1
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Pekkarinen M, Nordfors K, Uusi-Mäkelä J, Kytölä V, Hartewig A, Huhtala L, Rauhala M, Urhonen H, Häyrynen S, Afyounian E, Yli-Harja O, Zhang W, Helen P, Lohi O, Haapasalo H, Haapasalo J, Nykter M, Kesseli J, Rautajoki KJ. Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors. Life Sci Alliance 2024; 7:e202302088. [PMID: 38499326 PMCID: PMC10948937 DOI: 10.26508/lsa.202302088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
Atypical teratoid/rhabdoid tumors (AT/RTs) are pediatric brain tumors known for their aggressiveness and aberrant but still unresolved epigenetic regulation. To better understand their malignancy, we investigated how AT/RT-specific DNA hypermethylation was associated with gene expression and altered transcription factor binding and how it is linked to upstream regulation. Medulloblastomas, choroid plexus tumors, pluripotent stem cells, and fetal brain were used as references. A part of the genomic regions, which were hypermethylated in AT/RTs similarly as in pluripotent stem cells and demethylated in the fetal brain, were targeted by neural transcriptional regulators. AT/RT-unique DNA hypermethylation was associated with polycomb repressive complex 2 and linked to suppressed genes with a role in neural development and tumorigenesis. Activity of the several NEUROG/NEUROD pioneer factors, which are unable to bind to methylated DNA, was compromised via the suppressed expression or DNA hypermethylation of their target sites, which was also experimentally validated for NEUROD1 in medulloblastomas and AT/RT samples. These results highlight and characterize the role of DNA hypermethylation in AT/RT malignancy and halted neural cell differentiation.
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Affiliation(s)
- Meeri Pekkarinen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kristiina Nordfors
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Unit of Pediatric Hematology and Oncology, Tampere University Hospital, Tampere, Finland
| | - Joonas Uusi-Mäkelä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ville Kytölä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Anja Hartewig
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Laura Huhtala
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Minna Rauhala
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Henna Urhonen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Sergei Häyrynen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ebrahim Afyounian
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Olli Yli-Harja
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Pauli Helen
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Olli Lohi
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Hannu Haapasalo
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Joonas Haapasalo
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Juha Kesseli
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kirsi J Rautajoki
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
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2
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Zheng D, Zhang Y, Yang S, Su N, Bakhoum M, Zhang G, Naderinezhad S, Mao Z, Wang Z, Zhou T, Li W. Androgen deprivation induces neuroendocrine phenotypes in prostate cancer cells through CREB1/EZH2-mediated downregulation of REST. Cell Death Discov 2024; 10:246. [PMID: 38777812 PMCID: PMC11111810 DOI: 10.1038/s41420-024-02031-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Although effective initially, prolonged androgen deprivation therapy (ADT) promotes neuroendocrine differentiation (NED) and prostate cancer (PCa) progression. It is incompletely understood how ADT transcriptionally induces NE genes in PCa cells. CREB1 and REST are known to positively and negatively regulate neuronal gene expression in the brain, respectively. No direct link between these two master neuronal regulators has been elucidated in the NED of PCa. We show that REST mRNA is downregulated in NEPC cell and mouse models, as well as in patient samples. Phenotypically, REST overexpression increases ADT sensitivity, represses NE genes, inhibits colony formation in culture, and xenograft tumor growth of PCa cells. As expected, ADT downregulates REST in PCa cells in culture and in mouse xenografts. Interestingly, CREB1 signaling represses REST expression. In studying the largely unclear mechanism underlying transcriptional repression of REST by ADT, we found that REST is a direct target of EZH2 epigenetic repression. Finally, genetic rescue experiments demonstrated that ADT induces NED through EZH2's repression of REST, which is enhanced by ADT-activated CREB1 signaling. In summary, our study has revealed a key pathway underlying NE gene upregulation by ADT, as well as established novel relationships between CREB1 and REST, and between EZH2 and REST, which may also have implications in other cancer types and in neurobiology.
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Affiliation(s)
- Dayong Zheng
- Texas Therapeutics Institute; Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Oncology, Shunde Hospital, Southern Medical University, Foshan, China
- The First People's Hospital of Shunde, Foshan, China
| | - Yan Zhang
- Texas Therapeutics Institute; Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Pain, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sukjin Yang
- Texas Therapeutics Institute; Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ning Su
- Texas Therapeutics Institute; Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Michael Bakhoum
- Texas Therapeutics Institute; Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Guoliang Zhang
- Texas Therapeutics Institute; Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Samira Naderinezhad
- Texas Therapeutics Institute; Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Zhengmei Mao
- Texas Therapeutics Institute; Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zheng Wang
- Texas Therapeutics Institute; Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ting Zhou
- Texas Therapeutics Institute; Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Wenliang Li
- Texas Therapeutics Institute; Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.
- University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
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3
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Liu NQ, Paassen I, Custers L, Zeller P, Teunissen H, Ayyildiz D, He J, Buhl JL, Hoving EW, van Oudenaarden A, de Wit E, Drost J. SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors. Nat Commun 2023; 14:7762. [PMID: 38040699 PMCID: PMC10692191 DOI: 10.1038/s41467-023-43498-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 11/10/2023] [Indexed: 12/03/2023] Open
Abstract
Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer, yet their contribution to tumorigenesis remains in many cases poorly understood. Here, we study derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids reveals a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently reveal patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 activates patient-specific epigenetic reprogramming underlying MRT tumorigenesis.
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Affiliation(s)
- Ning Qing Liu
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Hematology, Erasmus Medical Center (MC) Cancer Institute, Rotterdam, the Netherlands
| | - Irene Paassen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Lars Custers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Peter Zeller
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute-KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Dilara Ayyildiz
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Jiayou He
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Juliane Laura Buhl
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Alexander van Oudenaarden
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute-KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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4
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Wang ZQ, Zhang ZC, Wu YY, Pi YN, Lou SH, Liu TB, Lou G, Yang C. Bromodomain and extraterminal (BET) proteins: biological functions, diseases, and targeted therapy. Signal Transduct Target Ther 2023; 8:420. [PMID: 37926722 PMCID: PMC10625992 DOI: 10.1038/s41392-023-01647-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/23/2023] [Accepted: 09/12/2023] [Indexed: 11/07/2023] Open
Abstract
BET proteins, which influence gene expression and contribute to the development of cancer, are epigenetic interpreters. Thus, BET inhibitors represent a novel form of epigenetic anticancer treatment. Although preliminary clinical trials have shown the anticancer potential of BET inhibitors, it appears that these drugs have limited effectiveness when used alone. Therefore, given the limited monotherapeutic activity of BET inhibitors, their use in combination with other drugs warrants attention, including the meaningful variations in pharmacodynamic activity among chosen drug combinations. In this paper, we review the function of BET proteins, the preclinical justification for BET protein targeting in cancer, recent advances in small-molecule BET inhibitors, and preliminary clinical trial findings. We elucidate BET inhibitor resistance mechanisms, shed light on the associated adverse events, investigate the potential of combining these inhibitors with diverse therapeutic agents, present a comprehensive compilation of synergistic treatments involving BET inhibitors, and provide an outlook on their future prospects as potent antitumor agents. We conclude by suggesting that combining BET inhibitors with other anticancer drugs and innovative next-generation agents holds great potential for advancing the effective targeting of BET proteins as a promising anticancer strategy.
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Affiliation(s)
- Zhi-Qiang Wang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Zhao-Cong Zhang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Yu-Yang Wu
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Ya-Nan Pi
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Sheng-Han Lou
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tian-Bo Liu
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Ge Lou
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China.
| | - Chang Yang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China.
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5
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Tran S, Plant-Fox AS, Chi SN, Narendran A. Current advances in immunotherapy for atypical teratoid rhabdoid tumor (ATRT). Neurooncol Pract 2023; 10:322-334. [PMID: 37457224 PMCID: PMC10346396 DOI: 10.1093/nop/npad005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2023] Open
Abstract
Atypical teratoid rhabdoid tumors (ATRT) are rare and aggressive embryonal tumors of central nervous system that typically affect children younger than 3 years of age. Given the generally poor outcomes of patients with ATRT and the significant toxicities associated with conventional multi-modal therapies, there is an urgent need for more novel approaches to treat ATRT, one such approach being immunotherapy. The recent rise of large-scale, multicenter interdisciplinary studies has delineated several molecular and genetic characteristics unique to ATRT. This review aims to describe currently available data on the tumor immune microenvironment of ATRT and its specific subtypes and to summarize the emerging clinical and preclinical results of immunotherapy-based approaches. It will also highlight the evolving knowledge of epigenetics on immunomodulation in this epigenetically influenced tumor, which may help guide the development of effective immunotherapeutic approaches in the future.
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Affiliation(s)
- Son Tran
- Departments of Oncology and Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ashley S Plant-Fox
- Division of Hematology, Stem Cell Transplant, and Neuro-Oncology, Ann & Robert H. Lurie Children’s Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Susan N Chi
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Aru Narendran
- Departments of Oncology and Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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6
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Soto-Castillo JJ, Llavata-Marti L, Fort-Culillas R, Andreu-Cobo P, Moreno R, Codony C, García Del Muro X, Alemany R, Piulats JM, Martin-Liberal J. SWI/SNF Complex Alterations in Tumors with Rhabdoid Features: Novel Therapeutic Approaches and Opportunities for Adoptive Cell Therapy. Int J Mol Sci 2023; 24:11143. [PMID: 37446319 DOI: 10.3390/ijms241311143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
The SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling complex is one of the most remarkably altered epigenetic regulators in cancer. Pathogenic mutations in genes encoding SWI/SNF-related proteins have been recently described in many solid tumors, including rare and aggressive malignancies with rhabdoid features with no standard therapies in advanced or metastatic settings. In recent years, clinical trials with targeted drugs aimed at restoring its function have shown discouraging results. However, preclinical data have found an association between these epigenetic alterations and response to immune therapy. Thus, the rationale for immunotherapy strategies in SWI/SNF complex alteration-related tumors is strong. Here, we review the SWI/SNF complex and how its dysfunction drives the oncogenesis of rhabdoid tumors and the proposed strategies to revert this alteration and promising novel therapeutic approaches, including immune checkpoint inhibition and adoptive cell therapy.
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Affiliation(s)
- Juan José Soto-Castillo
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Lucía Llavata-Marti
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 17007 Girona, Spain
| | - Roser Fort-Culillas
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 17007 Girona, Spain
| | - Pablo Andreu-Cobo
- Medical Oncology Department, Parc Tauli Hospital Universitari, 08208 Sabadell, Spain
| | - Rafael Moreno
- Cancer Immunotherapy Group, iPROCURE Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Carles Codony
- Cancer Immunotherapy Group, iPROCURE Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Xavier García Del Muro
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Ramon Alemany
- Cancer Immunotherapy Group, iPROCURE Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Josep M Piulats
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
- Cancer Immunotherapy Group, iPROCURE Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Juan Martin-Liberal
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
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7
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Vokshi BH, Davidson G, Tawanaie Pour Sedehi N, Helleux A, Rippinger M, Haller AR, Gantzer J, Thouvenin J, Baltzinger P, Bouarich R, Manriquez V, Zaidi S, Rao P, Msaouel P, Su X, Lang H, Tricard T, Lindner V, Surdez D, Kurtz JE, Bourdeaut F, Tannir NM, Davidson I, Malouf GG. SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance. Nat Commun 2023; 14:3034. [PMID: 37236926 DOI: 10.1038/s41467-023-38472-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Renal medullary carcinoma (RMC) is an aggressive tumour driven by bi-allelic loss of SMARCB1 and tightly associated with sickle cell trait. However, the cell-of-origin and oncogenic mechanism remain poorly understood. Using single-cell sequencing of human RMC, we defined transformation of thick ascending limb (TAL) cells into an epithelial-mesenchymal gradient of RMC cells associated with loss of renal epithelial transcription factors TFCP2L1, HOXB9 and MITF and gain of MYC and NFE2L2-associated oncogenic and ferroptosis resistance programs. We describe the molecular basis for this transcriptional switch that is reversed by SMARCB1 re-expression repressing the oncogenic and ferroptosis resistance programs leading to ferroptotic cell death. Ferroptosis resistance links TAL cell survival with the high extracellular medullar iron concentrations associated with sickle cell trait, an environment propitious to the mutagenic events associated with RMC development. This unique environment may explain why RMC is the only SMARCB1-deficient tumour arising from epithelial cells, differentiating RMC from rhabdoid tumours arising from neural crest cells.
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Affiliation(s)
- Bujamin H Vokshi
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Guillaume Davidson
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Nassim Tawanaie Pour Sedehi
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Alexandra Helleux
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Marc Rippinger
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Alexandre R Haller
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Justine Gantzer
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
- Department of Medical Oncology, Institut de Cancérologie Strasbourg Europe, 67200, Strasbourg, France
| | - Jonathan Thouvenin
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
- Department of Medical Oncology, Institut de Cancérologie Strasbourg Europe, 67200, Strasbourg, France
| | - Philippe Baltzinger
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Rachida Bouarich
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie Research Centre, 75005, Paris, France
| | - Valeria Manriquez
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie Research Centre, 75005, Paris, France
| | - Sakina Zaidi
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie Research Centre, 75005, Paris, France
| | - Priya Rao
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Pavlos Msaouel
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hervé Lang
- Department of Urology, CHRU Strasbourg, Strasbourg University, 67000, Strasbourg, France
| | - Thibault Tricard
- Department of Urology, CHRU Strasbourg, Strasbourg University, 67000, Strasbourg, France
| | - Véronique Lindner
- Department of Pathology, CHRU Strasbourg, Strasbourg University, 67200, Strasbourg, France
| | - Didier Surdez
- Balgrist University Hospital, University of Zurich, Zurich, Switzerland
- INSERM, U830, Pediatric Translational Research, PSL Research University, SIREDO Oncology Center, Institut Curie, Paris, France
| | - Jean-Emmanuel Kurtz
- Department of Medical Oncology, Institut de Cancérologie Strasbourg Europe, 67200, Strasbourg, France
| | - Franck Bourdeaut
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie Research Centre, 75005, Paris, France
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Irwin Davidson
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France.
- 'Équipe Labellisée' Ligue National contre le Cancer, Paris, France.
| | - Gabriel G Malouf
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France.
- Department of Medical Oncology, Institut de Cancérologie Strasbourg Europe, 67200, Strasbourg, France.
- 'Équipe Labellisée' Ligue National contre le Cancer, Paris, France.
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8
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Cocito C, Martin B, Giantini-Larsen AM, Valcarce-Aspegren M, Souweidane MM, Szalontay L, Dahmane N, Greenfield JP. Leptomeningeal dissemination in pediatric brain tumors. Neoplasia 2023; 39:100898. [PMID: 37011459 PMCID: PMC10124141 DOI: 10.1016/j.neo.2023.100898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 04/03/2023]
Abstract
Leptomeningeal disease (LMD) in pediatric brain tumors (PBTs) is a poorly understood and categorized phenomenon. LMD incidence rates, as well as diagnosis, treatment, and screening practices, vary greatly depending on the primary tumor pathology. While LMD is encountered most frequently in medulloblastoma, reports of LMD have been described across a wide variety of PBT pathologies. LMD may be diagnosed simultaneously with the primary tumor, at time of recurrence, or as primary LMD without a primary intraparenchymal lesion. Dissemination and seeding of the cerebrospinal fluid (CSF) involves a modified invasion-metastasis cascade and is often the result of direct deposition of tumor cells into the CSF. Cells develop select environmental advantages to survive the harsh, nutrient poor and turbulent environment of the CSF and leptomeninges. Improved understanding of the molecular mechanisms that underlie LMD, along with improved diagnostic and treatment approaches, will help the prognosis of children affected by primary brain tumors.
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9
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Sun CX, Daniel P, Bradshaw G, Shi H, Loi M, Chew N, Parackal S, Tsui V, Liang Y, Koptyra M, Adjumain S, Sun C, Chong WC, Fernando D, Drinkwater C, Tourchi M, Habarakada D, Sooraj D, Carvalho D, Storm PB, Baubet V, Sayles LC, Fernandez E, Nguyen T, Pörksen M, Doan A, Crombie DE, Panday M, Zhukova N, Dun MD, Ludlow LE, Day B, Stringer BW, Neeman N, Rubens JA, Raabe EH, Vinci M, Tyrrell V, Fletcher JI, Ekert PG, Dumevska B, Ziegler DS, Tsoli M, Syed Sulaiman NF, Loh AHP, Low SYY, Sweet-Cordero EA, Monje M, Resnick A, Jones C, Downie P, Williams B, Rosenbluh J, Gough D, Cain JE, Firestein R. Generation and multi-dimensional profiling of a childhood cancer cell line atlas defines new therapeutic opportunities. Cancer Cell 2023; 41:660-677.e7. [PMID: 37001527 DOI: 10.1016/j.ccell.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/21/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023]
Abstract
Pediatric solid and central nervous system tumors are the leading cause of cancer-related death among children. Identifying new targeted therapies necessitates the use of pediatric cancer models that faithfully recapitulate the patient's disease. However, the generation and characterization of pediatric cancer models has significantly lagged behind adult cancers, underscoring the urgent need to develop pediatric-focused cell line resources. Herein, we establish a single-site collection of 261 cell lines, including 224 pediatric cell lines representing 18 distinct extracranial and brain childhood tumor types. We subjected 182 cell lines to multi-omics analyses (DNA sequencing, RNA sequencing, DNA methylation), and in parallel performed pharmacological and genetic CRISPR-Cas9 loss-of-function screens to identify pediatric-specific treatment opportunities and biomarkers. Our work provides insight into specific pathway vulnerabilities in molecularly defined pediatric tumor classes and uncovers biomarker-linked therapeutic opportunities of clinical relevance. Cell line data and resources are provided in an open access portal.
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Affiliation(s)
- Claire Xin Sun
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Paul Daniel
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Gabrielle Bradshaw
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Hui Shi
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Melissa Loi
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Nicole Chew
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Sarah Parackal
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Vanessa Tsui
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Yuqing Liang
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Mateusz Koptyra
- Center for Data Driven Discovery in Biomedicine, Neurosurgery Department, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shazia Adjumain
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Christie Sun
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Wai Chin Chong
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Dasun Fernando
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Caroline Drinkwater
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Motahhareh Tourchi
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Dilru Habarakada
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Dhanya Sooraj
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Diana Carvalho
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, UK
| | - Phillip B Storm
- Center for Data Driven Discovery in Biomedicine, Neurosurgery Department, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Valerie Baubet
- Center for Data Driven Discovery in Biomedicine, Neurosurgery Department, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Leanne C Sayles
- Department of Pediatrics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Elisabet Fernandez
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, UK
| | - Thy Nguyen
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Mia Pörksen
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia; Department of Paediatrics, University of Lübeck, 23562 Lübeck, Germany
| | - Anh Doan
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Duncan E Crombie
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Monty Panday
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Nataliya Zhukova
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia; Children's Cancer Centre, Monash Children's Hospital, Monash Health, Clayton, VIC 3168, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3168, Australia
| | - Matthew D Dun
- Hunter Cancer Research Alliance, University of Newcastle, Callaghan, NSW 2308, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Louise E Ludlow
- Children's Cancer Centre Biobank, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Bryan Day
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Brett W Stringer
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Naama Neeman
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Jeffrey A Rubens
- Division of Pediatric Oncology, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Eric H Raabe
- Division of Pediatric Oncology, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Maria Vinci
- Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital-IRCCS, 00165 Rome, Italy
| | - Vanessa Tyrrell
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Jamie I Fletcher
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Paul G Ekert
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia; Centre for Cancer Immunotherapy, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Department of Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Biljana Dumevska
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - David S Ziegler
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia; Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Maria Tsoli
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Nur Farhana Syed Sulaiman
- Neurosurgical Service, KK Women's and Children's Hospital, Singapore 229899, Singapore; VIVA-KKH Paediatric Brain and Solid Tumours Programme, Singapore 229899, Singapore
| | - Amos Hong Pheng Loh
- VIVA-KKH Paediatric Brain and Solid Tumours Programme, Singapore 229899, Singapore; Duke-NUS Medical School, Singapore 169857, Singapore
| | - Sharon Yin Yee Low
- Neurosurgical Service, KK Women's and Children's Hospital, Singapore 229899, Singapore; VIVA-KKH Paediatric Brain and Solid Tumours Programme, Singapore 229899, Singapore; SingHealth-Duke NUS Neuroscience Academic Clinical Programme, Singapore 308433, Singapore; SingHealth-Duke NUS Paediatrics Academic Clinical Programme, Singapore 229899, Singapore
| | | | - Michelle Monje
- Department of Neurology, Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Adam Resnick
- Center for Data Driven Discovery in Biomedicine, Neurosurgery Department, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Chris Jones
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, UK
| | - Peter Downie
- Children's Cancer Centre, Monash Children's Hospital, Monash Health, Clayton, VIC 3168, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3168, Australia
| | - Bryan Williams
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Joseph Rosenbluh
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3168, Australia
| | - Daniel Gough
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Jason E Cain
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Ron Firestein
- Centre for Cancer Research, Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia; Department of Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia.
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10
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Säisä-Borreill S, Davidson G, Kleiber T, Thevenot A, Martin E, Mondot S, Blottière H, Helleux A, Mengus G, Plateroti M, Duluc I, Davidson I, Freund JN. General transcription factor TAF4 antagonizes epigenetic silencing by Polycomb to maintain intestine stem cell functions. Cell Death Differ 2023; 30:839-853. [PMID: 36639541 PMCID: PMC9984434 DOI: 10.1038/s41418-022-01109-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023] Open
Abstract
Taf4 (TATA-box binding protein-associated factor 4) is a subunit of the general transcription factor TFIID, a component of the RNA polymerase II pre-initiation complex that interacts with tissue-specific transcription factors to regulate gene expression. Properly regulated gene expression is particularly important in the intestinal epithelium that is constantly renewed from stem cells. Tissue-specific inactivation of Taf4 in murine intestinal epithelium during embryogenesis compromised gut morphogenesis and the emergence of adult-type stem cells. In adults, Taf4 loss impacted the stem cell compartment and associated Paneth cells in the stem cell niche, epithelial turnover and differentiation of mature cells, thus exacerbating the response to inflammatory challenge. Taf4 inactivation ex vivo in enteroids prevented budding formation and maintenance and caused broad chromatin remodeling and a strong reduction in the numbers of stem and progenitor cells with a concomitant increase in an undifferentiated cell population that displayed high activity of the Ezh2 and Suz12 components of Polycomb Repressive Complex 2 (PRC2). Treatment of Taf4-mutant enteroids with a specific Ezh2 inhibitor restored buddings, cell proliferation and the stem/progenitor compartment. Taf4 loss also led to increased PRC2 activity in cells of adult crypts associated with modification of the immune/inflammatory microenvironment that potentiated Apc-driven tumorigenesis. Our results reveal a novel function of Taf4 in antagonizing PRC2-mediated repression of the stem cell gene expression program to assure normal development, homeostasis, and immune-microenvironment of the intestinal epithelium.
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Affiliation(s)
- Susanna Säisä-Borreill
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Thomas Kleiber
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
- Orphazyme, Ole Maaloes 3, 2200, Copenhagen, Denmark
| | - Andréa Thevenot
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Elisabeth Martin
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Stanislas Mondot
- University Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Hervé Blottière
- University Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Alexandra Helleux
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Gabrielle Mengus
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Michelina Plateroti
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Isabelle Duluc
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Functional Genomics and Cancer, CNRS/Inserm/University of Strasbourg, 1 Rue Laurent Fries, 67404, Illkirch Cédex, France
| | - Jean-Noel Freund
- University of Strasbourg, Inserm, UMR-S1113/IRFAC, FHU ARRIMAGE, FMTS, 67200, Strasbourg, France.
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11
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Alva E, Rubens J, Chi S, Rosenberg T, Reddy A, Raabe EH, Margol A. Recent progress and novel approaches to treating atypical teratoid rhabdoid tumor. Neoplasia 2023; 37:100880. [PMID: 36773516 PMCID: PMC9929860 DOI: 10.1016/j.neo.2023.100880] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/12/2023] [Accepted: 01/23/2023] [Indexed: 02/11/2023]
Abstract
Atypical teratoid rhabdoid tumors (AT/RT) are malignant central nervous system (CNS) tumors that occur mostly in young children and have historically carried a very poor prognosis. While recent clinical trial results show that this tumor is curable, outcomes are still poor compared to other central nervous system embryonal tumors. We here review prior AT/RT clinical trials and highlight promising pre-clinical results that may inform novel clinical approaches to this aggressive cancer.
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Affiliation(s)
- Elizabeth Alva
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jeffrey Rubens
- Division of Pediatric Oncology, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Susan Chi
- Dana-Farber Cancer Institute, Children's Hospital Boston, Boston, MA, USA
| | - Tom Rosenberg
- Dana-Farber Cancer Institute, Children's Hospital Boston, Boston, MA, USA
| | - Alyssa Reddy
- Departments of Neurology and Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Eric H Raabe
- Division of Pediatric Oncology, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Ashley Margol
- Children's Hospital Los Angeles, Los Angeles, CA, USA; Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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12
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Guneri-Sozeri PY, Özden-Yılmaz G, Kisim A, Cakiroglu E, Eray A, Uzuner H, Karakülah G, Pesen-Okvur D, Senturk S, Erkek-Ozhan S. FLI1 and FRA1 transcription factors drive the transcriptional regulatory networks characterizing muscle invasive bladder cancer. Commun Biol 2023; 6:199. [PMID: 36805539 PMCID: PMC9941102 DOI: 10.1038/s42003-023-04561-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/07/2023] [Indexed: 02/22/2023] Open
Abstract
Bladder cancer is mostly present in the form of urothelium carcinoma, causing over 150,000 deaths each year. Its histopathological classification as muscle invasive (MIBC) and non-muscle invasive (NMIBC) is the most prominent aspect, affecting the prognosis and progression of this disease. In this study, we defined the active regulatory landscape of MIBC and NMIBC cell lines using H3K27ac ChIP-seq and used an integrative approach to combine our findings with existing data. Our analysis revealed FRA1 and FLI1 as two critical transcription factors differentially regulating MIBC regulatory landscape. We show that FRA1 and FLI1 regulate the genes involved in epithelial cell migration and cell junction organization. Knock-down of FRA1 and FLI1 in MIBC revealed the downregulation of several EMT-related genes such as MAP4K4 and FLOT1. Further, ChIP-SICAP performed for FRA1 and FLI1 enabled us to infer chromatin binding partners of these transcription factors and link this information with their target genes. Finally, we show that knock-down of FRA1 and FLI1 result in significant reduction of invasion capacity of MIBC cells towards muscle microenvironment using IC-CHIP assays. Our results collectively highlight the role of these transcription factors in selection and design of targeted options for treatment of MIBC.
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Affiliation(s)
- Perihan Yagmur Guneri-Sozeri
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey ,grid.21200.310000 0001 2183 9022Dokuz Eylül University Izmir International Biomedicine and Genome Institute, Inciralti, 35340 Izmir, Turkey
| | - Gülden Özden-Yılmaz
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey
| | - Asli Kisim
- grid.419609.30000 0000 9261 240XIzmir Institute of Technology, Urla, 35430 Izmir, Turkey
| | - Ece Cakiroglu
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey ,grid.21200.310000 0001 2183 9022Dokuz Eylül University Izmir International Biomedicine and Genome Institute, Inciralti, 35340 Izmir, Turkey
| | - Aleyna Eray
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey ,grid.21200.310000 0001 2183 9022Dokuz Eylül University Izmir International Biomedicine and Genome Institute, Inciralti, 35340 Izmir, Turkey
| | - Hamdiye Uzuner
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey ,grid.21200.310000 0001 2183 9022Dokuz Eylül University Izmir International Biomedicine and Genome Institute, Inciralti, 35340 Izmir, Turkey
| | - Gökhan Karakülah
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey ,grid.21200.310000 0001 2183 9022Dokuz Eylül University Izmir International Biomedicine and Genome Institute, Inciralti, 35340 Izmir, Turkey
| | - Devrim Pesen-Okvur
- grid.419609.30000 0000 9261 240XIzmir Institute of Technology, Urla, 35430 Izmir, Turkey
| | - Serif Senturk
- grid.21200.310000 0001 2183 9022Izmir Biomedicine and Genome Center, Inciralti, 35340 Izmir, Turkey ,grid.21200.310000 0001 2183 9022Dokuz Eylül University Izmir International Biomedicine and Genome Institute, Inciralti, 35340 Izmir, Turkey
| | - Serap Erkek-Ozhan
- Izmir Biomedicine and Genome Center, Inciralti, 35340, Izmir, Turkey.
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13
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Shinohara H, Sawado R, Nakagawa M, Hattori A, Yamagata K, Tauchi K, Ito J, Kuwahara Y, Okuda T, Ogawa C, Kitabayashi I. Dual targeting of EZH1 and EZH2 for the treatment of malignant rhabdoid tumors. Mol Ther Oncolytics 2022; 27:14-25. [PMID: 36212776 PMCID: PMC9529991 DOI: 10.1016/j.omto.2022.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 09/14/2022] [Indexed: 11/19/2022] Open
Abstract
Malignant rhabdoid tumors (MRTs) are rare and highly aggressive pediatric cancers with no standard of care. MRTs are characterized by loss of SMARCB1, which results in upregulated expression of enhancer of zeste homolog 2 (EZH2), which is responsible for the methylation of lysine 27 of histone H3 (H3K27me3), leading to the repression of gene expression. Although previous reports suggest EZH2 as an effective therapeutic target, the functions of EZH1, the other homolog of EZH, in MRT remain unknown. Here, we show that EZH1, as well as EZH2, contributes to MRT cell growth and H3K27 methylation. Depletion or selective inhibition of EZH2 led to a compensatory increase in EZH1 expression, and depletion of EZH1 enhanced the effect of EZH2 inhibition. EZH1/2 dual inhibitors suppressed MRT cell growth markedly, reflecting the reduction of H3K27me3 accumulation at one of the EZH1/2 targets, the CDKN2A locus. Dual inhibition of EZH1/2 in vivo suppressed tumor growth completely, with no significant adverse effects. These findings indicate that both EZH1 and EZH2 are potential targets for MRT therapy, and that EZH1/2 dual inhibitors may be promising therapeutic strategies for MRT.
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Affiliation(s)
- Haruka Shinohara
- Division of Hematological Malignancy, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo 104-0045, Japan
| | - Rie Sawado
- Division of Hematological Malignancy, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo 104-0045, Japan
| | - Makoto Nakagawa
- Division of Hematological Malignancy, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo 104-0045, Japan
- Department of Orthopaedic Surgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ayuna Hattori
- Division of Hematological Malignancy, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo 104-0045, Japan
- Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kazutsune Yamagata
- Division of Hematological Malignancy, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo 104-0045, Japan
| | - Kimiharu Tauchi
- Division of Hematological Malignancy, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo 104-0045, Japan
| | - Jumpei Ito
- Division of Hematological Malignancy, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo 104-0045, Japan
- Department of Pediatrics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, 160-8582 Tokyo, Japan
| | - Yasumichi Kuwahara
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Tsukasa Okuda
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Chitose Ogawa
- Department of Pediatric Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-Ku, Tokyo 104-0045, Japan
| | - Issay Kitabayashi
- Division of Hematological Malignancy, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo 104-0045, Japan
- Corresponding author Issay Kitabayashi, Division of Hematological Malignancy, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo 104-0045, Japan.
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14
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Akhoundova D, Rubin MA. Clinical application of advanced multi-omics tumor profiling: Shaping precision oncology of the future. Cancer Cell 2022; 40:920-938. [PMID: 36055231 DOI: 10.1016/j.ccell.2022.08.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/22/2022] [Accepted: 08/11/2022] [Indexed: 12/17/2022]
Abstract
Next-generation DNA sequencing technology has dramatically advanced clinical oncology through the identification of therapeutic targets and molecular biomarkers, leading to the personalization of cancer treatment with significantly improved outcomes for many common and rare tumor entities. More recent developments in advanced tumor profiling now enable dissection of tumor molecular architecture and the functional phenotype at cellular and subcellular resolution. Clinical translation of high-resolution tumor profiling and integration of multi-omics data into precision treatment, however, pose significant challenges at the level of prospective validation and clinical implementation. In this review, we summarize the latest advances in multi-omics tumor profiling, focusing on spatial genomics and chromatin organization, spatial transcriptomics and proteomics, liquid biopsy, and ex vivo modeling of drug response. We analyze the current stages of translational validation of these technologies and discuss future perspectives for their integration into precision treatment.
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Affiliation(s)
- Dilara Akhoundova
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland; Department of Medical Oncology, Inselspital, University Hospital of Bern, 3010 Bern, Switzerland
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland; Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, 3008 Bern, Switzerland.
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15
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Cooper GW, Hong AL. SMARCB1-Deficient Cancers: Novel Molecular Insights and Therapeutic Vulnerabilities. Cancers (Basel) 2022; 14:cancers14153645. [PMID: 35892904 PMCID: PMC9332782 DOI: 10.3390/cancers14153645] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Loss of SMARCB1 has been identified as the sole mutation in a number of rare pediatric and adult cancers, most of which have a poor prognosis despite intensive therapies including surgery, radiation, and chemotherapy. Thus, a more robust understanding of the mechanisms driving this set of cancers is vital to improving patient treatment and outcomes. This review outlines recent advances made in our understanding of the function of SMARCB1 and how these advances have been used to discover putative therapeutic vulnerabilities. Abstract SMARCB1 is a critical component of the BAF complex that is responsible for global chromatin remodeling. Loss of SMARCB1 has been implicated in the initiation of cancers such as malignant rhabdoid tumor (MRT), atypical teratoid rhabdoid tumor (ATRT), and, more recently, renal medullary carcinoma (RMC). These SMARCB1-deficient tumors have remarkably stable genomes, offering unique insights into the epigenetic mechanisms in cancer biology. Given the lack of druggable targets and the high mortality associated with SMARCB1-deficient tumors, a significant research effort has been directed toward understanding the mechanisms of tumor transformation and proliferation. Accumulating evidence suggests that tumorigenicity arises from aberrant enhancer and promoter regulation followed by dysfunctional transcriptional control. In this review, we outline key mechanisms by which loss of SMARCB1 may lead to tumor formation and cover how these mechanisms have been used for the design of targeted therapy.
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Affiliation(s)
- Garrett W. Cooper
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Andrew L. Hong
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
- Correspondence:
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16
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Zhang C, Li H. Molecular targeted therapies for pediatric atypical teratoid/rhabdoid tumors. Pediatr Investig 2022; 6:111-122. [PMID: 35774526 PMCID: PMC9218972 DOI: 10.1002/ped4.12325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/26/2022] [Indexed: 01/01/2023] Open
Affiliation(s)
- Chang Zhang
- Department of Neurosurgery Children's Hospital of Fudan University Shanghai China
| | - Hao Li
- Department of Neurosurgery Children's Hospital of Fudan University Shanghai China
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17
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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 DOI: 10.1158/1535-7163.mct-21-0646] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [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, Chicago, Illinois
| | - Yongzhan Zhang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | - Ali Zhang
- Department of Neurosurgical Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Takahiro Sasaki
- Department of Neurosurgical Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Andrea Piunti
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Amreena Suri
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Jun Watanabe
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Neurological Surgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kouki Abe
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Xingyao He
- Department of Neurosurgical Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Hiroaki Katagi
- Department of Neurosurgical Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Pankaj Bhalla
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Manabu Natsumeda
- Department of Neurological Surgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Lihua Zou
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Rintaro Hashizume
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Neuro-Oncology and Stem Cells Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
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18
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Drosos Y, Myers JA, Xu B, Mathias KM, Beane EC, Radko-Juettner S, Mobley RJ, Larsen ME, Piccioni F, Ma X, Low J, Hansen BS, Peters ST, Bhanu NV, Dhanda SK, Chen T, Upadhyaya SA, Pruett-Miller SM, Root DE, Garcia BA, Partridge JF, Roberts CW. NSD1 mediates antagonism between SWI/SNF and polycomb complexes and is required for transcriptional activation upon EZH2 inhibition. Mol Cell 2022; 82:2472-2489.e8. [DOI: 10.1016/j.molcel.2022.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/03/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
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19
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Carcamo S, Nguyen CB, Grossi E, Filipescu D, Alpsoy A, Dhiman A, Sun D, Narang S, Imig J, Martin TC, Parsons R, Aifantis I, Tsirigos A, Aguirre-Ghiso JA, Dykhuizen EC, Hasson D, Bernstein E. Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma. Cell Rep 2022; 39:110637. [PMID: 35385731 PMCID: PMC9013128 DOI: 10.1016/j.celrep.2022.110637] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/04/2022] [Accepted: 03/16/2022] [Indexed: 12/25/2022] Open
Abstract
ARID2 is the most recurrently mutated SWI/SNF complex member in melanoma; however, its tumor-suppressive mechanisms in the context of the chromatin landscape remain to be elucidated. Here, we model ARID2 deficiency in melanoma cells, which results in defective PBAF complex assembly with a concomitant genomic redistribution of the BAF complex. Upon ARID2 depletion, a subset of PBAF and shared BAF-PBAF-occupied regions displays diminished chromatin accessibility and associated gene expression, while BAF-occupied enhancers gain chromatin accessibility and expression of genes linked to the process of invasion. As a function of altered accessibility, the genomic occupancy of melanoma-relevant transcription factors is affected and significantly correlates with the observed transcriptional changes. We further demonstrate that ARID2-deficient cells acquire the ability to colonize distal organs in multiple animal models. Taken together, our results reveal a role for ARID2 in mediating BAF and PBAF subcomplex chromatin dynamics with consequences for melanoma metastasis.
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Affiliation(s)
- Saul Carcamo
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christie B Nguyen
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena Grossi
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan Filipescu
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aktan Alpsoy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Dan Sun
- Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sonali Narang
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York, NY 10016, USA
| | - Jochen Imig
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York, NY 10016, USA
| | - Tiphaine C Martin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ramon Parsons
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York, NY 10016, USA
| | - Aristotelis Tsirigos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, New York, NY 10016, USA; Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY 10016, USA
| | - Julio A Aguirre-Ghiso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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20
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Parkhurst A, Wang SZ, Findlay TR, Malebranche KJ, Odabas A, Alt J, Maxwell MJ, Kaur H, Peer CJ, Figg WD, Warren KE, Slusher BS, Eberhart CG, Raabe EH, Rubens JA. Dual mTORC1/2 inhibition compromises cell defenses against exogenous stress potentiating Obatoclax-induced cytotoxicity in atypical teratoid/rhabdoid tumors. Cell Death Dis 2022; 13:410. [PMID: 35484114 PMCID: PMC9050713 DOI: 10.1038/s41419-022-04868-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 04/08/2022] [Accepted: 04/19/2022] [Indexed: 11/09/2022]
Abstract
AbstractAtypical teratoid/rhabdoid tumors (AT/RT) are the most common malignant brain tumors of infancy and have a dismal 4-year event-free survival (EFS) of 37%. We have previously shown that mTOR activation contributes to AT/RT’s aggressive growth and poor survival. Targeting the mTOR pathway with the dual mTORC1/2 inhibitor TAK-228 slows tumor growth and extends survival in mice bearing orthotopic xenografts. However, responses are primarily cytostatic with limited durability. The aim of this study is to understand the impact of mTOR inhibitors on AT/RT signaling pathways and design a rational combination therapy to drive a more durable response to this promising therapy. We performed RNASeq, gene expression studies, and protein analyses to identify pathways disrupted by TAK-228. We find that TAK-228 decreases the expression of the transcription factor NRF2 and compromises AT/RT cellular defenses against oxidative stress and apoptosis. The BH3 mimetic, Obatoclax, is a potent inducer of oxidative stress and apoptosis in AT/RT. These complementary mechanisms of action drive extensive synergies between TAK-228 and Obatoclax slowing AT/RT cell growth and inducing apoptosis and cell death. Combination therapy activates the integrative stress response as determined by increased expression of phosphorylated EIF2α, ATF4, and CHOP, and disrupts the protective NOXA.MCL-1.BIM axis, forcing stressed cells to undergo apoptosis. Combination therapy is well tolerated in mice bearing orthotopic xenografts of AT/RT, slows tumor growth, and extends median overall survival. This novel combination therapy could be added to standard upfront therapies or used as a salvage therapy for relapsed disease to improve outcomes in AT/RT.
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21
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Epigenetic mechanisms in paediatric brain tumours: regulators lose control. Biochem Soc Trans 2022; 50:167-185. [PMID: 35076654 DOI: 10.1042/bst20201227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/28/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]
Abstract
Epigenetic mechanisms are essential to regulate gene expression during normal development. However, they are often disrupted in pathological conditions including tumours, where they contribute to their formation and maintenance through altered gene expression. In recent years, next generation genomic techniques has allowed a remarkable advancement of our knowledge of the genetic and molecular landscape of paediatric brain tumours and have highlighted epigenetic deregulation as a common hallmark in their pathogenesis. This review describes the main epigenetic dysregulations found in paediatric brain tumours, including at DNA methylation and histone modifications level, in the activity of chromatin-modifying enzymes and in the expression of non-coding RNAs. How these altered processes influence tumour biology and how they can be leveraged to dissect the molecular heterogeneity of these tumours and contribute to their classification is also addressed. Finally, the availability and value of preclinical models as well as the current clinical trials exploring targeting key epigenetic mediators in paediatric brain tumours are discussed.
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22
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Hasselblatt M, Thomas C, Federico A, Bens S, Hellström M, Casar‐Borota O, Kordes U, Neumann JE, Dottermusch M, Rodriguez FJ, Lo AC, Cheng S, Hendson G, Hukin J, Hartmann C, Koch A, Capper D, Siebert R, Paulus W, Nemes K, Johann PD, Frühwald MC, Kool M. Low‐grade diffusely infiltrative tumour (LGDIT), SMARCB1‐mutant: a clinical and histopathological distinct entity showing epigenetic similarity with ATRT‐MYC. Neuropathol Appl Neurobiol 2022; 48:e12797. [DOI: 10.1111/nan.12797] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/03/2022] [Accepted: 02/05/2022] [Indexed: 11/30/2022]
Affiliation(s)
| | - Christian Thomas
- Institute of Neuropathology University Hospital Münster Münster Germany
| | - Aniello Federico
- Hopp Children´s Cancer Center (KiTZ), Heidelberg Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg Germany
| | - Susanne Bens
- Institute of Human Genetics Ulm University & Ulm University Medical Center Ulm Germany
| | - Mats Hellström
- Dept. of Immunology, Genetics and Pathology, Rudbeck Laboratory Uppsala University Uppsala Sweden
| | - Olivera Casar‐Borota
- Dept. of Immunology, Genetics and Pathology, Rudbeck Laboratory Uppsala University Uppsala Sweden
- Dept. of Clinical Pathology Uppsala University Hospital Uppsala Sweden
| | - Uwe Kordes
- Dept. of Pediatric Hematology and Oncology University Medical Center, Hamburg‐Eppendorf Hamburg Germany
| | - Julia E. Neumann
- Institute of Neuropathology, University Medical Center, Hamburg‐Eppendorf Hamburg Germany
- Center for Molecular Neurobiology Hamburg (ZMNH) University Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Matthias Dottermusch
- Institute of Neuropathology, University Medical Center, Hamburg‐Eppendorf Hamburg Germany
- Center for Molecular Neurobiology Hamburg (ZMNH) University Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Fausto J. Rodriguez
- Dept. of Pathology The Johns Hopkins University School of Medicine Baltimore MD USA
| | - Andrea C. Lo
- Radiation Oncology British Columbia Cancer and University of British Columbia Vancouver Canada
| | - Sylvia Cheng
- Division of Hematology, Oncology & BMT, Department of Pediatrics University of British Columbia Vancouver Canada
| | - Glenda Hendson
- Dept. of Pathology, BC Women and Children's Hospital Vancouver Canada
| | - Juliette Hukin
- Division of Hematology, Oncology & BMT, Department of Pediatrics University of British Columbia Vancouver Canada
| | - Christian Hartmann
- Dept. of Neuropathology Institute of Pathology, Hannover Medical School Hannover Germany
| | - Arend Koch
- Charité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu Berlin, Dept. of Neuropathology Berlin Germany
| | - David Capper
- Charité ‐ Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu Berlin, Dept. of Neuropathology Berlin Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg Germany
| | - Reiner Siebert
- Institute of Human Genetics Ulm University & Ulm University Medical Center Ulm Germany
| | - Werner Paulus
- Institute of Neuropathology University Hospital Münster Münster Germany
| | - Karolina Nemes
- Pediatric and Adolescent Medicine, Swabian Childrens' Cancer Center University Childrens' Hospital Medical Center Augsburg and EU‐RHAB Registry Augsburg Germany
| | - Pascal D. Johann
- Hopp Children´s Cancer Center (KiTZ), Heidelberg Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg Germany
- Pediatric and Adolescent Medicine, Swabian Childrens' Cancer Center University Childrens' Hospital Medical Center Augsburg and EU‐RHAB Registry Augsburg Germany
| | - Michael C. Frühwald
- Pediatric and Adolescent Medicine, Swabian Childrens' Cancer Center University Childrens' Hospital Medical Center Augsburg and EU‐RHAB Registry Augsburg Germany
| | - Marcel Kool
- Hopp Children´s Cancer Center (KiTZ), Heidelberg Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg Germany
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
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23
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Rechberger JS, Nesvick CL, Daniels DJ. Atypical teratoid rhabdoid tumor (ATRT): disease mechanisms and potential drug targets. Expert Opin Ther Targets 2022; 26:187-192. [PMID: 35142587 DOI: 10.1080/14728222.2022.2040017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Julian S Rechberger
- Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, MN, United States.,Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Cody L Nesvick
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, United States
| | - David J Daniels
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, United States
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24
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Qi L, Lindsay H, Kogiso M, Du Y, Braun FK, Zhang H, Guo L, Zhao S, Injac SG, Baxter PA, Su JM, Xiao S, Erickson SW, Earley EJ, Teicher B, Smith MA, Li XN. Evaluation of an EZH2 inhibitor in patient-derived orthotopic xenograft models of pediatric brain tumors alone and in combination with chemo- and radiation therapies. J Transl Med 2022; 102:185-193. [PMID: 34802040 PMCID: PMC10228180 DOI: 10.1038/s41374-021-00700-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/09/2022] Open
Abstract
Brain tumors are the leading cause of cancer-related death in children. Tazemetostat is an FDA-approved enhancer of zeste homolog (EZH2) inhibitor. To determine its role in difficult-to-treat pediatric brain tumors, we examined EZH2 levels in a panel of 22 PDOX models and confirmed EZH2 mRNA over-expression in 9 GBM (34.6 ± 12.7-fold) and 11 medulloblastoma models (6.2 ± 1.7 in group 3, 6.0 ± 2.4 in group 4) accompanied by elevated H3K27me3 expression. Therapeutic efficacy was evaluated in 4 models (1 GBM, 2 medulloblastomas and 1 ATRT) via systematically administered tazemetostat (250 and 400 mg/kg, gavaged, twice daily) alone and in combination with cisplatin (5 mg/kg, i.p., twice) and/or radiation (2 Gy/day × 5 days). Compared with the untreated controls, tazemetostat significantly (Pcorrected < 0.05) prolonged survival times in IC-L1115ATRT (101% at 400 mg/kg) and IC-2305GBM (32% at 250 mg/kg, 45% at 400 mg/kg) in a dose-dependent manner. The addition of tazemetostat with radiation was evaluated in 3 models, with only one [IC-1078MB (group 4)] showing a substantial, though not statistically significant, prolongation in survival compared to radiation treatment alone. Combining tazemetostat (250 mg/kg) with cisplatin was not superior to cisplatin alone in any model. Analysis of in vivo drug resistance detected predominance of EZH2-negative cells in the remnant PDOX tumors accompanied by decreased H3K27me2 and H3K27me3 expressions. These data supported the use of tazemetostat in a subset of pediatric brain tumors and suggests that EZH2-negative tumor cells may have caused therapy resistance and should be prioritized for the search of new therapeutic targets.
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Affiliation(s)
- Lin Qi
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
- Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Pharmacology, School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Holly Lindsay
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Mari Kogiso
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Yuchen Du
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
- Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Frank K Braun
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Huiyuan Zhang
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Lei Guo
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Sibo Zhao
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Sarah G Injac
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Patricia A Baxter
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Jack Mf Su
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Sophie Xiao
- Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | | | | | | | - Xiao-Nan Li
- Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA.
- Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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Arakaki AKS, Szulzewsky F, Gilbert MR, Gujral TS, Holland EC. Utilizing preclinical models to develop targeted therapies for rare central nervous system cancers. Neuro Oncol 2021; 23:S4-S15. [PMID: 34725698 PMCID: PMC8561121 DOI: 10.1093/neuonc/noab183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Patients with rare central nervous system (CNS) tumors typically have a poor prognosis and limited therapeutic options. Historically, these cancers have been difficult to study due to small number of patients. Recent technological advances have identified molecular drivers of some of these rare cancers which we can now use to generate representative preclinical models of these diseases. In this review, we outline the advantages and disadvantages of different models, emphasizing the utility of various in vitro and ex vivo models for target discovery and mechanistic inquiry and multiple in vivo models for therapeutic validation. We also highlight recent literature on preclinical model generation and screening approaches for ependymomas, histone mutated high-grade gliomas, and atypical teratoid rhabdoid tumors, all of which are rare CNS cancers that have recently established genetic or epigenetic drivers. These preclinical models are critical to advancing targeted therapeutics for these rare CNS cancers that currently rely on conventional treatments.
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Affiliation(s)
- Aleena K S Arakaki
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Taranjit S Gujral
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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26
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Ding AS, Huq S, Casaos J, Raj D, Morales M, Zhao T, Kim T, Srivastava S, Pant A, Serra R, Gorelick NL, Brem H, Tyler B. Targeting of cyclin-dependent kinases in atypical teratoid rhabdoid tumors with multikinase inhibitor TG02. J Neurosurg Pediatr 2021:1-10. [PMID: 34479190 DOI: 10.3171/2021.5.peds20920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/21/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Atypical teratoid rhabdoid tumors (ATRTs) are aggressive pediatric brain tumors with no current standard of care and an estimated median patient survival of 12 to 18 months. Previous genetic analyses have implicated cyclin D1 and enhancer of zeste homolog 2 (EZH2), a histone methyltransferase that is implicated in many cancers, as key drivers of tumorigenicity in ATRTs. Since the effects of EZH2 and cyclin D1 are facilitated by a host of cyclin-dependent kinases (CDKs), the authors sought to investigate the potential therapeutic effects of targeting CDKs in ATRTs with the multi-CDK inhibitor, TG02. METHODS Human ATRT cell lines BT12, BT37, CHLA05, and CHLA06 were selected for investigation. The effects of TG02 on cell viability, proliferation, clonogenicity, and apoptosis were assessed via Cell Counting Kit-8 assays, cell counting, clonogenic assays, and flow cytometry, respectively. Similar methods were used to determine the effects of TG02 combined with radiation therapy (RT) or cisplatin. Synergism indices for TG02-cisplatin combination therapy were calculated using CompuSyn software. RESULTS TG02 was observed to significantly impair ATRT cell growth in vitro by limiting cell proliferation and clonogenicity, and by inducing apoptosis. TG02 inhibited ATRT cell proliferation and decreased cell viability in a dose-dependent manner with nanomolar half maximal effective concentration (EC50) values (BT12, 207.0 nM; BT37, 127.8 nM; CHLA05, 29.7 nM; CHLA06, 18.7 nM). TG02 (150 nM) dramatically increased the proportion of apoptotic ATRT cells 72 hours posttreatment (TG02 8.50% vs control 1.52% apoptotic cells in BT12, p < 0.0001; TG02 70.07% vs control 15.36%, p < 0.0001). Combination therapy studies revealed that TG02 acted as a potent radiosensitizer in ATRT cells (BT12 surviving fraction, RT 51.2% vs RT + TG02 21.7%). Finally, CompuSyn analysis demonstrated that TG02 acted synergistically with cisplatin against ATRT cells at virtually all therapeutic doses. These findings were consistent in cell lines that cover all three molecular subgroups of ATRTs. CONCLUSIONS The results of this investigation have established that TG02 is an effective therapeutic against ATRTs in vitro. Given the lack of standard therapy for ATRTs, these findings help fill an unmet need and support further study of TG02 as a potential therapeutic option for patients with this deadly disease.
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Affiliation(s)
- Andy S. Ding
- Hunterian Neurosurgical Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sakibul Huq
- Hunterian Neurosurgical Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joshua Casaos
- Hunterian Neurosurgical Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Divyaansh Raj
- Hunterian Neurosurgical Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Manuel Morales
- Hunterian Neurosurgical Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tianna Zhao
- Hunterian Neurosurgical Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Timothy Kim
- Hunterian Neurosurgical Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Siddhartha Srivastava
- Hunterian Neurosurgical Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ayush Pant
- Hunterian Neurosurgical Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Riccardo Serra
- Hunterian Neurosurgical Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Noah L. Gorelick
- Hunterian Neurosurgical Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Henry Brem
- Hunterian Neurosurgical Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Betty Tyler
- Hunterian Neurosurgical Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
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27
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β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture. Nat Commun 2021; 12:5240. [PMID: 34475390 PMCID: PMC8413440 DOI: 10.1038/s41467-021-25596-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/18/2021] [Indexed: 02/07/2023] Open
Abstract
β-actin is a crucial component of several chromatin remodeling complexes that control chromatin structure and accessibility. The mammalian Brahma-associated factor (BAF) is one such complex that plays essential roles in development and differentiation by regulating the chromatin state of critical genes and opposing the repressive activity of polycomb repressive complexes (PRCs). While previous work has shown that β-actin loss can lead to extensive changes in gene expression and heterochromatin organization, it is not known if changes in β-actin levels can directly influence chromatin remodeling activities of BAF and polycomb proteins. Here we conduct a comprehensive genomic analysis of β-actin knockout mouse embryonic fibroblasts (MEFs) using ATAC-Seq, HiC-seq, RNA-Seq and ChIP-Seq of various epigenetic marks. We demonstrate that β-actin levels can induce changes in chromatin structure by affecting the complex interplay between chromatin remodelers such as BAF/BRG1 and EZH2. Our results show that changes in β-actin levels and associated chromatin remodeling activities can not only impact local chromatin accessibility but also induce reversible changes in 3D genome architecture. Our findings reveal that β-actin-dependent chromatin remodeling plays a role in shaping the chromatin landscape and influences the regulation of genes involved in development and differentiation.
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28
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Plant-Fox AS, O'Halloran K, Goldman S. Pediatric brain tumors: the era of molecular diagnostics, targeted and immune-based therapeutics, and a focus on long term neurologic sequelae. Curr Probl Cancer 2021; 45:100777. [PMID: 34303558 DOI: 10.1016/j.currproblcancer.2021.100777] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022]
Abstract
Pediatric brain tumors are the second most common malignancy of childhood after acute leukemia and the number one cause of cancer-related mortality1. Over the past decade, advanced molecular diagnostics have led to the discovery of new molecularly-defined tumor types with prognostic and therapeutic implications. Methylation profiles, whole genome sequencing, and transcriptomics have defined subgroups and revealed heterogeneity within commonly defined tumor entities2,3. These findings have also revealed important differences between adult and pediatric brain tumors of similar histology. The majority of pediatric low grade gliomas (pLGG) are defined by alterations in the mitogen-activated protein kinase (MAPK) pathway including BRAFV600E point mutation, K1AA1549-BRAF fusion, and FGFR1 alterations as opposed to IDH1/2 mutations and 1p/19q co-deletion seen more frequently in adult low grade gliomas4. These findings have led to targeted therapies, namely BRAF and MEK inhibitors, which are currently being evaluated in phase III clinical trials and may soon supplant chemotherapy as standard of care for pLGG's. While targeted therapy trials for pediatric brain tumors have had significant success, immunotherapy remains a challenge in a group of tumors with generally lower mutational burden compared to adult tumors and relatively "cold" immune microenvironment. Despite this, a wide array of immunotherapy trials including vaccine therapies, immune checkpoint blockade, chimeric antigen receptor (CAR) T cells, and viral therapies are on-going. Unique to pediatrics, multiple clinical trials have sought to answer the question of whether the most malignant pediatric brain tumors in the youngest patients can be successfully treated with high dose chemotherapy in lieu of radiation to avoid devastating long-term neurocognitive deficits. Due to the collaborative work of multiple pediatric neuro-oncology consortiums, the recent history of pediatric brain tumor research is one of efficient translation from bench to bedside in a rare group of tumors resulting in significant progress in the field. Here, advances in the areas of molecular characterization, targeted and immune-based therapies, and reduction in long term co-morbidities will be reviewed.
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Affiliation(s)
- Ashley S Plant-Fox
- Ann and Robert H. Lurie Children's Hospital of Chicago. Division of Hematology/Oncology/Stem Cell Transplantation/Neuro-Oncology. Chicago, Illinois.
| | - Katrina O'Halloran
- Children's Hospital of Los Angeles. Division of Hematology/Oncology, Los Angeles, California
| | - Stewart Goldman
- Ann and Robert H. Lurie Children's Hospital of Chicago. Division of Hematology/Oncology/Stem Cell Transplantation/Neuro-Oncology. Chicago, Illinois
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29
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Krug B, Harutyunyan AS, Deshmukh S, Jabado N. Polycomb repressive complex 2 in the driver's seat of childhood and young adult brain tumours. Trends Cell Biol 2021; 31:814-828. [PMID: 34092471 DOI: 10.1016/j.tcb.2021.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 11/19/2022]
Abstract
Deregulation of the epigenome underlies oncogenesis in numerous primary brain tumours in children and young adults. In this review, we describe how recurrent mutations in isocitrate dehydrogenases or histone 3 variants (oncohistones) in gliomas, expression of the oncohistone mimic enhancer of Zeste homologs inhibiting protein (EZHIP) in a subgroup of ependymoma, and epigenetic alterations in other embryonal tumours promote oncogenicity. We review the proposed mechanisms of cellular transformation, current tumorigenesis models and their link to development. We further stress the narrow developmental windows permissive to their oncogenic potential and how this may stem from converging effects deregulating polycomb repressive complex (PRC)2 function and targets. As altered chromatin states may be reversible, improved understanding of aberrant cancer epigenomes could orient the design of effective therapies.
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Affiliation(s)
- Brian Krug
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Shriya Deshmukh
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, Canada; Division of Experimental Medicine, McGill University, Montreal, QC, Canada; Department of Pediatrics, McGill University, Montreal, QC, Canada; The Research Institute of the McGill University Health Center, Montreal, H4A 3J, Canada.
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30
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Peneder P, Stütz AM, Surdez D, Krumbholz M, Semper S, Chicard M, Sheffield NC, Pierron G, Lapouble E, Tötzl M, Ergüner B, Barreca D, Rendeiro AF, Agaimy A, Boztug H, Engstler G, Dworzak M, Bernkopf M, Taschner-Mandl S, Ambros IM, Myklebost O, Marec-Bérard P, Burchill SA, Brennan B, Strauss SJ, Whelan J, Schleiermacher G, Schaefer C, Dirksen U, Hutter C, Boye K, Ambros PF, Delattre O, Metzler M, Bock C, Tomazou EM. Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden. Nat Commun 2021; 12:3230. [PMID: 34050156 PMCID: PMC8163828 DOI: 10.1038/s41467-021-23445-w] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/29/2021] [Indexed: 12/19/2022] Open
Abstract
Sequencing of cell-free DNA in the blood of cancer patients (liquid biopsy) provides attractive opportunities for early diagnosis, assessment of treatment response, and minimally invasive disease monitoring. To unlock liquid biopsy analysis for pediatric tumors with few genetic aberrations, we introduce an integrated genetic/epigenetic analysis method and demonstrate its utility on 241 deep whole-genome sequencing profiles of 95 patients with Ewing sarcoma and 31 patients with other pediatric sarcomas. Our method achieves sensitive detection and classification of circulating tumor DNA in peripheral blood independent of any genetic alterations. Moreover, we benchmark different metrics for cell-free DNA fragmentation analysis, and we introduce the LIQUORICE algorithm for detecting circulating tumor DNA based on cancer-specific chromatin signatures. Finally, we combine several fragmentation-based metrics into an integrated machine learning classifier for liquid biopsy analysis that exploits widespread epigenetic deregulation and is tailored to cancers with low mutation rates. Clinical associations highlight the potential value of cfDNA fragmentation patterns as prognostic biomarkers in Ewing sarcoma. In summary, our study provides a comprehensive analysis of circulating tumor DNA beyond recurrent genetic aberrations, and it renders the benefits of liquid biopsy more readily accessible for childhood cancers.
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Affiliation(s)
- Peter Peneder
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Adrian M Stütz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Manuela Krumbholz
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Sabine Semper
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Mathieu Chicard
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Nathan C Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Eve Lapouble
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Marcus Tötzl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Bekir Ergüner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniele Barreca
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André F Rendeiro
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Erlangen, Germany
| | - Heidrun Boztug
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Gernot Engstler
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Michael Dworzak
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Marie Bernkopf
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | | | - Inge M Ambros
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ola Myklebost
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Perrine Marec-Bérard
- Pediatric Department, Hematology and Oncology Pediatric Institute, Centre Léon Bérard, Lyon, France
| | - Susan Ann Burchill
- Children's Cancer Research Group, Leeds Institute of Medical Research, St. James's University Hospital, Leeds, UK
| | - Bernadette Brennan
- Department of Pediatric Oncology, Royal Manchester Children's Hospital, Manchester, UK
| | - Sandra J Strauss
- Department of Oncology, UCL Cancer Institute, London, UK
- Department of Oncology, University College London Hospital, London, UK
| | - Jeremy Whelan
- Department of Oncology, University College London Hospital, London, UK
| | - Gudrun Schleiermacher
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Christiane Schaefer
- University Hospital Essen, Pediatrics III, West German Cancer Centre, Essen, Germany
| | - Uta Dirksen
- University Hospital Essen, Pediatrics III, West German Cancer Centre, Essen, Germany
| | - Caroline Hutter
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Kjetil Boye
- Department of Oncology, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Peter F Ambros
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Markus Metzler
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria.
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.
| | - Eleni M Tomazou
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
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31
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Ho B, Johann PD, Grabovska Y, De Dieu Andrianteranagna MJ, Yao F, Frühwald M, Hasselblatt M, Bourdeaut F, Williamson D, Huang A, Kool M. Molecular subgrouping of atypical teratoid/rhabdoid tumors-a reinvestigation and current consensus. Neuro Oncol 2021; 22:613-624. [PMID: 31889194 PMCID: PMC7229260 DOI: 10.1093/neuonc/noz235] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background Atypical teratoid/rhabdoid tumors (ATRTs) are known to exhibit molecular and clinical heterogeneity even though SMARCB1 inactivation is the sole recurrent genetic event present in nearly all cases. Indeed, recent studies demonstrated 3 molecular subgroups of ATRTs that are genetically, epigenetically, and clinically distinct. As these studies included different numbers of tumors, various subgrouping techniques, and naming, an international working group sought to align previous findings and to reach a consensus on nomenclature and clinicopathological significance of ATRT subgroups. Methods We integrated various methods to perform a meta-analysis on published and unpublished DNA methylation and gene expression datasets of ATRTs and associated clinicopathological data. Results In concordance with previous studies, the analyses identified 3 main molecular subgroups of ATRTs, for which a consensus was reached to name them ATRT-TYR, ATRT-SHH, and ATRT-MYC. The ATRT-SHH subgroup exhibited further heterogeneity, segregating further into 2 subtypes associated with a predominant supratentorial (ATRT-SHH-1) or infratentorial (ATRT-SHH-2) location. For each ATRT subgroup we provide an overview of its main molecular and clinical characteristics, including SMARCB1 alterations and pathway activation. Conclusions The introduction of a common classification, characterization, and nomenclature of ATRT subgroups will facilitate future research and serve as a common ground for subgrouping patient samples and ATRT models, which will aid in refining subgroup-based therapies for ATRT patients.
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Affiliation(s)
- Ben Ho
- Division of Hematology and Oncology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pascal D Johann
- Hopp Children's Cancer Center, Heidelberg, Germany.,Division of Pediatric Neuro-oncology, German Cancer Research Center and German Cancer Research Consortium, Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Yura Grabovska
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Mamy Jean De Dieu Andrianteranagna
- Departments of Genetics and of Oncopediatry and Young Adults, Curie Institute, Paris, France.,INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
| | - Fupan Yao
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Michael Frühwald
- University Children's Hospital Augsburg, Swabian Children's Cancer Center, Augsburg, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Franck Bourdeaut
- Departments of Genetics and of Oncopediatry and Young Adults, Curie Institute, Paris, France.,INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Annie Huang
- Division of Hematology and Oncology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Marcel Kool
- Hopp Children's Cancer Center, Heidelberg, Germany.,Division of Pediatric Neuro-oncology, German Cancer Research Center and German Cancer Research Consortium, Heidelberg, Germany
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32
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Panwalkar P, Pratt D, Chung C, Dang D, Le P, Martinez D, Bayliss JM, Smith KS, Adam M, Potter S, Northcott PA, Mascarenhas L, Shows J, Pawel B, Margol A, Huang A, Judkins AR, Venneti S. SWI/SNF complex heterogeneity is related to polyphenotypic differentiation, prognosis, and immune response in rhabdoid tumors. Neuro Oncol 2021; 22:785-796. [PMID: 31912158 DOI: 10.1093/neuonc/noaa004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Rhabdoid tumors (RTs) arise within (atypical teratoid/rhabdoid tumor [AT/RT]) or outside the brain (extra [e]CNS-RT) and are driven mainly by inactivation of the SWItch/sucrose nonfermentable (SWI/SNF) complex subunit SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1). A pathognomonic hallmark of RTs is heterogeneous multilineage differentiation, including anomalous neuronal differentiation in some eCNS-RTs. Because remodeling of the SWI/SNF complex regulates differentiation, we hypothesized that SWI/SNF Brahma-associated factors (BAF) and polybromo-associated BAF (PBAF) complex heterogeneity are related to both multilineage differentiation and clinical outcome. METHODS We performed an integrated analysis of SWI/SNF complex alterations in the developing kidney and cerebellum (most common regions of RT origin) in comparison to eCNS-RT (n = 14) and AT/RT (n = 25) tumors. RT samples were interrogated using immunohistochemistry, DNA methylation, and gene expression analyses. RESULTS The SWI/SNF BAF paralogs actin-like protein (ACTL)6A and ACTL6B were expressed in a mutually exclusive manner in the developing cerebellum and kidney. In contrast, a subset of eCNS-RTs lost mutual exclusivity and coexpressed both subunits. These tumors showed aberrant DNA methylation of genes that regulate neuronal and renal development and demonstrated immunohistochemical evidence of neuronal differentiation. In addition, low expression of the PBAF subunit polybromo-1 (PBRM1) identified a group of AT/RTs in younger children with better overall prognosis. PBRM1-low AT/RT and eCNS-RTs showed altered DNA methylation and gene expression in immune-related genes. PBRM1 knockdown resulted in lowering immunosuppressive cytokines, and PBRM1 levels in tumor samples showed an inverse relationship with cluster of differentiation (CD)8 cytotoxic T-cell infiltration. CONCLUSIONS Heterogeneity in SWI/SNF BAF (ACTL6A/ACTL6B) and PBAF (PBRM1) subunits is related to histogenesis, contributes to the immune microenvironment and prognosis in RTs, and may inform opportunities to develop immunotherapies.
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Affiliation(s)
- Pooja Panwalkar
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Drew Pratt
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Chan Chung
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Derek Dang
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Paul Le
- Department of Pathology, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel Martinez
- Department of Pathology, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jill M Bayliss
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kyle S Smith
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Mike Adam
- Division of Pediatric Urology and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Steven Potter
- Division of Pediatric Urology and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Leo Mascarenhas
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California, USA.,Department of Pediatrics, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Jared Shows
- Department of Pathology, Long Beach Memorial Medical Center/Miller Children's Hospital, Long Beach, California, USA
| | - Bruce Pawel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, California, USA
| | - Ashley Margol
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California, USA.,Department of Pediatrics, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Annie Huang
- Division of Hematology/Oncology, Department of Pediatrics, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine University of Southern California, Los Angeles, California, USA
| | - Sriram Venneti
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA
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33
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Hoffman LM, Richardson EA, Ho B, Margol A, Reddy A, Lafay-Cousin L, Chi S, Slavc I, Judkins A, Hasselblatt M, Bourdeaut F, Frühwald MC, Vibhakar R, Bouffet E, Huang A. Advancing biology-based therapeutic approaches for atypical teratoid rhabdoid tumors. Neuro Oncol 2021; 22:944-954. [PMID: 32129445 DOI: 10.1093/neuonc/noaa046] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Atypical teratoid rhabdoid tumor (ATRT) is a rare, highly malignant central nervous system cancer arising in infants and younger children, historically considered to be homogeneous, monogenic, and incurable. Recent use of intensified therapies has modestly improved survival for ATRT; however, a majority of patients will still succumb to their disease. While ATRTs almost universally exhibit loss of SMARCB1 (BAF47/INI1/SNF5), recent whole genome, transcriptome, and epigenomic analyses of large cohorts reveal previously underappreciated molecular heterogeneity. These discoveries provide novel insights into how SMARCB1 loss drives oncogenesis and confer specific therapeutic vulnerabilities, raising exciting prospects for molecularly stratified treatment for patients with ATRT.
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Affiliation(s)
- Lindsey M Hoffman
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - Elizabeth Anne Richardson
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ben Ho
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ashley Margol
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California, USA.,Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Alyssa Reddy
- Departments of Neurology and Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Lucie Lafay-Cousin
- Department of Pediatric Hematology Oncology and Blood and Marrow Transplantation, Alberta Children's Hospital, Calgary, Alberta, Canada.,Department of Paediatrics and Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Susan Chi
- Pediatric Medical Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.,Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Alexander Judkins
- Center for Personalized Medicine, Children's Hospital of Los Angeles.,Pathology and Laboratory Medicine, Children's Hospital of Los Angeles.,Department of Pathology, Keck School of Medicine University of Southern California, Los Angeles, California, USA
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Franck Bourdeaut
- Curie Institute, Integrated Cancer Research Site, Paris, France.,Departments of Genetics and of Oncopediatry and Young Adults, Curie Institute, Paris, France.,INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
| | - Michael C Frühwald
- Swabian Children's Cancer Center, University Children's Hospital, University Hospital Augsburg, Augsburg, Germany.,Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, University of Münster, Münster, Germany.,EU-RHAB Registry Working Group, Augsburg, Germany
| | - Rajeev Vibhakar
- Department of Pediatrics, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA.,Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado, USA.,Department of Neurosurgery, University of Colorado Denver, Aurora, Colorado, USA
| | - Eric Bouffet
- Child Health Evaluative Sciences, SickKids Research Institute, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada.,Division of Hematology/Oncology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Annie Huang
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada.,Division of Hematology/Oncology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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34
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Custers L, Khabirova E, Coorens THH, Oliver TRW, Calandrini C, Young MD, Vieira Braga FA, Ellis P, Mamanova L, Segers H, Maat A, Kool M, Hoving EW, van den Heuvel-Eibrink MM, Nicholson J, Straathof K, Hook L, de Krijger RR, Trayers C, Allinson K, Behjati S, Drost J. Somatic mutations and single-cell transcriptomes reveal the root of malignant rhabdoid tumours. Nat Commun 2021; 12:1407. [PMID: 33658498 PMCID: PMC7930245 DOI: 10.1038/s41467-021-21675-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 02/05/2021] [Indexed: 11/08/2022] Open
Abstract
Malignant rhabdoid tumour (MRT) is an often lethal childhood cancer that, like many paediatric tumours, is thought to arise from aberrant fetal development. The embryonic root and differentiation pathways underpinning MRT are not firmly established. Here, we study the origin of MRT by combining phylogenetic analyses and single-cell mRNA studies in patient-derived organoids. Comparison of somatic mutations shared between cancer and surrounding normal tissues places MRT in a lineage with neural crest-derived Schwann cells. Single-cell mRNA readouts of MRT differentiation, which we examine by reverting the genetic driver mutation underpinning MRT, SMARCB1 loss, suggest that cells are blocked en route to differentiating into mesenchyme. Quantitative transcriptional predictions indicate that combined HDAC and mTOR inhibition mimic MRT differentiation, which we confirm experimentally. Our study defines the developmental block of MRT and reveals potential differentiation therapies.
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Affiliation(s)
- Lars Custers
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
- Oncode Institute, 3584CS, Utrecht, the Netherlands
| | | | - Tim H H Coorens
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Camilla Calandrini
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
- Oncode Institute, 3584CS, Utrecht, the Netherlands
| | - Matthew D Young
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
| | | | - Peter Ellis
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
| | - Heidi Segers
- Department of Pediatric Hemato-Oncology, University Hospital Leuven, Leuven, Belgium
| | - Arie Maat
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
- Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center DKFZ and German Cancer Consortium DKTK, 69120, Heidelberg, Germany
| | - Eelco W Hoving
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
| | | | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Karin Straathof
- UCL Great Ormond Street Hospital Institute of Child Health Biomedical Research Centre, London, WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
| | - Liz Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
- Department of Pathology, University Medical Center Utrecht, 3584CX, Utrecht, the Netherlands
| | - Claire Trayers
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Kieren Allinson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands.
- Oncode Institute, 3584CS, Utrecht, the Netherlands.
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35
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Abstract
The key differences between tumors arising in children and those in adults stem from the cellular origin of cancer at different ages, with adult cancers arising within aging cell hierarchies, as a consequence of accumulated damage and mutagenesis, in contrast to childhood tumors that are born in aberrantly developing tissues. A distinct biological property of childhood tumor cells-a block of developmental maturation-may hold the key to advancing the treatment of childhood cancer beyond cytotoxic strategies.
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Affiliation(s)
- Sam Behjati
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Division of Pediatric Neurooncology, Heidelberg, Germany
- Heidelberg University Hospital, Department of Pediatric Hematology and Oncology, Heidelberg, Germany
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36
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Custers L, Paassen I, Drost J. In vitro Modeling of Embryonal Tumors. Front Cell Dev Biol 2021; 9:640633. [PMID: 33718380 PMCID: PMC7952537 DOI: 10.3389/fcell.2021.640633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/25/2021] [Indexed: 01/06/2023] Open
Abstract
A subset of pediatric tumors affects very young children and are thought to arise during fetal life. A common theme is that these embryonal tumors hijack developmental programs, causing a block in differentiation and, as a consequence, unrestricted proliferation. Embryonal tumors, therefore typically maintain an embryonic gene signature not found in their differentiated progeny. Still, the processes underpinning malignant transformation remain largely unknown, which is hampering therapeutic innovation. To gain more insight into these processes, in vitro and in vivo research models are indispensable. However, embryonic development is an extremely dynamic process with continuously changing cellular identities, making it challenging to define cells-of-origin. This is crucial for the development of representative models, as targeting the wrong cell or targeting a cell within an incorrect developmental time window can result in completely different phenotypes. Recent innovations in in vitro cell models may provide more versatile platforms to study embryonal tumors in a scalable manner. In this review, we outline different in vitro models that can be explored to study embryonal tumorigenesis and for therapy development.
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Affiliation(s)
- Lars Custers
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Irene Paassen
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
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37
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Pyziak K, Sroka-Porada A, Rzymski T, Dulak J, Łoboda A. Potential of enhancer of zeste homolog 2 inhibitors for the treatment of SWI/SNF mutant cancers and tumor microenvironment modulation. Drug Dev Res 2021; 82:730-753. [PMID: 33565092 DOI: 10.1002/ddr.21796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 12/17/2022]
Abstract
Enhancer of zeste homolog 2 (EZH2), a catalytic component of polycomb repressive complex 2 (PRC2), is commonly overexpressed or mutated in many cancer types, both of hematological and solid nature. Till now, plenty of EZH2 small molecule inhibitors have been developed and some of them have already been tested in clinical trials. Most of these inhibitors, however, are effective only in limited cases in the context of EZH2 gain-of-function mutated tumors such as lymphomas. Other cancer types with aberrant EZH2 expression and function require alternative approaches for successful treatment. One possibility is to exploit synthetic lethal strategy, which is based on the phenomenon that concurrent loss of two genes is detrimental but the deletion of either of them leaves cell viable. In the context of EZH2/PRC2, the most promising synthetic lethal target seems to be SWItch/Sucrose Non-Fermentable chromatin remodeling complex (SWI/SNF), which is known to counteract PRC2 functions. SWI/SNF is heavily involved in carcinogenesis and its subunits have been found mutated in approximately 20% of tumors of different kinds. In the current review, we summarize the existing knowledge of synthetic lethal relationships between EZH2/PRC2 and components of the SWI/SNF complex and discuss in detail the potential application of existing EZH2 inhibitors in cancer patients harboring mutations in SWI/SNF proteins. We also highlight recent discoveries of EZH2 involvement in tumor microenvironment regulation and consequences for future therapies. Although clinical studies are limited, the fundamental research might help to understand which patients are most likely to benefit from therapies using EZH2 inhibitors.
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Affiliation(s)
- Karolina Pyziak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.,Biology R&D, Ryvu Therapeutics S.A., Kraków, Poland
| | | | | | - Józef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Agnieszka Łoboda
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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38
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Chasse MH, Johnson BK, Boguslawski EA, Sorensen KM, Rosien JE, Kang MH, Reynolds CP, Heo L, Madaj ZB, Beddows I, Foxa GE, Kitchen‐Goosen SM, Williams BO, Triche TJ, Grohar PJ. Mithramycin induces promoter reprogramming and differentiation of rhabdoid tumor. EMBO Mol Med 2021; 13:e12640. [PMID: 33332735 PMCID: PMC7863405 DOI: 10.15252/emmm.202012640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 12/21/2022] Open
Abstract
Rhabdoid tumor (RT) is a pediatric cancer characterized by the inactivation of SMARCB1, a subunit of the SWI/SNF chromatin remodeling complex. Although this deletion is the known oncogenic driver, there are limited effective therapeutic options for these patients. Here we use unbiased screening of cell line panels to identify a heightened sensitivity of rhabdoid tumor to mithramycin and the second-generation analogue EC8042. The sensitivity of MMA and EC8042 was superior to traditional DNA damaging agents and linked to the causative mutation of the tumor, SMARCB1 deletion. Mithramycin blocks SMARCB1-deficient SWI/SNF activity and displaces the complex from chromatin to cause an increase in H3K27me3. This triggers chromatin remodeling and enrichment of H3K27ac at chromHMM-defined promoters to restore cellular differentiation. These effects occurred at concentrations not associated with DNA damage and were not due to global chromatin remodeling or widespread gene expression changes. Importantly, a single 3-day infusion of EC8042 caused dramatic regressions of RT xenografts, recapitulated the increase in H3K27me3, and cellular differentiation described in vitro to completely cure three out of eight mice.
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Affiliation(s)
| | | | | | | | | | - Min H Kang
- Texas Tech University Health Sciences CenterLubbockTXUSA
| | | | - Lyong Heo
- Van Andel Research InstituteGrand RapidsMIUSA
| | | | - Ian Beddows
- Van Andel Research InstituteGrand RapidsMIUSA
| | | | | | | | | | - Patrick J Grohar
- Van Andel Research InstituteGrand RapidsMIUSA
- The Children's Hospital of PhiladelphiaPhiladelphiaPAUSA
- University of PennsylvaniaPerelman School of MedicinePhiladelphiaPAUSA
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39
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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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40
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Olkhova LV, Kushel YV, Kadyrov SU, Melikyan AG, Gorelyshev SK, Popov VE, Schultz EI, Ryzhova MV, Zheludkova OG. [Influence of resection quality on postoperative outcomes in children with atypical teratoid-rhabdoid tumor of the central nervous system]. ZHURNAL VOPROSY NEIROKHIRURGII IMENI N. N. BURDENKO 2021; 85:17-25. [PMID: 33864665 DOI: 10.17116/neiro20218502117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The purpose of this study was to assess the influence of resection quality on overall survival and disease-free survival in children with atypical teratoid-rhabdoid tumors (ATRT). The study included children younger than 18 years old for the period from 2008 to 2019. There were 134 interventions in 105 patients with ATRT including 11 redo resections («second-look» surgery) and 18 procedures for tumor recurrence. Age of patients ranged from 2 to 168 months (median 21 months). Patients with supratentorial tumors prevailed (50.5%), infratentorial neoplasms were diagnosed in 45.7% of patients, spinal cord lesion - 3.8% of cases. At the first stage, all patients underwent surgical treatment. Total resection was achieved in 34 (32.4%) patients, subtotal - 37 (35.2%) patients, partial resection - 30 (28.6%) patients. Biopsy was performed in 4 (3.8%) patients. Quality of resection and age at surgery significantly influenced overall and disease-free survival. Extended resection of tumor followed by adjuvant chemo- and radiotherapy are required to improve survival although ATRTs are high-grade neoplasms with poor prognosis.
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Affiliation(s)
- L V Olkhova
- Children's Clinical Hospital of the Pirogov Russian National Medical University, Moscow, Russia
| | - Yu V Kushel
- Burdenko Neurosurgical Center, Moscow, Russia
| | | | | | | | - V E Popov
- Vladimirsky Moscow Regional Research Clinical Institute, Moscow, Russia
| | - E I Schultz
- Burdenko Neurosurgical Center, Moscow, Russia
| | - M V Ryzhova
- Burdenko Neurosurgical Center, Moscow, Russia
| | - O G Zheludkova
- Voino-Yasenetsky Research and Practical Center for Specialized Medical Care, Moscow, Russia
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41
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Understanding the epigenetic landscape and cellular architecture of childhood brain tumors. Neurochem Int 2020; 144:104940. [PMID: 33333210 DOI: 10.1016/j.neuint.2020.104940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/12/2020] [Indexed: 11/22/2022]
Abstract
Pediatric brain tumors are the leading cancer-related cause of death in children and adolescents in the United States, affecting on average 1 in 2000 children per year. Recent advances in cancer genomics have led to profound discoveries about the underlying molecular biology and ontogeny of these tumors. In particular, these studies have revealed epigenetic dysregulation to be one of the main hallmarks of pediatric brain tumorigenesis. In this review, we will highlight a number of important recent findings about the nature of this dysregulation in different types of pediatric brain tumors as well as examine their implications for preclinical research and clinical practice. Specifically, we discuss the emergence of methylation signatures as tools for tumor stratification/classification while also highlighting the importance of mutations that directly affect the epigenome and clarifying their impact on risk stratification and pediatric brain tumor biology. We then incorporate recent advances in our understanding of pediatric brain tumor cellular architecture and emphasize the link between epigenetic dysregulation and the "stalled" development seen in many of these malignant neoplasms. Lastly, we explore recentwork investigating the use of these mutated epigenomic regulators as therapeutic targets and extrapolate their utility in overcoming this "stalling" to halt tumor growth.
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42
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Paik S, Maule F, Gallo M. Dysregulation of chromatin organization in pediatric and adult brain tumors: oncoepigenomic contributions to tumorigenesis and cancer stem cell properties. Genome 2020; 64:326-336. [PMID: 33075237 DOI: 10.1139/gen-2020-0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The three-dimensional (3D) organization of the genome is a crucial enabler of cell fate, identity, and function. In this review, we will focus on the emerging role of altered 3D genome organization in the etiology of disease, with a special emphasis on brain cancers. We discuss how different genetic alterations can converge to disrupt the epigenome in childhood and adult brain tumors, by causing aberrant DNA methylation and by affecting the amounts and genomic distribution of histone post-translational modifications. We also highlight examples that illustrate how epigenomic alterations have the potential to affect 3D genome architecture in brain tumors. Finally, we will propose the concept of "epigenomic erosion" to explain the transition from stem-like cells to differentiated cells in hierarchically organized brain cancers.
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Affiliation(s)
- Seungil Paik
- Arnie Charbonneau Cancer Institute, Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Arnie Charbonneau Cancer Institute, Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Francesca Maule
- Arnie Charbonneau Cancer Institute, Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Arnie Charbonneau Cancer Institute, Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Marco Gallo
- Arnie Charbonneau Cancer Institute, Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Arnie Charbonneau Cancer Institute, Alberta Children's Hospital Research Institute, Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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Atypical teratoid rhabdoid tumor: molecular insights and translation to novel therapeutics. J Neurooncol 2020; 150:47-56. [PMID: 33021733 DOI: 10.1007/s11060-020-03639-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Atypical teratoid rhabdoid tumor (ATRT) is a rare, often lethal brain tumor of childhood characterized by a complex epigenetic landscape amongst a simple genetic background. Recent molecular studies have defined key biologic events that contribute to tumorigenesis and molecular subtypes of ATRT. METHODS Seminal studies on ATRT are reviewed with an emphasis on molecular pathogenesis and its relevance to novel therapeutics. RESULTS In this review, we summarize the key clinicopathologic and molecular features of ATRT, completed and ongoing clinical trials and outline the translational potential of novel insights into the molecular pathogenesis of this tumor. CONCLUSIONS SMARCB1 loss is the key genetic event in ATRT pathogenesis that leads to widespread epigenetic dysregulation and loss of lineage-specific enhancers. Current work is defining subtype-specific treatments that target underlying molecular derangements that drive tumorigenesis.
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Chen G, Zhou H, Liu B, Wang Y, Zhao J, Giancotti FG, Long J. A heterotrimeric SMARCB1-SMARCC2 subcomplex is required for the assembly and tumor suppression function of the BAF chromatin-remodeling complex. Cell Discov 2020; 6:66. [PMID: 33024572 PMCID: PMC7506551 DOI: 10.1038/s41421-020-00196-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 07/21/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Guidong Chen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Hao Zhou
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
- Department of Cancer Biology and David H Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Beibei Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Yan Wang
- Department of Cancer Biology and David H Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Jianchun Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Filippo G. Giancotti
- Department of Cancer Biology and David H Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX 77230 USA
| | - Jiafu Long
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
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45
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Parisian AD, Koga T, Miki S, Johann PD, Kool M, Crawford JR, Furnari FB. SMARCB1 loss interacts with neuronal differentiation state to block maturation and impact cell stability. Genes Dev 2020; 34:1316-1329. [PMID: 32912900 PMCID: PMC7528703 DOI: 10.1101/gad.339978.120] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/14/2020] [Indexed: 01/23/2023]
Abstract
Atypical teratoid rhabdoid tumors (ATRTs) are challenging pediatric brain cancers that are predominantly associated with inactivation of the gene SMARCB1, a conserved subunit of the chromatin remodeling BAF complex, which has known contributions to developmental processes. To identify potential interactions between SMARCB1 loss and the process of neural development, we introduced an inducible SMARCB1 loss-of-function system into human induced pluripotent stem cells (iPSCs) that were subjected to either directed neuronal differentiation or differentiation into cerebral organoids. Using this system, we identified substantial differences in the downstream effects of SMARCB1 loss depending on differentiation state and identified an interaction between SMARCB1 loss and neural differentiation pressure that causes a resistance to terminal differentiation and a defect in maintenance of a normal cell state. Our results provide insight into how SMARCB1 loss might interact with neural development in the process of ATRT tumorigenesis.
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Affiliation(s)
- Alison D Parisian
- Ludwig Institute for Cancer Research, La Jolla, California 92093, USA.,Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California 92093, USA
| | - Tomoyuki Koga
- Ludwig Institute for Cancer Research, La Jolla, California 92093, USA.,Department of Neurosurgery, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Shunichiro Miki
- Ludwig Institute for Cancer Research, La Jolla, California 92093, USA
| | - Pascal D Johann
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Princess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - John R Crawford
- Department of Neurosciences and Pediatrics, University of California at San Diego, San Diego, California 92093, USA; Rady Children's Hospital at San Diego, San Diego, California 92123, USA
| | - Frank B Furnari
- Ludwig Institute for Cancer Research, La Jolla, California 92093, USA.,Moores Cancer Center, University of California at San Diego, La Jolla, California 92093, USA.,Department of Pathology, University of California at San Diego, La Jolla, California 92093, USA
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46
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Xue Y, Zhu X, Meehan B, Venneti S, Martinez D, Morin G, Maïga RI, Chen H, Papadakis AI, Johnson RM, O'Sullivan MJ, Erdreich-Epstein A, Gotlieb WH, Park M, Judkins AR, Pelletier J, Foulkes WD, Rak J, Huang S. SMARCB1 loss induces druggable cyclin D1 deficiency via upregulation of MIR17HG in atypical teratoid rhabdoid tumors. J Pathol 2020; 252:77-87. [PMID: 32558936 DOI: 10.1002/path.5493] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/27/2020] [Accepted: 06/10/2020] [Indexed: 01/04/2023]
Abstract
Atypical teratoid rhabdoid tumor (ATRT) is a fatal pediatric malignancy of the central neural system lacking effective treatment options. It belongs to the rhabdoid tumor family and is usually caused by biallelic inactivation of SMARCB1, encoding a key subunit of SWI/SNF chromatin remodeling complexes. Previous studies proposed that SMARCB1 loss drives rhabdoid tumor by promoting cell cycle through activating transcription of cyclin D1 while suppressing p16. However, low cyclin D1 protein expression is observed in most ATRT patient tumors. The underlying mechanism and therapeutic implication of this molecular trait remain unknown. Here, we show that SMARCB1 loss in ATRT leads to the reduction of cyclin D1 expression by upregulating MIR17HG, a microRNA (miRNA) cluster known to generate multiple miRNAs targeting CCND1. Furthermore, we find that this cyclin D1 deficiency in ATRT results in marked in vitro and in vivo sensitivity to the CDK4/6 inhibitor palbociclib as a single agent. Our study identifies a novel genetic interaction between SMARCB1 and MIR17HG in regulating cyclin D1 in ATRT and suggests a rationale to treat ATRT patients with FDA-approved CDK4/6 inhibitors. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Yibo Xue
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Xianbing Zhu
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Brian Meehan
- Department of Pediatrics, McGill University, and Research Institute of McGill University Health Centre, Montreal Children's Hospital, Montreal, Canada
| | - Sriram Venneti
- Pathology and Neuropathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel Martinez
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Geneviève Morin
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Rayelle I Maïga
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Hongbo Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, PR China
| | - Andreas I Papadakis
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Radia M Johnson
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Maureen J O'Sullivan
- School of Medicine, University of Dublin, Trinity College, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Anat Erdreich-Epstein
- Departments of Pediatrics and Pathology, The Saban Research Institute at Children's Hospital Los Angeles and the Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Walter H Gotlieb
- Division of Gynecologic Oncology, Segal Cancer Center, Jewish General Hospital, McGill University, Montreal, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Canada.,Department of Medical Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Canada.,Department of Medical Genetics and Cancer Research Program, McGill University Health Centre, Montreal, Canada
| | - Janusz Rak
- Department of Pediatrics, McGill University, and Research Institute of McGill University Health Centre, Montreal Children's Hospital, Montreal, Canada
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
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47
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Perla A, Fratini L, Cardoso PS, Nör C, Brunetto AT, Brunetto AL, de Farias CB, Jaeger M, Roesler R. Histone Deacetylase Inhibitors in Pediatric Brain Cancers: Biological Activities and Therapeutic Potential. Front Cell Dev Biol 2020; 8:546. [PMID: 32754588 PMCID: PMC7365945 DOI: 10.3389/fcell.2020.00546] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022] Open
Abstract
Brain cancers are the leading cause of cancer-related deaths in children. Biological changes in these tumors likely include epigenetic deregulation during embryonal development of the nervous system. Histone acetylation is one of the most widely investigated epigenetic processes, and histone deacetylase inhibitors (HDACis) are increasingly important candidate treatments in many cancer types. Here, we review advances in our understanding of how HDACis display antitumor effects in experimental models of specific pediatric brain tumor types, i.e., medulloblastoma (MB), ependymoma (EPN), pediatric high-grade gliomas (HGGs), and rhabdoid and atypical teratoid/rhabdoid tumors (ATRTs). We also discuss clinical perspectives for the use of HDACis in the treatment of pediatric brain tumors.
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Affiliation(s)
- Alexandre Perla
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Lívia Fratini
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Paula S Cardoso
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Carolina Nör
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - André T Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Children's Cancer Institute, Porto Alegre, Brazil
| | - Algemir L Brunetto
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Children's Cancer Institute, Porto Alegre, Brazil
| | - Caroline Brunetto de Farias
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Children's Cancer Institute, Porto Alegre, Brazil
| | - Mariane Jaeger
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Children's Cancer Institute, Porto Alegre, Brazil
| | - Rafael Roesler
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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48
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Theruvath J, Sotillo E, Mount CW, Graef CM, Delaidelli A, Heitzeneder S, Labanieh L, Dhingra S, Leruste A, Majzner RG, Xu P, Mueller S, Yecies DW, Finetti MA, Williamson D, Johann PD, Kool M, Pfister S, Hasselblatt M, Frühwald MC, Delattre O, Surdez D, Bourdeaut F, Puget S, Zaidi S, Mitra SS, Cheshier S, Sorensen PH, Monje M, Mackall CL. Locoregionally administered B7-H3-targeted CAR T cells for treatment of atypical teratoid/rhabdoid tumors. Nat Med 2020; 26:712-719. [PMID: 32341579 DOI: 10.1038/s41591-020-0821-8] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 03/06/2020] [Indexed: 01/01/2023]
Abstract
Atypical teratoid/rhabdoid tumors (ATRTs) typically arise in the central nervous system (CNS) of children under 3 years of age. Despite intensive multimodal therapy (surgery, chemotherapy and, if age permits, radiotherapy), median survival is 17 months1,2. We show that ATRTs robustly express B7-H3/CD276 that does not result from the inactivating mutations in SMARCB1 (refs. 3,4), which drive oncogenesis in ATRT, but requires residual SWItch/Sucrose Non-Fermentable (SWI/SNF) activity mediated by BRG1/SMARCA4. Consistent with the embryonic origin of ATRT5,6, B7-H3 is highly expressed on the prenatal, but not postnatal, brain. B7-H3.BB.z-chimeric antigen receptor (CAR) T cells administered intracerebroventricularly or intratumorally mediate potent antitumor effects against cerebral ATRT xenografts in mice, with faster kinetics, greater potency and reduced systemic levels of inflammatory cytokines compared to CAR T cells administered intravenously. CAR T cells administered ICV also traffic from the CNS into the periphery; following clearance of ATRT xenografts, B7-H3.BB.z-CAR T cells administered intracerebroventricularly or intravenously mediate antigen-specific protection from tumor rechallenge, both in the brain and periphery. These results identify B7-H3 as a compelling therapeutic target for this largely incurable pediatric tumor and demonstrate important advantages of locoregional compared to systemic delivery of CAR T cells for the treatment of CNS malignancies.
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Affiliation(s)
- Johanna Theruvath
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Elena Sotillo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher W Mount
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Claus Moritz Graef
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Sabine Heitzeneder
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Louai Labanieh
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Shaurya Dhingra
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Amaury Leruste
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Robbie G Majzner
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Peng Xu
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sabine Mueller
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.,Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.,Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Derek W Yecies
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Martina A Finetti
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Pascal D Johann
- Hopp Children's Cancer Center Heidelberg, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - Stefan Pfister
- Hopp Children's Cancer Center Heidelberg, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, Münster University Hospital, Münster, Germany
| | - Michael C Frühwald
- University Children's Hospital Augsburg, Swabian Children's Cancer Center, Augsburg, Germany.,EU-RHAB Registry Center, Augsburg, Germany
| | - Olivier Delattre
- Paris Sciences Lettres Research University, INSERM U830, Paris, France.,Paris Sciences Lettres Research University, SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Didier Surdez
- Paris Sciences Lettres Research University, INSERM U830, Paris, France.,Paris Sciences Lettres Research University, SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Franck Bourdeaut
- Paris Sciences Lettres Research University, INSERM U830, Paris, France.,Paris Sciences Lettres Research University, SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Stephanie Puget
- Paris University, Necker-Enfants Malades Hospital, Department of Neurosurgery, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sakina Zaidi
- Paris Sciences Lettres Research University, INSERM U830, Paris, France.,Paris Sciences Lettres Research University, SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Siddhartha S Mitra
- Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Samuel Cheshier
- Division of Pediatric Neurosurgery, Department of Neurosurgery, Primary Children's Hospital and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Michelle Monje
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Institute for Stem Cell and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Crystal L Mackall
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA. .,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Chen F, Mei W, Lu W, Zeng T, Kang D, Wu X, You H. Atypical Teratoid/Rhabdoid Tumor Originated From the Trigeminal Nerve in a Young Male Adult: Case Report and Review of the Literature. Front Neurol 2020; 11:265. [PMID: 32373048 PMCID: PMC7186469 DOI: 10.3389/fneur.2020.00265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/20/2020] [Indexed: 11/17/2022] Open
Abstract
Atypical teratoid/rhabdoid tumor (AT/RT) is a highly malignant central nervous system neoplasm predominantly found in children under the age of 3 years, and is extremely rare in adults. There is no specific clinical presentations or radiological features in reported cases of AT/RT. Diagnosis of brain AT/RT is mainly dependent on the classical pathological characteristics. We report a rare case of AT/RT arising from the trigeminal nerve and leading to progressively multiple cranial nerve palsies in a 25-year-old male patient. Microsurgical resection of the tumor has been performed and confirmed the diagnosis by postoperative pathology. To our knowledge, this is the second case of adult-onset AT/RT originating from the trigeminal nerve.
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Affiliation(s)
- Fuxiang Chen
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Wenzhong Mei
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Wen Lu
- Department of Disease Prevention and Healthcare, Fujian Provincial Hospital, Fuzhou, China
| | - Tiefa Zeng
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Dezhi Kang
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xiyue Wu
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Honghai You
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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50
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The SWI/SNF complex in cancer - biology, biomarkers and therapy. Nat Rev Clin Oncol 2020; 17:435-448. [PMID: 32303701 DOI: 10.1038/s41571-020-0357-3] [Citation(s) in RCA: 278] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2020] [Indexed: 12/11/2022]
Abstract
Cancer genome-sequencing studies have revealed a remarkably high prevalence of mutations in genes encoding subunits of the SWI/SNF chromatin-remodelling complexes, with nearly 25% of all cancers harbouring aberrations in one or more of these genes. A role for such aberrations in tumorigenesis is evidenced by cancer predisposition in both carriers of germline loss-of-function mutations and genetically engineered mouse models with inactivation of any of several SWI/SNF subunits. Whereas many of the most frequently mutated oncogenes and tumour-suppressor genes have been studied for several decades, the cancer-promoting role of mutations in SWI/SNF genes has been recognized only more recently, and thus comparatively less is known about these alterations. Consequently, increasing research interest is being focused on understanding the prognostic and, in particular, the potential therapeutic implications of mutations in genes encoding SWI/SNF subunits. Herein, we review the burgeoning data on the mechanisms by which mutations affecting SWI/SNF complexes promote cancer and describe promising emerging opportunities for targeted therapy, including immunotherapy with immune-checkpoint inhibitors, presented by these mutations. We also highlight ongoing clinical trials open specifically to patients with cancers harbouring mutations in certain SWI/SNF genes.
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