51
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Mo J, Liu F, Sun X, Huang H, Tan K, Zhao X, Li R, Jiang W, Sui Y, Chen X, Shen K, Zhang L, Ma J, Zhao K, Tang Y. Inhibition of the FACT Complex Targets Aberrant Hedgehog Signaling and Overcomes Resistance to Smoothened Antagonists. Cancer Res 2021; 81:3105-3120. [PMID: 33853831 DOI: 10.1158/0008-5472.can-20-3186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/05/2021] [Accepted: 04/12/2021] [Indexed: 11/16/2022]
Abstract
Hedgehog signaling is aberrantly activated in hematologic malignancies and solid tumors, and targeting it is a promising therapeutic strategy against these cancers. Resistance to clinically available hedgehog-targeted Smoothened inhibitor (SMOi) drugs has become a critical issue in hedgehog-driven cancer treatment. Our previous studies identified inhibition of BET and CDK7 as two epigenetic/transcriptional-targeted therapeutic strategies for overcoming SMOi resistance, providing a promising direction for anti-hedgehog drug development. To uncover additional strategies for inhibiting aberrant hedgehog activity, here we performed CRISPR-Cas9 screening with an single-guide RNA library targeting epigenetic and transcriptional modulators in hedgehog-driven medulloblastoma cells, combined with tumor dataset analyses. Structure specific recognition protein 1 (SSRP1), a subunit of facilitates chromatin transcription (FACT) complex, was identified as a hedgehog-induced essential oncogene and therapeutic target in hedgehog-driven cancer. The FACT inhibitor CBL0137, which has entered clinical trials for cancer, effectively suppressed in vitro and in vivo growth of multiple SMOi-responsive and SMOi-resistant hedgehog-driven cancer models. Mechanistically, CBL0137 exerted anti-hedgehog activity by targeting transcription of GLI1 and GLI2, which are core transcription factors of the hedgehog pathway. SSRP1 bound the promoter regions of GLI1 and GLI2, while CBL0137 treatment substantially disrupted these interactions. Moreover, CBL0137 synergized with BET or CDK7 inhibitors to antagonize aberrant hedgehog pathway and growth of hedgehog-driven cancer models. Taken together, these results identify FACT inhibition as a promising epigenetic/transcriptional-targeted therapeutic strategy for treating hedgehog-driven cancers and overcoming SMOi resistance. SIGNIFICANCE: This study identifies FACT inhibition as an anti-hedgehog therapeutic strategy for overcoming resistance to Smoothened inhibitors and provides preclinical support for initiating clinical trials of FACT-targeted drug CBL0137 against hedgehog-driven cancers.
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Affiliation(s)
- Jialin Mo
- Research Center of Translational Medicine, Shanghai Children's Hospital, State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Fang Liu
- Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Xi Sun
- Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Hongting Huang
- Department of Hepatic Surgery and Liver Transplantation Center, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Kezhe Tan
- Research Center of Translational Medicine, Shanghai Children's Hospital, State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Xiaojing Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, P.R. China
| | - Rui Li
- Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Wenyan Jiang
- Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Yi Sui
- Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Xiaosong Chen
- Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Kunwei Shen
- Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, P.R. China
| | - Jie Ma
- Department of Pediatric Neurosurgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.
| | - Kewen Zhao
- Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.
| | - Yujie Tang
- Research Center of Translational Medicine, Shanghai Children's Hospital, State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China.
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52
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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: 42] [Impact Index Per Article: 14.0] [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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53
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Holdhof D, Johann PD, Spohn M, Bockmayr M, Safaei S, Joshi P, Masliah-Planchon J, Ho B, Andrianteranagna M, Bourdeaut F, Huang A, Kool M, Upadhyaya SA, Bendel AE, Indenbirken D, Foulkes WD, Bush JW, Creytens D, Kordes U, Frühwald MC, Hasselblatt M, Schüller U. Atypical teratoid/rhabdoid tumors (ATRTs) with SMARCA4 mutation are molecularly distinct from SMARCB1-deficient cases. Acta Neuropathol 2021; 141:291-301. [PMID: 33331994 PMCID: PMC7847432 DOI: 10.1007/s00401-020-02250-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022]
Abstract
Atypical teratoid/rhabdoid tumors (ATRTs) are very aggressive childhood malignancies of the central nervous system. The underlying genetic cause are inactivating bi-allelic mutations in SMARCB1 or (rarely) in SMARCA4. ATRT-SMARCA4 have been associated with a higher frequency of germline mutations, younger age, and an inferior prognosis in comparison to SMARCB1 mutated cases. Based on their DNA methylation profiles and transcriptomics, SMARCB1 mutated ATRTs have been divided into three distinct molecular subgroups: ATRT-TYR, ATRT-SHH, and ATRT-MYC. These subgroups differ in terms of age at diagnosis, tumor location, type of SMARCB1 alterations, and overall survival. ATRT-SMARCA4 are, however, less well understood, and it remains unknown, whether they belong to one of the described ATRT subgroups. Here, we examined 14 ATRT-SMARCA4 by global DNA methylation analyses. We show that they form a separate group segregating from SMARCB1 mutated ATRTs and from other SMARCA4-deficient tumors like small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) or SMARCA4 mutated extra-cranial malignant rhabdoid tumors. In contrast, medulloblastoma (MB) samples with heterozygous SMARCA4 mutations do not group separately, but with established MB subgroups. RNA sequencing of ATRT-SMARCA4 confirmed the clustering results based on DNA methylation profiling and displayed an absence of typical signature genes upregulated in SMARCB1 deleted ATRT. In summary, our results suggest that, in line with previous clinical observations, ATRT-SMARCA4 should be regarded as a distinct molecular subgroup.
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Affiliation(s)
- Dörthe Holdhof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), 20251, Hamburg, Germany
| | - Pascal D Johann
- Paediatric and Adolescent Medicine, Swabian Childrens' Cancer Center Augsburg, Augsburg, Germany
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Heidelberg, Germany
| | - Michael Spohn
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), 20251, Hamburg, Germany
| | - Michael Bockmayr
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), 20251, Hamburg, Germany
- Institute of Pathology, Corporate Member of Freie Universität Berlin, Charité, Universitätsmedizin Berlin, Humboldt-Universität Zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Sepehr Safaei
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), 20251, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Piyush Joshi
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Heidelberg, Germany
| | - Julien Masliah-Planchon
- INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
| | - Ben Ho
- Division of Hematology and Oncology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Mamy Andrianteranagna
- INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
- INSERM U900, CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Curie Institute, Paris, France
| | - Franck Bourdeaut
- INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
- Departments of Genetics and of Oncopediatry and Young Adults, Curie Institute, Paris, France
| | - Annie Huang
- INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Santhosh A Upadhyaya
- Department of Oncology, St Jude Children's Research Hospital, Department of Pediatrics, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Anne E Bendel
- Children's Hospitals and Clinics of Minnesota, Minneapolis, MN, USA
| | - Daniela Indenbirken
- Heinrich-Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jonathan W Bush
- Division of Anatomical Pathology, British Columbia Children's Hospital and Women's Hospital and Health Center, Vancouver, BC, Canada
- University of British Columbia, Vancouver, BC, Canada
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Uwe Kordes
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael C Frühwald
- Paediatric and Adolescent Medicine, Swabian Childrens' Cancer Center Augsburg, Augsburg, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, N63 (HPI), 20251, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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54
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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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55
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Nemes K, Bens S, Kachanov D, Teleshova M, Hauser P, Simon T, Tippelt S, Woessmann W, Beck O, Flotho C, Grigull L, Driever PH, Schlegel PG, Khurana C, Hering K, Kolb R, Leipold A, Abbink F, Gil-Da-Costa MJ, Benesch M, Kerl K, Lowis S, Marques CH, Graf N, Nysom K, Vokuhl C, Melchior P, Kröncke T, Schneppenheim R, Kordes U, Gerss J, Siebert R, Furtwängler R, Frühwald MC. Clinical and genetic risk factors define two risk groups of extracranial malignant rhabdoid tumours (eMRT/RTK). Eur J Cancer 2020; 142:112-122. [PMID: 33249395 DOI: 10.1016/j.ejca.2020.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/29/2020] [Accepted: 10/07/2020] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Extracranial rhabdoid tumours are rare, highly aggressive malignancies primarily affecting young children. The EU-RHAB registry was initiated in 2009 to prospectively collect data of rhabdoid tumour patients treated according to the EU-RHAB therapeutic framework. METHODS We evaluated 100 patients recruited within EU-RHAB (2009-2018). Tumours and matching blood samples were examined for SMARCB1 mutations by sequencing and cytogenetics. RESULTS A total of 70 patients presented with extracranial, extrarenal tumours (eMRT) and 30 with renal rhabdoid tumours (RTK). Nine patients demonstrated synchronous tumours. Distant metastases at diagnosis (M+) were present in 35% (35/100), localised disease (M0) with (LN+) and without (LN-) loco-regional lymph node involvement in 65% (65/100). SMARCB1 germline mutations (GLM) were detected in 21% (17/81 evaluable) of patients. The 5-year overall survival (OS) and event-free survival (EFS) rates were 45.8 ± 5.4% and 35.2 ± 5.1%, respectively. On univariate analyses, age at diagnosis (≥12 months), M0-stage, absence of synchronous tumours, absence of a GLM, gross total resection (GTR), radiotherapy and achieving a CR were significantly associated with favourable outcomes. In an adjusted multivariate model presence of a GLM, M+ and lack of a GTR were the strongest significant negative predictors of outcome. CONCLUSIONS We suggest to stratify patients with localised disease (M0), GTR+ and without proof of a GLM (5-year OS 72.2 ± 9.9%) as 'standard risk'. Patients presenting with one of the features M+ and/or GTR- and/or GLM+ belong to a high risk group (5-year, OS 32.5 ± 6.2%). These patients need novel therapeutic strategies such as combinations of targeted agents with conventional chemotherapy or novel experimental approaches ideally within international phase I/II trials.
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Affiliation(s)
- Karolina Nemes
- Paediatrics and Adolescent Medicine, Swabian Children's Cancer Center, University Medical Center Augsburg, Germany
| | - Susanne Bens
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Ulm, Germany
| | - Denis Kachanov
- National Scientific and Practical Center of Pediatric Hematology, Oncology and Immunology named after Dmitry Rogachev, Moscow, Russian Federation
| | - Margarita Teleshova
- National Scientific and Practical Center of Pediatric Hematology, Oncology and Immunology named after Dmitry Rogachev, Moscow, Russian Federation
| | - Peter Hauser
- Department of Pediatric Oncology, 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Thorsten Simon
- Department of Pediatric Hematology and Oncology, University Children's Hospital of Cologne, Cologne, Germany
| | - Stephan Tippelt
- Department of Pediatric Hematology and Oncology, Pediatrics III, University Hospital of Essen, Essen, Germany
| | - Wilhelm Woessmann
- Department of Pediatric Hematology and Oncology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Olaf Beck
- Department of Pediatric Hematology, Oncology & Hemostaseology, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Christian Flotho
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium, Heidelberg, Germany
| | - Lorenz Grigull
- Department of Pediatric Hematology and Oncology, Children's Hospital of Hannover, Hannover, Germany
| | - Pablo H Driever
- Department of Pediatric Oncology and Hematology, Charité - University Hospital Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | - Claudia Khurana
- Department of Pediatric Hematology and Oncology, Children's Hospital of Bielefeld, Germany
| | - Kathrin Hering
- Department of Radiotherapy and Radiation Oncology, Leipzig University, Leipzig, Germany
| | - Reinhard Kolb
- Department of Pediatrics, Children's Center, Hospital of Oldenburg, Oldenburg, Germany
| | | | - Floor Abbink
- Department of Pediatric Hematology and Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Maria J Gil-Da-Costa
- Pediatric Hemathology and Oncology Division, University Hospital S. João Alameda Hernani Monteiro, Porto, Portugal
| | - Martin Benesch
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Austria
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany
| | - Stephen Lowis
- School of Clinical Sciences, University of Bristol, London, UK
| | - Carmen H Marques
- Pediatric Onco-hematology Unit, Niño Jesús Hospital, Madrid, Spain
| | - Norbert Graf
- Department of Pediatric Hematology and Oncology, University of Saarland, Homburg, Germany
| | - Karsten Nysom
- Department of Paediatrics and Adolescent Medicine, Neuroscience Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Christian Vokuhl
- Department of Pathology, Section of Pediatric Pathology, University Hospital Bonn, Bonn, Germany
| | - Patrick Melchior
- Department of Radiation Oncology, University of Saarland, Homburg, Germany
| | - Thomas Kröncke
- Department of Diagnostic and Interventional Radiology, University Hospital Augsburg, Augsburg, Germany
| | - Reinhard Schneppenheim
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Uwe Kordes
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joachim Gerss
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Ulm, Germany
| | - Rhoikos Furtwängler
- Department of Pediatric Hematology and Oncology, University of Saarland, Homburg, Germany
| | - Michael C Frühwald
- Paediatrics and Adolescent Medicine, Swabian Children's Cancer Center, University Medical Center Augsburg, Germany.
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56
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Kling T, Wenger A, Carén H. DNA methylation-based age estimation in pediatric healthy tissues and brain tumors. Aging (Albany NY) 2020; 12:21037-21056. [PMID: 33168783 PMCID: PMC7695434 DOI: 10.18632/aging.202145] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/03/2020] [Indexed: 12/20/2022]
Abstract
Several DNA methylation clocks have been developed to reflect chronological age of human tissues, but most clocks have been trained on adult samples. The rapid methylome changes in children and the role of epigenetics in pediatric tumors calls for tools accurately estimating methylation age in children. We aimed to evaluate seven methylation clocks in multiple tissues from healthy children to inform future studies on the optimal clock for pediatric cohorts, and analyzed the methylation age in brain tumors. We found that clocks trained on pediatric samples were the best in all tested tissues, highlighting the need for dedicated clocks. For blood samples, the Skin and blood clock had the best correlation with chronological age, while PedBE was the most accurate for saliva and buccal samples, and Horvath for brain tissue. Horvath methylation age was accelerated in pediatric brain tumors and the acceleration was subtype-specific for atypical teratoid rhabdoid tumor (ATRT), ependymoma, medulloblastoma and glioma. The subtypes with the highest acceleration corresponded to the worst prognostic categories in ATRT, ependymoma and glioma, whereas the relationship was reversed in medulloblastoma. This suggests that methylation age has potential as a prognostic biomarker in pediatric brain tumors and should be further explored.
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Affiliation(s)
- Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Wenger
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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57
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Leruste A, Chauvin C, Pouponnot C, Bourdeaut F, Waterfall JJ, Piaggio E. Immune responses in genomically simple SWI/SNF-deficient cancers. Cancer 2020; 127:172-180. [PMID: 33079397 DOI: 10.1002/cncr.33172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/27/2020] [Accepted: 07/23/2020] [Indexed: 01/09/2023]
Affiliation(s)
- Amaury Leruste
- Translational Research in Pediatric Oncology (RTOP) team, INSERM U830, Curie Institute Research Center, PSL Research University, Paris, France.,SIREDO Pediatric Cancer Center, Curie Institute, Paris, France.,Translational Research Department, Curie Institute Research Center, PSL Research University, Paris, France
| | - Céline Chauvin
- Translational Research in Pediatric Oncology (RTOP) team, INSERM U830, Curie Institute Research Center, PSL Research University, Paris, France.,SIREDO Pediatric Cancer Center, Curie Institute, Paris, France.,Translational Research Department, Curie Institute Research Center, PSL Research University, Paris, France
| | - Celio Pouponnot
- CNRS UMR 3347, INSERM U1021, Curie Institute Research Center, PSL Research University, Orsay, France
| | - Franck Bourdeaut
- Translational Research in Pediatric Oncology (RTOP) team, INSERM U830, Curie Institute Research Center, PSL Research University, Paris, France.,SIREDO Pediatric Cancer Center, Curie Institute, Paris, France.,Translational Research Department, Curie Institute Research Center, PSL Research University, Paris, France
| | - Joshua J Waterfall
- Translational Research Department, Curie Institute Research Center, PSL Research University, Paris, France.,Integrative Functional Genomics of Cancer (IFGC) team, INSERM U830, Curie Institute Research Center, PSL Research University, Paris, France
| | - Eliane Piaggio
- Translational Research Department, Curie Institute Research Center, PSL Research University, Paris, France.,Translational Immunotherapy (TransImm) team, INSERM U932, Curie Institute Research Center, PSL Research University, Paris, France
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58
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Nacev BA, Jones KB, Intlekofer AM, Yu JSE, Allis CD, Tap WD, Ladanyi M, Nielsen TO. The epigenomics of sarcoma. Nat Rev Cancer 2020; 20:608-623. [PMID: 32782366 PMCID: PMC8380451 DOI: 10.1038/s41568-020-0288-4] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/26/2020] [Indexed: 12/11/2022]
Abstract
Epigenetic regulation is critical to physiological control of development, cell fate, cell proliferation, genomic integrity and, fundamentally, transcriptional regulation. This epigenetic control occurs at multiple levels including through DNA methylation, histone modification, nucleosome remodelling and modulation of the 3D chromatin structure. Alterations in genes that encode chromatin regulators are common among mesenchymal neoplasms, a collection of more than 160 tumour types including over 60 malignant variants (sarcomas) that have unique and varied genetic, biological and clinical characteristics. Herein, we review those sarcomas in which chromatin pathway alterations drive disease biology. Specifically, we emphasize examples of dysregulation of each level of epigenetic control though mechanisms that include alterations in metabolic enzymes that regulate DNA methylation and histone post-translational modifications, mutations in histone genes, subunit loss or fusions in chromatin remodelling and modifying complexes, and disruption of higher-order chromatin structure. Epigenetic mechanisms of tumorigenesis have been implicated in mesenchymal tumours ranging from chondroblastoma and giant cell tumour of bone to chondrosarcoma, malignant peripheral nerve sheath tumour, synovial sarcoma, epithelioid sarcoma and Ewing sarcoma - all diseases that present in a younger patient population than most cancers. Finally, we review current and potential future approaches for the development of sarcoma therapies based on this emerging understanding of chromatin dysregulation.
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Affiliation(s)
- Benjamin A Nacev
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- The Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Kevin B Jones
- Department of Orthopaedics, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrew M Intlekofer
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamie S E Yu
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - C David Allis
- The Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Torsten O Nielsen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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59
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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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60
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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: 11] [Impact Index Per Article: 2.8] [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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61
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Yasui H, Valind A, Karlsson J, Pietras C, Jansson C, Wille J, Romerius P, Backman T, Gisselsson D. A dynamic mutational landscape associated with an inter-regionally diverse immune response in malignant rhabdoid tumour. J Pathol 2020; 252:22-28. [PMID: 32542645 DOI: 10.1002/path.5490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/11/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022]
Abstract
Malignant rhabdoid tumour (MRT) is a childhood neoplasm of high malignancy characterised by biallelic mutation and/or loss of the epigenetic master regulator SMARCB1, accompanied by no or few other oncogenic drivers. In spite of their generally low mutational burden, an intratumoural T-cell response has been reported in a subset of MRTs, indicating that immune checkpoint inhibition may be considered a viable therapy option for some patients. We assess here the evolution over time and space of predicted neoantigens and indicators of immune checkpoint status in two MRT patients who progressed under treatment. Both patients showed an accumulation of novel clonal and subclonal mutations, including predicted neoantigens, in metastases compared to their inferred ancestral clones in the primary tumours. The first patient had peritoneal metastases from an MRT of the liver. Clonal deconvolution revealed polyclonal seeding from the primary tumour to a single metastatic site, followed by a local subclonal burst of mutations. The second patient had a renal MRT with multiple pulmonary metastases, each of which could be traced back to a single genetically unique founder cell, with formation of novel subclones in two metastases. Both patients showed a regionally heterogeneous landscape of predicted neoantigens and of tumour-infiltrating lymphocytes expressing CD8 and PD1. In both patients, some tumour regions fulfilled established criteria for PD-L1 positivity (> 1% of tumour cells), while others did not. This suggests that even in a tumour type like MRT, with a single driver mutation, there can be heterogeneity in neoantigen repertoire, immune response, and biomarkers for checkpoint blockade among sampled locations. This must be taken into account when assessing progressed MRT patients for checkpoint inhibition therapy. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Hiroaki Yasui
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Obstetrics and Gynaecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Paediatrics, Skåne University Hospital, Lund, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Christina Pietras
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Caroline Jansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Joakim Wille
- Paediatric Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Patrik Romerius
- Paediatric Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Torbjörn Backman
- Paediatric Surgery, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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62
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Forrest SJ, Al-Ibraheemi A, Doan D, Ward A, Clinton CM, Putra J, Pinches RS, Kadoch C, Chi SN, DuBois SG, Leavey PJ, LeBoeuf NR, Mullen E, Collins N, Church AJ, Janeway KA. Genomic and Immunologic Characterization of INI1-Deficient Pediatric Cancers. Clin Cancer Res 2020; 26:2882-2890. [PMID: 32122923 PMCID: PMC10947260 DOI: 10.1158/1078-0432.ccr-19-3089] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/22/2020] [Accepted: 02/26/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Several aggressive pediatric cancers harbor alterations in SMARCB1, including rhabdoid tumors, epithelioid sarcoma, and chordoma. As tumor profiling has become more routine in clinical care, we investigated the relationship between SMARCB1 genetic variants identified by next-generation sequencing (NGS) and INI1 protein expression. Therapeutic approaches for INI1-deficient tumors are limited. Early reports suggest a potential role for immune checkpoint inhibition in these patients. Thus, we also investigated PD-L1 and CD8 expression in INI1-negative pediatric brain and solid tumors. EXPERIMENTAL DESIGN We performed immunohistochemistry (IHC) for INI1 and immune markers (PD-L1, CD8, and CD163) and NGS on tumor samples from 43 pediatric patients who had tumors with INI1 loss on previous IHC or SMARCB1 genomic alterations on prior somatic sequencing. RESULTS SMARCB1 two-copy deletions and inactivating mutations on NGS were associated with loss of INI1 protein expression. Single-copy deletion of SMARCB1 was not predictive of INI1 loss in tumor histologies not known to be INI1-deficient. In the 27 cases with INI1 loss and successful tumor sequencing, 24 (89%) had a SMARCB1 alteration detected. In addition, 47% (14/30) of the patients with INI1-negative tumors had a tumor specimen that was PD-L1 positive and 60% (18/30) had positive or rare CD8 staining. We report on 3 patients with INI1-negative tumors with evidence of disease control on immune checkpoint inhibitors. CONCLUSIONS A significant proportion of the INI1-negative tumors express PD-L1, and PD-L1 positivity was associated with extracranial tumor site. These results suggest that clinical trials of immune checkpoint inhibitors are warranted in INI1-negative pediatric cancers.
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Affiliation(s)
- Suzanne J Forrest
- Department of Pediatric Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Boston, Massachusetts.
| | - Alyaa Al-Ibraheemi
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Duong Doan
- Department of Pediatric Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Boston, Massachusetts
| | - Abigail Ward
- Department of Pediatric Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Boston, Massachusetts
| | - Catherine M Clinton
- Department of Pediatric Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Boston, Massachusetts
| | - Juan Putra
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - R Seth Pinches
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Susan N Chi
- Department of Pediatric Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Boston, Massachusetts
| | - Steven G DuBois
- Department of Pediatric Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Boston, Massachusetts
| | - Patrick J Leavey
- Department of Pediatric Hematology-Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Nicole R LeBoeuf
- Department of Dermatology, Center for Cutaneous Oncology, Dana-Farber/Brigham and Women's Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Elizabeth Mullen
- Department of Pediatric Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Boston, Massachusetts
| | - Natalie Collins
- Department of Pediatric Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Boston, Massachusetts
| | - Alanna J Church
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Katherine A Janeway
- Department of Pediatric Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Boston, Massachusetts.
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63
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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: 300] [Impact Index Per Article: 75.0] [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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64
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Calandrini C, Schutgens F, Oka R, Margaritis T, Candelli T, Mathijsen L, Ammerlaan C, van Ineveld RL, Derakhshan S, de Haan S, Dolman E, Lijnzaad P, Custers L, Begthel H, Kerstens HHD, Visser LL, Rookmaaker M, Verhaar M, Tytgat GAM, Kemmeren P, de Krijger RR, Al-Saadi R, Pritchard-Jones K, Kool M, Rios AC, van den Heuvel-Eibrink MM, Molenaar JJ, van Boxtel R, Holstege FCP, Clevers H, Drost J. An organoid biobank for childhood kidney cancers that captures disease and tissue heterogeneity. Nat Commun 2020; 11:1310. [PMID: 32161258 PMCID: PMC7066173 DOI: 10.1038/s41467-020-15155-6] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/21/2020] [Indexed: 01/02/2023] Open
Abstract
Kidney tumours are among the most common solid tumours in children, comprising distinct subtypes differing in many aspects, including cell-of-origin, genetics, and pathology. Pre-clinical cell models capturing the disease heterogeneity are currently lacking. Here, we describe the first paediatric cancer organoid biobank. It contains tumour and matching normal kidney organoids from over 50 children with different subtypes of kidney cancer, including Wilms tumours, malignant rhabdoid tumours, renal cell carcinomas, and congenital mesoblastic nephromas. Paediatric kidney tumour organoids retain key properties of native tumours, useful for revealing patient-specific drug sensitivities. Using single cell RNA-sequencing and high resolution 3D imaging, we further demonstrate that organoid cultures derived from Wilms tumours consist of multiple different cell types, including epithelial, stromal and blastemal-like cells. Our organoid biobank captures the heterogeneity of paediatric kidney tumours, providing a representative collection of well-characterised models for basic cancer research, drug-screening and personalised medicine. Pre-clinical cell culture models capturing the heterogeneity of childhood kidney tumours are limited. Here, the authors establish and characterise an organoid biobank of tumour and matched normal organoid cultures from over 50 children with different subtypes of kidney cancer.
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Affiliation(s)
- Camilla Calandrini
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Frans Schutgens
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,University Medical Center, Department of Nephrology and Hypertension, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Rurika Oka
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Thanasis Margaritis
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Tito Candelli
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Luka Mathijsen
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Carola Ammerlaan
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,University Medical Center, Department of Nephrology and Hypertension, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Ravian L van Ineveld
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Sepide Derakhshan
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Sanne de Haan
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Emmy Dolman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Philip Lijnzaad
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Lars Custers
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Harry Begthel
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Hindrik H D Kerstens
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Lindy L Visser
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Maarten Rookmaaker
- University Medical Center, Department of Nephrology and Hypertension, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Marianne Verhaar
- University Medical Center, Department of Nephrology and Hypertension, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Godelieve A M Tytgat
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,University Medical Center, Department of Pathology, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Reem Al-Saadi
- University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Kathy Pritchard-Jones
- University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,Hopp Children's Cancer Center (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Anne C Rios
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | | | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Ruben van Boxtel
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Hans Clevers
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.,Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Jarno Drost
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.
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65
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Finetti MA, Grabovska Y, Bailey S, Williamson D. Translational genomics of malignant rhabdoid tumours: Current impact and future possibilities. Semin Cancer Biol 2020; 61:30-41. [PMID: 31923457 DOI: 10.1016/j.semcancer.2019.12.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022]
Abstract
Malignant Rhabdoid Tumours (MRT) are the quintessential example of an epigenetic cancer. Mutation of a single gene, SMARCB1 or more rarely SMARCA4, is capable of causing one of the most aggressive and lethal cancers of early childhood and infancy. SMARCB1 encodes a core subunit of the SWI/SNF complex and its mutation evokes genome-wide downstream effects which may be counteracted therapeutically. Here we review and discuss the use of translational genomics in the study of MRT biology and the ways in which this has impacted clinical practice or may do so in the future. First, the diagnosis and definition of MRT and the transition from a histopathological to a molecular definition. Second, epigenetic and transcriptomic subgroups within MRT, their defining features and potential prognostic or therapeutic significance. Third, functional genomic studies of MRT by mouse modelling and forced re-expression of SMARCB1 in MRT cells. Fourth, studies of underlying epigenetic mechanisms (e.g. EZH2, HDACs) or deregulated kinases (e.g. PDGFR, FGFR1) and the potential therapeutic opportunities these provide. Finally, we discuss likely future directions and proffer opinion on how future translational genomics should be integrated into future biological/clinical studies to select and evaluate the best anti-MRT therapeutic agents.
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Affiliation(s)
- Martina A Finetti
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK
| | - Yura Grabovska
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK
| | - Simon Bailey
- 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.
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Abstract
Carcinogen-induced cancers typically have high mutation burdens and an inflamed microenvironment and thus are poised to respond to immune checkpoint inhibitors (ICIs). However, cancers with loss-of-function mutations in the SWI/SNF complex have few additional mutations yet also have an inflamed immunophenotype and should respond to ICI therapy.
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Affiliation(s)
- Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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