-UMR 6293, Clermont-Ferrand 63001, France.,GReD Laboratory, Clermont Auvergne University, Clermont-Ferrand 63000, France
| | - Bruno Pereira
- Biostatistics Department , DRCI, Clermont-Ferrand Hospital , Clermont-Ferrand 63003 , France
| | | | - Franck Court
- INSERM-U1103 and.,CNRS-UMR 6293, Clermont-Ferrand 63001, France.,GReD Laboratory, Clermont Auvergne University, Clermont-Ferrand 63000, France
| | - Julian Biau
- Clermont Auvergne University, EA 7283 CREaT, Clermont-Ferrand 63000, France.,Radiotherapy Department, Jean Perrin Center, Clermont-Ferrand 63011, France
| | - Afonso Almeida Pinto
- Department of Neurosurgery , Braga Hospital , Braga 4710-243 São Victor , Portugal
| | - Jean-Louis Kémény
- Department of Anatomopathology , Clermont-Ferrand Hospital , Clermont-Ferrand 63003 , France
| | - Toufic Khalil
- Department of Neurosurgery, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France.,Clermont Auvergne University, EA 7282 IGCNC, Clermont-Ferrand 63000, France
| | - Lucie Karayan-Tapon
- INSERM-U935, Poitiers 86021, France.,Poitiers University, Poitiers 86000, France.,Cancer Biology Laboratory, Poitiers Hospital, Poitiers 86021, France
| | - Pierre Verrelle
- Clermont Auvergne University, EA 7283 CREaT, Clermont-Ferrand 63000, France.,Radiotherapy Department, Jean Perrin Center, Clermont-Ferrand 63011, France.,INSERM U2021 CNRS UMR3347, Curie Institute, Orsay 91405, France
| | - Bruno Marques Costa
- School of Health Sciences, Life and Health Sciences Research Institute (ICVS), Braga 4710-057, Portugal and.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Braga 4710-057, Portugal
| | - Philippe Arnaud
- INSERM-U1103 and.,CNRS-UMR 6293, Clermont-Ferrand 63001, France.,GReD Laboratory, Clermont Auvergne University, Clermont-Ferrand 63000, France
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