1
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Rojo-Pardillo M, Godefroid L, Dom G, Lefort A, Libert F, Robaye B, Maenhaut C. Understanding the Dosage-Dependent Role of Dicer1 in Thyroid Tumorigenesis. Int J Mol Sci 2024; 25:10701. [PMID: 39409030 PMCID: PMC11476720 DOI: 10.3390/ijms251910701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/27/2024] [Accepted: 10/02/2024] [Indexed: 10/19/2024] Open
Abstract
Tumors originating from thyroid follicular cells are the most common endocrine tumors, with rising incidence. Despite a generally good prognosis, up to 20% of patients experience recurrence and persistence, highlighting the need to identify the underlying molecular mechanisms. Dicer1 has been found to be altered in papillary thyroid cancer (PTC). Studies suggest that Dicer1 functions as a haploinsufficient tumor suppressor gene: partial loss promotes tumorigenesis, while complete loss prevents it. To investigate the effects of partial or total Dicer1 loss in PTC in vitro, we generated stable Dicer1 (+/-) cell lines from TPC1 using CRISPR-Cas9, though no Dicer1 (-/-) lines could be produced. Therefore, siRNA against Dicer1 was transfected into Dicer1 (+/-) cell lines to further decrease its expression. Transcriptomic analysis revealed changes in proliferation and cell locomotion. BrdU staining indicated a slow-down of the cell cycle, with fewer cells in S phase and more in G0-G1-phase. Additionally, transwell assays showed decreased invasion and migration after Dicer1 knockdown by siRNA. Moreover, Dicer1 overexpression led to decreased proliferation, invasion, and increased apoptosis. Our findings deepen the understanding of Dicer1's role in thyroid cancer, demonstrating that both complete elimination and overexpression of Dicer1 inhibit thyroid oncogenesis, highlighting Dicer1 as a promising target for novel therapeutic strategies.
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Affiliation(s)
- María Rojo-Pardillo
- IRIBHM J. E. Dumont, Université Libre de Bruxelles, 1070 Brussels, Belgium; (M.R.-P.)
| | - Ludivine Godefroid
- IRIBHM J. E. Dumont, Université Libre de Bruxelles, 1070 Brussels, Belgium; (M.R.-P.)
| | - Geneviève Dom
- IRIBHM J. E. Dumont, Université Libre de Bruxelles, 1070 Brussels, Belgium; (M.R.-P.)
| | - Anne Lefort
- IRIBHM J. E. Dumont, Université Libre de Bruxelles, 1070 Brussels, Belgium; (M.R.-P.)
- BRIGHTcore Facility, 1070 Brussels, Belgium
| | - Frederick Libert
- IRIBHM J. E. Dumont, Université Libre de Bruxelles, 1070 Brussels, Belgium; (M.R.-P.)
- BRIGHTcore Facility, 1070 Brussels, Belgium
| | - Bernard Robaye
- IRIBHM J. E. Dumont, Université Libre de Bruxelles, Campus Charleroi, 6041 Charleroi, Belgium
| | - Carine Maenhaut
- IRIBHM J. E. Dumont, Université Libre de Bruxelles, 1070 Brussels, Belgium; (M.R.-P.)
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2
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Sánchez J, Ingaramo M, Gervé M, Thomas M, Boccaccio G, Dekanty A. FOXO-mediated repression of Dicer1 regulates metabolism, stress resistance, and longevity in Drosophila. Proc Natl Acad Sci U S A 2023; 120:e2216539120. [PMID: 37014862 PMCID: PMC10104520 DOI: 10.1073/pnas.2216539120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/04/2023] [Indexed: 04/05/2023] Open
Abstract
The adipose tissue plays a crucial role in metabolism and physiology, affecting animal lifespan and susceptibility to disease. In this study, we present evidence that adipose Dicer1 (Dcr-1), a conserved type III endoribonuclease involved in miRNA processing, plays a crucial role in the regulation of metabolism, stress resistance, and longevity. Our results indicate that the expression of Dcr-1 in murine 3T3L1 adipocytes is responsive to changes in nutrient levels and is subject to tight regulation in the Drosophila fat body, analogous to human adipose and hepatic tissues, under various stress and physiological conditions such as starvation, oxidative stress, and aging. The specific depletion of Dcr-1 in the Drosophila fat body leads to changes in lipid metabolism, enhanced resistance to oxidative and nutritional stress, and is associated with a significant increase in lifespan. Moreover, we provide mechanistic evidence showing that the JNK-activated transcription factor FOXO binds to conserved DNA-binding sites in the dcr-1 promoter, directly repressing its expression in response to nutrient deprivation. Our findings emphasize the importance of FOXO in controlling nutrient responses in the fat body by suppressing Dcr-1 expression. This mechanism coupling nutrient status with miRNA biogenesis represents a novel and previously unappreciated function of the JNK-FOXO axis in physiological responses at the organismal level.
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Affiliation(s)
- Juan A. Sánchez
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe3000, Argentina
| | - María C. Ingaramo
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe3000, Argentina
| | - María P. Gervé
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe3000, Argentina
| | - Maria G. Thomas
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas and Instituto Leloir, Buenos Aires1405, Argentina
| | - Graciela L. Boccaccio
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas and Instituto Leloir, Buenos Aires1405, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires1428, Argentina
| | - Andrés Dekanty
- Instituto de Agrobiotecnología del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe3000, Argentina
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe3000, Argentina
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3
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Hanna JA, Langdon CG, Garcia MR, Benton A, Lanman NA, Finkelstein D, Rehg JE, Hatley ME. Genetic context of oncogenic drivers dictates vascular sarcoma development in
aP2‐Cre
mice. J Pathol 2022; 257:109-124. [PMID: 35066877 PMCID: PMC9007915 DOI: 10.1002/path.5873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/06/2022] [Accepted: 01/20/2022] [Indexed: 12/02/2022]
Abstract
Angiosarcomas are aggressive vascular sarcomas that arise from endothelial cells and have an extremely poor prognosis. Because of the rarity of angiosarcomas, knowledge of molecular drivers and optimized treatment strategies is lacking, highlighting the need for in vivo models to study the disease. Previously, we generated genetically engineered mouse models of angiosarcoma driven by aP2‐Cre‐mediated biallelic loss of Dicer1 or conditional activation of KrasG12D with Cdkn2a loss that histologically and genetically resemble human tumors. In the present study, we found that DICER1 functions as a potent tumor suppressor and its deletion, in combination with either KRASG12D expression or Cdkn2a loss, is associated with angiosarcoma development. Independent of the genetic driver, the mTOR pathway was activated in all murine angiosarcoma models. Direct activation of the mTOR pathway by conditional deletion of Tsc1 with aP2‐Cre resulted in tumors that resemble intermediate grade human kaposiform hemangioendotheliomas, indicating that mTOR activation was not sufficient to drive the malignant angiosarcoma phenotype. Genetic dissection of the spectrum of vascular tumors identified genes specifically regulated in the aggressive murine angiosarcomas that are also enriched in human angiosarcoma. The genetic dissection driving the transition across the malignant spectrum of endothelial sarcomas provides an opportunity to identify key determinants of the malignant phenotype, novel therapies for angiosarcoma, and novel in vivo models to further explore angiosarcoma pathogenesis. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Jason A. Hanna
- Department of Oncology St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis TN 38105 USA
- Department of Biological Sciences Purdue University 201 S. University Street West Lafayette IN 47906 USA
- Purdue University Center for Cancer Research Purdue University West Lafayette, IN, 47907 USA
| | - Casey G. Langdon
- Department of Oncology St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis TN 38105 USA
| | - Matthew R. Garcia
- Department of Oncology St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis TN 38105 USA
| | - Annaleigh Benton
- Department of Biological Sciences Purdue University 201 S. University Street West Lafayette IN 47906 USA
- Purdue University Center for Cancer Research Purdue University West Lafayette, IN, 47907 USA
| | - Nadia A. Lanman
- Department of Comparative Pathobiology Purdue University 201 S. University Street West Lafayette IN 47906 USA
- Purdue University Center for Cancer Research Purdue University West Lafayette, IN, 47907 USA
| | - David Finkelstein
- Department of Computational Biology St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis TN 38105 USA
| | - Jerold E. Rehg
- Department of Pathology St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis TN 38105 USA
| | - Mark E. Hatley
- Department of Oncology St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis TN 38105 USA
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4
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Gao J, Shi H, Juhlin CC, Larsson C, Lui WO. Merkel cell polyomavirus T-antigens regulate DICER1 mRNA stability and translation through HSC70. iScience 2021; 24:103264. [PMID: 34761184 PMCID: PMC8567380 DOI: 10.1016/j.isci.2021.103264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/13/2021] [Accepted: 10/09/2021] [Indexed: 01/07/2023] Open
Abstract
Merkel cell carcinoma is an aggressive skin malignancy, mostly caused by Merkel cell polyomavirus (MCPyV). MCPyV T-antigens can induce mature microRNA expressions through the DnaJ domain, but its underlying mechanism is still unknown. Here, we report that the T-antigens induce protein expression and mRNA stability of DICER1, a key factor in microRNA biogenesis, through heat shock cognate 70 (HSC70). HSC70 directly interacts with the AU-rich elements (ARE) of DICER1 mRNA in both coding and 3′ untranslated region in the presence of MCPyV T-antigen. The T-antigen/HSC70 interaction could induce luciferase activity of synthetic ARE-containing reporter, as well as the stability of ARE-containing mRNAs, suggesting a broader role of MCPyV T-antigens in regulating multiple mRNAs via HSC70. These findings highlight a new role for the interaction of HSC70 and MCPyV T-antigens in mRNA regulation and an undescribed regulatory mechanism of DICER1 mRNA stability and translation through its direct interaction with HSC70. MCPyV T-antigen and HSC70 interaction regulates DICER1 expression HSC70 directly binds to ARE in the 3′UTR of DICER1 for expression regulation An unknown motif in DICER1 CDS is also required for its expression regulation by LT The LT-HSC70 interaction can regulate other ARE-containing mRNAs
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Affiliation(s)
- Jiwei Gao
- Department of Oncology-Pathology, Karolinska Institutet; BioClinicum, Karolinska University Hospital, 171 64 Solna, Sweden
| | - Hao Shi
- Department of Oncology-Pathology, Karolinska Institutet; BioClinicum, Karolinska University Hospital, 171 64 Solna, Sweden
| | - C Christofer Juhlin
- Department of Oncology-Pathology, Karolinska Institutet; BioClinicum, Karolinska University Hospital, 171 64 Solna, Sweden.,Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, 171 64 Solna, Sweden
| | - Catharina Larsson
- Department of Oncology-Pathology, Karolinska Institutet; BioClinicum, Karolinska University Hospital, 171 64 Solna, Sweden
| | - Weng-Onn Lui
- Department of Oncology-Pathology, Karolinska Institutet; BioClinicum, Karolinska University Hospital, 171 64 Solna, Sweden
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5
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Homayoonfal M, Asemi Z, Yousefi B. Targeting microRNAs with thymoquinone: a new approach for cancer therapy. Cell Mol Biol Lett 2021; 26:43. [PMID: 34627167 PMCID: PMC8502376 DOI: 10.1186/s11658-021-00286-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/27/2021] [Indexed: 02/08/2023] Open
Abstract
Cancer is a global disease involving transformation of normal cells into tumor types via numerous mechanisms, with mortality among all generations, in spite of the breakthroughs in chemotherapy, radiotherapy and/or surgery for cancer treatment. Since one in six deaths is due to cancer, it is one of the overriding priorities of world health. Recently, bioactive natural compounds have been widely recognized due to their therapeutic effects for treatment of various chronic disorders, notably cancer. Thymoquinone (TQ), the most valuable constituent of black cumin seeds, has shown anti-cancer characteristics in a wide range of animal models. The revolutionary findings have revealed TQ's ability to regulate microRNA (miRNA) expression, offering a promising approach for cancer therapy. MiRNAs are small noncoding RNAs that modulate gene expression by means of variation in features of mRNA. MiRNAs manage several biological processes including gene expression and cellular signaling pathways. Accordingly, miRNAs can be considered as hallmarks for cancer diagnosis, prognosis and therapy. The purpose of this study was to review the various molecular mechanisms by which TQ exerts its potential as an anti-cancer agent through modulating miRNAs.
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Affiliation(s)
- Mina Homayoonfal
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran
| | - Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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6
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Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS. Multisite Evaluation of Next-Generation Methods for Small RNA Quantification. J Biomol Tech 2021; 31:47-56. [PMID: 31966025 DOI: 10.7171/jbt.20-3102-001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Small RNAs (smRNAs) are important regulators of many biologic processes and are now most frequently characterized using Illumina sequencing. However, although standard RNA sequencing library preparation has become routine in most sequencing facilities, smRNA sequencing library preparation has historically been challenging because of high input requirements, laborious protocols involving gel purifications, inability to automate, and a lack of benchmarking standards. Additionally, studies have suggested that many of these methods are nonlinear and do not accurately reflect the amounts of smRNAs in vivo. Recently, a number of new kits have become available that permit lower input amounts and less laborious, gel-free protocol options. Several of these new kits claim to reduce RNA ligase-dependent sequence bias through novel adapter modifications and to lessen adapter-dimer contamination in the resulting libraries. With the increasing number of smRNA kits available, understanding the relative strengths of each method is crucial for appropriate experimental design. In this study, we systematically compared 9 commercially available smRNA library preparation kits as well as NanoString probe hybridization across multiple study sites. Although several of the new methodologies do reduce the amount of artificially over- and underrepresented microRNAs (miRNAs), we observed that none of the methods was able to remove all of the bias in the library preparation. Identical samples prepared with different methods show highly varied levels of different miRNAs. Even so, many methods excelled in ease of use, lower input requirement, fraction of usable reads, and reproducibility across sites. These differences may help users select the most appropriate methods for their specific question of interest.
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Affiliation(s)
- Zachary T Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, Indiana, USA
| | | | - Fred W Kolling
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Carol S Ringelberg
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Ashley LeClerc
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA
| | - Yuriy O Alekseyev
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA.,Department of Pathology and Laboratory Medicine, Boston University, Boston, Massachusetts, USA
| | - Jun Fan
- Genomic Core Facility, Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, USA
| | - Jessica W Podnar
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Holly S Stevenson
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Gary Sommerville
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shipra Gupta
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Maura Berkeley
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Julie Koeman
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Allison R Scott
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - Jeffrey Malik
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - Kara L Pivarski
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Xinkun Wang
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Gina Kuffel
- Loyola Genomics Facility, Loyola University Chicago, Maywood, Illinois, USA
| | - Tania E Mesa
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Andrew T Smith
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Yoko Takata
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Thomas L Volkert
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jennifer A Love
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Yanping Zhang
- Interdisciplinary Center for Biotechnology Research Gene Expression and Genotyping, University of Florida, Gainsville, Florida, USA
| | - Jun Wang
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Xiaoling Xuei
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Stuart S Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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7
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MicroRNAs Regulating Autophagy in Neurodegeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1208:191-264. [PMID: 34260028 DOI: 10.1007/978-981-16-2830-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Social and economic impacts of neurodegenerative diseases (NDs) become more prominent in our constantly aging population. Currently, due to the lack of knowledge about the aetiology of most NDs, only symptomatic treatment is available for patients. Hence, researchers and clinicians are in need of solid studies on pathological mechanisms of NDs. Autophagy promotes degradation of pathogenic proteins in NDs, while microRNAs post-transcriptionally regulate multiple signalling networks including autophagy. This chapter will critically discuss current research advancements in the area of microRNAs regulating autophagy in NDs. Moreover, we will introduce basic strategies and techniques used in microRNA research. Delineation of the mechanisms contributing to NDs will result in development of better approaches for their early diagnosis and effective treatment.
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8
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Kim O, Park EY, Klinkebiel DL, Pack SD, Shin YH, Abdullaev Z, Emerson RE, Coffey DM, Kwon SY, Creighton CJ, Kwon S, Chang EC, Chiang T, Yatsenko AN, Chien J, Cheon DJ, Yang-Hartwich Y, Nakshatri H, Nephew KP, Behringer RR, Fernández FM, Cho CH, Vanderhyden B, Drapkin R, Bast RC, Miller KD, Karpf AR, Kim J. In vivo modeling of metastatic human high-grade serous ovarian cancer in mice. PLoS Genet 2020; 16:e1008808. [PMID: 32497036 PMCID: PMC7297383 DOI: 10.1371/journal.pgen.1008808] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/16/2020] [Accepted: 04/28/2020] [Indexed: 01/03/2023] Open
Abstract
Metastasis is responsible for 90% of human cancer mortality, yet it remains a challenge to model human cancer metastasis in vivo. Here we describe mouse models of high-grade serous ovarian cancer, also known as high-grade serous carcinoma (HGSC), the most common and deadliest human ovarian cancer type. Mice genetically engineered to harbor Dicer1 and Pten inactivation and mutant p53 robustly replicate the peritoneal metastases of human HGSC with complete penetrance. Arising from the fallopian tube, tumors spread to the ovary and metastasize throughout the pelvic and peritoneal cavities, invariably inducing hemorrhagic ascites. Widespread and abundant peritoneal metastases ultimately cause mouse deaths (100%). Besides the phenotypic and histopathological similarities, mouse HGSCs also display marked chromosomal instability, impaired DNA repair, and chemosensitivity. Faithfully recapitulating the clinical metastases as well as molecular and genomic features of human HGSC, this murine model will be valuable for elucidating the mechanisms underlying the development and progression of metastatic ovarian cancer and also for evaluating potential therapies. Rarely does an experimental model fully replicate the clinical metastases of a human malignancy. Faithfully representing the clinical metastases of human high-grade serous ovarian cancer with complete penetrance, coupled with histopathological, molecular, and genomic similarities, these mouse models, particularly one harboring mutant p53, will be vital to elucidating the underlying pathogenesis of human ovarian cancer. In-depth understanding of the development and progression of ovarian cancer is crucial to medical advances in the early detection, effective treatment, and prevention of ovarian cancer. Also, these robust mouse models, as well as cell lines established from the mouse primary and metastatic tumors, will serve as useful preclinical tools to evaluate therapeutic target genes and new therapies in ovarian cancer.
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Affiliation(s)
- Olga Kim
- Department of Biochemistry and Molecular Biology, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Eun Young Park
- Department of Biochemistry and Molecular Biology, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - David L. Klinkebiel
- Department of Biochemistry and Molecular Biology, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Svetlana D. Pack
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yong-Hyun Shin
- Department of Biochemistry and Molecular Biology, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Robert E. Emerson
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Donna M. Coffey
- Department of Pathology and Genomic Medicine, Houston Methodist and Weill Cornell Medical College, Houston, Texas, United States of America
| | - Sun Young Kwon
- Department of Pathology, School of Medicine, Keimyung University, Daegu, Republic of Korea
| | - Chad J. Creighton
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sanghoon Kwon
- Research and Development Center, Bioway Inc, Seoul, Republic of Korea
| | - Edmund C. Chang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alexander N. Yatsenko
- Department of Obstetrics, Gynecology & Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jeremy Chien
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California, United States of America
| | - Dong-Joo Cheon
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, United States of America
| | - Yang Yang-Hartwich
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Kenneth P. Nephew
- Medical Sciences Program, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Richard R. Behringer
- Departments of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chi-Heum Cho
- Department of Obstetrics and Gynecology, School of Medicine, Keimyung University, Daegu, Republic of Korea
| | - Barbara Vanderhyden
- Department of Cellular and Molecular Medicine, University of Ottawa, and Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Robert C. Bast
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Kathy D. Miller
- Department of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine Indianapolis, Indiana, United States of America
| | - Adam R. Karpf
- Eppley Institute for Cancer Research, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Jaeyeon Kim
- Department of Biochemistry and Molecular Biology, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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9
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Wu X, Chen X, Liu H, He ZW, Wang Z, Wei LJ, Wang WY, Zhong S, He Q, Zhang Z, Ou R, Gao J, Lei Y, Yang W, Song G, Jin Y, Zhou L, Xu Y, Tang KF. Rescuing Dicer expression in inflamed colon tissues alleviates colitis and prevents colitis-associated tumorigenesis. Am J Cancer Res 2020; 10:5749-5762. [PMID: 32483416 PMCID: PMC7254990 DOI: 10.7150/thno.41894] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/04/2020] [Indexed: 12/13/2022] Open
Abstract
Chronic inflammation is known to promote carcinogenesis; Dicer heterozygous mice are more likely to develop colitis-associated tumors. This study investigates whether Dicer is downregulated in inflamed colon tissues before malignancy occurs and whether increasing Dicer expression in inflamed colon tissues can alleviate colitis and prevent colitis-associated tumorigenesis. Methods: Gene expression in colon tissues was analyzed by immunohistochemistry, immunoblots, and real-time RT-PCR. Hydrogen peroxide or N-acetyl-L-cysteine was used to induce or alleviate oxidative stress, respectively. Mice were given azoxymethane followed by dextran sulfate sodium to induce colitis and colon tumors. Berberine, anastrozole, or pranoprofen was used to rescue Dicer expression in inflammatory colon tissues. Results: Oxidative stress repressed Dicer expression in inflamed colon tissues by inducing miR-215 expression. Decreased Dicer expression increased DNA damage and cytosolic DNA and promoted interleukin-6 expression upon hydrogen peroxide treatment. Dicer overexpression in inflamed colon tissues alleviated inflammation and repressed colitis-associated carcinogenesis. Furthermore, we found that anastrozole, berberine, and pranoprofen could promote Dicer expression and protect cells from hydrogen peroxide-induced DNA damage, thereby reducing cytosolic DNA and partially repressing interleukin-6 expression upon hydrogen peroxide treatment. Rescuing Dicer expression using anastrozole, berberine, or pranoprofen in inflamed colon tissues alleviated colitis and prevented colitis-associated tumorigenesis. Conclusions: Dicer was downregulated in inflamed colon tissues before malignancy occurred. Decreased Dicer expression further exaggerated inflammation, which may promote carcinogenesis. Anastrozole, berberine, and pranoprofen alleviated colitis and colitis-associated tumorigenesis by promoting Dicer expression. Our study provides insight into potential colitis treatment and colitis-associated colon cancer prevention strategies.
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10
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Davis AJ, Tsinkevich M, Rodencal J, Abbas HA, Su XH, Gi YJ, Fang B, Rajapakshe K, Coarfa C, Gunaratne PH, Koomen JM, Tsai KY, Flores ER. TAp63-Regulated miRNAs Suppress Cutaneous Squamous Cell Carcinoma through Inhibition of a Network of Cell-Cycle Genes. Cancer Res 2020; 80:2484-2497. [PMID: 32156775 DOI: 10.1158/0008-5472.can-19-1892] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 01/18/2020] [Accepted: 03/05/2020] [Indexed: 12/26/2022]
Abstract
TAp63 is a p53 family member and potent tumor and metastasis suppressor. Here, we show that TAp63-/- mice exhibit an increased susceptibility to ultraviolet radiation-induced cutaneous squamous cell carcinoma (cuSCC). A human-to-mouse comparison of cuSCC tumors identified miR-30c-2* and miR-497 as underexpressed in TAp63-deficient cuSCC. Reintroduction of these miRNAs significantly inhibited the growth of cuSCC cell lines and tumors. Proteomic profiling of cells expressing either miRNA showed downregulation of cell-cycle progression and mitosis-associated proteins. A mouse to human and cross-platform comparison of RNA-sequencing and proteomics data identified a 7-gene signature, including AURKA, KIF18B, PKMYT1, and ORC1, which were overexpressed in cuSCC. Knockdown of these factors in cuSCC cell lines suppressed tumor cell proliferation and induced apoptosis. In addition, selective inhibition of AURKA suppressed cuSCC cell proliferation, induced apoptosis, and showed antitumor effects in vivo. Finally, treatment with miR-30c-2* or miR-497 miRNA mimics was highly effective in suppressing cuSCC growth in vivo. Our data establish TAp63 as an essential regulator of novel miRNAs that can be therapeutically targeted for potent suppression of cuSCC. SIGNIFICANCE: This study provides preclinical evidence for the use of miR-30c-2*/miR-497 delivery and AURKA inhibition in the treatment of cuSCC, which currently has no FDA-approved targeted therapies.See related commentary by Parrales and Iwakuma, p. 2439.
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Affiliation(s)
- Andrew John Davis
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Maksym Tsinkevich
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jason Rodencal
- Department of Biology, Stanford University School of Medicine, Stanford, California
| | - Hussein A Abbas
- Hematology/Oncology Fellowship Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiao-Hua Su
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Young-Jin Gi
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bin Fang
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kimal Rajapakshe
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Preethi H Gunaratne
- Department of Biology and Biochemistry, University of Houston, Houston, Texas
| | - John M Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kenneth Y Tsai
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Elsa R Flores
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
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11
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Gutbrod MJ, Martienssen RA. Conserved chromosomal functions of RNA interference. Nat Rev Genet 2020; 21:311-331. [PMID: 32051563 DOI: 10.1038/s41576-019-0203-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/21/2022]
Abstract
RNA interference (RNAi), a cellular process through which small RNAs target and regulate complementary RNA transcripts, has well-characterized roles in post-transcriptional gene regulation and transposon repression. Recent studies have revealed additional conserved roles for RNAi proteins, such as Argonaute and Dicer, in chromosome function. By guiding chromatin modification, RNAi components promote chromosome segregation during both mitosis and meiosis and regulate chromosomal and genomic dosage response. Small RNAs and the RNAi machinery also participate in the resolution of DNA damage. Interestingly, many of these lesser-studied functions seem to be more strongly conserved across eukaryotes than are well-characterized functions such as the processing of microRNAs. These findings have implications for the evolution of RNAi since the last eukaryotic common ancestor, and they provide a more complete view of the functions of RNAi.
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Affiliation(s)
- Michael J Gutbrod
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Robert A Martienssen
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. .,Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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12
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Vedanayagam J, Chatila WK, Aksoy BA, Majumdar S, Skanderup AJ, Demir E, Schultz N, Sander C, Lai EC. Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis. Nat Commun 2019; 10:3682. [PMID: 31417090 PMCID: PMC6695490 DOI: 10.1038/s41467-019-11610-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 07/25/2019] [Indexed: 11/09/2022] Open
Abstract
Somatic mutations in the RNase IIIb domain of DICER1 arise in cancer and disrupt the cleavage of 5' pre-miRNA arms. Here, we characterize an unstudied, recurrent, mutation (S1344L) in the DICER1 RNase IIIa domain in tumors from The Cancer Genome Atlas (TCGA) project and MSK-IMPACT profiling. RNase IIIa/b hotspots are absent from most cancers, but are notably enriched in uterine cancers. Systematic analysis of TCGA small RNA datasets show that DICER1 RNase IIIa-S1344L tumors deplete 5p-miRNAs, analogous to RNase IIIb hotspot samples. Structural and evolutionary coupling analyses reveal constrained proximity of RNase IIIa-S1344 to the RNase IIIb catalytic site, rationalizing why mutation of this site phenocopies known hotspot alterations. Finally, examination of DICER1 hotspot endometrial tumors reveals derepression of specific miRNA target signatures. In summary, comprehensive analyses of DICER1 somatic mutations and small RNA data reveal a mechanistic aspect of pre-miRNA processing that manifests in specific cancer settings.
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Affiliation(s)
- Jeffrey Vedanayagam
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Walid K Chatila
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.,Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Bülent Arman Aksoy
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.,Immunology and Microbiology Department, Medical University of South Carolina, Charleston, SC, 29412, USA
| | - Sonali Majumdar
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Anders Jacobsen Skanderup
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Emek Demir
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Oregon Health and Science University, Computational Biology Program, Portland, OR, 97239, USA
| | - Nikolaus Schultz
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chris Sander
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA. .,cBio Center, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. .,Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Eric C Lai
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA. .,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
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13
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Kasai M, Ishida R, Nakahara K, Okumura K, Aoki K. Mesenchymal cell differentiation and diseases: involvement of translin/TRAX complexes and associated proteins. Ann N Y Acad Sci 2018; 1421:37-45. [PMID: 29740830 DOI: 10.1111/nyas.13690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 02/22/2018] [Accepted: 03/01/2018] [Indexed: 12/22/2022]
Abstract
Translin and translin-associated factor X (translin/TRAX) proteins have been implicated in a variety of cellular activities central to nucleic acid metabolism. Accumulating evidence indicates that translin/TRAX complexes participate in processes ensuring the replication of DNA, as well as cell division. Significant progress has been made in understanding the roles of translin/TRAX complexes in RNA metabolism, such as through RNA-induced silencing complex activation or the microRNA depletion that occurs in Dicer deficiency. At the cellular level, translin-deficient (Tsn-/- ) mice display delayed endochondral ossification or progressive bone marrow failure with ectopic osteogenesis and adipogenesis, suggesting involvement in mesenchymal cell differentiation. In this review, we summarize the molecular and cellular functions of translin homo-octamer and translin/TRAX hetero-octamer. Finally, we discuss the multifaceted roles of translin, TRAX, and associated proteins in the healthy and disease states.
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Affiliation(s)
- Masataka Kasai
- Juntendo University School of Medicine, Atopy Research Center, Tokyo, Japan.,Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Reiko Ishida
- Center for Stem Cell and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Nakahara
- National Institution for Academic Degrees and Quality Enhancement of Higher Education, Tokyo, Japan
| | - Ko Okumura
- Juntendo University School of Medicine, Atopy Research Center, Tokyo, Japan
| | - Katsunori Aoki
- Occupational Health Department, Sony Corporate Service Corporation, Kanagawa, Japan
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14
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De Vita A, Mercatali L, Miserocchi G, Liverani C, Spadazzi C, Recine F, Bongiovanni A, Pieri F, Cavaliere D, Fausti V, Amadori D, Ibrahim T. Establishment of a Primary Culture of Patient-derived Soft Tissue Sarcoma. J Vis Exp 2018. [PMID: 29708525 DOI: 10.3791/56767] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Soft tissue sarcomas (STS) represent a spectrum of heterogeneous malignancies with a difficult diagnosis, classification, and management. To date, more than 50 histological subtypes of these rare solid tumors have been identified. Thus, due to their extraordinary diversity and low incidence, our understanding of the biology of these tumors is still limited. Patient-derived cultures represent the ideal platform to study STS pathophysiology and pharmacology. We thus developed a human preclinical model of STS starting from tumor specimens harvested from patients undergoing surgical resection. Patient-derived STS cell cultures were obtained from the surgical specimens by collagenase digestion and isolated by filtration. Cells were counted, seeded, and left for 14 days in standard monolayer cultures and then processed by downstream analysis. Before performing molecular or pharmaceutical analyses, the establishment of STS primary cultures was confirmed through the evaluation of cytomorphologic features and, when available, immunohistochemical markers. This method represents a useful tool 1) to study the natural history of these poorly explored malignancies and 2) to test the effects of different drugs in an effort to learn more about their mechanisms of action.
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Affiliation(s)
- Alessandro De Vita
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS;
| | - Laura Mercatali
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS
| | - Giacomo Miserocchi
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS
| | - Chiara Liverani
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS
| | - Chiara Spadazzi
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS
| | - Federica Recine
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS
| | - Alberto Bongiovanni
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS
| | | | - Davide Cavaliere
- Unit of Surgery and Advanced Oncologic Therapies, Morgagni-Pierantoni Hospital
| | - Valentina Fausti
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS
| | - Dino Amadori
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS
| | - Toni Ibrahim
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS
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15
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Kim Y, Kang YG, Choe JY, Lee D, Shin C, Hong SW, Lee DK. RNA Interference-Mediated Gene Silencing by Branched Tripodal RNAs Does Not Require Dicer Processing. Nucleic Acid Ther 2018; 28:44-49. [PMID: 29195056 DOI: 10.1089/nat.2017.0681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Specific gene silencing through RNA interference (RNAi) holds great promise as the next-generation therapeutic development platform. Previously, we have shown that branched, tripodal interfering RNA (tiRNA) structures could simultaneously trigger RNAi-mediated gene silencing of three target genes with 38 nt-long guide strands associated with Argonaute 2. Herein, we show that the branched RNA structure can trigger effective gene silencing in Dicer knockout cell line, demonstrating that the Dicer-mediated processing is not required for tiRNA activity. The finding of this study confirms the flexibility of the structure of RNAi triggers as well as the length of the guide strand in RNAi-mediated gene silencing.
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Affiliation(s)
- Yanghee Kim
- 1 Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University , Suwon, Republic of Korea
| | - Young Gyu Kang
- 1 Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University , Suwon, Republic of Korea
| | - Jeong Yong Choe
- 1 Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University , Suwon, Republic of Korea
| | - Dooyoung Lee
- 2 Department of Agricultural Biotechnology, Seoul National University , Seoul, Republic of Korea
| | - Chanseok Shin
- 2 Department of Agricultural Biotechnology, Seoul National University , Seoul, Republic of Korea
| | - Sun Woo Hong
- 3 OliX Pharmaceuticals, Inc. , Suwon, Republic of Korea
| | - Dong-Ki Lee
- 1 Global Research Laboratory for RNAi Medicine, Department of Chemistry, Sungkyunkwan University , Suwon, Republic of Korea
- 3 OliX Pharmaceuticals, Inc. , Suwon, Republic of Korea
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16
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Mansouri S, Singh S, Alamsahebpour A, Burrell K, Li M, Karabork M, Ekinci C, Koch E, Solaroglu I, Chang JT, Wouters B, Aldape K, Zadeh G. DICER governs characteristics of glioma stem cells and the resulting tumors in xenograft mouse models of glioblastoma. Oncotarget 2018; 7:56431-56446. [PMID: 27421140 PMCID: PMC5302925 DOI: 10.18632/oncotarget.10570] [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: 03/17/2016] [Accepted: 05/19/2016] [Indexed: 12/21/2022] Open
Abstract
The RNAse III endonuclease DICER is a key regulator of microRNA (miRNA) biogenesis and is frequently decreased in a variety of malignancies. We characterized the role of DICER in glioblastoma (GB), specifically demonstrating its effects on the ability of glioma stem-like cells (GSCs) to form tumors in a mouse model of GB. DICER silencing in GSCs reduced their stem cell characteristics, while tumors arising from these cells were more aggressive, larger in volume, and displayed a higher proliferation index and lineage differentiation. The resulting tumors, however, were more sensitive to radiation treatment. Our results demonstrate that DICER silencing enhances the tumorigenic potential of GSCs, providing a platform for analysis of specific relevant miRNAs and development of potentially novel therapies against GB.
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Affiliation(s)
- Sheila Mansouri
- Princess Margaret Cancer Centre and MacFeeters-Hamilton Centre for Neuro-Oncology Research, Toronto, ON, Canada
| | - Sanjay Singh
- Princess Margaret Cancer Centre and MacFeeters-Hamilton Centre for Neuro-Oncology Research, Toronto, ON, Canada
| | - Amir Alamsahebpour
- Princess Margaret Cancer Centre and MacFeeters-Hamilton Centre for Neuro-Oncology Research, Toronto, ON, Canada
| | - Kelly Burrell
- Princess Margaret Cancer Centre and MacFeeters-Hamilton Centre for Neuro-Oncology Research, Toronto, ON, Canada
| | - Mira Li
- Princess Margaret Cancer Centre and MacFeeters-Hamilton Centre for Neuro-Oncology Research, Toronto, ON, Canada
| | - Merve Karabork
- School of Medicine, Koç University, Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
| | - Can Ekinci
- School of Medicine, Koç University, Rumelifeneri Yolu, Sariyer, Istanbul, Turkey
| | - Elizabeth Koch
- Ontario Cancer Institute and Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Ihsan Solaroglu
- School of Medicine, Koç University, Rumelifeneri Yolu, Sariyer, Istanbul, Turkey.,Loma Linda University, School of Medicine, Loma Linda, CA, USA
| | - Jeffery T Chang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas, Houston, TX, USA
| | - Bradly Wouters
- Ontario Cancer Institute and Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, Toronto, ON, Canada.,Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Kenneth Aldape
- Princess Margaret Cancer Centre and MacFeeters-Hamilton Centre for Neuro-Oncology Research, Toronto, ON, Canada
| | - Gelareh Zadeh
- Princess Margaret Cancer Centre and MacFeeters-Hamilton Centre for Neuro-Oncology Research, Toronto, ON, Canada.,Department of Neurosurgery, Toronto Western Hospital, University Health Network, 4W-436, Toronto, ON, Canada
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17
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Hanna JA, Drummond CJ, Garcia MR, Go JC, Finkelstein D, Rehg JE, Hatley ME. Biallelic Dicer1 Loss Mediated by aP2-Cre Drives Angiosarcoma. Cancer Res 2017; 77:6109-6118. [PMID: 28916654 DOI: 10.1158/0008-5472.can-17-1262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/11/2017] [Accepted: 09/12/2017] [Indexed: 12/14/2022]
Abstract
Angiosarcoma is an aggressive vascular sarcoma with an extremely poor prognosis. Because of the relative rarity of this disease, its molecular drivers and optimal treatment strategies are obscure. DICER1 is an RNase III endoribonuclease central to miRNA biogenesis, and germline DICER1 mutations result in a cancer predisposition syndrome, associated with an increased risk of many tumor types. Here, we show that biallelic Dicer1 deletion with aP2-Cre drives aggressive and metastatic angiosarcoma independent of other genetically engineered oncogenes or tumor suppressor loss. Angiosarcomas in aP2-Cre;Dicer1Flox/- mice histologically and genetically resemble human angiosarcoma. miR-23 target genes, including the oncogenes Ccnd1 as well as Adam19, Plau, and Wsb1 that promote invasiveness and metastasis, were enriched in mouse and human angiosarcoma. These studies illustrate that Dicer1 can function as a traditional loss-of-function tumor suppressor gene, and they provide a fully penetrant animal model for the study of angiosarcoma development and metastasis. Cancer Res; 77(22); 6109-18. ©2017 AACR.
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Affiliation(s)
- Jason A Hanna
- Department of Oncology, Molecular Oncology Division, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Catherine J Drummond
- Department of Oncology, Molecular Oncology Division, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Matthew R Garcia
- Department of Oncology, Molecular Oncology Division, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jonathan C Go
- Department of Oncology, Molecular Oncology Division, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jerold E Rehg
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mark E Hatley
- Department of Oncology, Molecular Oncology Division, St. Jude Children's Research Hospital, Memphis, Tennessee.
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18
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Dicer loss and recovery induce an oncogenic switch driven by transcriptional activation of the oncofetal Imp1-3 family. Genes Dev 2017; 31:674-687. [PMID: 28446596 PMCID: PMC5411708 DOI: 10.1101/gad.296301.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/20/2017] [Indexed: 12/16/2022]
Abstract
JnBaptiste et al. present analysis of the gene expression and phenotypic changes associated with global miRNA restoration in miRNA-deficient fibroblasts. This analysis uncovers a miRNA-repressed network containing oncofetal genes Imp1–3 that is up-regulated upon Dicer loss and is resistant to resilencing by complete restoration of miRNA activity. MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression critical for organismal viability. Changes in miRNA activity are common in cancer, but how these changes relate to subsequent alterations in transcription and the process of tumorigenesis is not well understood. Here, we report a deep transcriptional, oncogenic network regulated by miRNAs. We present analysis of the gene expression and phenotypic changes associated with global miRNA restoration in miRNA-deficient fibroblasts. This analysis uncovers a miRNA-repressed network containing oncofetal genes Imp1, Imp2, and Imp3 (Imp1–3) that is up-regulated primarily transcriptionally >100-fold upon Dicer loss and is resistant to resilencing by complete restoration of miRNA activity. This Dicer-resistant epigenetic switch confers tumorigenicity to these cells. Let-7 targets Imp1–3 are required for this tumorigenicity and feed back to reinforce and sustain expression of the oncogenic network. Together, these Dicer-resistant genes constitute an mRNA expression signature that is present in numerous human cancers and is associated with poor survival.
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19
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Roden C, Mastriano S, Wang N, Lu J. microRNA Expression Profiling: Technologies, Insights, and Prospects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 888:409-21. [PMID: 26663195 DOI: 10.1007/978-3-319-22671-2_21] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Since the early days of microRNA (miRNA) research, miRNA expression profiling technologies have provided important tools toward both better understanding of the biological functions of miRNAs and using miRNA expression as potential diagnostics. Multiple technologies, such as microarrays, next-generation sequencing, bead-based detection system, single-molecule measurements, and quantitative RT-PCR, have enabled accurate quantification of miRNAs and the subsequent derivation of key insights into diverse biological processes. As a class of ~22 nt long small noncoding RNAs, miRNAs present unique challenges in expression profiling that require careful experimental design and data analyses. We will particularly discuss how normalization and the presence of miRNA isoforms can impact data interpretation. We will present one example in which the consideration in data normalization has provided insights that helped to establish the global miRNA expression as a tumor suppressor. Finally, we discuss two future prospects of using miRNA profiling technologies to understand single cell variability and derive new rules for the functions of miRNA isoforms.
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Affiliation(s)
- Christine Roden
- Department of Genetics, Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, 10 Amistad Street, Rm 237C, New Haven, CT, 06520-8005, USA
| | - Stephen Mastriano
- Department of Genetics, Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, 10 Amistad Street, Rm 237C, New Haven, CT, 06520-8005, USA
| | - Nayi Wang
- The Biomedical Engineering Graduate Program, New Haven, CT, 06520, USA
| | - Jun Lu
- Department of Genetics, Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, 10 Amistad Street, Rm 237C, New Haven, CT, 06520-8005, USA. .,Yale Center for RNA Science and Medicine, New Haven, CT, 06520, USA.
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20
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Re-evaluation of the roles of DROSHA, Export in 5, and DICER in microRNA biogenesis. Proc Natl Acad Sci U S A 2016; 113:E1881-9. [PMID: 26976605 DOI: 10.1073/pnas.1602532113] [Citation(s) in RCA: 311] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Biogenesis of canonical microRNAs (miRNAs) involves multiple steps: nuclear processing of primary miRNA (pri-miRNA) by DROSHA, nuclear export of precursor miRNA (pre-miRNA) by Export in 5 (XPO5), and cytoplasmic processing of pre-miRNA by DICER. To gain a deeper understanding of the contribution of each of these maturation steps, we deleted DROSHA, XPO5, and DICER in the same human cell line, and analyzed their effects on miRNA biogenesis. Canonical miRNA production was completely abolished in DROSHA-deleted cells, whereas we detected a few DROSHA-independent miRNAs including three previously unidentified noncanonical miRNAs (miR-7706, miR-3615, and miR-1254). In contrast to DROSHA knockout, many canonical miRNAs were still detected without DICER albeit at markedly reduced levels. In the absence of DICER, pre-miRNAs are loaded directly onto AGO and trimmed at the 3' end, yielding miRNAs from the 5' strand (5p miRNAs). Interestingly, in XPO5 knockout cells, most miRNAs are affected only modestly, suggesting that XPO5 is necessary but not critical for miRNA maturation. Our study demonstrates an essential role of DROSHA and an important contribution of DICER in the canonical miRNA pathway, and reveals that the function of XPO5 can be complemented by alternative mechanisms. Thus, this study allows us to understand differential contributions of key biogenesis factors, and provides with valuable resources for miRNA research.
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21
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Swahari V, Nakamura A, Deshmukh M. The paradox of dicer in cancer. Mol Cell Oncol 2016; 3:e1155006. [PMID: 27314098 PMCID: PMC4909435 DOI: 10.1080/23723556.2016.1155006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 02/10/2016] [Accepted: 02/11/2016] [Indexed: 12/22/2022]
Abstract
Dicer has been well studied in cancer; however, deciphering its exact function in tumorigenesis continues to be a challenge. While partial suppression or truncation of Dicer promotes tumorigenesis, its complete deletion inhibits tumor growth. Here, we discuss this Dicer cancer conundrum in the context of its recently discovered role in the DNA damage response.
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Affiliation(s)
- Vijay Swahari
- Neuroscience Center, University of North Carolina at Chapel Hill , North Carolina
| | - Ayumi Nakamura
- Neuroscience Center, University of North Carolina at Chapel Hill , North Carolina
| | - Mohanish Deshmukh
- Neuroscience Center, University of North Carolina at Chapel Hill , North Carolina
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22
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Francia S, Cabrini M, Matti V, Oldani A, d'Adda di Fagagna F. DICER, DROSHA and DNA damage response RNAs are necessary for the secondary recruitment of DNA damage response factors. J Cell Sci 2016; 129:1468-76. [PMID: 26906421 PMCID: PMC4852722 DOI: 10.1242/jcs.182188] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/09/2016] [Indexed: 12/18/2022] Open
Abstract
The DNA damage response (DDR) plays a central role in preserving genome integrity. Recently, we reported that the endoribonucleases DICER and DROSHA contribute to DDR activation by generating small non-coding RNAs, termed DNA damage response RNA (DDRNA), carrying the sequence of the damaged locus. It is presently unclear whether DDRNAs act by promoting the primary recognition of DNA lesions or the secondary recruitment of DDR factors into cytologically detectable foci and consequent signal amplification. Here, we demonstrate that DICER and DROSHA are dispensable for primary recruitment of the DDR sensor NBS1 to DNA damage sites. Instead, the accumulation of the DDR mediators MDC1 and 53BP1 (also known as TP53BP1), markers of secondary recruitment, is reduced in DICER- or DROSHA-inactivated cells. In addition, NBS1 (also known as NBN) primary recruitment is resistant to RNA degradation, consistent with the notion that RNA is dispensable for primary recognition of DNA lesions. We propose that DICER, DROSHA and DDRNAs act in the response to DNA damage after primary recognition of DNA lesions and, together with γH2AX, are essential for enabling the secondary recruitment of DDR factors and fuel the amplification of DDR signaling. Summary: We show that DICER, DROSHA and DNA damage response RNAs are necessary for the secondary recruitment of DNA damage response factors but not essential for primary recognition of DNA lesions.
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Affiliation(s)
- Sofia Francia
- IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, Milan 20139, Italy Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, Pavia 27100, Italy
| | - Matteo Cabrini
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, Pavia 27100, Italy
| | - Valentina Matti
- IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, Milan 20139, Italy
| | - Amanda Oldani
- IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, Milan 20139, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, Milan 20139, Italy Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, Pavia 27100, Italy
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23
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MicroRNA Biogenesis and Hedgehog-Patched Signaling Cooperate to Regulate an Important Developmental Transition in Granule Cell Development. Genetics 2016; 202:1105-18. [PMID: 26773048 DOI: 10.1534/genetics.115.184176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/10/2016] [Indexed: 12/20/2022] Open
Abstract
The Dicer1, Dcr-1 homolog (Drosophila) gene encodes a type III ribonuclease required for the canonical maturation and functioning of microRNAs (miRNAs). Subsets of miRNAs are known to regulate normal cerebellar granule cell development, in addition to the growth and progression of medulloblastoma, a neoplasm that often originates from granule cell precursors. Multiple independent studies have also demonstrated that deregulation of Sonic Hedgehog (Shh)-Patched (Ptch) signaling, through miRNAs, is causative of granule cell pathologies. In the present study, we investigated the genetic interplay between miRNA biogenesis and Shh-Ptch signaling in granule cells of the cerebellum by way of the Cre/lox recombination system in genetically engineered models of Mus musculus (mouse). We demonstrate that, although the miRNA biogenesis and Shh-Ptch-signaling pathways, respectively, regulate the opposing growth processes of cerebellar hypoplasia and hyperplasia leading to medulloblastoma, their concurrent deregulation was nonadditive and did not bring the growth phenotypes toward an expected equilibrium. Instead, mice developed either hypoplasia or medulloblastoma, but of a greater severity. Furthermore, some genotypes were bistable, whereby subsets of mice developed hypoplasia or medulloblastoma. This implies that miRNAs and Shh-Ptch signaling regulate an important developmental transition in granule cells of the cerebellum. We also conclusively show that the Dicer1 gene encodes a haploinsufficient tumor suppressor gene for Ptch1-induced medulloblastoma, with the monoallielic loss of Dicer1 more severe than biallelic loss. These findings exemplify how genetic interplay between pathways may produce nonadditive effects with a substantial and unpredictable impact on biology. Furthermore, these findings suggest that the functional dosage of Dicer1 may nonadditively influence a wide range of Shh-Ptch-dependent pathologies.
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24
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Galicia-Vázquez G, Chu J, Pelletier J. eIF4AII is dispensable for miRNA-mediated gene silencing. RNA (NEW YORK, N.Y.) 2015; 21:1826-33. [PMID: 26286746 PMCID: PMC4574758 DOI: 10.1261/rna.052225.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/21/2015] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that regulate gene expression through partial complementary base-pairing to the 3' untranslated region (UTR) of target mRNAs. Inhibition of translation initiation has been identified as an early event of miRNA-mediated gene repression, but the underlying mechanistic details of this process are not well understood. Recently, eukaryotic initiation factor (eIF) 4AII was identified as a critical modulator of miRNA activity with depletion of this factor alleviating miRNA-mediated gene repression. Using the CRISPR/Cas9-editing system, we generated a novel cell line in which expression of eIF4AII was eliminated. The absence of eIF4AII does not affect cell viability, proliferation, or global mRNA translation. Importantly, we show that eIF4AII is dispensable for miRNA-mediated gene silencing.
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Affiliation(s)
| | - Jennifer Chu
- Department of Biochemistry, McGill University, Montreal, Québec H3G 1Y6, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Québec H3G 1Y6, Canada The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Québec H3G 1Y6, Canada Department of Oncology, McGill University, Montreal, Québec H3G 1Y6, Canada
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25
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Asada K, Canestrari E, Fu X, Li Z, Makowski E, Wu YC, Mito JK, Kirsch DG, Baraban J, Paroo Z. Rescuing dicer defects via inhibition of an anti-dicing nuclease. Cell Rep 2015; 9:1471-81. [PMID: 25457613 DOI: 10.1016/j.celrep.2014.10.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 09/23/2014] [Accepted: 10/09/2014] [Indexed: 01/12/2023] Open
Abstract
Genetic defects in the microRNA (miRNA) generating enzyme, dicer, are increasingly linked to disease. Loss of miRNA in dicer deficiency is thought to be due to loss of miRNA-generating activity. Here, we demonstrate a catabolic mechanism driving miRNA depletion in dicer deficiency. We developed a Dicer-antagonist assay revealing a pre-miRNA degrading enzyme that competes with pre-miRNA processing. We purified this pre-miRNA degrading activity using an unbiased chromatographic procedure and identified the ribonuclease complex Translin/Trax (TN/TX). In wild-type dicer backgrounds, pre-miRNA processing was dominant. However, in dicer-deficient contexts, TN/TX broadly suppressed miRNA. These findings indicate that miRNA depletion in dicer deficiency is due to the combined loss of miRNA-generating activity and catabolic function of TN/TX. Importantly, inhibition of TN/TX mitigated loss of both miRNA and tumor suppression with dicer haploinsufficiency. These studies reveal a potentially druggable target for restoring miRNA function in cancers and emerging dicer deficiencies.
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26
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Chen J, Wang Y, McMonechy MK, Anglesio MS, Yang W, Senz J, Maines-Bandiera S, Rosner J, Trigo-Gonzalez G, Grace Cheng SW, Kim J, Matzuk MM, Morin GB, Huntsman DG. Recurrent DICER1 hotspot mutations in endometrial tumours and their impact on microRNA biogenesis. J Pathol 2015; 237:215-25. [PMID: 26033159 DOI: 10.1002/path.4569] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 03/15/2015] [Accepted: 05/22/2015] [Indexed: 12/18/2022]
Abstract
DICER1 plays a critical role in microRNA (miRNA) biogenesis. Recurrent somatic 'hotspot' mutations at the four metal-binding sites within the RNase IIIb domain of DICER1 were identified in ovarian sex cord-stromal tumours and have since been described in other paediatric tumours. In this study, we screened the RNase IIIb domain of DICER1 in 290 endometrial tumours and identified six cases with hotspot mutations, including two cases affected by an atypical G1809R mutation directly adjacent to a metal-binding site. Using Illumina and Sanger targeted resequencing, we observed and validated biallelic DICER1 mutations in several cases with hotspot mutations. Through in vitro DICER1 cleavage assays, small RNA deep sequencing and real-time PCR, we demonstrated that mutations adding a positively charged side chain to residue 1809 have similar detrimental effects on 5p miRNA production to mutations at the metal-binding sites. As expected, 5p miRNAs were globally reduced in tumours and cell lines with hotspot mutations. Pathway analysis of gene expression profiles indicated that genes de-repressed due to loss of 5p miRNAs are strongly associated with pathways regulating the cell cycle. Using a Dicer1-null mouse cell line model, we found that expression of DICER1 hotspot mutants promoted cell proliferation, whereas wild-type (WT) DICER1 inhibited cell proliferation. Furthermore, targets of let-7 family miRNAs are enriched among the up-regulated genes, suggesting that loss of let-7 may be impacting downstream pathways. Our results reveal that DICER1 hotspot mutations are implicated in common malignancies and may constitute a unique oncogenic pathway.
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Affiliation(s)
- Jiamin Chen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Center for Translational and Applied Genomics, BC Cancer Agency, Vancouver, BC, Canada
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Center for Translational and Applied Genomics, BC Cancer Agency, Vancouver, BC, Canada
| | - Melissa K McMonechy
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Center for Translational and Applied Genomics, BC Cancer Agency, Vancouver, BC, Canada
| | - Michael S Anglesio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Winnie Yang
- Center for Translational and Applied Genomics, BC Cancer Agency, Vancouver, BC, Canada
| | - Janine Senz
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sarah Maines-Bandiera
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jamie Rosner
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
| | | | - S W Grace Cheng
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Jaeyeon Kim
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Martin M Matzuk
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Gregg B Morin
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada.,Center for Translational and Applied Genomics, BC Cancer Agency, Vancouver, BC, Canada
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27
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Zindy F, Lee Y, Kawauchi D, Ayrault O, Merzoug LB, Li Y, McKinnon PJ, Roussel MF. Dicer Is Required for Normal Cerebellar Development and to Restrain Medulloblastoma Formation. PLoS One 2015; 10:e0129642. [PMID: 26091048 PMCID: PMC4474721 DOI: 10.1371/journal.pone.0129642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/11/2015] [Indexed: 11/18/2022] Open
Abstract
Dicer, a ribonuclease III enzyme, is required for the maturation of microRNAs. To assess its role in cerebellar and medulloblastoma development, we genetically deleted Dicer in Nestin-positive neural progenitors and in mice lacking one copy for the Sonic Hedgehog receptor, Patched 1. We found that conditional loss of Dicer in mouse neural progenitors induced massive Trp53-independent apoptosis in all proliferative zones of the brain and decreased proliferation of cerebellar granule progenitors at embryonic day 15.5 leading to abnormal cerebellar development and perinatal lethality. Loss of one copy of Dicer significantly accelerated the formation of mouse medulloblastoma of the Sonic Hedgehog subgroup in Patched1-heterozygous mice. We conclude that Dicer is required for proper cerebellar development, and to restrain medulloblastoma formation.
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Affiliation(s)
- Frederique Zindy
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Youngsoo Lee
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Daisuke Kawauchi
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Olivier Ayrault
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Leila Ben Merzoug
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Yang Li
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Peter J. McKinnon
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Martine F. Roussel
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
- * E-mail:
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28
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Dicer1 imparts essential survival cues in Notch-driven T-ALL via miR-21-mediated tumor suppressor Pdcd4 repression. Blood 2015; 126:993-1004. [PMID: 25979949 DOI: 10.1182/blood-2014-12-618892] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 05/07/2015] [Indexed: 02/07/2023] Open
Abstract
The modulatory function of individual microRNAs (miRNAs) in Notch-driven T-cell acute lymphoblastic leukemias (T-ALLs) has recently been established. Although protumorigenic and tumor-suppressive miRNAs are implicated in disease onset in murine models of Notch-driven T-cell leukemia, whether Dicer1-processed miRNAs are essential for Notch-driven T-ALL is currently unknown. Here we used conditional and inducible genetic loss-of-function approaches to test whether the development and maintenance of Notch-driven T-ALL was dependent on Dicer1 function. Mice with specific inactivation of both Dicer1 alleles in the T-cell lineage did not develop Notch-driven T-ALL. In contrast, loss of 1 functional Dicer1 allele did not significantly perturb T-ALL onset and tumor progression. Inducible inactivation of Dicer1 in early stage polyclonal T-ALL cells was sufficient to abrogate T-ALL progression in leukemic mice, whereas late-stage monoclonal T-ALL cells were counterselected against loss of Dicer1. Lineage-tracing experiments revealed that Dicer1 deficiency led to the induction of apoptosis in T-ALL cells, whereas cell cycle progression remained unaltered. Through microarray-based miRNA profiling, we identified miR-21 as a previously unrecognized miRNA deregulated in both mouse and human T-ALL. Herein, we demonstrate that miR-21 regulates T-ALL cell survival via repression of the tumor suppressor Pdcd4.
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29
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Karreth FA, Reschke M, Ruocco A, Ng C, Chapuy B, Léopold V, Sjoberg M, Keane TM, Verma A, Ala U, Tay Y, Wu D, Seitzer N, Velasco-Herrera MDC, Bothmer A, Fung J, Langellotto F, Rodig SJ, Elemento O, Shipp MA, Adams DJ, Chiarle R, Pandolfi PP. The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell 2015; 161:319-32. [PMID: 25843629 DOI: 10.1016/j.cell.2015.02.043] [Citation(s) in RCA: 259] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 12/19/2014] [Accepted: 02/02/2015] [Indexed: 12/14/2022]
Abstract
Research over the past decade has suggested important roles for pseudogenes in physiology and disease. In vitro experiments demonstrated that pseudogenes contribute to cell transformation through several mechanisms. However, in vivo evidence for a causal role of pseudogenes in cancer development is lacking. Here, we report that mice engineered to overexpress either the full-length murine B-Raf pseudogene Braf-rs1 or its pseudo "CDS" or "3' UTR" develop an aggressive malignancy resembling human diffuse large B cell lymphoma. We show that Braf-rs1 and its human ortholog, BRAFP1, elicit their oncogenic activity, at least in part, as competitive endogenous RNAs (ceRNAs) that elevate BRAF expression and MAPK activation in vitro and in vivo. Notably, we find that transcriptional or genomic aberrations of BRAFP1 occur frequently in multiple human cancers, including B cell lymphomas. Our engineered mouse models demonstrate the oncogenic potential of pseudogenes and indicate that ceRNA-mediated microRNA sequestration may contribute to the development of cancer.
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Affiliation(s)
- Florian A Karreth
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Markus Reschke
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Anna Ruocco
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Christopher Ng
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Bjoern Chapuy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Valentine Léopold
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Marcela Sjoberg
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, UK
| | - Thomas M Keane
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, UK
| | - Akanksha Verma
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Ugo Ala
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yvonne Tay
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - David Wu
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10021, USA
| | - Nina Seitzer
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | - Anne Bothmer
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jacqueline Fung
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Fernanda Langellotto
- Department of Pathology, Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Margaret A Shipp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, UK
| | - Roberto Chiarle
- Department of Pathology, Children's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Molecular Biotechnology and Health Sciences, University of Torino, 10124 Torino, Italy
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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30
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Wagh PK, Gardner MA, Ma X, Callahan M, Shannon JM, Wert SE, Messinger YH, Dehner LP, Hill DA, Wikenheiser-Brokamp KA. Cell- and developmental stage-specific Dicer1 ablation in the lung epithelium models cystic pleuropulmonary blastoma. J Pathol 2015; 236:41-52. [PMID: 25500911 DOI: 10.1002/path.4500] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/25/2014] [Accepted: 12/10/2014] [Indexed: 01/19/2023]
Abstract
Inherited syndromes provide unique opportunities to identify key regulatory mechanisms governing human disease. We previously identified germline loss-of-function DICER1 mutations in a human syndrome defined by the childhood lung neoplasm pleuropulmonary blastoma (PPB), which arises during lung development. DICER1 regulates many biological processes critical in development and disease pathogenesis. Significant challenges in defining the role of DICER1 in human disease are identifying cause-effect relationships and generating manipulatable systems that model the complexity of organ development and disease pathogenesis. Here we report the generation of a murine model for PPB and demonstrate that precise temporal and cell type-specific Dicer1 ablation is necessary and sufficient for the development of cystic lungs that histologically and phenotypically model PPB. Dicer1 ablation in the distal airway epithelium during early stages of lung development resulted in a cystic lung phenotype indistinguishable from PPB, whereas DICER1 function was not required for development of the proximal airway epithelium or during later stages of organogenesis. Mechanistic studies demonstrate that Dicer1 loss results in epithelial cell death, followed by cystic airway dilatation accompanied by epithelial and mesenchymal proliferation. These studies define precise temporal and epithelial cell type-specific DICER1 functions in the developing lung and demonstrate that loss of these DICER1 functions is sufficient for the development of cystic PPB. These results also provide evidence that PPB arise through a novel mechanism of non-cell-autonomous tumour initiation, in which the genetic abnormality initiating the neoplasm does not occur in the cells that ultimately transform, but rather occurs in a benign-appearing epithelial cell component that predisposes underlying mesenchymal cells to malignant transformation.
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Affiliation(s)
- Purnima K Wagh
- Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, OH, USA
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31
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Tarabichi M, Antoniou A, Saiselet M, Pita JM, Andry G, Dumont JE, Detours V, Maenhaut C. Systems biology of cancer: entropy, disorder, and selection-driven evolution to independence, invasion and "swarm intelligence". Cancer Metastasis Rev 2014; 32:403-21. [PMID: 23615877 PMCID: PMC3843370 DOI: 10.1007/s10555-013-9431-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Our knowledge of the biology of solid cancer has greatly progressed during the last few years, and many excellent reviews dealing with the various aspects of this biology have appeared. In the present review, we attempt to bring together these subjects in a general systems biology narrative. It starts from the roles of what we term entropy of signaling and noise in the initial oncogenic events, to the first major transition of tumorigenesis: the independence of the tumor cell and the switch in its physiology, i.e., from subservience to the organism to its own independent Darwinian evolution. The development after independence involves a constant dynamic reprogramming of the cells and the emergence of a sort of collective intelligence leading to invasion and metastasis and seldom to the ultimate acquisition of immortality through inter-individual infection. At each step, the probability of success is minimal to infinitesimal, but the number of cells possibly involved and the time scale account for the relatively high occurrence of tumorigenesis and metastasis in multicellular organisms.
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Affiliation(s)
| | | | | | - J. M. Pita
- IRIBHM, Brussels, Belgium
- UIPM, Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOFG) and CEDOC, FCM, Universidade Nova de Lisboa, 1169-056 Lisboa, Portugal
| | - G. Andry
- J. Bordet Institute, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | | | | | - C. Maenhaut
- IRIBHM, Brussels, Belgium
- WELBIO, Wallonia, Belgium
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32
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Moyret-Lalle C, Ruiz E, Puisieux A. Epithelial-mesenchymal transition transcription factors and miRNAs: “Plastic surgeons” of breast cancer. World J Clin Oncol 2014; 5:311-322. [PMID: 25114847 PMCID: PMC4127603 DOI: 10.5306/wjco.v5.i3.311] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/18/2014] [Accepted: 06/27/2014] [Indexed: 02/06/2023] Open
Abstract
Growing evidence suggests that breast cancer cell plasticity arises due to a partial reactivation of epithelial-mesenchymal transition (EMT) programs in order to give cells pluripotency, leading to a stemness-like phenotype. A complete EMT would be a dead end program that would render cells unable to fully metastasize to distant organs. Evoking the EMT-mesenchymal-to-epithelial transition (MET) cascade promotes successful colonization of distal target tissues. It is unlikely that direct reprogramming or trans-differentiation without passing through a pluripotent stage would be the preferred mechanism during tumor progression. This review focuses on key EMT transcriptional regulators, EMT-transcription factors involved in EMT (TFs) and the miRNA pathway, which are deregulated in breast cancer, and discusses their implications in cancer cell plasticity. Cross-regulation between EMT-TFs and miRNAs, where miRNAs act as co-repressors or co-activators, appears to be a pivotal mechanism for breast cancer cells to acquire a stem cell-like state, which is implicated both in breast metastases and tumor recurrence. As a master regulator of miRNA biogenesis, the ribonuclease type III endonuclease Dicer plays a central role in EMT-TFs/miRNAs regulating networks. All these EMT-MET key regulators represent valuable new prognostic and predictive markers for breast cancer as well as promising new targets for drug-resistant breast cancers.
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Lyle S, Hoover K, Colpan C, Zhu Z, Matijasevic Z, Jones SN. Dicer cooperates with p53 to suppress DNA damage and skin carcinogenesis in mice. PLoS One 2014; 9:e100920. [PMID: 24979267 PMCID: PMC4076203 DOI: 10.1371/journal.pone.0100920] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 06/02/2014] [Indexed: 11/17/2022] Open
Abstract
Dicer is required for the maturation of microRNA, and loss of Dicer and miRNA processing has been found to alter numerous biological events during embryogenesis, including the development of mammalian skin and hair. We have previously examined the role of miRNA biogenesis in mouse embryonic fibroblasts and found that deletion of Dicer induces cell senescence regulated, in part, by the p53 tumor suppressor. Although Dicer and miRNA molecules are thought to have either oncogenic or tumor suppressing roles in various types of cancer, a role for Dicer and miRNAs in skin carcinogenesis has not been established. Here we show that perinatal ablation of Dicer in the skin of mice leads to loss of fur in adult mice, increased epidermal cell proliferation and apoptosis, and the accumulation of widespread DNA damage in epidermal cells. Co-ablation of Dicer and p53 did not alter the timing or extent of fur loss, but greatly reduced survival of Dicer-skin ablated mice, as these mice developed multiple and highly aggressive skin carcinomas. Our results describe a new mouse model for spontaneous basal and squamous cell tumorigenesis. Furthermore, our findings reveal that loss of Dicer in the epidermis induces extensive DNA damage, activation of the DNA damage response and p53-dependent apoptosis, and that Dicer and p53 cooperate to suppress mammalian skin carcinogenesis.
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MESH Headings
- Animals
- Animals, Newborn
- Apoptosis
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- Carcinogenesis/pathology
- Carcinoma, Basal Cell/genetics
- Carcinoma, Basal Cell/metabolism
- Carcinoma, Basal Cell/mortality
- Carcinoma, Basal Cell/pathology
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/mortality
- Carcinoma, Squamous Cell/pathology
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/metabolism
- DNA Damage
- Fetus
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Neoplastic
- Hair/metabolism
- Hair/pathology
- Mice
- Mice, Transgenic
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Ribonuclease III/genetics
- Ribonuclease III/metabolism
- Skin/metabolism
- Skin/pathology
- Skin Neoplasms/genetics
- Skin Neoplasms/metabolism
- Skin Neoplasms/mortality
- Skin Neoplasms/pathology
- Survival Analysis
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
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Affiliation(s)
- Stephen Lyle
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Kathleen Hoover
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Cansu Colpan
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Zhiqing Zhu
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Zdenka Matijasevic
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Stephen N. Jones
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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34
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Adams CM, Eischen CM. Cell survival is dicey without Dicer. Mol Cell Oncol 2014; 1:e961825. [PMID: 25558471 PMCID: PMC4279215 DOI: 10.4161/23723548.2014.961825] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 07/25/2014] [Accepted: 07/29/2014] [Indexed: 06/04/2023]
Abstract
The cellular requirements of Dicer, an essential miRNA processing enzyme, and the consequences of altered levels of it on tumorigenesis are incompletely understood. We review the effects of Dicer loss in cells of different origin and whether loss of p53 permits cell survival and growth in the absence of Dicer.
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Affiliation(s)
- Clare M Adams
- Department of Pathology, Microbiology and Immunology; Vanderbilt University Medical Center; Nashville, TN USA
| | - Christine M Eischen
- Department of Pathology, Microbiology and Immunology; Vanderbilt University Medical Center; Nashville, TN USA
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35
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Adams CM, Eischen CM. Inactivation of p53 is insufficient to allow B cells and B-cell lymphomas to survive without Dicer. Cancer Res 2014; 74:3923-34. [PMID: 24840646 DOI: 10.1158/0008-5472.can-13-1866] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Inactivation of p53, the master regulator of cellular stress and damage signals, often allows cells that should die or senesce to live. Loss of Dicer, an RNase III-like enzyme critical in microRNA biogenesis, causes embryonic lethality and activation of the p53 pathway. Several nonhematopoietic cell types that contain inactivated p53 have been shown to survive Dicer deletion, suggesting that p53 loss may protect cells from the negative consequences of Dicer deletion. However, here, we report that loss of p53 did not provide a survival advantage to B cells, as they underwent rapid apoptosis upon Dicer deletion. Moreover, a deficiency in p53 neither rescued the Dicer deletion-induced delay in Myc-driven B-cell lymphomagenesis, nor allowed a single B-cell lymphoma to develop with biallelic deletion of Dicer. A p53 deficiency did, however, restore the pre-B/B-cell phenotype and CD19 surface expression of the lymphomas that emerged in conditional Dicer knockout Eμ-myc transgenic mice. Moreover, p53 loss in transformed B cells did not confer protection from apoptosis, as Dicer deletion in established p53-null B-cell lymphomas induced apoptosis, and all of the 1,260 B-cell lymphoma clones analyzed that survived Cre-mediated Dicer deletion retained at least one allele of Dicer. Moreover, Dicer deletion in lymphomas in vivo reduced tumor burden and prolonged survival. Therefore, inactivation of p53 is insufficient to allow untransformed B cells and B-cell lymphomas to survive without Dicer, presenting a potential therapeutic opportunity for the treatment of B-cell lymphomas.
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Affiliation(s)
- Clare M Adams
- Authors' Affiliation: Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Christine M Eischen
- Authors' Affiliation: Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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36
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Chen S, Xue Y, Wu X, Le C, Bhutkar A, Bell EL, Zhang F, Langer R, Sharp PA. Global microRNA depletion suppresses tumor angiogenesis. Genes Dev 2014; 28:1054-67. [PMID: 24788094 PMCID: PMC4035535 DOI: 10.1101/gad.239681.114] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chen et al. depleted microRNAs from tumors by knocking out Dicer1 and found that these tumors are highly hypoxic but poorly vascularized. Factor inhibiting HIF-1 (FIH1) was derepressed in the tumors and suppressed HIF transcription. Depleting FIH1 reversed the phenotypes of microRNA-deficient cells, including HIF transcription activity, VEGF production, tumor hypoxia, and angiogenesis. This study suggests that microRNAs promote tumor responses to hypoxia and angiogenesis by repressing FIH1. MicroRNAs delicately regulate the balance of angiogenesis. Here we show that depletion of all microRNAs suppresses tumor angiogenesis. We generated microRNA-deficient tumors by knocking out Dicer1. These tumors are highly hypoxic but poorly vascularized, suggestive of deficient angiogenesis signaling. Expression profiling revealed that angiogenesis genes were significantly down-regulated as a result of the microRNA deficiency. Factor inhibiting hypoxia-inducible factor 1 (HIF-1), FIH1, is derepressed under these conditions and suppresses HIF transcription. Knocking out FIH1 using CRISPR/Cas9-mediated genome engineering reversed the phenotypes of microRNA-deficient cells in HIF transcriptional activity, VEGF production, tumor hypoxia, and tumor angiogenesis. Using multiplexed CRISPR/Cas9, we deleted regions in FIH1 3′ untranslated regions (UTRs) that contain microRNA-binding sites, which derepresses FIH1 protein and represses hypoxia response. These data suggest that microRNAs promote tumor responses to hypoxia and angiogenesis by repressing FIH1.
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Affiliation(s)
- Sidi Chen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Yuan Xue
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Xuebing Wu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Cong Le
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Arjun Bhutkar
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Eric L Bell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Feng Zhang
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Robert Langer
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Phillip A Sharp
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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37
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Morris JP, Greer R, Russ HA, von Figura G, Kim GE, Busch A, Lee J, Hertel KJ, Kim S, Mcmanus M, Hebrok M. Dicer regulates differentiation and viability during mouse pancreatic cancer initiation. PLoS One 2014; 9:e95486. [PMID: 24788257 PMCID: PMC4006805 DOI: 10.1371/journal.pone.0095486] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 03/26/2014] [Indexed: 12/13/2022] Open
Abstract
miRNA levels are altered in pancreatic ductal adenocarcinoma (PDA), the most common and lethal pancreatic malignancy, and intact miRNA processing is essential for lineage specification during pancreatic development. However, the role of miRNA processing in PDA has not been explored. Here we study the role of miRNA biogenesis in PDA development by deleting the miRNA processing enzyme Dicer in a PDA mouse model driven by oncogenic Kras. We find that loss of Dicer accelerates Kras driven acinar dedifferentiation and acinar to ductal metaplasia (ADM), a process that has been shown to precede and promote the specification of PDA precursors. However, unconstrained ADM also displays high levels of apoptosis. Dicer loss does not accelerate development of Kras driven PDA precursors or PDA, but surprisingly, we observe that mouse PDA can develop without Dicer, although at the expense of proliferative capacity. Our data suggest that intact miRNA processing is involved in both constraining pro-tumorigenic changes in pancreatic differentiation as well as maintaining viability during PDA initiation.
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Affiliation(s)
- John P. Morris
- Diabetes Center, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Renee Greer
- Diabetes Center, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Holger A. Russ
- Diabetes Center, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Guido von Figura
- Diabetes Center, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Grace E. Kim
- Department of Pathology, University of California San Francisco, San Francisco, California, United States of America
| | - Anke Busch
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, United States of America
| | - Jonghyeob Lee
- Department of Developmental Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Klemens J. Hertel
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, United States of America
| | - Seung Kim
- Department of Developmental Biology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Michael Mcmanus
- Diabetes Center, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Matthias Hebrok
- Diabetes Center, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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38
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MiRNA-99a directly regulates AGO2 through translational repression in hepatocellular carcinoma. Oncogenesis 2014; 3:e97. [PMID: 24732044 PMCID: PMC4007193 DOI: 10.1038/oncsis.2014.11] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 03/05/2014] [Accepted: 03/06/2014] [Indexed: 12/12/2022] Open
Abstract
The regulation network consisting of microRNAs (miRNAs) and their target genes remains largely elusive in hepatocellular carcinoma (HCC), especially the reciprocal loop between specific miRNAs and the miRNA processing machinery. In this study, we found that miR-99a was remarkably decreased in 111 of 152 (73.03%) primary HCC tissues and low-level expression of miR-99a was correlated with low tumor differentiation (P=0.001), liver cirrhosis (P=0.015), poor tumor-free survival (P=0.004) and overall survival (P=0.006) for HCC patients. By restoration of miR-99a, the HCC growth could be considerably inhibited both in vitro and in vivo. Subsequently, Argonaute-2 (Ago2), a central component of RNA-induced silencing complex, was found to be directly regulated by miR-99a via translational repression. Overexpression of Ago2 could partly impair the inhibitory effect of miR-99a on HCC cells in vitro. Then, we demonstrated that Ago2 was upregulated in HCC tissues at both RNA and protein levels and the expression of AGO2 protein and miR-99a was negatively correlated within detected HCC tissues (r=−0.727, P=0.004). Interestingly, the tumorigenicity of Ago2-knockdown HCC cells was severely impaired (4/10 vs 10/10, P<0.05), and this was in contrast to the miR-99a-overexpressing HCC cells. Functionally, the increased AGO2 protein could specifically facilitate oncogenic miR-21 to repress its targeted gene phosphatase and tensin homolog (Pten) in HCC, whereas leave the regulatory capacity of let-7a on its targeted oncogenes almost unaltered. In summary, our study has revealed a novel pathway for the tumor suppressor miR-99a to control tumor growth in HCC, via its downstream signaling of AGO2/miR-21/PTEN. In addition, this study provides potential strategies for HCC therapy by reintroduction of miRNA suppressors.
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39
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Palanichamy JK, Rao DS. miRNA dysregulation in cancer: towards a mechanistic understanding. Front Genet 2014; 5:54. [PMID: 24672539 PMCID: PMC3957189 DOI: 10.3389/fgene.2014.00054] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/02/2014] [Indexed: 12/17/2022] Open
Abstract
It is now well known that gene expression is intricately regulated inside each cell especially in mammals. There are multiple layers of gene regulation active inside a cell at a given point of time. Gene expression is regulated post-transcriptionally by microRNAs and other factors. Mechanistically, microRNAs are known to bind to the 3’ UTR of mRNAs and cause repression of gene expression and the number of known microRNAs continues to increase every day. Dysregulated microRNA signatures in different types of cancer are being uncovered consistently implying their importance in cellular homeostasis. However when studied in isolation in mouse models, clear-cut cellular and molecular mechanisms have been described only for a select few microRNAs. What is the reason behind this discrepancy? Are microRNAs small players in gene regulation helping only to fine tune gene expression? Or are their roles tissue and cell type-specific with single-cell level effects on mRNA expression and microRNA threshold levels? Or does it all come down to the technical limitations of high-throughput techniques, resulting in false positive results? In this review, we will assess the challenges facing the field and potential avenues for resolving the cellular and molecular mechanisms of these small but important regulators of gene expression.
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Affiliation(s)
| | - Dinesh S Rao
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, CA, USA ; Jonsson Comprehensive Cancer Center, University of California Los Angeles, CA, USA ; Broad Stem Cell Research Center, University of California Los Angeles, CA, USA ; Division of Biology, California Institute of Technology Pasadena, CA, USA
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40
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Stokowy T, Eszlinger M, Świerniak M, Fujarewicz K, Jarząb B, Paschke R, Krohn K. Analysis options for high-throughput sequencing in miRNA expression profiling. BMC Res Notes 2014; 7:144. [PMID: 24625073 PMCID: PMC4007773 DOI: 10.1186/1756-0500-7-144] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 02/28/2014] [Indexed: 12/11/2022] Open
Abstract
Background Recently high-throughput sequencing (HTS) using next generation sequencing techniques became useful in digital gene expression profiling. Our study introduces analysis options for HTS data based on mapping to miRBase or counting and grouping of identical sequence reads. Those approaches allow a hypothesis free detection of miRNA differential expression. Methods We compare our results to microarray and qPCR data from one set of RNA samples. We use Illumina platforms for microarray analysis and miRNA sequencing of 20 samples from benign follicular thyroid adenoma and malignant follicular thyroid carcinoma. Furthermore, we use three strategies for HTS data analysis to evaluate miRNA biomarkers for malignant versus benign follicular thyroid tumors. Results High correlation of qPCR and HTS data was observed for the proposed analysis methods. However, qPCR is limited in the differential detection of miRNA isoforms. Moreover, we illustrate a much broader dynamic range of HTS compared to microarrays for small RNA studies. Finally, our data confirm hsa-miR-197-3p, hsa-miR-221-3p, hsa-miR-222-3p and both hsa-miR-144-3p and hsa-miR-144-5p as potential follicular thyroid cancer biomarkers. Conclusions Compared to microarrays HTS provides a global profile of miRNA expression with higher specificity and in more detail. Summarizing of HTS reads as isoform groups (analysis pipeline B) or according to functional criteria (seed analysis pipeline C), which better correlates to results of qPCR are promising new options for HTS analysis. Finally, data opens future miRNA research perspectives for HTS and indicates that qPCR might be limited in validating HTS data in detail.
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Affiliation(s)
| | | | | | | | | | | | - Knut Krohn
- Interdisciplinary Center for Clinical Research (IZKF), University of Leipzig, Liebigstr, 21, 04103 Leipzig, Germany.
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41
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Kumar MS, Armenteros-Monterroso E, East P, Chakravorty P, Matthews N, Winslow MM, Downward J. HMGA2 functions as a competing endogenous RNA to promote lung cancer progression. Nature 2013; 505:212-7. [PMID: 24305048 PMCID: PMC3886898 DOI: 10.1038/nature12785] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 10/16/2013] [Indexed: 01/02/2023]
Abstract
Non-small-cell lung cancer (NSCLC) is the most prevalent histological cancer subtype worldwide. As the majority of patients present with invasive, metastatic disease, it is vital to understand the basis for lung cancer progression. Hmga2 is highly expressed in metastatic lung adenocarcinoma, in which it contributes to cancer progression and metastasis. Here we show that Hmga2 promotes lung cancer progression in mouse and human cells by operating as a competing endogenous RNA (ceRNA) for the let-7 microRNA (miRNA) family. Hmga2 can promote the transformation of lung cancer cells independent of protein-coding function but dependent upon the presence of let-7 sites; this occurs without changes in the levels of let-7 isoforms, suggesting that Hmga2 affects let-7 activity by altering miRNA targeting. These effects are also observed in vivo, where Hmga2 ceRNA activity drives lung cancer growth, invasion and dissemination. Integrated analysis of miRNA target prediction algorithms and metastatic lung cancer gene expression data reveals the TGF-β co-receptor Tgfbr3 (ref. 12) as a putative target of Hmga2 ceRNA function. Tgfbr3 expression is regulated by the Hmga2 ceRNA through differential recruitment to Argonaute 2 (Ago2), and TGF-β signalling driven by Tgfbr3 is important for Hmga2 to promote lung cancer progression. Finally, analysis of NSCLC-patient gene-expression data reveals that HMGA2 and TGFBR3 are coordinately regulated in NSCLC-patient material, a vital corollary to ceRNA function. Taken together, these results suggest that Hmga2 promotes lung carcinogenesis both as a protein-coding gene and as a non-coding RNA; such dual-function regulation of gene-expression networks reflects a novel means by which oncogenes promote disease progression.
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Affiliation(s)
- Madhu S Kumar
- Signal Transduction Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Elena Armenteros-Monterroso
- Signal Transduction Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Philip East
- Bioinformatics and Biostatistics Group, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Probir Chakravorty
- Bioinformatics and Biostatistics Group, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Nik Matthews
- Advanced Sequencing Facility, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Monte M Winslow
- Department of Genetics, Department of Pathology, the Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Julian Downward
- 1] Signal Transduction Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK [2] Lung Cancer Group, Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
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42
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Jeker LT, Bluestone JA. MicroRNA regulation of T-cell differentiation and function. Immunol Rev 2013; 253:65-81. [PMID: 23550639 DOI: 10.1111/imr.12061] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are emerging as key controllers of T-cell differentiation and function. Their expression is dynamically regulated by extracellular signals such as costimulation and cytokine signals. miRNAs set thresholds for gene expression and optimize protein concentrations of genetic networks. Absence of individual miRNAs can lead to severe immune dysfunction. In this study, we review emerging principles and provide examples of important functions exerted by miRNAs. Although our understanding of miRNA function in T-cell differentiation is still rudimentary, the available evidence leaves no doubt that these small post-transcriptional regulators are indispensable for proper functioning of the immune system.
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Affiliation(s)
- Lukas T Jeker
- Diabetes Center, University of California San Francisco, San Francisco, CA 94143, USA
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43
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miR-26a enhances miRNA biogenesis by targeting Lin28B and Zcchc11 to suppress tumor growth and metastasis. Oncogene 2013; 33:4296-306. [PMID: 24056962 DOI: 10.1038/onc.2013.385] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 07/12/2013] [Accepted: 08/09/2013] [Indexed: 02/06/2023]
Abstract
Human cancers often exhibit attenuated microRNA (miRNA) biogenesis and global underexpression of miRNAs; thus, targeting the miRNA biogenesis pathway represents a novel strategy for cancer therapy. Here, we report that miR-26a enhances miRNA biogenesis, which acts as a common mechanism partially accounting for miR-26a function in diverse cancers including melanoma, prostate and liver cancer. miR-26a was broadly reduced in multiple cancers, and overexpression of miR-26a significantly suppressed tumor growth and metastasis both in vitro and in vivo, including melanoma, prostate and liver cancers. Notably, miR-26a overexpression was accompanied by global upregulation of miRNAs, especially let-7, and let-7 expression was concordant with miR-26a expression in cancer cell lines, xenograft tumors and normal human tissues, underscoring their biological relevance. We showed that miR-26a directly targeted Lin28B and Zcchc11-two critical repressors of let-7 maturation. Furthermore, we have demonstrated that Zcchc11 promoted tumor growth and metastasis, and it was prominently overexpressed in human cancers. Our findings thus provide a novel mechanism by which a miRNA acts as a modulator of miRNA biogenesis. These results also define a role of the miR-26a and Zcchc11 in tumorigenesis and metastasis and have implications to develop new strategies for cancer therapy.
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44
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Zhang B, Chen H, Zhang L, Dakhova O, Zhang Y, Lewis MT, Creighton CJ, Ittmann MM, Xin L. A dosage-dependent pleiotropic role of Dicer in prostate cancer growth and metastasis. Oncogene 2013; 33:3099-108. [PMID: 23851498 PMCID: PMC3916938 DOI: 10.1038/onc.2013.281] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/25/2013] [Accepted: 05/24/2013] [Indexed: 12/12/2022]
Abstract
Dicer is as an RNase III enzyme essential for the maturation of the majority of microRNAs. Recent studies have revealed down-regulation or hemizygous loss of Dicer in many tumor models and demonstrated that suppressing Dicer activity enhances tumorigenic activities of lung and breast cancer cells, which support Dicer as a haploinsufficient tumor suppressor in these cancer models. Surprisingly, we found that knocking down Dicer expression suppresses the growth and tumorigenic capacity of human prostate cancer cell lines, but enhances migratory capacities of some prostate cancer cell lines. Dicer is up-regulated in human prostate cancer specimens, but lower Dicer expression portends a shorter time to recurrence. Complete ablation of Dicer activity in a Pten null mouse model for prostate cancer significantly halts tumor growth and progression, demonstrating that microRNAs play a critical role in maintaining cancer cell fitness. In comparison, hemizygous loss of Dicer in the same model also reduces primary tumor burden, but induces a more locally invasive phenotype and causes seminal vesicle obstruction at high penetrance. Disrupting Dicer activity leads to an increase in apoptosis and senescence in these models, presumably through up-regulation of P16/INK4a and P27/Kip1. Collectively, these results highlight a pleotropic role of Dicer in tumorigenesis that is not only dosage-dependent but also tissue context-dependent.
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Affiliation(s)
- B Zhang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - H Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - L Zhang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - O Dakhova
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Y Zhang
- Dan L. Duncan Cancer Center, Houston, TX, USA
| | - M T Lewis
- 1] Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA [2] Dan L. Duncan Cancer Center, Houston, TX, USA
| | | | - M M Ittmann
- 1] Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA [2] Dan L. Duncan Cancer Center, Houston, TX, USA
| | - L Xin
- 1] Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA [2] Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA [3] Dan L. Duncan Cancer Center, Houston, TX, USA
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Gurtan AM, Ravi A, Rahl PB, Bosson AD, JnBaptiste CK, Bhutkar A, Whittaker CA, Young RA, Sharp PA. Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts. Genes Dev 2013; 27:941-54. [PMID: 23630078 DOI: 10.1101/gad.215376.113] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
MicroRNAs (miRNAs) are critical to proliferation, differentiation, and development. Here, we characterize gene expression in murine Dicer-null adult mesenchymal stem cell lines, a fibroblast cell type. Loss of Dicer leads to derepression of let-7 targets at levels that exceed 10-fold to 100-fold with increases in transcription. Direct and indirect targets of this miRNA belong to a mid-gestation embryonic program that encompasses known oncofetal genes as well as oncogenes not previously associated with an embryonic state. Surprisingly, this mid-gestation program represents a distinct period that occurs between the pluripotent state of the inner cell mass at embryonic day 3.5 (E3.5) and the induction of let-7 upon differentiation at E10.5. Within this mid-gestation program, we characterize the let-7 target Nr6a1, an embryonic transcriptional repressor that regulates gene expression in adult fibroblasts following miRNA loss. In total, let-7 is required for the continual suppression of embryonic gene expression in adult cells, a mechanism that may underlie its tumor-suppressive function.
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Affiliation(s)
- Allan M Gurtan
- David H. Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts 02139, USA
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46
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Jeker LT, Zhou X, Blelloch R, Bluestone JA. DGCR8-mediated production of canonical microRNAs is critical for regulatory T cell function and stability. PLoS One 2013; 8:e66282. [PMID: 23741528 PMCID: PMC3669207 DOI: 10.1371/journal.pone.0066282] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 05/08/2013] [Indexed: 02/01/2023] Open
Abstract
Regulatory T cells (Treg) are integral for immune homeostasis. Here we demonstrate that canonical microRNAs (miRNAs) are required for Treg function because mice with DGCR8-deficient Treg cells spontaneously develop a scurfy-like disease. Using genetic lineage marking we show that absence of miRNAs leads to reduced FoxP3 expression in Treg cells in vivo. In vitro culture of purified DGCR8-deficient Treg leads to a loss of FoxP3 expression. We conclude that canonical miRNAs are essential to maintain stable FoxP3 expression and Treg function. Thus, signals interfering with miRNA homeostasis might contribute to autoimmune diseases.
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Affiliation(s)
- Lukas T. Jeker
- Diabetes Center and the Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Department of Pathology, University of California San Francisco, San Francisco, California, United States of America
| | - Xuyu Zhou
- Diabetes Center and the Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America,
| | - Jeffrey A. Bluestone
- Diabetes Center and the Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Department of Pathology, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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47
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Insulin receptor tyrosine kinase substrate activates EGFR/ERK signalling pathway and promotes cell proliferation of hepatocellular carcinoma. Cancer Lett 2013; 337:96-106. [PMID: 23693078 DOI: 10.1016/j.canlet.2013.05.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Revised: 05/07/2013] [Accepted: 05/14/2013] [Indexed: 11/21/2022]
Abstract
Insulin receptor tyrosine kinase substrate (IRTKS) is closely associated with actin remodelling and membrane protrusion, but its role in the pathogenesis of malignant tumours, including hepatocellular carcinoma (HCC), is still unknown. In this study, we showed that IRTKS was frequently upregulated in HCC samples, and its expression level was significantly associated with tumour size. Enforced expression of IRTKS in human HCC cell lines significantly promoted their proliferation and colony formation in vitro, and their capacity to develop tumour xenografts in vivo, whereas knockdown of IRTKS resulted in the opposite effects. Furthermore, the bromodeoxyuridine (BrdU) incorporation analyses and propidium iodide staining indicated that IRTKS can promote the entry into S phase of cell cycle progression. Significantly, IRTKS can interact with epidermal growth factor receptor (EGFR), results in the phosphorylation of extracellular signal-regulated kinase (ERK). By contrast, inhibition of ERK activation can attenuate the effects of IRTKS overexpression on cellular proliferation. Taken together, these data demonstrate that IRTKS promotes the proliferation of HCC cells by enhancing EGFR-ERK signalling pathway.
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48
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The transcriptional consequences of somatic amplifications, deletions, and rearrangements in a human lung squamous cell carcinoma. Neoplasia 2013; 14:1075-86. [PMID: 23226101 DOI: 10.1593/neo.121380] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 09/25/2012] [Accepted: 09/28/2012] [Indexed: 12/16/2022] Open
Abstract
Lung cancer causes more deaths, worldwide, than any other cancer. Several histologic subtypes exist. Currently, there is a dearth of targeted therapies for treating one of the main subtypes: squamous cell carcinoma (SCC). As for many cancers, lung SCC karyotypes are often highly anomalous owing to large somatic structural variants, some of which are seen repeatedly in lung SCC, indicating a potential causal association for genes therein. We chose to characterize a lung SCC genome to unprecedented detail and integrate our findings with the concurrently characterized transcriptome. We aimed to ascertain how somatic structural changes affected gene expression within the cell in ways that could confer a pathogenic phenotype. We sequenced the genomes of a lung SCC cell line (LUDLU-1) and its matched lymphocyte cell line (AGLCL) to more than 50x coverage. We also sequenced the transcriptomes of LUDLU-1 and a normal bronchial epithelium cell line (LIMM-NBE1), resulting in more than 600 million aligned reads per sample, including both coding and non-coding RNA (ncRNA), in a strand-directional manner. We also captured small RNA (<30 bp). We discovered significant, but weak, correlations between copy number and expression for protein-coding genes, antisense transcripts, long intergenic ncRNA, and microRNA (miRNA). We found that miRNA undergo the largest change in overall expression pattern between the normal bronchial epithelium and the tumor cell line. We found evidence of transcription across the novel genomic sequence created from six somatic structural variants. For each part of our integrated analysis, we highlight candidate genes that have undergone the largest expression changes.
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Moore LM, Kivinen V, Liu Y, Annala M, Cogdell D, Liu X, Liu CG, Sawaya R, Yli-Harja O, Shmulevich I, Fuller GN, Zhang W, Nykter M. Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma. J Pathol 2013; 229:449-59. [PMID: 23007860 DOI: 10.1002/path.4109] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 12/21/2022]
Abstract
Altered expression of oncogenic and tumour-suppressing microRNAs (miRNAs) is widely associated with tumourigenesis. However, the regulatory mechanisms underlying these alterations are poorly understood. We sought to shed light on the deregulation of miRNA biogenesis promoting the aberrant miRNA expression profiles identified in these tumours. Using sequencing technology to perform both whole-transcriptome and small RNA sequencing of glioma patient samples, we examined precursor and mature miRNAs to directly evaluate the miRNA maturation process, and examined expression profiles for genes involved in the major steps of miRNA biogenesis. We found that ratios of mature to precursor forms of a large number of miRNAs increased with the progression from normal brain to low-grade and then to high-grade gliomas. The expression levels of genes involved in each of the three major steps of miRNA biogenesis (nuclear processing, nucleo-cytoplasmic transport, and cytoplasmic processing) were systematically altered in glioma tissues. Survival analysis of an independent data set demonstrated that the alteration of genes involved in miRNA maturation correlates with survival in glioma patients. Direct quantification of miRNA maturation with deep sequencing demonstrated that deregulation of the miRNA biogenesis pathway is a hallmark for glioma genesis and progression.
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Affiliation(s)
- Lynette M Moore
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
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Thangavel C, Boopathi E, Ertel A, Lim M, Addya S, Fortina P, Witkiewicz AK, Knudsen ES. Regulation of miR106b cluster through the RB pathway: mechanism and functional targets. Cell Cycle 2012; 12:98-111. [PMID: 23255112 DOI: 10.4161/cc.23029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The RB pathway plays a critical role in proliferation control that is commonly subverted in tumor development. However, restoration of RB pathway function can be elicited in many tumor cells by the inhibition of CDK4/6 activity that leads to dephosphorylation of RB and subsequent repression of E2F-mediated transcription. In this context, active RB/E2F complexes inhibit the expression of a critical program of coding genes that promote cell cycle progression. However, the non-coding RNA target genes downstream from RB that could be relevant for tumor biology remain obscure. Here, miRNA gene expression profiling identified the miR106b cluster as being efficiently repressed with CDK4/6 inhibition in an E2F and RB-dependent manner. Importantly, the miR106B-cluster is intragenic of MCM7, and through a series of functional studies, the basis of MCM7 regulation and concordant expression of the miRNA species within the 106b cluster was determined. Importantly, RB-mediated repression of the 106b cluster enhances the transcript levels of p21Cip1 and PTEN. These data provide a mechanistic basis for cross-talk between the RB pathway and p21 and PTEN through the regulation of the MCM7/miR106b locus.
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