1
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Mello SS, Sinow C, Raj N, Mazur PK, Bieging-Rolett K, Broz DK, Imam JFC, Vogel H, Wood LD, Sage J, Hirose T, Nakagawa S, Rinn J, Attardi LD. Neat1 is a p53-inducible lincRNA essential for transformation suppression. Genes Dev 2017; 31:1095-1108. [PMID: 28698299 PMCID: PMC5538433 DOI: 10.1101/gad.284661.116] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 05/26/2017] [Indexed: 12/12/2022]
Abstract
Mello et al. identify Neat1, a ncRNA constituent of paraspeckles, as a p53 target gene that plays a crucial role in suppressing transformation in response to oncogenic signals. The p53 gene is mutated in over half of all cancers, reflecting its critical role as a tumor suppressor. Although p53 is a transcriptional activator that induces myriad target genes, those p53-inducible genes most critical for tumor suppression remain elusive. Here, we leveraged p53 ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) and RNA-seq (RNA sequencing) data sets to identify new p53 target genes, focusing on the noncoding genome. We identify Neat1, a noncoding RNA (ncRNA) constituent of paraspeckles, as a p53 target gene broadly induced by mouse and human p53 in different cell types and by diverse stress signals. Using fibroblasts derived from Neat1−/− mice, we examined the functional role of Neat1 in the p53 pathway. We found that Neat1 is dispensable for cell cycle arrest and apoptosis in response to genotoxic stress. In sharp contrast, Neat1 plays a crucial role in suppressing transformation in response to oncogenic signals. Neat1 deficiency enhances transformation in oncogene-expressing fibroblasts and promotes the development of premalignant pancreatic intraepithelial neoplasias (PanINs) and cystic lesions in KrasG12D-expressing mice. Neat1 loss provokes global changes in gene expression, suggesting a mechanism by which its deficiency promotes neoplasia. Collectively, these findings identify Neat1 as a p53-regulated large intergenic ncRNA (lincRNA) with a key role in suppressing transformation and cancer initiation, providing fundamental new insight into p53-mediated tumor suppression.
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Affiliation(s)
- Stephano S Mello
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Carolyn Sinow
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Nitin Raj
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Pawel K Mazur
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kathryn Bieging-Rolett
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Daniela Kenzelmann Broz
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jamie F Conklin Imam
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Hannes Vogel
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Laura D Wood
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - John Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Laura D Attardi
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
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2
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Schmitt AM, Garcia JT, Hung T, Flynn RA, Shen Y, Qu K, Payumo AY, Peres-da-Silva A, Broz DK, Baum R, Guo S, Chen JK, Attardi LD, Chang HY. An inducible long noncoding RNA amplifies DNA damage signaling. Nat Genet 2016; 48:1370-1376. [PMID: 27668660 PMCID: PMC5083181 DOI: 10.1038/ng.3673] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/22/2016] [Indexed: 12/17/2022]
Abstract
Long noncoding RNAs (lncRNAs) are prevalent genes with frequently precise regulation but mostly unknown functions. Here we demonstrate that lncRNAs guide the organismal DNA damage response. DNA damage activated transcription of the DINO (Damage Induced Noncoding) lncRNA via p53. DINO was required for p53-dependent gene expression, cell cycle arrest and apoptosis in response to DNA damage, and DINO expression was sufficient to activate damage signaling and cell cycle arrest in the absence of DNA damage. DINO bound to p53 protein and promoted its stabilization, mediating a p53 auto-amplification loop. Dino knockout or promoter inactivation in mice dampened p53 signaling and ameliorated acute radiation syndrome in vivo. Thus, inducible lncRNA can create a feedback loop with its cognate transcription factor to amplify cellular signaling networks.
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Affiliation(s)
- Adam M Schmitt
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Julia T Garcia
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Tiffany Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Ying Shen
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Kun Qu
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Alexander Y Payumo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Ashwin Peres-da-Silva
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | | | - Rachel Baum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Shuling Guo
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Laura D Attardi
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
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3
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Hor H, Francescatto L, Bartesaghi L, Ortega-Cubero S, Kousi M, Lorenzo-Betancor O, Jiménez-Jiménez FJ, Gironell A, Clarimón J, Drechsel O, Agúndez JAG, Kenzelmann Broz D, Chiquet-Ehrismann R, Lleó A, Coria F, García-Martin E, Alonso-Navarro H, Martí MJ, Kulisevsky J, Hor CN, Ossowski S, Chrast R, Katsanis N, Pastor P, Estivill X. Missense mutations in TENM4, a regulator of axon guidance and central myelination, cause essential tremor. Hum Mol Genet 2015; 24:5677-86. [PMID: 26188006 DOI: 10.1093/hmg/ddv281] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/13/2015] [Indexed: 12/16/2022] Open
Abstract
Essential tremor (ET) is a common movement disorder with an estimated prevalence of 5% of the population aged over 65 years. In spite of intensive efforts, the genetic architecture of ET remains unknown. We used a combination of whole-exome sequencing and targeted resequencing in three ET families. In vitro and in vivo experiments in oligodendrocyte precursor cells and zebrafish were performed to test our findings. Whole-exome sequencing revealed a missense mutation in TENM4 segregating in an autosomal-dominant fashion in an ET family. Subsequent targeted resequencing of TENM4 led to the discovery of two novel missense mutations. Not only did these two mutations segregate with ET in two additional families, but we also observed significant over transmission of pathogenic TENM4 alleles across the three families. Consistent with a dominant mode of inheritance, in vitro analysis in oligodendrocyte precursor cells showed that mutant proteins mislocalize. Finally, expression of human mRNA harboring any of three patient mutations in zebrafish embryos induced defects in axon guidance, confirming a dominant-negative mode of action for these mutations. Our genetic and functional data, which is corroborated by the existence of a Tenm4 knockout mouse displaying an ET phenotype, implicates TENM4 in ET. Together with previous studies of TENM4 in model organisms, our studies intimate that processes regulating myelination in the central nervous system and axon guidance might be significant contributors to the genetic burden of this disorder.
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Affiliation(s)
- Hyun Hor
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, Spain, Universitat Pompeu Fabra (UPF), Barcelona, Spain, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain, CRG CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Catalonia 08003, Spain,
| | - Ludmila Francescatto
- Center for Human Disease Modeling, Duke University, Duke University Medical Center, Durham NC 27710, USA
| | - Luca Bartesaghi
- Department of Medical Genetics, University of Lausanne, Lausanne 1005, Switzerland, Department of Neuroscience and Department of Clinical Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Sara Ortega-Cubero
- Neurogenetics Laboratory, Division of Neurosciences, Center for Applied Medical Research (CIMA), and Department of Neurology, Clínica Universidad de Navarra, University of Navarra School of Medicine and Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Pamplona, Navarra 31008, Spain
| | - Maria Kousi
- Center for Human Disease Modeling, Duke University, Duke University Medical Center, Durham NC 27710, USA
| | - Oswaldo Lorenzo-Betancor
- Neurogenetics Laboratory, Division of Neurosciences, Center for Applied Medical Research (CIMA), and Department of Neurology, Clínica Universidad de Navarra, University of Navarra School of Medicine and Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Pamplona, Navarra 31008, Spain
| | - Felix J Jiménez-Jiménez
- Section of Neurology, Hospital Universitario del Sureste, Arganda del Rey, Madrid 28030, Spain
| | - Alexandre Gironell
- Movement Disorders Unit, Neurology Department, Hospital de Sant Pau, Barcelona, Spain, Sant Pau Biomedical Research Institute, Barcelona, Spain
| | - Jordi Clarimón
- Sant Pau Biomedical Research Institute, Barcelona, Spain, Universitat Autònoma de Barcelona and CIBERNED, Barcelona, Catalonia 08026, Spain
| | - Oliver Drechsel
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, Spain, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Daniela Kenzelmann Broz
- Faculty of Sciences and Department of Biomedicine, Friedrich Miescher Institute of Biomedical Research, Novartis Research Foundation and University of Basel, Basel 4058, Switzerland
| | - Ruth Chiquet-Ehrismann
- Faculty of Sciences and Department of Biomedicine, Friedrich Miescher Institute of Biomedical Research, Novartis Research Foundation and University of Basel, Basel 4058, Switzerland
| | - Alberto Lleó
- Sant Pau Biomedical Research Institute, Barcelona, Spain
| | - Francisco Coria
- Clinic for Nervous Disorders, Service of Neurology, Son Espases University Hospital, Palma de Mallorca 07120, Spain
| | - Elena García-Martin
- Department of Biochemistry and Molecular Biology, University of Extremadura, Cáceres 10071, Spain
| | | | - Maria J Martí
- Movement Disorders Unit, Neurology Service, Hospital Clinic, CIBERNED and Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia 08036, Spain and
| | - Jaume Kulisevsky
- Movement Disorders Unit, Neurology Department, Hospital de Sant Pau, Barcelona, Spain, Universitat Autònoma de Barcelona and CIBERNED, Barcelona, Catalonia 08026, Spain
| | - Charlotte N Hor
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, Spain, Universitat Pompeu Fabra (UPF), Barcelona, Spain, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain, CRG CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Catalonia 08003, Spain
| | - Stephan Ossowski
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, Spain, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roman Chrast
- Department of Medical Genetics, University of Lausanne, Lausanne 1005, Switzerland, Department of Neuroscience and Department of Clinical Neuroscience, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Duke University Medical Center, Durham NC 27710, USA
| | - Pau Pastor
- Neurogenetics Laboratory, Division of Neurosciences, Center for Applied Medical Research (CIMA), and Department of Neurology, Clínica Universidad de Navarra, University of Navarra School of Medicine and Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Pamplona, Navarra 31008, Spain,
| | - Xavier Estivill
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, Spain, Universitat Pompeu Fabra (UPF), Barcelona, Spain, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain, CRG CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Catalonia 08003, Spain, Dexeus Women's Health, University Hospital Quiron-Dexeus, Barcelona, Catalonia 08028, Spain
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Brady CA, Broz DK, Jiang D, Mello SS, Bieging K, Johnson TM, Jarvis LA, Kozak MM, Basak S, Attardi LD. Abstract IA4: Deconstructing p53 pathways in vivo. Cancer Res 2013. [DOI: 10.1158/1538-7445.fbcr13-ia4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The activation of the p53 protein by cellular stress signals is fundamental for tumor suppression but also promotes pathological states, such as provoking the side effects of genotoxic cancer therapies. To better understand the mechanisms of p53 action in different contexts, we have leveraged both mouse genetic and genomic approaches. First, we have used mouse genetics to define transcriptional programs involved in p53 function in different in vivo settings, specifically by generating a panel of p53 transcriptional activation domain mutant knock-in mouse strains. These include strains expressing p53 mutants in the first (p5325,26), second (p5353,54), or both transactivation domains (p5325,26,53,54). We have observed that p5325,26 is severely compromised for transactivation of most classical p53 target genes, but retains the ability to activate a subset of p53 targets, while p5325,26,53,54 lacks transactivation activity completely. Interestingly, although unable to induce apoptosis or cell cycle arrest in response to acute DNA damage signals, p5325,26 retains full activity in suppressing cancers of a wide range of types, indicating that robust transactivation of most canonical p53 targets is dispensable for tumor suppression. Importantly, as p5325,26 activates only a subset of p53-dependent genes, yet retains tumor suppressor activity, it has helped to define a small set of novel p53-inducible tumor suppression-associated genes, which we are currently analyzing in detail. Second, we have utilized genomic approaches to better understand p53 function. Using ChIP-sequencing and RNA-sequencing to analyze transcriptional programs in acute DNA damage-treated mouse embryo fibroblasts, our studies have revealed an extensive p53-regulated autophagy program that contributes to p53 responses. Together, these approaches will help better define the transcriptional networks important for p53 action in different settings.
Citation Format: Colleen A. Brady, Daniela Kenzelmann Broz, Dadi Jiang, Stephano Spano Mello, Kathryn Bieging, Thomas M. Johnson, Leslie A. Jarvis, Margaret M. Kozak, Shashwati Basak, Laura D. Attardi. Deconstructing p53 pathways in vivo. [abstract]. In: Proceedings of the Third AACR International Conference on Frontiers in Basic Cancer Research; Sep 18-22, 2013; National Harbor, MD. Philadelphia (PA): AACR; Cancer Res 2013;73(19 Suppl):Abstract nr IA4.
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Affiliation(s)
| | | | - Dadi Jiang
- Stanford University School of Medicine, Stanford, CA
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Abstract
The mechanisms by which the TP53/TRP53 transcription factor acts as a tumor suppressor remain incompletely understood. To gain new insights into TP53/TRP53 biology, we used ChIP-seq and RNA-seq technologies to define global TRP53 transcriptional networks in primary cells subjected to DNA damage. Intriguingly, we identified a TRP53-regulated autophagy program, which can be coordinately regulated by the TRP53 family members TRP63 and TRP73 in certain settings. While autophagy is not involved in TRP53-dependent cell cycle arrest, it contributes to both TRP53-driven apoptosis in response to DNA damage and TRP53-mediated transformation suppression. Collectively, our genome-wide analyses reveal a profound role for TRP53 in regulating autophagy, through an extensive transcriptional network, and have demonstrated an important role for this program in promoting TRP53-mediated apoptosis and tumor suppression.
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Affiliation(s)
- Daniela Kenzelmann Broz
- Division of Radiation and Cancer Biology; Department of Radiation Oncology; Stanford University School of Medicine; Stanford, CA USA
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Kenzelmann Broz D, Spano Mello S, Bieging KT, Jiang D, Dusek RL, Brady CA, Sidow A, Attardi LD. Global genomic profiling reveals an extensive p53-regulated autophagy program contributing to key p53 responses. Genes Dev 2013; 27:1016-31. [PMID: 23651856 DOI: 10.1101/gad.212282.112] [Citation(s) in RCA: 312] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The mechanisms by which the p53 tumor suppressor acts remain incompletely understood. To gain new insights into p53 biology, we used high-throughput sequencing to analyze global p53 transcriptional networks in primary mouse embryo fibroblasts in response to DNA damage. Chromatin immunoprecipitation sequencing reveals 4785 p53-bound sites in the genome located near 3193 genes involved in diverse biological processes. RNA sequencing analysis shows that only a subset of p53-bound genes is transcriptionally regulated, yielding a list of 432 p53-bound and regulated genes. Interestingly, we identify a host of autophagy genes as direct p53 target genes. While the autophagy program is regulated predominantly by p53, the p53 family members p63 and p73 contribute to activation of this autophagy gene network. Induction of autophagy genes in response to p53 activation is associated with enhanced autophagy in diverse settings and depends on p53 transcriptional activity. While p53-induced autophagy does not affect cell cycle arrest in response to DNA damage, it is important for both robust p53-dependent apoptosis triggered by DNA damage and transformation suppression by p53. Together, our data highlight an intimate connection between p53 and autophagy through a vast transcriptional network and indicate that autophagy contributes to p53-dependent apoptosis and cancer suppression.
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Affiliation(s)
- Daniela Kenzelmann Broz
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305, USA
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Abstract
p53 is a crucial tumor suppressor, as evidenced by the high propensity for p53 mutation during human cancer development. Already more than a decade ago, p53 knockout mice confirmed that p53 is critical for preventing tumorigenesis. More recently, a host of p53 knock-in mouse strains has been generated, with the aim of either more precisely modeling p53 mutations in human cancer or better understanding p53's regulation and downstream activities. In the first category, several mouse strains expressing mutant p53 proteins corresponding to human-tumor-derived mutants have demonstrated that mutant p53 is not equivalent to loss of p53 but additionally exhibits gain-of-function properties, promoting invasive and metastatic phenotypes. The second class of p53 knock-in mouse models expressing engineered p53 mutants has also provided new insight into p53 function. For example, mice expressing p53 mutants lacking specific posttranslational modification sites have revealed that these modifications serve to modulate p53 responses in vivo in a cell-type- and stress-specific manner rather than being absolutely required for p53 stabilization and activation as suggested by in vitro experiments. Additionally, studies of p53 mouse models have established that both p53-driven cell-cycle arrest and apoptosis responses contribute to tumor suppression and that activation of p53 by oncogenic stress imposes an important barrier to tumorigenesis. Finally, the use of mouse strains expressing temporally regulatable p53 has demonstrated that p53 loss is not only required for tumor development but also required for tumor maintenance, suggesting that p53 restoration in human cancer patients may be a promising therapeutic strategy. These sophisticated p53 mouse models have taught us important lessons, and new mouse models will certainly continue to reveal interesting and perhaps surprising aspects of p53's complex biology.
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