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Ishi Y, Zhang Y, Zhang A, Sasaki T, Piunti A, Suri A, Watanabe J, Abe K, He X, Katagi H, Bhalla P, Natsumeda M, Zou L, Shilatifard A, Hashizume R. Therapeutic Targeting of EZH2 and BET BRD4 in Pediatric Rhabdoid Tumors. Mol Cancer Ther 2022; 21:715-726. [PMID: 35247919 PMCID: PMC9081147 DOI: 10.1158/1535-7163.mct-21-0646] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/20/2021] [Accepted: 02/10/2022] [Indexed: 11/16/2022]
Abstract
Aberrant activity of the H3K27 modifiers EZH2 and BRD4 is an important oncogenic driver for atypical teratoid/rhabdoid tumor (AT/RT), and each is potentially a possible therapeutic target for treating AT/RT. We, therefore, determined whether targeting distinct histone modifier activities was an effective approach for treating AT/RT. The effects of EZH2 and BRD4 inhibition on histone modification, cell proliferation, and cell invasion were analyzed by immunoblotting, MTS assay, colony formation assay, and cell invasion assay. RNA- and chromatin immunoprecipitation-sequencing were used to determine transcriptional and epigenetic changes in AT/RT cells treated with EZH2 and BRD4 inhibitors. We treated mice bearing human AT/RT xenografts with EZH2 and BRD4 inhibitors. Intracranial tumor growth was monitored by bioluminescence imaging, and the therapeutic response was evaluated by animal survival. AT/RT cells showed elevated levels of H3K27 trimethylation (H3K27me3) and H3K27 acetylation (H3K27ac), with expression of EZH2 and BRD4, and lack of SMARCB1 proteins. Targeted inhibition of EZH2 and BRD4 activities reduced cell proliferation and invasiveness of AT/RT in association with decreasing H3K27me3 and H3K27ac. Differential genomic occupancy of H3K27me3 and H3K27ac regulated specific gene expression in response to EZH2 and BRD4 inhibitions. A combination of EZH2 and BRD4 inhibition increased the therapeutic benefit in vitro and in vivo, outperforming either monotherapy. Overall, histones H3K27me3 and H3K27ac were elevated in AT/RT cells and distributed in distinct chromatin regions to regulate specific gene expression and to promote AT/RT growth. Targeting EZH2 and BRD4 activity is, therefore, a potential combination therapy for AT/RT.
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Affiliation(s)
- Yukitomo Ishi
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL, 60611, USA
| | - Yongzhan Zhang
- Department of Biochemistry & Molecular Genetics, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL, 60611, USA
- Institute of Molecular Health Sciences, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Ali Zhang
- Department of Neurosurgical Surgery, Northwestern University Feinberg School of Medicine, 300 East Superior Street, Chicago, IL, 60611, USA
| | - Takahiro Sasaki
- Department of Neurosurgical Surgery, Northwestern University Feinberg School of Medicine, 300 East Superior Street, Chicago, IL, 60611, USA
| | - Andrea Piunti
- Department of Biochemistry & Molecular Genetics, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL, 60611, USA
| | - Amreena Suri
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL, 60611, USA
| | - Jun Watanabe
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL, 60611, USA
- Department of Neurological Surgery, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, Japan
| | - Kouki Abe
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL, 60611, USA
| | - Xingyao He
- Department of Neurosurgical Surgery, Northwestern University Feinberg School of Medicine, 300 East Superior Street, Chicago, IL, 60611, USA
| | - Hiroaki Katagi
- Department of Neurosurgical Surgery, Northwestern University Feinberg School of Medicine, 300 East Superior Street, Chicago, IL, 60611, USA
| | - Pankaj Bhalla
- Department of Dermatology, Northwestern University Feinberg School of Medicine, 300 East Superior Street, Chicago, IL, 60611, USA
| | - Manabu Natsumeda
- Department of Neurological Surgery, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, Japan
| | - Lihua Zou
- Department of Biochemistry & Molecular Genetics, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL, 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry & Molecular Genetics, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL, 60611, USA
| | - Rintaro Hashizume
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL, 60611, USA
- Department of Biochemistry & Molecular Genetics, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Chicago, IL, 60611, USA
- Neuro-Oncology and Stem Cells Transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 East Chicago Avenue, Chicago, IL, 60611, USA
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Johann PD. Invited Review: Dysregulation of chromatin remodellers in paediatric brain tumours - SMARCB1 and beyond. Neuropathol Appl Neurobiol 2021; 46:57-72. [PMID: 32307752 DOI: 10.1111/nan.12616] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/21/2020] [Indexed: 12/13/2022]
Abstract
Mutations in chromatin remodelling genes occur in approximately 25% of all human tumours (Kadoch et al. Nat Genet 45: 592-601, 2013). The spectrum of alterations is broad and comprises single nucleotide variants, insertion/deletions and more complex structural variations. The single most often affected remodelling complex is the SWI/SNF complex (SWItch/sucrose non-fermentable). In the field of paediatric neuro-oncology, the spectrum of affected genes implicated in epigenetic remodelling is narrower with SMARCB1 and SMARCA4 being the most frequent. The low mutation frequencies in many of the SWI/SNF mutant entities underline the fact that perturbed chromatin remodelling is the most salient factor in tumourigenesis and could thus be a potential therapeutic opportunity. Here, I review the genetic basis of aberrant chromatin remodelling in paediatric brain tumours and discuss their impact on the epigenome in the respective entities, mainly medulloblastomas and rhabdoid tumours.
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Affiliation(s)
- P D Johann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Heidelberg, Germany.,Department of Paediatric Haematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
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Kitahama K, Iijima S, Sumiishi A, Hayashi A, Nagahama K, Saito K, Sasaki N, Kobayashi K, Shimizu S, Nagane M, Shibahara J. Reduced H3K27me3 levels in diffuse gliomas: association with 1p/19q codeletion and difference from H3K27me3 loss in malignant peripheral nerve sheath tumors. Brain Tumor Pathol 2020; 38:23-29. [PMID: 32989606 DOI: 10.1007/s10014-020-00382-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/17/2020] [Indexed: 12/18/2022]
Abstract
Trimethylation of histone H3 at lysine 27 (H3K27me3) acts as a transcriptional repressor of target genes. Recent immunohistochemical studies have reported a loss of H3K27me3 modification in diffuse (especially 1p/19q-codeleted) gliomas. However, we did not observe H3K27me3 loss in diffuse gliomas using routine immunostaining conditions for the detection of H3K27me3 loss in malignant peripheral nerve sheath tumors (MPNSTs). Therefore, we conducted immunohistochemical analysis of surgically resected specimens to understand the differences in the H3K27me3 status in MPNSTs and diffuse gliomas and evaluate the diagnostic utility of H3K27me3 immunohistochemistry. Staining with a standard 1:200 dilution of the C36B11 antibody showed a complete loss of H3K27me3 in 5 out of 11 MPNSTs, whereas most diffuse gliomas (149/151, 98.7%) showed diffuse immunoreactivity. At a 1:2000 antibody dilution, 12.6% (19/151) of the diffuse gliomas showed H3K27me3 loss, which was significantly associated with 1p/19q codeletion (P < 0.001). H3K27me3 loss predicted 1p/19q codeletion in IDH-mutant gliomas with lower sensitivity (56.2%) and higher specificity (100%) than ATRX retention or p53 negative result. In conclusion, reduction in H3K27me3 levels was associated with 1p/19q codeletion in diffuse gliomas; however, the extent of reduction differed from that in MPNSTs, and the results depended on the immunostaining conditions.
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Affiliation(s)
- Keiichiro Kitahama
- Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo, 181-8611, Japan
| | - Shohei Iijima
- Department of Neurosurgery, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo, 181-8611, Japan
| | - Ayumi Sumiishi
- Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo, 181-8611, Japan
| | - Akimasa Hayashi
- Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo, 181-8611, Japan
| | - Kiyotaka Nagahama
- Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo, 181-8611, Japan
| | - Kuniaki Saito
- Department of Neurosurgery, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo, 181-8611, Japan
| | - Nobuyoshi Sasaki
- Department of Neurosurgery, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo, 181-8611, Japan
| | - Keiichi Kobayashi
- Department of Neurosurgery, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo, 181-8611, Japan
| | - Saki Shimizu
- Department of Neurosurgery, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo, 181-8611, Japan
| | - Motoo Nagane
- Department of Neurosurgery, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo, 181-8611, Japan
| | - Junji Shibahara
- Department of Pathology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo, 181-8611, Japan.
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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. Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation. Cancer Cell 2019; 35:95-110.e8. [PMID: 30595504 PMCID: PMC6341227 DOI: 10.1016/j.ccell.2018.11.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 05/30/2018] [Accepted: 11/21/2018] [Indexed: 12/27/2022]
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.
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Affiliation(s)
- Serap Erkek
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany; Izmir Biomedicine and Genome Center, 35340 Izmir, Turkey
| | - Pascal D Johann
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Martina A Finetti
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, NE2 Newcastle Upon Tyne, UK
| | - Yiannis Drosos
- Department of Oncology, St Jude Children's Research Hospital, 38105 Memphis, USA
| | - Hsien-Chao Chou
- Department of Oncology, St Jude Children's Research Hospital, 38105 Memphis, USA
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Dominik Sturm
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - David T W Jones
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marina Rhyzova
- Department of Neuropathology, Burdenko Neurosurgical Institute, 125047 Moscow, Russia
| | - Stephan Wolf
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jan-Philipp Mallm
- Genome Organization & Function Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, 69120 Heidelberg, Germany
| | - Katja Beck
- Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, 69120 Heidelberg, Germany
| | - Olaf Witt
- Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Michael C Frühwald
- University Children's Hospital Augsburg, Swabian Children's Cancer Center, 86156 Augsburg, Germany; EU-RHAB Registry Center, 86156 Augsburg, Germany
| | - Paul A Northcott
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 38105 Memphis, TN, USA
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, 69120 Heidelberg, Germany
| | - Roland Eils
- Genome Organization & Function Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Amar Gajjar
- Department of Oncology, St Jude Children's Research Hospital, 38105 Memphis, USA
| | - Charles W M Roberts
- Department of Oncology, St Jude Children's Research Hospital, 38105 Memphis, USA
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, NE2 Newcastle Upon Tyne, UK
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, 48149 Münster, Germany
| | - Lukas Chavez
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Stefan M Pfister
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Marcel Kool
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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