Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation

Serap Erkek; Pascal D. Johann; Martina A. Finetti; Yiannis Drosos; Hsien Chao Chou; Marc Zapatka; Dominik Sturm; David T.W. Jones; Andrey Korshunov; Marina Rhyzova; Stephan Wolf; Jan Philipp Mallm; Katja Beck; Olaf Witt; Andreas E. Kulozik; Michael C. Frühwald; Paul A. Northcott; Jan O. Korbel; Peter Lichter; Roland Eils; Amar Gajjar; Charles W.M. Roberts; Daniel Williamson; Martin Hasselblatt; Lukas Chavez; Stefan M. Pfister; Marcel Kool

doi:10.1016/j.ccell.2018.11.014

Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation

Serap Erkek, Pascal D. Johann, Martina A. Finetti, Yiannis Drosos, Hsien Chao Chou, Marc Zapatka, Dominik Sturm, David T.W. Jones, Andrey Korshunov, Marina Rhyzova, Stephan Wolf, Jan Philipp Mallm, Katja Beck, Olaf Witt, Andreas E. Kulozik, Michael C. Frühwald, Paul A. Northcott, Jan O. Korbel, Peter Lichter, Roland EilsAmar Gajjar, Charles W.M. Roberts, Daniel Williamson, Martin Hasselblatt, Lukas Chavez, Stefan M. Pfister, Marcel Kool

Onderzoeksoutput: Bijdrage aan tijdschrift › Artikel › peer review

64 Citaten (Scopus)

Samenvatting

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.

Originele taal-2	Engels
Pagina's (van-tot)	95-110.e8
Tijdschrift	Cancer Cell
Volume	35
Nummer van het tijdschrift	1
DOI's	https://doi.org/10.1016/j.ccell.2018.11.014
Status	Gepubliceerd - 14 jan. 2019
Extern gepubliceerd	Ja

Toegang tot document

10.1016/j.ccell.2018.11.014

Citeer dit

Erkek, S., Johann, P. D., Finetti, M. A., Drosos, Y., Chou, H. C., Zapatka, M., Sturm, D., Jones, D. T. W., Korshunov, A., Rhyzova, M., Wolf, S., Mallm, J. P., Beck, K., Witt, O., Kulozik, A. E., Frühwald, M. C., Northcott, P. A., Korbel, J. O., Lichter, P., ... Kool, M. (2019). Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation. Cancer Cell, 35(1), 95-110.e8. https://doi.org/10.1016/j.ccell.2018.11.014

@article{395ea8ebe663454093e78c9ad591b6ab,

title = "Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation",

abstract = "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.",

keywords = "atypical teratoid rhabdoid tumor, chromatin states, EZH2, pediatric brain tumor, SMARCA4, SMARCB1",

author = "Serap Erkek and Johann, {Pascal D.} and Finetti, {Martina A.} and Yiannis Drosos and Chou, {Hsien Chao} and Marc Zapatka and Dominik Sturm and Jones, {David T.W.} and Andrey Korshunov and Marina Rhyzova and Stephan Wolf and Mallm, {Jan Philipp} and Katja Beck and Olaf Witt and Kulozik, {Andreas E.} and Fr{\"u}hwald, {Michael C.} and Northcott, {Paul A.} and Korbel, {Jan O.} and Peter Lichter and Roland Eils and Amar Gajjar and Roberts, {Charles W.M.} and Daniel Williamson and Martin Hasselblatt and Lukas Chavez and Pfister, {Stefan M.} and Marcel Kool",

note = "Publisher Copyright: {\textcopyright} 2018 Elsevier Inc.",

year = "2019",

month = jan,

day = "14",

doi = "10.1016/j.ccell.2018.11.014",

language = "English",

volume = "35",

pages = "95--110.e8",

journal = "Cancer Cell",

issn = "1535-6108",

publisher = "Cell Press",

number = "1",

}

Erkek, S, Johann, PD, Finetti, MA, Drosos, Y, Chou, HC, Zapatka, M, Sturm, D, Jones, DTW, Korshunov, A, Rhyzova, M, Wolf, S, Mallm, JP, Beck, K, Witt, O, Kulozik, AE, Frühwald, MC, Northcott, PA, Korbel, JO, Lichter, P, Eils, R, Gajjar, A, Roberts, CWM, Williamson, D, Hasselblatt, M, Chavez, L, Pfister, SM & Kool, M 2019, 'Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation', Cancer Cell, vol. 35, nr. 1, blz. 95-110.e8. https://doi.org/10.1016/j.ccell.2018.11.014

TY - JOUR

T1 - Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation

AU - Erkek, Serap

AU - Johann, Pascal D.

AU - Finetti, Martina A.

AU - Drosos, Yiannis

AU - Chou, Hsien Chao

AU - Zapatka, Marc

AU - Sturm, Dominik

AU - Jones, David T.W.

AU - Korshunov, Andrey

AU - Rhyzova, Marina

AU - Wolf, Stephan

AU - Mallm, Jan Philipp

AU - Beck, Katja

AU - Witt, Olaf

AU - Kulozik, Andreas E.

AU - Frühwald, Michael C.

AU - Northcott, Paul A.

AU - Korbel, Jan O.

AU - Lichter, Peter

AU - Eils, Roland

AU - Gajjar, Amar

AU - Roberts, Charles W.M.

AU - Williamson, Daniel

AU - Hasselblatt, Martin

AU - Chavez, Lukas

AU - Pfister, Stefan M.

AU - Kool, Marcel

PY - 2019/1/14

Y1 - 2019/1/14

N2 - 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.

AB - 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.

KW - atypical teratoid rhabdoid tumor

KW - chromatin states

KW - EZH2

KW - pediatric brain tumor

KW - SMARCA4

KW - SMARCB1

UR - http://www.scopus.com/inward/record.url?scp=85060052550&partnerID=8YFLogxK

U2 - 10.1016/j.ccell.2018.11.014

DO - 10.1016/j.ccell.2018.11.014

M3 - Article

C2 - 30595504

AN - SCOPUS:85060052550

SN - 1535-6108

VL - 35

SP - 95-110.e8

JO - Cancer Cell

JF - Cancer Cell

IS - 1

ER -

Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation

Samenvatting

Toegang tot document

Vingerafdruk

Citeer dit