51
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Yu L, Jearawiriyapaisarn N, Lee MP, Hosoya T, Wu Q, Myers G, Lim KC, Kurita R, Nakamura Y, Vojtek AB, Rual JF, Engel JD. BAP1 regulation of the key adaptor protein NCoR1 is critical for γ-globin gene repression. Genes Dev 2018; 32:1537-1549. [PMID: 30463901 PMCID: PMC6295165 DOI: 10.1101/gad.318436.118] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/02/2018] [Indexed: 12/31/2022]
Abstract
Human globin gene production transcriptionally "switches" from fetal to adult synthesis shortly after birth and is controlled by macromolecular complexes that enhance or suppress transcription by cis elements scattered throughout the locus. The DRED (direct repeat erythroid-definitive) repressor is recruited to the ε-globin and γ-globin promoters by the orphan nuclear receptors TR2 (NR2C1) and TR4 (NR2C2) to engender their silencing in adult erythroid cells. Here we found that nuclear receptor corepressor-1 (NCoR1) is a critical component of DRED that acts as a scaffold to unite the DNA-binding and epigenetic enzyme components (e.g., DNA methyltransferase 1 [DNMT1] and lysine-specific demethylase 1 [LSD1]) that elicit DRED function. We also describe a potent new regulator of γ-globin repression: The deubiquitinase BRCA1-associated protein-1 (BAP1) is a component of the repressor complex whose activity maintains NCoR1 at sites in the β-globin locus, and BAP1 inhibition in erythroid cells massively induces γ-globin synthesis. These data provide new mechanistic insights through the discovery of novel epigenetic enzymes that mediate γ-globin gene repression.
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Affiliation(s)
- Lei Yu
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Natee Jearawiriyapaisarn
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Mary P Lee
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Tomonori Hosoya
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Qingqing Wu
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Greggory Myers
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Kim-Chew Lim
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Ryo Kurita
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Anne B Vojtek
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Jean-François Rual
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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52
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Chromatin modifiers Mdm2 and RNF2 prevent RNA:DNA hybrids that impair DNA replication. Proc Natl Acad Sci U S A 2018; 115:E11311-E11320. [PMID: 30413623 DOI: 10.1073/pnas.1809592115] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The p53-Mdm2 system is key to tumor suppression. We have recently reported that p53 as well as Mdm2 are capable of supporting DNA replication fork progression. On the other hand, we found that Mdm2 is a modifier of chromatin, modulating polycomb repressor complex (PRC)-driven histone modifications. Here we show that, similar to Mdm2 knockdown, the depletion of PRC members impairs DNA synthesis, as determined in fiber assays. In particular, the ubiquitin ligase and PRC1 component RNF2/Ring1B is required to support DNA replication, similar to Mdm2. Moreover, the Ring finger domain of Mdm2 is not only essential for its ubiquitin ligase activity, but also for proper DNA replication. Strikingly, Mdm2 overexpression can rescue RNF2 depletion with regard to DNA replication fork progression, and vice versa, strongly suggesting that the two ubiquitin ligases perform overlapping functions in this context. H2A overexpression also rescues fork progression upon depletion of Mdm2 or RNF2, but only when the ubiquitination sites K118/K119 are present. Depleting the H2A deubiquitinating enzyme BAP1 reduces the fork rate, suggesting that both ubiquitination and deubiquitination of H2A are required to support fork progression. The depletion of Mdm2 elicits the accumulation of RNA/DNA hybrids, suggesting R-loop formation as a mechanism of impaired DNA replication. Accordingly, RNase H overexpression or the inhibition of the transcription elongation kinase CDK9 each rescues DNA replication upon depletion of Mdm2 or RNF2. Taken together, our results suggest that chromatin modification by Mdm2 and PRC1 ensures smooth DNA replication through the avoidance of R-loop formation.
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53
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Daou S, Barbour H, Ahmed O, Masclef L, Baril C, Sen Nkwe N, Tchelougou D, Uriarte M, Bonneil E, Ceccarelli D, Mashtalir N, Tanji M, Masson JY, Thibault P, Sicheri F, Yang H, Carbone M, Therrien M, Affar EB. Monoubiquitination of ASXLs controls the deubiquitinase activity of the tumor suppressor BAP1. Nat Commun 2018; 9:4385. [PMID: 30349006 PMCID: PMC6197237 DOI: 10.1038/s41467-018-06854-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 09/19/2018] [Indexed: 12/21/2022] Open
Abstract
The tumor suppressor and deubiquitinase (DUB) BAP1 and its Drosophila ortholog Calypso assemble DUB complexes with the transcription regulators Additional sex combs-like (ASXL1, ASXL2, ASXL3) and Asx respectively. ASXLs and Asx use their DEUBiquitinase ADaptor (DEUBAD) domain to stimulate BAP1/Calypso DUB activity. Here we report that monoubiquitination of the DEUBAD is a general feature of ASXLs and Asx. BAP1 promotes DEUBAD monoubiquitination resulting in an increased stability of ASXL2, which in turn stimulates BAP1 DUB activity. ASXL2 monoubiquitination is directly catalyzed by UBE2E family of Ubiquitin-conjugating enzymes and regulates mammalian cell proliferation. Remarkably, Calypso also regulates Asx monoubiquitination and transgenic flies expressing monoubiquitination-defective Asx mutant exhibit developmental defects. Finally, the protein levels of ASXL2, BAP1 and UBE2E enzymes are highly correlated in mesothelioma tumors suggesting the importance of this signaling axis for tumor suppression. We propose that monoubiquitination orchestrates a molecular symbiosis relationship between ASXLs and BAP1.
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Affiliation(s)
- Salima Daou
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Haithem Barbour
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Oumaima Ahmed
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Louis Masclef
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Caroline Baril
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Nadine Sen Nkwe
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Daméhan Tchelougou
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Maxime Uriarte
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer, Laboratory of Proteomics and Bioanalytical Mass Spectrometry, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Derek Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Nazar Mashtalir
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Mika Tanji
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Jean-Yves Masson
- CHU de Quebec Research Center (Oncology Axis), Laval University Cancer Research Center, 9 McMahon, Quebec, PQ, G1R 2J6, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Laboratory of Proteomics and Bioanalytical Mass Spectrometry, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Haining Yang
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Michele Carbone
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, University of Montréal, Montréal, QC, H3T 1J4, Canada. .,Département de pathologie et biologie cellulaire, University of Montréal, Montréal, QC, H3C 3J7, Canada.
| | - El Bachir Affar
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada.
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54
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Patrone S, Maric I, Rutigliani M, Lanza F, Puntoni M, Banelli B, Rancati S, Angelini G, Amaro A, Ligorio P, Defferrari C, Castagnetta M, Bandelloni R, Mosci C, DeCensi A, Romani M, Pfeffer U, Viaggi S, Coviello DA. Prognostic value of chromosomal imbalances, gene mutations, and BAP1 expression in uveal melanoma. Genes Chromosomes Cancer 2018; 57:387-400. [PMID: 29689622 DOI: 10.1002/gcc.22541] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 12/27/2022] Open
Abstract
Uveal melanoma (UM) exhibits recurring chromosomal abnormalities and gene driver mutations, which are related to tumor evolution/progression. Almost half of the patients with UM develop distant metastases, predominantly to the liver, and so far there are no effective adjuvant therapies. An accurate UM genetic profile could assess the individual patient's metastatic risk, and provide the basis to determine an individualized targeted therapeutic strategy for each UM patient. To investigate the presence of specific chromosomal and gene alterations, BAP1 protein expression, and their relationship with distant progression free survival (DPFS), we analyzed tumor samples from 63 UM patients (40 men and 23 women, with a median age of 64 years), who underwent eye enucleation by a single cancer ophthalmologist from December 2005 to June 2016. UM samples were screened for the presence of losses/gains in chromosomes 1p, 3, 6p, and 8q, and for mutations in GNAQ, GNA11, BAP1, SF3B1, and EIF1AX. BAP1 protein expression was detected by immunohistochemistry (IHC). Multivariate analysis showed that the presence of monosomy 3, 8q gain, and loss of BAP1 protein were significantly associated to DPFS, while BAP1 gene mutation was not, mainly due to the presence of metastatic UM cases with negative BAP1 IHC and no BAP1 mutation detected by Sanger sequencing. Loss of BAP1 protein expression and monosomy 3 represent the strongest predictors of metastases, and may have important implications for implementation of patient surveillance, properly designed clinical trials enrollment, and adjuvant therapy.
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Affiliation(s)
- Serena Patrone
- Department of Internal Medicine (DIMI), University of Genoa, Genova, Italy
| | - Irena Maric
- Department of Earth Sciences, Environment, and Life (DISTAV), University of Genoa, Genova, Italy.,Department of Biotherapy, Ospedale Policlinico San Martino, Genova, Italy
| | | | - Francesco Lanza
- Department of Ocular Oncology Unit, E.O. Ospedali Galliera, Genova, Italy
| | - Matteo Puntoni
- Department of Clinical Trial Unit/Scientific Direction, E.O. Ospedali Galliera, Genova, Italy
| | - Barbara Banelli
- Department of Tumor Epigenetics Unit, Ospedale Policlinico San Martino, Genova, Italy.,Department of Health Sciences, University of Genoa, Genova, Italy
| | - Silvia Rancati
- Department of Earth Sciences, Environment, and Life (DISTAV), University of Genoa, Genova, Italy
| | - Giovanna Angelini
- Department of Molecular Pathology Unit, Ospedale Policlinico San Martino, Genova, Italy
| | - Adriana Amaro
- Department of Molecular Pathology Unit, Ospedale Policlinico San Martino, Genova, Italy
| | - Paolo Ligorio
- Department of Ocular Oncology Unit, E.O. Ospedali Galliera, Genova, Italy
| | | | - Mauro Castagnetta
- Department of Human Genetics Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | | | - Carlo Mosci
- Department of Ocular Oncology Unit, E.O. Ospedali Galliera, Genova, Italy
| | - Andrea DeCensi
- Department of Medical Oncology Unit, E.O. Ospedali Galliera, Genova, Italy
| | - Massimo Romani
- Department of Tumor Epigenetics Unit, Ospedale Policlinico San Martino, Genova, Italy
| | - Urlich Pfeffer
- Department of Molecular Pathology Unit, Ospedale Policlinico San Martino, Genova, Italy
| | - Silvia Viaggi
- Department of Earth Sciences, Environment, and Life (DISTAV), University of Genoa, Genova, Italy.,Department of Human Genetics Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Domenico A Coviello
- Department of Human Genetics Laboratory, E.O. Ospedali Galliera, Genova, Italy
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55
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Bellush JM, Whitehouse I. DNA replication through a chromatin environment. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0287. [PMID: 28847824 DOI: 10.1098/rstb.2016.0287] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2017] [Indexed: 01/03/2023] Open
Abstract
Compaction of the genome into the nuclear space is achieved by wrapping DNA around octameric assemblies of histone proteins to form nucleosomes, the fundamental repeating unit of chromatin. Aside from providing a means by which to fit larger genomes into the cell, chromatinization of DNA is a crucial means by which the cell regulates access to the genome. While the complex role that chromatin plays in gene transcription has been appreciated for a long time, it is now also apparent that crucial aspects of DNA replication are linked to the biology of chromatin. This review will focus on recent advances in our understanding of how the chromatin environment influences key aspects of DNA replication.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- James M Bellush
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.,BCMB Graduate Program, Weill Cornell Medical College, 1300 York Avenue, New York, NY, USA
| | - Iestyn Whitehouse
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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56
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Poli J, Gasser SM, Papamichos-Chronakis M. The INO80 remodeller in transcription, replication and repair. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0290. [PMID: 28847827 DOI: 10.1098/rstb.2016.0290] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2017] [Indexed: 02/06/2023] Open
Abstract
The accessibility of eukaryotic genomes to the action of enzymes involved in transcription, replication and repair is maintained despite the organization of DNA into nucleosomes. This access is often regulated by the action of ATP-dependent nucleosome remodellers. The INO80 class of nucleosome remodellers has unique structural features and it is implicated in a diverse array of functions, including transcriptional regulation, DNA replication and DNA repair. Underlying these diverse functions is the catalytic activity of the main ATPase subunit, which in the context of a multisubunit complex can shift nucleosomes and carry out histone dimer exchange. In vitro studies showed that INO80 promotes replication fork progression on a chromatin template, while in vivo it was shown to facilitate replication fork restart after stalling and to help evict RNA polymerase II at transcribed genes following the collision of a replication fork with transcription. More recent work in yeast implicates INO80 in the general eviction and degradation of nucleosomes following high doses of oxidative DNA damage. Beyond these replication and repair functions, INO80 was shown to repress inappropriate transcription at promoters in the opposite direction to the coding sequence. Here we discuss the ways in which INO80's diverse functions help maintain genome integrity.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,University of Montpellier and Centre de Recherche en Biologie Cellulaire (CRBM), UMR5237, CNRS, Montpellier 34095, Cedex 5, France
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland .,Faculty of Natural Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Manolis Papamichos-Chronakis
- Institute for Cell and Molecular Biosciences, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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57
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Hu J, Liu J, Chen A, Lyu J, Ai G, Zeng Q, Sun Y, Chen C, Wang J, Qiu J, Wu Y, Cheng J, Shi X, Song L. Ino80 promotes cervical cancer tumorigenesis by activating Nanog expression. Oncotarget 2018; 7:72250-72262. [PMID: 27750218 PMCID: PMC5342159 DOI: 10.18632/oncotarget.12667] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/10/2016] [Indexed: 02/03/2023] Open
Abstract
Ino80 ATPase is an integral component of the INO80 ATP-dependent chromatin-remodeling complex, which regulates transcription, DNA repair and replication. We found that Ino80 was highly expressed in cervical cancer cell lines and tumor samples. Ino80 knockdown inhibited cervical cancer cell proliferation, induced G0/G1 phase cell cycle arrest in vitro and suppressed tumor growth in vivo. However, Ino80 knockdown did not affect cell apoptosis, migration or invasion in vitro. Ino80 overexpression promoted proliferation in the H8 immortalized cervical epithelial cell line, which has low endogenous Ino80 expression as compared to cervical cancer cell lines. Ino80 bound to the Nanog transcription start site (TSS) and enhanced its expression in cervical cancer cells. Nanog overexpression in Ino80 knockdown cell lines promoted cell proliferation. This study demonstrated for the first time that Ino80 was upregulated in cervical cancer and promoted cell proliferation and tumorigenesis. Our findings suggest that Ino80 may be a potential therapeutic target for the treatment of cervical cancer.
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Affiliation(s)
- Jing Hu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jie Liu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Aozheng Chen
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jia Lyu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Guihai Ai
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiongjing Zeng
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Sun
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunxia Chen
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinbo Wang
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jin Qiu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Wu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiajing Cheng
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.,The First Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiujuan Shi
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liwen Song
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
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58
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Wang Z, Wang XY, Li J, Zhu WW. Prognostic and Clinicopathological Significance of BAP1 Protein Expression in Different Types of Cancer—A Meta-Analysis. Genet Test Mol Biomarkers 2018; 22:115-126. [PMID: 29266978 DOI: 10.1089/gtmb.2017.0176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Zheng Wang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institutes of Cancer Metastasis, Fudan University, Shanghai, China
| | - Xiang-Yu Wang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institutes of Cancer Metastasis, Fudan University, Shanghai, China
| | - Juan Li
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institutes of Cancer Metastasis, Fudan University, Shanghai, China
| | - Wen-Wei Zhu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institutes of Cancer Metastasis, Fudan University, Shanghai, China
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59
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Miller A, Hendrich B. Chromatin Remodelling Proteins and Cell Fate Decisions in Mammalian Preimplantation Development. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2018; 229:3-14. [PMID: 29177761 DOI: 10.1007/978-3-319-63187-5_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The very first cell divisions in mammalian embryogenesis produce a ball of cells, each with the potential to form any cell in the developing embryo or placenta. At some point, the embryo produces enough cells that some are located on the outside of the embryo, while others are completely surrounded by other cells. It is at this point that cells undergo the very first lineage commitment event: outer cells form the trophectoderm and lose the potential to form embryonic lineages, while inner cells form the Inner Cell Mass, which retain embryonic potential. Cell identity is defined by gene expression patterns, and gene expression is largely controlled by how the DNA is packaged into chromatin. A number of protein complexes exist which are able to use the energy of ATP to remodel chromatin: that is, to alter the nucleosome topology of chromatin. Here, we summarise the evidence that chromatin remodellers play essential roles in the successful completion of preimplantation development in mammals and describe recent efforts to understand the molecular mechanisms through which chromatin remodellers facilitate the successful completion of the first cell fate decisions in mammalian embryogenesis.
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Affiliation(s)
- Anzy Miller
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Brian Hendrich
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK. .,Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
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60
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Lee SA, Lee HS, Hur SK, Kang SW, Oh GT, Lee D, Kwon J. INO80 haploinsufficiency inhibits colon cancer tumorigenesis via replication stress-induced apoptosis. Oncotarget 2017; 8:115041-115053. [PMID: 29383140 PMCID: PMC5777752 DOI: 10.18632/oncotarget.22984] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/17/2017] [Indexed: 12/20/2022] Open
Abstract
The INO80 chromatin-remodeling complex performs functions in many chromosomal processes that are crucial for genome stability, such as DNA replication and stalled replication fork recovery. Although these functions suggest that INO80 acts as a tumor suppressor, its specific role in tumorigenesis has remained obscure. Here, we show that a haploinsufficient mutation of Ino80, the catalytic ATPase of the INO80 complex, decreased intestinal adenomatous polyps and increased survival in an Apcmin/+ mouse model of colon cancer. Experiments using tumors obtained from Apcmin/+ mice and cells from human colon cancers showed that this Ino80 defect induced stalled replication forks, the concomitant activation of ATR-Chk1 signaling and an increase in apoptosis, suggesting that Ino80 haploinsufficiency inhibited colon cancer tumorigenesis by activating replication stress-induced ATR-Chk1 signaling to increase apoptosis. Importantly, in human colon cancer, we observed that the INO80 subunits were frequently present in high copy numbers and exhibited a high rate of amplification and increased protein expression. These results show that in contrast to our original prediction that INO80 acts as a tumor suppressor, INO80 actually functions oncogenically to promote colon tumorigenesis. INO80 therefore represents a novel therapeutic target in colon cancer. The results of this study also reinforce the emerging notion that while genomic instability can promote tumorigenesis, in certain genetic contexts, it can also act as a tumor suppressor.
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Affiliation(s)
- Shin-Ai Lee
- Department of Life Science, Ewha Womans University, Seodaemun-gu, Seoul, 03760, Korea
- The Research Center for Cellular Homeostasis, Ewha Womans University, Seodaemun-gu, Seoul, 03760, Korea
| | - Han-Sae Lee
- Department of Life Science, Ewha Womans University, Seodaemun-gu, Seoul, 03760, Korea
- The Research Center for Cellular Homeostasis, Ewha Womans University, Seodaemun-gu, Seoul, 03760, Korea
| | - Shin-Kyoung Hur
- Department of Life Science, Ewha Womans University, Seodaemun-gu, Seoul, 03760, Korea
| | - Sang Won Kang
- Department of Life Science, Ewha Womans University, Seodaemun-gu, Seoul, 03760, Korea
- The Research Center for Cellular Homeostasis, Ewha Womans University, Seodaemun-gu, Seoul, 03760, Korea
| | - Goo Taeg Oh
- Department of Life Science, Ewha Womans University, Seodaemun-gu, Seoul, 03760, Korea
| | - Daekee Lee
- Department of Life Science, Ewha Womans University, Seodaemun-gu, Seoul, 03760, Korea
| | - Jongbum Kwon
- Department of Life Science, Ewha Womans University, Seodaemun-gu, Seoul, 03760, Korea
- The Research Center for Cellular Homeostasis, Ewha Womans University, Seodaemun-gu, Seoul, 03760, Korea
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61
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Ge J, Hu W, Zhou H, Yu J, Sun C, Chen W. Ubiquitin carboxyl-terminal hydrolase isozyme L5 inhibits human glioma cell migration and invasion via downregulating SNRPF. Oncotarget 2017; 8:113635-113649. [PMID: 29371935 PMCID: PMC5768352 DOI: 10.18632/oncotarget.23071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/14/2017] [Indexed: 12/14/2022] Open
Abstract
Ubiquitin C-terminal Hydrolase-L5 (UCH-L5/UCH37), a member of the deubiquitinases (DUBs), suppresses protein degeneration via removing ubiquitin from the distal subunit of the polyubiquitin chain. The activity of UCH-L5 is enhanced when UCH-L5 combines with proteasome 19S regulatory subunit by Rpn13/Admr1 receptor and inhibited when UCH-L5 interacts with NFRKB. But the role of UCH-L5 in gliomas remains unknown. In this study, analysis of 19 frozen and 51 paraffin-embedded clinic pathological cases showed that UCH-L5 expression in glioma tissues was lower than normal brain tissues. In vitro, we found that UCH-L5 could inhibit migration and invasion of U87MG and U251 cells. It has been reported that the expression of SNRPN, SNRPF, and CKLF was abnormal in gliomas or other tumors. We also found that SNRPF-siRNA, SNRPN-siRNA and CKLF-siRNA could inhibit migration and invasion of U87MG cells. And knockdown of UCH-L5 expression improved both mRNA expression and protein level of SNRPF. The relationship between UCH-L5 and SNRPF was further confirmed in 293T cells. Our study showed that UCH-L5 could inhibit migration and invasion of glioma cells via down regulating expression of SNRPF. And the above findings suggest that UCH-L5 may inhibit occurrence and metastasis of gliomas.
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Affiliation(s)
- Jiafeng Ge
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Weiwei Hu
- Department of Neurosurgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Hui Zhou
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Juan Yu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Chongran Sun
- Department of Neurosurgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Weilin Chen
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China.,Department of Immunology, Shenzhen University School of Medicine, Shenzhen 518060, China
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62
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Carbone M, Kanodia S, Chao A, Miller A, Wali A, Weissman D, Adjei A, Baumann F, Boffetta P, Buck B, de Perrot M, Dogan AU, Gavett S, Gualtieri A, Hassan R, Hesdorffer M, Hirsch FR, Larson D, Mao W, Masten S, Pass HI, Peto J, Pira E, Steele I, Tsao A, Woodard GA, Yang H, Malik S. Consensus Report of the 2015 Weinman International Conference on Mesothelioma. J Thorac Oncol 2017; 11:1246-1262. [PMID: 27453164 PMCID: PMC5551435 DOI: 10.1016/j.jtho.2016.04.028] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/31/2016] [Accepted: 04/26/2016] [Indexed: 01/31/2023]
Abstract
On November 9 and 10, 2015, the International Conference on Mesothelioma in Populations Exposed to Naturally Occurring Asbestiform Fibers was held at the University of Hawaii Cancer Center in Honolulu, Hawaii. The meeting was cosponsored by the International Association for the Study of Lung Cancer, and the agenda was designed with significant input from staff at the U.S. National Cancer Institute and National Institute of Environmental Health Sciences. A multidisciplinary group of participants presented updates reflecting a range of disciplinary perspectives, including mineralogy, geology, epidemiology, toxicology, biochemistry, molecular biology, genetics, public health, and clinical oncology. The group identified knowledge gaps that are barriers to preventing and treating malignant mesothelioma (MM) and the required next steps to address barriers. This manuscript reports the group’s efforts and focus on strategies to limit risk to the population and reduce the incidence of MM. Four main topics were explored: genetic risk, environmental exposure, biomarkers, and clinical interventions. Genetics plays a critical role in MM when the disease occurs in carriers of germline BRCA1 associated protein 1 mutations. Moreover, it appears likely that, in addition to BRCA1 associated protein 1, other yet unknown genetic variants may also influence the individual risk for development of MM, especially after exposure to asbestos and related mineral fibers. MM is an almost entirely preventable malignancy as it is most often caused by exposure to commercial asbestos or mineral fibers with asbestos-like health effects, such as erionite. In the past in North America and in Europe, the most prominent source of exposure was related to occupation. Present regulations have reduced occupational exposure in these countries; however, some people continue to be exposed to previously installed asbestos in older construction and other settings. Moreover, an increasing number of people are being exposed in rural areas that contain noncommercial asbestos, erionite, and other mineral fibers in soil or rock (termed naturally occurring asbestos [NOA]) and are being developed. Public health authorities, scientists, residents, and other affected groups must work together in the areas where exposure to asbestos, including NOA, has been documented in the environment to mitigate or reduce this exposure. Although a blood biomarker validated to be effective for use in screening and identifying MM at an early stage in asbestos/ NOA-exposed populations is not currently available, novel biomarkers presented at the meeting, such as high mobility group box 1 and fibulin-3, are promising. There was general agreement that current treatment for MM, which is based on surgery and standard chemotherapy, has a modest effect on the overall survival (OS), which remains dismal. Additionally, although much needed novel therapeutic approaches for MM are being developed and explored in clinical trials, there is a critical need to invest in prevention research, in which there is a great opportunity to reduce the incidence and mortality from MM.
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Affiliation(s)
- Michele Carbone
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, Hawaii.
| | - Shreya Kanodia
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, Hawaii; Samuel Oschin Comprehensive Cancer Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Ann Chao
- Center for Global Health, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Aubrey Miller
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Anil Wali
- Center to Reduce Cancer Health Disparities, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - David Weissman
- Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia
| | | | | | - Paolo Boffetta
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brenda Buck
- Department of Geoscience, University of Nevada Las Vegas, Las Vegas, Nevada
| | - Marc de Perrot
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - A Umran Dogan
- Chemical and Biochemical Engineering Department and Center for Global and Regional Environmental Research, University of Iowa, Iowa City, Iowa
| | - Steve Gavett
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
| | | | - Raffit Hassan
- Thoracic Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland
| | - Mary Hesdorffer
- Mesothelioma Applied Research Foundation, Alexandria, Virginia
| | - Fred R Hirsch
- University of Colorado Cancer Center, Denver, Colorado
| | - David Larson
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Weimin Mao
- Cancer Research Institute, Zhejiang Cancer Hospital and Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology of Zhejiang, Hangzhou, People's Republic of China
| | - Scott Masten
- National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Harvey I Pass
- Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York
| | - Julian Peto
- Cancer Research UK, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Enrico Pira
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| | - Ian Steele
- Notre Dame Integrated Imaging Facility, Notre Dame University, Notre Dame, Indiana
| | - Anne Tsao
- Department of Thoracic and Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Gavitt Alida Woodard
- Thoracic Surgery, University of California at San Francisco, San Francisco, California
| | - Haining Yang
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Shakun Malik
- Cancer Therapy Evaluation Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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63
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Nishi R. Balancing act: To be, or not to be ubiquitylated. Mutat Res 2017; 803-805:43-50. [PMID: 28764946 DOI: 10.1016/j.mrfmmm.2017.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/30/2017] [Accepted: 07/17/2017] [Indexed: 01/13/2023]
Abstract
DNA double-strand breaks (DSBs) are one of the most deleterious DNA lesions. Appropriate repair of DSB either by homologous recombination or non-homologous end-joining is critical for maintaining genome stability and fitness. DSB repair cooperates with cellular signalling networks, namely DSB response (DDR), which plays pivotal roles in the choice of DSB repair pathway, orchestrating recruitment of DDR factors to site of damage, transcription suppression and cell cycle checkpoint activation. It has been revealed that these mechanisms are strictly regulated, in time and space, by complex and minute ubiquitylation-mediated reactions. Furthermore, balancing the ubiquitylation status of the DDR and DSB repair proteins by deubiquitylation, which is carried out by deubiquitylating enzymes (DUBs), is also found to be important. Recent findings have uncovered that DUBs are involved in various aspects of both DDR and DSB repair by counteracting non-proteolytic ubiquitylations in addition to protecting substrates from proteasomal degradation by removing proteolytic ubiquitylation. An advanced understanding of the detailed molecular mechanisms of the "balancing act" between ubiquitylation and deubiquitylation will provide novel therapeutic targets for diseases caused by dysfunction of DDR and DSB repair.
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Affiliation(s)
- Ryotaro Nishi
- Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Shiga, 525-8577, Japan.
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64
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Pardo M, Yu L, Shen S, Tate P, Bode D, Letney BL, Quelle DE, Skarnes W, Choudhary JS. Myst2/Kat7 histone acetyltransferase interaction proteomics reveals tumour-suppressor Niam as a novel binding partner in embryonic stem cells. Sci Rep 2017; 7:8157. [PMID: 28811661 PMCID: PMC5557939 DOI: 10.1038/s41598-017-08456-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/10/2017] [Indexed: 12/28/2022] Open
Abstract
MYST histone acetyltransferases have crucial functions in transcription, replication and DNA repair and are hence implicated in development and cancer. Here we characterise Myst2/Kat7/Hbo1 protein interactions in mouse embryonic stem cells by affinity purification coupled to mass spectrometry. This study confirms that in embryonic stem cells Myst2 is part of H3 and H4 histone acetylation complexes similar to those described in somatic cells. We identify a novel Myst2-associated protein, the tumour suppressor protein Niam (Nuclear Interactor of ARF and Mdm2). Human NIAM is involved in chromosome segregation, p53 regulation and cell proliferation in somatic cells, but its role in embryonic stem cells is unknown. We describe the first Niam embryonic stem cell interactome, which includes proteins with roles in DNA replication and repair, transcription, splicing and ribosome biogenesis. Many of Myst2 and Niam binding partners are required for correct embryonic development, implicating Myst2 and Niam in the cooperative regulation of this process and suggesting a novel role for Niam in embryonic biology. The data provides a useful resource for exploring Myst2 and Niam essential cellular functions and should contribute to deeper understanding of organism early development and survival as well as cancer. Data are available via ProteomeXchange with identifier PXD005987.
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Affiliation(s)
- Mercedes Pardo
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom.
| | - Lu Yu
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Shihpei Shen
- Stem Cell Engineering, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Cold Genesys Inc., Santa Ana, CA, USA
| | - Peri Tate
- Stem Cell Engineering, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Daniel Bode
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Wellcome Trust PhD Program, Cambridge Stem Cell Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Blake L Letney
- Departments of Pharmacology and Pathology, The University of Iowa and Holden Comprehensive Cancer Center, Iowa City, IA, 52242, USA
| | - Dawn E Quelle
- Departments of Pharmacology and Pathology, The University of Iowa and Holden Comprehensive Cancer Center, Iowa City, IA, 52242, USA
| | - William Skarnes
- Stem Cell Engineering, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Jyoti S Choudhary
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
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65
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Moon S, Lee YK, Lee SW, Um SJ. Suppressive role of OGT-mediated O-GlcNAcylation of BAP1 in retinoic acid signaling. Biochem Biophys Res Commun 2017; 492:89-95. [PMID: 28802580 DOI: 10.1016/j.bbrc.2017.08.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
Abstract
BRCA1-associated protein 1 (BAP1) has been implicated in diverse biological functions, including tumor suppression. However, its regulation via glycosylation and its role in embryonic stem (ES) cells are poorly defined. BAP1 was recently reported to interact with O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT). Here, we confirmed the physical interaction and investigated its functional significance. The O-GlcNAcylation of BAP1, which requires OGT, was examined in vivo and in vitro, and was proven using alloxan, an OGT inhibitor. OGT promoted the BAP1-induced repression of retinoic acid (RA)-induced RA receptor (RAR) activation. The repressive activity of BAP1 was relieved by alloxan but exacerbated by PUGNAc, an O-GlcNAcase (OGA) inhibitor. Finally, we addressed the role of O-GlcNAcylation in the RA-induced differentiation of murine ES cells. Alkaline phosphatase staining revealed the cooperation of RA and alloxan for impairing the pluripotency of ES cells. This cooperation was also observed by measuring the size of embryonic bodies and the expression of Sox2, a pluripotency marker. Overall, our data suggest that OGT-mediated O-GlcNAcylation of BAP1 prefers the maintenance of pluripotency, whereas its inhibition facilitates RA-induced differentiation in ES cells.
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Affiliation(s)
- Seungtae Moon
- Department of Integrative Bioscience & Biotechnology/Institute of Bioscience, BK21 Graduate Program, Sejong University, Seoul 05006, South Korea
| | - Yong-Kyu Lee
- Department of Integrative Bioscience & Biotechnology/Institute of Bioscience, BK21 Graduate Program, Sejong University, Seoul 05006, South Korea
| | - Sang-Wang Lee
- Department of Integrative Bioscience & Biotechnology/Institute of Bioscience, BK21 Graduate Program, Sejong University, Seoul 05006, South Korea
| | - Soo-Jong Um
- Department of Integrative Bioscience & Biotechnology/Institute of Bioscience, BK21 Graduate Program, Sejong University, Seoul 05006, South Korea.
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66
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Molecular architecture of polycomb repressive complexes. Biochem Soc Trans 2017; 45:193-205. [PMID: 28202673 PMCID: PMC5310723 DOI: 10.1042/bst20160173] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/24/2016] [Accepted: 12/02/2016] [Indexed: 01/05/2023]
Abstract
The polycomb group (PcG) proteins are a large and diverse family that epigenetically repress the transcription of key developmental genes. They form three broad groups of polycomb repressive complexes (PRCs) known as PRC1, PRC2 and Polycomb Repressive DeUBiquitinase, each of which modifies and/or remodels chromatin by distinct mechanisms that are tuned by having variable compositions of core and accessory subunits. Until recently, relatively little was known about how the various PcG proteins assemble to form the PRCs; however, studies by several groups have now allowed us to start piecing together the PcG puzzle. Here, we discuss some highlights of recent PcG structures and the insights they have given us into how these complexes regulate transcription through chromatin.
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67
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Wang XY, Wang Z, Huang JB, Ren XD, Ye D, Zhu WW, Qin LX. Tissue-specific significance of BAP1 gene mutation in prognostic prediction and molecular taxonomy among different types of cancer. Tumour Biol 2017; 39:1010428317699111. [PMID: 28618948 DOI: 10.1177/1010428317699111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BAP1 is an emerging tumor suppressor whose inactivating mutations have been found to play critical roles in tumor development. This study was conducted to elucidate the potential value of BAP1 mutation in guiding prognostic prediction and clinical stratification. We conducted a comprehensive analysis of relevant studies from multiple databases, to determine the impact of BAP1 mutation on the overall survival and disease-free survival of patients in various cancers. A total of 2457 patients from 21 studies were included in the final analysis. Although the pooled results demonstrated that BAP1 mutation was a negative indicator of overall survival (hazard ratio = 1.73; 95% confidence interval = 1.23-2.42) and disease-free survival (hazard ratio = 2.25; 95% confidence interval = 1.47-3.45), this prognostic value was only applicable to uveal melanoma and clear cell renal cell carcinoma, but not to malignant pleural mesothelioma or cholangiocarcinoma. Consistently, BAP1 mutation was correlated with critical clinicopathological features only in uveal melanoma and clear cell renal cell carcinoma. In uveal melanoma, BAP1 mutation and SF3B1/EIF1AX mutations were negatively correlated, and BAP1-mutant tumors indicated significant worse prognosis than SF3B1/EIF1AX-mutant tumors ( p = 0.028). While in clear cell renal cell carcinoma, BAP1 mutation was mutually exclusive with PBRM1 mutations, and BAP1-mutant clear cell renal cell carcinomas also showed significantly worse prognosis than PBRM1-mutant clear cell renal cell carcinomas ( p = 0.001). Our study revealed a unique tissue-specific significance of BAP1 mutation in prognostic prediction among different types of cancer. Clinically, combining detection of BAP1 mutation and other driver mutations may further allow for a more precise molecular taxonomy to stratify patients into distinct subgroups in uveal melanoma and clear cell renal cell carcinoma.
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Affiliation(s)
- Xiang-Yu Wang
- 1 Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Zheng Wang
- 1 Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Jian-Bo Huang
- 1 Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Xu-Dong Ren
- 1 Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Dan Ye
- 1 Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China.,2 Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wen-Wei Zhu
- 1 Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Lun-Xiu Qin
- 1 Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
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68
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Bononi A, Yang H, Giorgi C, Patergnani S, Pellegrini L, Su M, Xie G, Signorato V, Pastorino S, Morris P, Sakamoto G, Kuchay S, Gaudino G, Pass HI, Napolitano A, Pinton P, Jia W, Carbone M. Germline BAP1 mutations induce a Warburg effect. Cell Death Differ 2017; 24:1694-1704. [PMID: 28665402 PMCID: PMC5596430 DOI: 10.1038/cdd.2017.95] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/09/2017] [Accepted: 02/24/2017] [Indexed: 12/26/2022] Open
Abstract
Carriers of heterozygous germline BAP1 mutations (BAP1+/−) develop cancer. We studied plasma from 16 BAP1+/− individuals from 2 families carrying different germline BAP1 mutations and 30 BAP1 wild-type (BAP1WT) controls from these same families. Plasma samples were analyzed by liquid chromatography time-of-flight mass spectrometry (LC-TOF-MS), ultra-performance liquid chromatography triple quadrupole mass spectrometry (UPLC-TQ-MS), and gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). We found a clear separation in the metabolic profile between BAP1WT and BAP1+/− individuals. We confirmed the specificity of the data in vitro using 12 cell cultures of primary fibroblasts we derived from skin punch biopsies from 12/46 of these same individuals, 6 BAP1+/− carriers and 6 controls from both families. BAP1+/− fibroblasts displayed increased aerobic glycolysis and lactate secretion, and reduced mitochondrial respiration and ATP production compared with BAP1WT. siRNA-mediated downregulation of BAP1 in primary BAP1WT fibroblasts and in primary human mesothelial cells, led to the same reduced mitochondrial respiration and increased aerobic glycolysis as we detected in primary fibroblasts from carriers of BAP1+/− mutations. The plasma and cell culture results were highly reproducible and were specifically and only linked to BAP1 status and not to gender, age or family, or cell type, and required an intact BAP1 catalytic activity. Accordingly, we were able to build a metabolomic model capable of predicting BAP1 status with 100% accuracy using data from human plasma. Our data provide the first experimental evidence supporting the hypothesis that aerobic glycolysis, also known as the ‘Warburg effect’, does not necessarily occur as an adaptive process that is consequence of carcinogenesis, but rather that it may also predate malignancy by many years and facilitate carcinogenesis.
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Affiliation(s)
- Angela Bononi
- Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Haining Yang
- Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Carlotta Giorgi
- Department of Morphology-Surgery-Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Simone Patergnani
- Department of Morphology-Surgery-Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Laura Pellegrini
- Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Mingming Su
- Metabolomics Unit, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Guoxiang Xie
- Metabolomics Unit, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Valentina Signorato
- Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA.,Department of Morphology-Surgery-Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Sandra Pastorino
- Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Paul Morris
- Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Greg Sakamoto
- Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Shafi Kuchay
- Cancer Center, New York University, New York, NY 10016, USA
| | - Giovanni Gaudino
- Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Harvey I Pass
- Cancer Center, New York University, New York, NY 10016, USA
| | - Andrea Napolitano
- Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Paolo Pinton
- Department of Morphology-Surgery-Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Wei Jia
- Metabolomics Unit, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Michele Carbone
- Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
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69
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BAP1 regulates IP3R3-mediated Ca 2+ flux to mitochondria suppressing cell transformation. Nature 2017; 546:549-553. [PMID: 28614305 PMCID: PMC5581194 DOI: 10.1038/nature22798] [Citation(s) in RCA: 282] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 04/28/2017] [Indexed: 12/18/2022]
Abstract
BRCA1-associated protein 1 (BAP1) is a potent tumor suppressor gene that modulates environmental carcinogenesis1-3. All carriers of inherited heterozygous germline BAP1 inactivating mutations (BAP1+/-) developed one and often several BAP1-/- malignancies in their lifetime4, mostly malignant mesothelioma (MM), uveal melanoma (UVM)2,5, etc6-10. Moreover, BAP1 acquired biallelic mutations are frequent in human cancers8,11-14. BAP1 tumor suppressor activity has been attributed to its nuclear localization where BAP1 helps maintaining genome integrity15-17. The possible activity of BAP1 in the cytoplasm was unknown. Cells with reduced levels of BAP1 exhibit chromosomal abnormalities and decreased DNA repair by homologous recombination18, indicating that BAP1 dosage is critical. Cells with extensive DNA damage should die and not grow into malignancies. We discovered that BAP1 localizes at the endoplasmic reticulum (ER). Here BAP1 binds, deubiquitylates and stabilizes type-3 inositol-1,4,5-trisphosphate-receptor (IP3R3), modulating calcium (Ca2+) release from the ER into the cytosol and mitochondria, promoting apoptosis. Reduced levels of BAP1 in BAP1+/- carriers caused reduction of both IP3R3 levels and Ca2+ flux, preventing BAP1+/- cells that had accumulated DNA damage from executing apoptosis. A higher fraction of cells exposed to either ionizing or ultraviolet radiation, or to asbestos, survived genotoxic stress resulting in a higher rate of cellular transformation. We propose that the high incidence of cancers in BAP1+/- carriers results from the combined reduced nuclear and cytoplasmic BAP1 activities. Our data provide a mechanistic rationale for the powerful ability of BAP1 to regulate gene-environment interaction.
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70
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Rees DM, Willhoft O, Lin CL, Bythell-Douglas R, Wigley DB. Production and Assay of Recombinant Multisubunit Chromatin Remodeling Complexes. Methods Enzymol 2017; 592:27-47. [PMID: 28668124 DOI: 10.1016/bs.mie.2017.03.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
We have developed a novel system to facilitate the rapid and easy cloning of multiple genes (>10) in under a week. Using this system we have been able to successfully clone, overexpress, and purify a number of large multimeric proteins from insect cells, including the chromatin remodeling complexes SWR1 and INO80. Using Förster resonance energy transfer (FRET)-based assays we have demonstrated that our overexpressed enzymes have activities comparable to those purified from sources where the proteins are expressed under their endogenous promoters.
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Affiliation(s)
- David M Rees
- Section of Structural Biology, Imperial College London, London, United Kingdom
| | - Oliver Willhoft
- Section of Structural Biology, Imperial College London, London, United Kingdom
| | - Chia-Liang Lin
- Section of Structural Biology, Imperial College London, London, United Kingdom
| | | | - Dale B Wigley
- Section of Structural Biology, Imperial College London, London, United Kingdom.
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71
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Prado F, Maya D. Regulation of Replication Fork Advance and Stability by Nucleosome Assembly. Genes (Basel) 2017; 8:genes8020049. [PMID: 28125036 PMCID: PMC5333038 DOI: 10.3390/genes8020049] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/04/2017] [Accepted: 01/16/2017] [Indexed: 12/13/2022] Open
Abstract
The advance of replication forks to duplicate chromosomes in dividing cells requires the disassembly of nucleosomes ahead of the fork and the rapid assembly of parental and de novo histones at the newly synthesized strands behind the fork. Replication-coupled chromatin assembly provides a unique opportunity to regulate fork advance and stability. Through post-translational histone modifications and tightly regulated physical and genetic interactions between chromatin assembly factors and replisome components, chromatin assembly: (1) controls the rate of DNA synthesis and adjusts it to histone availability; (2) provides a mechanism to protect the integrity of the advancing fork; and (3) regulates the mechanisms of DNA damage tolerance in response to replication-blocking lesions. Uncoupling DNA synthesis from nucleosome assembly has deleterious effects on genome integrity and cell cycle progression and is linked to genetic diseases, cancer, and aging.
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Affiliation(s)
- Felix Prado
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), Spanish National Research Council (CSIC), Seville 41092, Spain.
| | - Douglas Maya
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), Spanish National Research Council (CSIC), Seville 41092, Spain.
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72
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Kurat CF, Yeeles JTP, Patel H, Early A, Diffley JFX. Chromatin Controls DNA Replication Origin Selection, Lagging-Strand Synthesis, and Replication Fork Rates. Mol Cell 2017; 65:117-130. [PMID: 27989438 PMCID: PMC5222724 DOI: 10.1016/j.molcel.2016.11.016] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/17/2016] [Accepted: 11/07/2016] [Indexed: 11/16/2022]
Abstract
The integrity of eukaryotic genomes requires rapid and regulated chromatin replication. How this is accomplished is still poorly understood. Using purified yeast replication proteins and fully chromatinized templates, we have reconstituted this process in vitro. We show that chromatin enforces DNA replication origin specificity by preventing non-specific MCM helicase loading. Helicase activation occurs efficiently in the context of chromatin, but subsequent replisome progression requires the histone chaperone FACT (facilitates chromatin transcription). The FACT-associated Nhp6 protein, the nucleosome remodelers INO80 or ISW1A, and the lysine acetyltransferases Gcn5 and Esa1 each contribute separately to maximum DNA synthesis rates. Chromatin promotes the regular priming of lagging-strand DNA synthesis by facilitating DNA polymerase α function at replication forks. Finally, nucleosomes disrupted during replication are efficiently re-assembled into regular arrays on nascent DNA. Our work defines the minimum requirements for chromatin replication in vitro and shows how multiple chromatin factors might modulate replication fork rates in vivo.
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Affiliation(s)
- Christoph F Kurat
- Clare Hall Laboratory, Francis Crick Institute, South Mimms, Hertfordshire EN6 3LD, UK
| | - Joseph T P Yeeles
- Clare Hall Laboratory, Francis Crick Institute, South Mimms, Hertfordshire EN6 3LD, UK
| | - Harshil Patel
- Lincoln's Inn Fields Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Anne Early
- Clare Hall Laboratory, Francis Crick Institute, South Mimms, Hertfordshire EN6 3LD, UK
| | - John F X Diffley
- Clare Hall Laboratory, Francis Crick Institute, South Mimms, Hertfordshire EN6 3LD, UK.
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73
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Alabert C, Jasencakova Z, Groth A. Chromatin Replication and Histone Dynamics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:311-333. [PMID: 29357065 DOI: 10.1007/978-981-10-6955-0_15] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Inheritance of the DNA sequence and its proper organization into chromatin is fundamental for genome stability and function. Therefore, how specific chromatin structures are restored on newly synthesized DNA and transmitted through cell division remains a central question to understand cell fate choices and self-renewal. Propagation of genetic information and chromatin-based information in cycling cells entails genome-wide disruption and restoration of chromatin, coupled with faithful replication of DNA. In this chapter, we describe how cells duplicate the genome while maintaining its proper organization into chromatin. We reveal how specialized replication-coupled mechanisms rapidly assemble newly synthesized DNA into nucleosomes, while the complete restoration of chromatin organization including histone marks is a continuous process taking place throughout the cell cycle. Because failure to reassemble nucleosomes at replication forks blocks DNA replication progression in higher eukaryotes and leads to genomic instability, we further underline the importance of the mechanistic link between DNA replication and chromatin duplication.
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Affiliation(s)
- Constance Alabert
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Zuzana Jasencakova
- Biotech Research and Innovation Centre (BRIC), Health and Medical Faculty, University of Copenhagen, Copenhagen, Denmark
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), Health and Medical Faculty, University of Copenhagen, Copenhagen, Denmark.
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74
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Improving the Accuracy of Mesothelioma Diagnosis in China. J Thorac Oncol 2016; 12:714-723. [PMID: 28007630 DOI: 10.1016/j.jtho.2016.12.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 12/12/2022]
Abstract
INTRODUCTION In the Western world, malignant mesothelioma (MM) is most prevalent in the pleura of older males who have been professionally exposed to asbestos. Information about MM from rapidly industrializing countries such as China is minimal. There is concern that a proportion of MM diagnoses in China may be incorrect because most Chinese physicians do not have experience diagnosing this rare cancer. We recently reported an unusually high incidence of peritoneal MM among eastern Chinese female patients. Here, we review the accuracy of MM diagnoses in China and provide suggestions to improve the accuracy of diagnosis. METHODS We reviewed 92 pathological diagnosis of MM in 2002-2015 from two reference centers in the province of Zhejiang in eastern China. We performed a large set of immunohistochemistry analyses to increase the reliability of the diagnosis. RESULTS We confirmed the MM diagnosis in 12 of 34 of the pleural tumors (35.3%), in 38 of 56 of the peritoneal tumors (67.9%), and in two of two of the MMs of the tunica vaginalis (100%). MMs were characterized by tumor cells showing nuclear Wilms tumor 1 and calretinin staining and by strong membranous staining for cytokeratin CAM5.2. The results of staining for the epithelial markers carcinoembryonic antigen, thyroid transcription factor-1, MOC31, BerEP4, p63, p40, paired box 8, ER and PR were negative. BRCA1 associated protein 1 nuclear staining was lost in percentages similar to what has been reported for samples from Western countries. CONCLUSIONS Our findings suggest that MM-especially in its pleural localization-is often misdiagnosed in eastern China. Identifying pitfalls and possible solutions in the pathological diagnosis of MM will affect both the standard of care and research in China.
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75
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Festuccia N, Gonzalez I, Navarro P. The Epigenetic Paradox of Pluripotent ES Cells. J Mol Biol 2016; 429:1476-1503. [PMID: 27988225 DOI: 10.1016/j.jmb.2016.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 12/15/2022]
Abstract
The propagation and maintenance of gene expression programs are at the foundation of the preservation of cell identity. A large and complex set of epigenetic mechanisms enables the long-term stability and inheritance of transcription states. A key property of authentic epigenetic regulation is being independent from the instructive signals used for its establishment. This makes epigenetic regulation, particularly epigenetic silencing, extremely robust and powerful to lock regulatory states and stabilise cell identity. In line with this, the establishment of epigenetic silencing during development restricts cell potency and maintains the cell fate choices made by transcription factors (TFs). However, how more immature cells that have not yet established their definitive fate maintain their transitory identity without compromising their responsiveness to signalling cues remains unclear. A paradigmatic example is provided by pluripotent embryonic stem (ES) cells derived from a transient population of cells of the blastocyst. Here, we argue that ES cells represent an interesting "epigenetic paradox": even though they are captured in a self-renewing state characterised by extremely efficient maintenance of their identity, which is a typical manifestation of robust epigenetic regulation, they seem not to heavily rely on classical epigenetic mechanisms. Indeed, self-renewal strictly depends on the TFs that previously instructed their undifferentiated identity and relies on a particular signalling-dependent chromatin state where repressive chromatin marks play minor roles. Although this "epigenetic paradox" may underlie their exquisite responsiveness to developmental cues, it suggests that alternative mechanisms to faithfully propagate gene regulatory states might be prevalent in ES cells.
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Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Inma Gonzalez
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France.
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76
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Papadopoulou T, Richly H. On-site remodeling at chromatin: How multiprotein complexes are rebuilt during DNA repair and transcriptional activation. Bioessays 2016; 38:1130-1140. [PMID: 27599465 DOI: 10.1002/bies.201600094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this review, we discuss a novel on-site remodeling function that is mediated by the H2A-ubiquitin binding protein ZRF1. ZRF1 facilitates the remodeling of multiprotein complexes at chromatin and lies at the heart of signaling processes that occur at DNA damage sites and during transcriptional activation. In nucleotide excision repair ZRF1 remodels E3 ubiquitin ligase complexes at the damage site. During embryonic stem cell differentiation, it contributes to retinoic acid-mediated gene activation by altering the subunit composition of the Mediator complex. We postulate that ZRF1 operates in conjunction with cellular remodeling machines and suggest that on-site remodeling might be a hallmark of many chromatin-associated signaling pathways. We discuss yet unexplored functions of ZRF1-mediated remodeling in replication and double strand break repair. In conclusion, we postulate that on-site remodeling of multiprotein complexes is essential for the timing of chromatin signaling processes.
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Affiliation(s)
- Thaleia Papadopoulou
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Holger Richly
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology (IMB), Mainz, Germany.
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77
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García-Rodríguez N, Wong RP, Ulrich HD. Functions of Ubiquitin and SUMO in DNA Replication and Replication Stress. Front Genet 2016; 7:87. [PMID: 27242895 PMCID: PMC4865505 DOI: 10.3389/fgene.2016.00087] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 04/27/2016] [Indexed: 12/14/2022] Open
Abstract
Complete and faithful duplication of its entire genetic material is one of the essential prerequisites for a proliferating cell to maintain genome stability. Yet, during replication DNA is particularly vulnerable to insults. On the one hand, lesions in replicating DNA frequently cause a stalling of the replication machinery, as most DNA polymerases cannot cope with defective templates. This situation is aggravated by the fact that strand separation in preparation for DNA synthesis prevents common repair mechanisms relying on strand complementarity, such as base and nucleotide excision repair, from working properly. On the other hand, the replication process itself subjects the DNA to a series of hazardous transformations, ranging from the exposure of single-stranded DNA to topological contortions and the generation of nicks and fragments, which all bear the risk of inducing genomic instability. Dealing with these problems requires rapid and flexible responses, for which posttranslational protein modifications that act independently of protein synthesis are particularly well suited. Hence, it is not surprising that members of the ubiquitin family, particularly ubiquitin itself and SUMO, feature prominently in controlling many of the defensive and restorative measures involved in the protection of DNA during replication. In this review we will discuss the contributions of ubiquitin and SUMO to genome maintenance specifically as they relate to DNA replication. We will consider cases where the modifiers act during regular, i.e., unperturbed stages of replication, such as initiation, fork progression, and termination, but also give an account of their functions in dealing with lesions, replication stalling and fork collapse.
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78
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Qiu Z, Elsayed Z, Peterkin V, Alkatib S, Bennett D, Landry JW. Ino80 is essential for proximal-distal axis asymmetry in part by regulating Bmp4 expression. BMC Biol 2016; 14:18. [PMID: 26975355 PMCID: PMC4790052 DOI: 10.1186/s12915-016-0238-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 02/16/2016] [Indexed: 12/12/2022] Open
Abstract
Background Understanding how embryos specify asymmetric axes is a major focus of biology. While much has been done to discover signaling pathways and transcription factors important for axis specification, comparatively little is known about how epigenetic regulators are involved. Epigenetic regulators operate downstream of signaling pathways and transcription factors to promote nuclear processes, most prominently transcription. To discover novel functions for these complexes in axis establishment during early embryonic development, we characterized phenotypes of a mouse knockout (KO) allele of the chromatin remodeling Ino80 ATPase. Results Ino80 KO embryos implant, but fail to develop beyond the egg cylinder stage. Ino80 KO embryonic stem cells (ESCs) are viable and maintain alkaline phosphatase activity, which is suggestive of pluripotency, but they fail to fully differentiate as either embryoid bodies or teratomas. Gene expression analysis of Ino80 KO early embryos by in situ hybridization and embryoid bodies by RT-PCR shows elevated Bmp4 expression and reduced expression of distal visceral endoderm (DVE) markers Cer1, Hex, and Lefty1. In culture, Bmp4 maintains stem cell pluripotency and when overexpressed is a known negative regulator of DVE differentiation in the early embryo. Consistent with the early embryo, we observed upregulated Bmp4 expression and down-regulated Cer1, Hex, and Lefty1 expression when Ino80 KO ESCs are differentiated in a monolayer. Molecular studies in these same cells demonstrate that Ino80 bound to the Bmp4 promoter regulates its chromatin structure, which correlates with enhanced SP1 binding. These results in combination suggest that Ino80 directly regulates the chromatin structure of the Bmp4 promoter with consequences to gene expression. Conclusions In contrast to Ino80 KO differentiated cells, our experiments show that undifferentiated Ino80 KO ESCs are viable, but fail to differentiate in culture and in the early embryo. Ino80 KO ESCs and the early embryo up-regulate Bmp4 expression and down-regulate the expression of DVE markers Cer1, Hex and Lefty1. Based on this data, we propose a model where the Ino80 chromatin remodeling complex represses Bmp4 expression in the early embryo, thus promoting DVE differentiation and successful proximal-distal axis establishment. These results are significant because they show that epigenetic regulators have specific roles in establishing embryonic axes. By further characterizing these complexes, we will deepen our understanding of how the mammalian embryo is patterned by epigenetic regulators. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0238-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhijun Qiu
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Zeinab Elsayed
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Veronica Peterkin
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Suehyb Alkatib
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Dorothy Bennett
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
| | - Joseph W Landry
- Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA.
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BAP1/ASXL1 recruitment and activation for H2A deubiquitination. Nat Commun 2016; 7:10292. [PMID: 26739236 PMCID: PMC4729829 DOI: 10.1038/ncomms10292] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/26/2015] [Indexed: 12/22/2022] Open
Abstract
The deubiquitinating enzyme BAP1 is an important tumor suppressor that has drawn attention in the clinic since its loss leads to a variety of cancers. BAP1 is activated by ASXL1 to deubiquitinate mono-ubiquitinated H2A at K119 in Polycomb gene repression, but the mechanism of this reaction remains poorly defined. Here we show that the BAP1 C-terminal extension is important for H2A deubiquitination by auto-recruiting BAP1 to nucleosomes in a process that does not require the nucleosome acidic patch. This initial encounter-like complex is unproductive and needs to be activated by the DEUBAD domains of ASXL1, ASXL2 or ASXL3 to increase BAP1's affinity for ubiquitin on H2A, to drive the deubiquitination reaction. The reaction is specific for Polycomb modifications of H2A as the complex cannot deubiquitinate the DNA damage-dependent ubiquitination at H2A K13/15. Our results contribute to the molecular understanding of this important tumor suppressor.
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80
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Carbone M, Flores EG, Emi M, Johnson TA, Tsunoda T, Behner D, Hoffman H, Hesdorffer M, Nasu M, Napolitano A, Powers A, Minaai M, Baumann F, Bryant-Greenwood P, Lauk O, Kirschner MB, Weder W, Opitz I, Pass HI, Gaudino G, Pastorino S, Yang H. Combined Genetic and Genealogic Studies Uncover a Large BAP1 Cancer Syndrome Kindred Tracing Back Nine Generations to a Common Ancestor from the 1700s. PLoS Genet 2015; 11:e1005633. [PMID: 26683624 PMCID: PMC4686043 DOI: 10.1371/journal.pgen.1005633] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/08/2015] [Indexed: 01/31/2023] Open
Abstract
We recently discovered an inherited cancer syndrome caused by BRCA1-Associated Protein 1 (BAP1) germline mutations, with high incidence of mesothelioma, uveal melanoma and other cancers and very high penetrance by age 55. To identify families with the BAP1 cancer syndrome, we screened patients with family histories of multiple mesotheliomas and melanomas and/or multiple cancers. We identified four families that shared an identical BAP1 mutation: they lived across the US and did not appear to be related. By combining family histories, molecular genetics, and genealogical approaches, we uncovered a BAP1 cancer syndrome kindred of ~80,000 descendants with a core of 106 individuals, whose members descend from a couple born in Germany in the early 1700s who immigrated to North America. Their descendants spread throughout the country with mutation carriers affected by multiple malignancies. Our data show that, once a proband is identified, extended analyses of these kindreds, using genomic and genealogical studies to identify the most recent common ancestor, allow investigators to uncover additional branches of the family that may carry BAP1 mutations. Using this knowledge, we have identified new branches of this family carrying BAP1 mutations. We have also implemented early-detection strategies that help identify cancers at early-stage, when they can be cured (melanomas) or are more susceptible to therapy (MM and other malignancies). Germline BAP1 mutations cause a cancer syndrome characterized by high incidence of mesothelioma (MM), uveal melanoma and other cancers, and by very high penetrance, as all individuals carrying BAP1 mutations developed at least one, and usually several, malignancies throughout their lives. Through screening MM patients with histories of multiple cancers, we found four supposedly unrelated patients that shared an identical germline BAP1 mutation. We investigated whether this BAP1 mutation occurred in a ‘hot-spot’ for “de novo” mutations or whether these four MM patients shared a common ancestor. Using molecular genomics analyses we found that they are related. By genealogic studies we traced their ancestor to a couple that emigrated from Germany to North America in the early 1700’s; we traced the subsequent migration of their descendants, who are now living in at least three different US States. Our findings demonstrate that BAP1 mutations are transmitted among subsequent generations over the course of centuries. This knowledge and methodology is being used to identify additional branches of the family carrying BAP1 mutations. Our study shows that the application of modern genomic analyses, coupled with “classical” family histories collected by the treating physician, and with genealogical searches, offer a powerful strategy to identify high-risk germline BAP1 mutation carriers that will benefit from genetic counseling and early detection cancer screening.
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Affiliation(s)
- Michele Carbone
- Thoracic Oncology Program, University of Hawai‘i Cancer Center, Honolulu, Hawai’i, United States of America
- * E-mail: (MC); (HY)
| | - Erin G. Flores
- Thoracic Oncology Program, University of Hawai‘i Cancer Center, Honolulu, Hawai’i, United States of America
| | - Mitsuru Emi
- Thoracic Oncology Program, University of Hawai‘i Cancer Center, Honolulu, Hawai’i, United States of America
| | - Todd A. Johnson
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan
| | - Tatsuhiko Tsunoda
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan
| | - Dusty Behner
- Thoracic Oncology Program, University of Hawai‘i Cancer Center, Honolulu, Hawai’i, United States of America
| | - Harriet Hoffman
- Genealogy from the Hart, Honolulu, Hawai’i, United States of America
| | - Mary Hesdorffer
- Mesothelioma Applied Research Foundation, Alexandria, Virginia, United States of America
| | - Masaki Nasu
- Thoracic Oncology Program, University of Hawai‘i Cancer Center, Honolulu, Hawai’i, United States of America
| | - Andrea Napolitano
- Thoracic Oncology Program, University of Hawai‘i Cancer Center, Honolulu, Hawai’i, United States of America
| | - Amy Powers
- Thoracic Oncology Program, University of Hawai‘i Cancer Center, Honolulu, Hawai’i, United States of America
| | - Michael Minaai
- Thoracic Oncology Program, University of Hawai‘i Cancer Center, Honolulu, Hawai’i, United States of America
| | - Francine Baumann
- Thoracic Oncology Program, University of Hawai‘i Cancer Center, Honolulu, Hawai’i, United States of America
| | - Peter Bryant-Greenwood
- Thoracic Oncology Program, University of Hawai‘i Cancer Center, Honolulu, Hawai’i, United States of America
| | - Olivia Lauk
- Klinik für Thoraxchirurgie Universitätsspital, Zürich, Switzerland
| | | | - Walter Weder
- Klinik für Thoraxchirurgie Universitätsspital, Zürich, Switzerland
| | - Isabelle Opitz
- Klinik für Thoraxchirurgie Universitätsspital, Zürich, Switzerland
| | - Harvey I. Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York, United States of America
| | - Giovanni Gaudino
- Thoracic Oncology Program, University of Hawai‘i Cancer Center, Honolulu, Hawai’i, United States of America
| | - Sandra Pastorino
- Thoracic Oncology Program, University of Hawai‘i Cancer Center, Honolulu, Hawai’i, United States of America
| | - Haining Yang
- Thoracic Oncology Program, University of Hawai‘i Cancer Center, Honolulu, Hawai’i, United States of America
- * E-mail: (MC); (HY)
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Abstract
Both proteolytic and nonproteolytic functions of ubiquitination are essential regulatory mechanisms for promoting DNA repair and the DNA damage response in mammalian cells. Deubiquitinating enzymes (DUBs) have emerged as key players in the maintenance of genome stability. In this minireview, we discuss the recent findings on human DUBs that participate in genome maintenance, with a focus on the role of DUBs in the modulation of DNA repair and DNA damage signaling.
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82
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Serber DW, Runge JS, Menon DU, Magnuson T. The Mouse INO80 Chromatin-Remodeling Complex Is an Essential Meiotic Factor for Spermatogenesis. Biol Reprod 2015; 94:8. [PMID: 26607718 PMCID: PMC4809561 DOI: 10.1095/biolreprod.115.135533] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/16/2015] [Indexed: 11/21/2022] Open
Abstract
The ability to faithfully transmit genetic information across generations via the germ cells is a critical aspect of mammalian reproduction. The process of germ cell development requires a number of large-scale modulations of chromatin within the nucleus. One such occasion arises during meiotic recombination, when hundreds of DNA double-strand breaks are induced and subsequently repaired, enabling the transfer of genetic information between homologous chromosomes. The inability to properly repair DNA damage is known to lead to an arrest in the developing germ cells and sterility within the animal. Chromatin-remodeling activity, and in particular the BRG1 subunit of the SWI/SNF complex, has been shown to be required for successful completion of meiosis. In contrast, remodeling complexes of the ISWI and CHD families are required for postmeiotic processes. Little is known regarding the contribution of the INO80 family of chromatin-remodeling complexes, which is a particularly interesting candidate due to its well described functions during DNA double-strand break repair. Here we show that INO80 is expressed in developing spermatocytes during the early stages of meiotic prophase I. Based on this information, we used a conditional allele to delete the INO80 core ATPase subunit, thereby eliminating INO80 chromatin-remodeling activity in this lineage. The loss of INO80 resulted in an arrest during meiosis associated with a failure to repair DNA damage during meiotic recombination.
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Affiliation(s)
- Daniel W Serber
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - John S Runge
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Debashish U Menon
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Terry Magnuson
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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83
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Qin J, Zhou Z, Chen W, Wang C, Zhang H, Ge G, Shao M, You D, Fan Z, Xia H, Liu R, Chen C. BAP1 promotes breast cancer cell proliferation and metastasis by deubiquitinating KLF5. Nat Commun 2015; 6:8471. [PMID: 26419610 PMCID: PMC4598844 DOI: 10.1038/ncomms9471] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 08/25/2015] [Indexed: 02/06/2023] Open
Abstract
The transcription factor KLF5 is highly expressed in basal-like breast cancer and promotes breast cancer cell proliferation, survival, migration and tumour growth. Here we show that, in breast cancer cells, KLF5 is stabilized by the deubiquitinase (DUB) BAP1. With a genome-wide siRNA library screen of DUBs, we identify BAP1 as a bona fide KLF5 DUB. BAP1 interacts directly with KLF5 and stabilizes KLF5 via deubiquitination. KLF5 is in the BAP1/HCF-1 complex, and this newly identified complex promotes cell cycle progression partially by inhibiting p27 gene expression. Furthermore, BAP1 knockdown inhibits tumorigenicity and lung metastasis, which can be rescued partially by ectopic expression of KLF5. Collectively, our findings not only identify BAP1 as the DUB for KLF5, but also reveal a critical mechanism that regulates KLF5 expression in breast cancer. Our findings indicate that BAP1 could be a potential therapeutic target for breast and other cancers. The zinc finger-containing transcription factor KLF5 drives cell proliferation and migration. Here, the authors show that the debuquitinase BAP1 directly stabilizes KLF5, thus promoting basal-like breast cancer cell-cycle progression and metastasis.
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Affiliation(s)
- Junying Qin
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Collaborative Innovation Center for Cancer Medicine, Kunming, Yunnan 650223, China.,Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Zhongmei Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Collaborative Innovation Center for Cancer Medicine, Kunming, Yunnan 650223, China
| | - Wenlin Chen
- Department of Breast Surgery, Breast Cancer Clinical Research Center, Cancer Hospital, Kunming Medical University, Kunming, Yunnan 650031, China
| | - Chunyan Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Collaborative Innovation Center for Cancer Medicine, Kunming, Yunnan 650223, China.,Graduate School of the Chinese Academy of Sciences, Beijing 100039, China.,Department of Pathology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
| | - Hailin Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Collaborative Innovation Center for Cancer Medicine, Kunming, Yunnan 650223, China
| | - Guangzhe Ge
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Collaborative Innovation Center for Cancer Medicine, Kunming, Yunnan 650223, China.,Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Ming Shao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Collaborative Innovation Center for Cancer Medicine, Kunming, Yunnan 650223, China.,Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Dingyun You
- Kunming Medical University, Kunming, Yunnan 650031, China
| | - Zhixiang Fan
- Kunming Medical University, Kunming, Yunnan 650031, China
| | - Houjun Xia
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Collaborative Innovation Center for Cancer Medicine, Kunming, Yunnan 650223, China
| | - Rong Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Collaborative Innovation Center for Cancer Medicine, Kunming, Yunnan 650223, China
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Collaborative Innovation Center for Cancer Medicine, Kunming, Yunnan 650223, China
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84
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Daou S, Hammond-Martel I, Mashtalir N, Barbour H, Gagnon J, Iannantuono NVG, Nkwe NS, Motorina A, Pak H, Yu H, Wurtele H, Milot E, Mallette FA, Carbone M, Affar EB. The BAP1/ASXL2 Histone H2A Deubiquitinase Complex Regulates Cell Proliferation and Is Disrupted in Cancer. J Biol Chem 2015; 290:28643-63. [PMID: 26416890 DOI: 10.1074/jbc.m115.661553] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Indexed: 01/03/2023] Open
Abstract
The deubiquitinase (DUB) and tumor suppressor BAP1 catalyzes ubiquitin removal from histone H2A Lys-119 and coordinates cell proliferation, but how BAP1 partners modulate its function remains poorly understood. Here, we report that BAP1 forms two mutually exclusive complexes with the transcriptional regulators ASXL1 and ASXL2, which are necessary for maintaining proper protein levels of this DUB. Conversely, BAP1 is essential for maintaining ASXL2, but not ASXL1, protein stability. Notably, cancer-associated loss of BAP1 expression results in ASXL2 destabilization and hence loss of its function. ASXL1 and ASXL2 use their ASXM domains to interact with the C-terminal domain (CTD) of BAP1, and these interactions are required for ubiquitin binding and H2A deubiquitination. The deubiquitination-promoting effect of ASXM requires intramolecular interactions between catalytic and non-catalytic domains of BAP1, which generate a composite ubiquitin-binding interface (CUBI). Notably, the CUBI engages multiple interactions with ubiquitin involving (i) the ubiquitin carboxyl hydrolase catalytic domain of BAP1, which interacts with the hydrophobic patch of ubiquitin, and (ii) the CTD domain, which interacts with a charged patch of ubiquitin. Significantly, we identified cancer-associated mutations of BAP1 that disrupt the CUBI and notably an in-frame deletion in the CTD that inhibits its interaction with ASXL1/2 and DUB activity and deregulates cell proliferation. Moreover, we demonstrated that BAP1 interaction with ASXL2 regulates cell senescence and that ASXL2 cancer-associated mutations disrupt BAP1 DUB activity. Thus, inactivation of the BAP1/ASXL2 axis might contribute to cancer development.
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Affiliation(s)
- Salima Daou
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Ian Hammond-Martel
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Nazar Mashtalir
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Haithem Barbour
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Jessica Gagnon
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Nicholas V G Iannantuono
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Nadine Sen Nkwe
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Alena Motorina
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Helen Pak
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Helen Yu
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Hugo Wurtele
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Eric Milot
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Frédérick A Mallette
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Michele Carbone
- the Thoracic Oncology Program, University of Hawaii Cancer Center, Honolulu, Hawaii 96813
| | - El Bachir Affar
- From the Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, Québec H3C 3J7, Canada and
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85
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Peng J, Ma J, Li W, Mo R, Zhang P, Gao K, Jin X, Xiao J, Wang C, Fan J. Stabilization of MCRS1 by BAP1 prevents chromosome instability in renal cell carcinoma. Cancer Lett 2015; 369:167-74. [PMID: 26300492 DOI: 10.1016/j.canlet.2015.08.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/17/2015] [Accepted: 08/17/2015] [Indexed: 01/21/2023]
Abstract
Characterization of the exome and genome of carcinoma (ccRCC) by next-generation sequencing identified numerous genetic alternations. BRCA1-associated protein-1 (BAP1) was identified as one of the most frequently mutated genes in ccRCC, suggesting that BAP1 is a potential key driver for ccRCC cancer initiation and progression. However, how BAP1 mutations contribute to ccRCC remains to be elucidated. BAP1 is a nuclear de-ubiquitinating enzyme and cleaves the ubiquitin chain from the substrates. Here, we identified MCRS1 as a bona fide substrate for BAP1. MCRS1 is a component of the centrosome proteins, and plays an essential role in spindle assembly. BAP1 binds to MCRS1 and stabilizes MCRS1 by de-ubiquitination. BAP1 contributes to chromosome stability partially via MCRS1. A positive correlation was identified between BAP1 and MCRS1 expression in ccRCC tissues. Both BAP1 loss and MCRS1 down-regulation in ccRCC were associated with adverse clinicopathological features. This study revealed a novel mechanism for BAP1 involved in MCRS1 stability regulation, and provided insight in understanding the relationship between BAP1 mutations and chromosome instability in ccRCC.
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Affiliation(s)
- Jingtao Peng
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, 100 Haining Road, Shanghai 200080, China
| | - Jian Ma
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, 100 Haining Road, Shanghai 200080, China
| | - Weiguo Li
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, 100 Haining Road, Shanghai 200080, China
| | - Ren Mo
- Department of Urology, Inner Mongolia Autonomous Region Peoples Hospital, 20 Zhaowuda Road, Hohhot 010017, China
| | - Pingzhao Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Kun Gao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Xiaofeng Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Jiantao Xiao
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, 100 Haining Road, Shanghai 200080, China
| | - Chenji Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China.
| | - Jie Fan
- Department of Urology, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, 100 Haining Road, Shanghai 200080, China.
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86
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Ghasemi M, Pawar H, Mishra RK, Brahmachari V. The functional diversity of Drosophila Ino80 in development. Mech Dev 2015; 138 Pt 2:113-121. [PMID: 26253267 DOI: 10.1016/j.mod.2015.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022]
Abstract
Ino80 is well known as a chromatin remodeling protein with the catalytic function of DNA dependent ATPase and is highly conserved across phyla. Ino80 in human and Drosophila is known to form the Ino80 complex in association with the DNA binding protein Ying-Yang 1 (YY1)/Pleiohomeotic (Pho) the Drosophila homologue. We have earlier reported that Ino80 sub-family of proteins has two functional domains, namely, the DNA dependent ATPase and the DNA binding domain. In the background of the essential role of dIno80 in development, we provide evidence of Pho independent function of dIno80 in development and analyze the dual role of dIno80 in activation as well as repression in the context of the homeotic gene Scr (sex combs reduced) in imaginal discs. This differential effect of dIno80 in different imaginal discs suggests the contextual function of dIno80 as an Enhancer of Trithorax and Polycomb (ETP). We speculate on the role of dIno80 as a chromatin remodeler on one hand and a potential recruiter of epigenetic regulatory complexes on the other.
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Affiliation(s)
- Mohsen Ghasemi
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Hema Pawar
- Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Vani Brahmachari
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India.
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87
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Napolitano A, Pellegrini L, Dey A, Larson D, Tanji M, Flores EG, Kendrick B, Lapid D, Powers A, Kanodia S, Pastorino S, Pass HI, Dixit V, Yang H, Carbone M. Minimal asbestos exposure in germline BAP1 heterozygous mice is associated with deregulated inflammatory response and increased risk of mesothelioma. Oncogene 2015; 35:1996-2002. [PMID: 26119930 DOI: 10.1038/onc.2015.243] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/16/2015] [Accepted: 04/20/2015] [Indexed: 01/04/2023]
Abstract
Germline BAP1 mutations predispose to several cancers, in particular malignant mesothelioma. Mesothelioma is an aggressive malignancy generally associated with professional exposure to asbestos. However, to date, we found that none of the mesothelioma patients carrying germline BAP1 mutations were professionally exposed to asbestos. We hypothesized that germline BAP1 mutations might influence the asbestos-induced inflammatory response that is linked to asbestos carcinogenesis, thereby increasing the risk of developing mesothelioma after minimal exposure. Using a BAP1(+/-) mouse model, we found that, compared with their wild-type littermates, BAP1(+/-) mice exposed to low-dose asbestos fibers showed significant alterations of the peritoneal inflammatory response, including significantly higher levels of pro-tumorigenic alternatively polarized M2 macrophages, and lower levels of several chemokines and cytokines. Consistent with these data, BAP1(+/-) mice had a significantly higher incidence of mesothelioma after exposure to very low doses of asbestos, doses that rarely induced mesothelioma in wild-type mice. Our findings suggest that minimal exposure to carcinogenic fibers may significantly increase the risk of malignant mesothelioma in genetically predisposed individuals carrying germline BAP1 mutations, possibly via alterations of the inflammatory response.
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Affiliation(s)
- A Napolitano
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA.,Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - L Pellegrini
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A Dey
- Department of Discovery Oncology, Genentech, South San Francisco, CA, USA
| | - D Larson
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - M Tanji
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - E G Flores
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - B Kendrick
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - D Lapid
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A Powers
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - S Kanodia
- Department of Biomedical Sciences and Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - S Pastorino
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - H I Pass
- Department of Cardiothoracic Surgery, New York University, New York, NY, USA
| | - V Dixit
- Department of Discovery Oncology, Genentech, South San Francisco, CA, USA
| | - H Yang
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - M Carbone
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
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88
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Bravo M, Nicolini F, Starowicz K, Barroso S, Calés C, Aguilera A, Vidal M. Polycomb RING1A/RING1B-dependent histone H2A monoubiquitylation at pericentromeric regions promotes S phase progression. J Cell Sci 2015; 128:3660-71. [DOI: 10.1242/jcs.173021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 08/12/2015] [Indexed: 12/22/2022] Open
Abstract
Functions of Polycomb products extend beyond their well known activity as transcriptional regulators to include genome duplication processes. Polycomb activities in DNA replication and DNA damage repair are unclear, particularly without induced replicative stress. We have used a cellular model of conditionally inactive Polycomb E3 ligases (RING1A and RING1B) that monoubiquitylate lysine 119 of histone H2A (H2AK119Ub) to examine DNA replication in unperturbed cells. We identify slow elongation and fork stalling during DNA replication, associated to the accumulation of mid and late S cells. Signs of replicative stress and colocalization of double strand breaks with chromocenters, the sites of coalesced pericentromeric heterocromatic (PCH) domains, were enriched in cells at mid S, the stage at which PCH is replicated. Altered replication was rescued by targeted monoubiquitylation of PCH through methyl-CpG binding domain protein 1. The acute senescence associated to the depletion of RING1 proteins, mediated by CDKN1A/p21 upregulation, could be uncoupled from a response to DNA damage. These findings link cell proliferation and Polycomb RING1A/B to S phase progression through a specific function in PCH replication.
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Affiliation(s)
- Mónica Bravo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Fabio Nicolini
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Katarzyna Starowicz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Sonia Barroso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, 41092 Sevilla, Spain
| | - Carmela Calés
- Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28029 Madrid, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, 41092 Sevilla, Spain
| | - Miguel Vidal
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
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89
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Kwon SJ, Lee SK, Na J, Lee SA, Lee HS, Park JH, Chung JK, Youn H, Kwon J. Targeting BRG1 chromatin remodeler via its bromodomain for enhanced tumor cell radiosensitivity in vitro and in vivo. Mol Cancer Ther 2014; 14:597-607. [PMID: 25504753 DOI: 10.1158/1535-7163.mct-14-0372] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Radiotherapy treats cancer by inducing DNA double-strand breaks (DSB) in tumor cells using ionizing radiation. However, DNA repair in tumor cells often leads to radioresistance and unsuccessful outcome. Inhibition of DNA repair by targeting repair proteins can increase radiosensitivity of tumor cells. The BRG1 chromatin remodeling enzyme assists DSB repair by stimulating γ-H2AX formation and BRG1 binding to acetylated histones at DSBs via bromodomain (BRD) is critical for this activity. Here, we show that ectopic expression of BRG1-BRD inhibited γ-H2AX and DSB repair after irradiation and increased the radiosensitivity in various human cancer cells, including HT29 colon cancer. Dimerization of BRG1-BRD, increasing its chromatin binding affinity, aggravated the defects in γ-H2AX and DSB repair and further enhanced the radiosensitivity. While little affecting the upstream ATM activation, BRG1-BRD in irradiated HT29 cells inhibited the recruitment of 53BP1 to damaged chromatin, the downstream event of γ-H2AX, and compromised the G2-M checkpoint and increased apoptosis. Importantly, in a xenograft mouse model, BRG1-BRD increased the radiosensitivity of HT29 tumors, which was further enhanced by dimerization. These data suggest that BRG1-BRD radiosensitizes tumor cells by a dominant negative activity against BRG1, which disrupts γ-H2AX and its downstream 53BP1 pathways, leading to inefficient DNA repair, G2-M checkpoint defect, and increased apoptosis. This work therefore identifies BRG1-BRD as a novel tumor radiosensitizer and its action mechanism, providing the first example of chromatin remodeler as a target for improving cancer radiotherapy.
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Affiliation(s)
- Su-Jung Kwon
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Korea
| | - Seul-Ki Lee
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Korea
| | - Juri Na
- Department of Nuclear Medicine and Biomedical Sciences, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Shin-Ai Lee
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Korea
| | - Han-Sae Lee
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Korea
| | - Ji-Hye Park
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Korea
| | - June-Key Chung
- Department of Nuclear Medicine and Biomedical Sciences, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea. Tumor Microenvironment Global Core Research Center, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hyewon Youn
- Department of Nuclear Medicine and Biomedical Sciences, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea. Tumor Microenvironment Global Core Research Center, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea. Cancer Imaging Center, Seoul National University Hospital, Jongno-Gu, Seoul, Korea.
| | - Jongbum Kwon
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Korea.
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