Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation.
Binding Sites
Brain
/ metabolism
Cell Line, Tumor
Chromatin
/ metabolism
Chromatin Immunoprecipitation
Epigenomics
/ methods
Gene Expression Regulation, Neoplastic
Histones
/ metabolism
Humans
Polycomb-Group Proteins
/ metabolism
Repressor Proteins
/ metabolism
Rhabdoid Tumor
/ metabolism
SMARCB1 Protein
/ chemistry
Sequence Analysis, DNA
Survival Analysis
Teratoma
/ metabolism
EZH2
SMARCA4
SMARCB1
atypical teratoid rhabdoid tumor
chromatin states
pediatric brain tumor
Journal
Cancer cell
ISSN: 1878-3686
Titre abrégé: Cancer Cell
Pays: United States
ID NLM: 101130617
Informations de publication
Date de publication:
14 01 2019
14 01 2019
Historique:
received:
13
09
2017
revised:
30
05
2018
accepted:
21
11
2018
pubmed:
1
1
2019
medline:
19
10
2019
entrez:
1
1
2019
Statut:
ppublish
Résumé
Biallelic inactivation of SMARCB1, encoding a member of the SWI/SNF chromatin remodeling complex, is the hallmark genetic aberration of atypical teratoid rhabdoid tumors (ATRT). Here, we report how loss of SMARCB1 affects the epigenome in these tumors. Using chromatin immunoprecipitation sequencing (ChIP-seq) on primary tumors for a series of active and repressive histone marks, we identified the chromatin states differentially represented in ATRTs compared with other brain tumors and non-neoplastic brain. Re-expression of SMARCB1 in ATRT cell lines enabled confirmation of our genome-wide findings for the chromatin states. Additional generation of ChIP-seq data for SWI/SNF and Polycomb group proteins and the transcriptional repressor protein REST determined differential dependencies of SWI/SNF and Polycomb complexes in regulation of diverse gene sets in ATRTs.
Identifiants
pubmed: 30595504
pii: S1535-6108(18)30535-X
doi: 10.1016/j.ccell.2018.11.014
pmc: PMC6341227
mid: NIHMS1515494
pii:
doi:
Substances chimiques
Chromatin
0
Histones
0
Polycomb-Group Proteins
0
RE1-silencing transcription factor
0
Repressor Proteins
0
SMARCB1 Protein
0
SMARCB1 protein, human
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
95-110.e8Subventions
Organisme : NCI NIH HHS
ID : P30 CA021765
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA113794
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA172152
Pays : United States
Informations de copyright
Copyright © 2018 Elsevier Inc. All rights reserved.
Références
Nat Med. 2015 Dec;21(12):1491-6
pubmed: 26552009
Cancer Cell. 2016 Apr 11;29(4):464-476
pubmed: 27070701
Acta Neuropathol. 2017 Nov;134(5):817-818
pubmed: 28815304
Nucleic Acids Res. 2013 Jan;41(Database issue):D970-6
pubmed: 23066107
Pediatr Blood Cancer. 2017 Mar;64(3):
pubmed: 27555605
Epigenetics. 2014 Nov;9(11):1485-95
pubmed: 25482055
PLoS Comput Biol. 2014 Jun 12;10(6):e1003671
pubmed: 24922058
Cancer Cell. 2016 Dec 12;30(6):891-908
pubmed: 27960086
Bioinformatics. 2015 Jan 15;31(2):166-9
pubmed: 25260700
Acta Neuropathol. 2010 Nov;120(5):553-66
pubmed: 20882288
Genes Dev. 2015 Dec 15;29(24):2547-62
pubmed: 26637281
Cell. 2016 Nov 17;167(5):1145-1149
pubmed: 27863232
Ann Oncol. 2017 Feb 1;28(2):254-269
pubmed: 28426098
Proc Natl Acad Sci U S A. 2011 Mar 1;108(9):3665-70
pubmed: 21307310
Nat Commun. 2017 Mar 06;8:14648
pubmed: 28262751
Cancer Res. 2009 Oct 15;69(20):8094-101
pubmed: 19789351
Eur J Cancer. 2006 Sep;42(14):2326-34
pubmed: 16908131
Acta Neuropathol. 2014 Sep;128(3):453-6
pubmed: 25060813
Biochemistry. 2016 Mar 22;55(11):1600-14
pubmed: 26836503
Cancer Cell. 2016 Mar 14;29(3):394-406
pubmed: 26977886
Cancer Manag Res. 2016 Sep 16;8:115-125
pubmed: 27695363
Neuro Oncol. 2013 Feb;15(2):149-60
pubmed: 23190500
PLoS Genet. 2008 Oct;4(10):e1000242
pubmed: 18974828
Nat Protoc. 2007;2(4):933-8
pubmed: 17446892
Appl Immunohistochem Mol Morphol. 2016 Nov/Dec;24(10):729-737
pubmed: 26469332
Nature. 2015 Feb 19;518(7539):317-30
pubmed: 25693563
Genome Biol. 2010;11(3):R25
pubmed: 20196867
Proc Natl Acad Sci U S A. 2013 May 7;110(19):7922-7
pubmed: 23620515
Nature. 2012 Sep 6;489(7414):57-74
pubmed: 22955616
Science. 2012 Dec 14;338(6113):1465-9
pubmed: 23239736
Cold Spring Harb Perspect Biol. 2014 Nov 03;6(11):a019331
pubmed: 25367972
Genome Biol. 2014 Feb 03;15(2):R29
pubmed: 24485249
Front Oncol. 2012 Sep 12;2:114
pubmed: 22988546
Nat Methods. 2012 Feb 28;9(3):215-6
pubmed: 22373907
Anticancer Res. 2016 Aug;36(8):3883-7
pubmed: 27466490
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Epigenetics Chromatin. 2009 Dec 02;2(1):16
pubmed: 19954516
Cancer Genet. 2014 Sep;207(9):365-72
pubmed: 24853101
Nature. 2016 Feb 4;530(7588):57-62
pubmed: 26814967
Cancer Cell. 2010 Oct 19;18(4):316-28
pubmed: 20951942
Am J Hum Genet. 2010 Feb 12;86(2):279-84
pubmed: 20137775
Bioinformatics. 2010 Apr 1;26(7):966-8
pubmed: 20147306
Genome Res. 2013 Jan;23(1):60-73
pubmed: 22964890
Acta Neuropathol. 2014 Nov;128(5):743-53
pubmed: 25200322
Annu Rev Pathol. 2015;10:145-71
pubmed: 25387058
Neuro Oncol. 2016 Jun;18(6):764-78
pubmed: 26755072
Science. 2005 Feb 18;307(5712):1098-101
pubmed: 15718470
Nat Genet. 2013 Jun;45(6):592-601
pubmed: 23644491
Nat Genet. 2017 Feb;49(2):289-295
pubmed: 27941797
Cancer Cell. 2016 Mar 14;29(3):379-393
pubmed: 26923874