201
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Schmitt K, Molfenter B, Laureano NK, Tawk B, Bieg M, Hostench XP, Weichenhan D, Ullrich ND, Shang V, Richter D, Stögbauer F, Schroeder L, de Bem Prunes B, Visioli F, Rados PV, Jou A, Plath M, Federspil PA, Thierauf J, Döscher J, Weissinger SE, Hoffmann TK, Wagner S, Wittekindt C, Ishaque N, Eils R, Klussmann JP, Holzinger D, Plass C, Abdollahi A, Freier K, Weichert W, Zaoui K, Hess J. Somatic mutations and promotor methylation of the ryanodine receptor 2 is a common event in the pathogenesis of head and neck cancer. Int J Cancer 2019; 145:3299-3310. [PMID: 31135957 DOI: 10.1002/ijc.32481] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 12/31/2022]
Abstract
Genomic sequencing projects unraveled the mutational landscape of head and neck squamous cell carcinoma (HNSCC) and provided a comprehensive catalog of somatic mutations. However, the limited number of significant cancer-related genes obtained so far only partially explains the biological complexity of HNSCC and hampers the development of novel diagnostic biomarkers and therapeutic targets. We pursued a multiscale omics approach based on whole-exome sequencing, global DNA methylation and gene expression profiling data derived from tumor samples of the HIPO-HNC cohort (n = 87), and confirmed new findings with datasets from The Cancer Genome Atlas (TCGA). Promoter methylation was confirmed by MassARRAY analysis and protein expression was assessed by immunohistochemistry and immunofluorescence staining. We discovered a set of cancer-related genes with frequent somatic mutations and high frequency of promoter methylation. This included the ryanodine receptor 2 (RYR2), which showed variable promoter methylation and expression in both tumor samples and cell lines. Immunohistochemical staining of tissue sections unraveled a gradual loss of RYR2 expression from normal mucosa via dysplastic lesion to invasive cancer and indicated that reduced RYR2 expression in adjacent tissue and precancerous lesions might serve as risk factor for unfavorable prognosis and upcoming malignant conversion. In summary, our data indicate that impaired RYR2 function by either somatic mutation or epigenetic silencing is a common event in HNSCC pathogenesis. Detection of RYR2 expression and/or promoter methylation might enable risk assessment for malignant conversion of dysplastic lesions.
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Affiliation(s)
- Katrin Schmitt
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Britta Molfenter
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Natalia Koerich Laureano
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Oral Pathology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Bouchra Tawk
- Division of Molecular and Translational Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg University Hospital, and Translational Radiation Oncology, German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Bieg
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), and Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - Xavier Pastor Hostench
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), and Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - Dieter Weichenhan
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nina D Ullrich
- Institute of Physiology and Pathophysiology, Division of Cardiovascular Physiology, Heidelberg University, Heidelberg, Germany
| | - Viny Shang
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniela Richter
- Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden, Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Fabian Stögbauer
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Lea Schroeder
- Division of Molecular Diagnostics of Oncogenic Infections, Infection, Inflammation and Cancer Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bianca de Bem Prunes
- Oral Pathology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Fernanda Visioli
- Oral Pathology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | - Adriana Jou
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michaela Plath
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Philippe A Federspil
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Julia Thierauf
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Johannes Döscher
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Ulm, Ulm, Germany
| | | | - Thomas K Hoffmann
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Ulm, Ulm, Germany
| | - Steffen Wagner
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Giessen, Germany
| | - Claus Wittekindt
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Giessen, Germany
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), and Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), and Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Heidelberg, Germany
| | - Jens P Klussmann
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, Cologne, Germany
| | - Dana Holzinger
- Division of Molecular Diagnostics of Oncogenic Infections, Infection, Inflammation and Cancer Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Amir Abdollahi
- Division of Molecular and Translational Radiation Oncology, Heidelberg Ion Therapy Center (HIT), Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg University Hospital, and Translational Radiation Oncology, German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kolja Freier
- Department of Oral and Maxillofacial Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University Munich (TUM), and German Cancer Consortium (DKTK) partner site, Munich, Germany
| | - Karim Zaoui
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Jochen Hess
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
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202
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Abstract
BCOR is a gene that encodes for an epigenetic regulator involved in the specification of cell differentiation and body structure development and takes part in the noncanonical polycomb repressive complex 1. This review provides a comprehensive summary of BCOR’s involvement in oncology, illustrating that various BCOR aberrations, such as the internal tandem duplications of the PCGF Ub-like fold discriminator domain and different gene fusions (mainly BCOR–CCNB3, BCOR–MAML3 and ZC3H7B–BCOR), represent driver elements of various sarcomas such as clear cell sarcoma of the kidney, primitive mesenchymal myxoid tumor of infancy, small round blue cell sarcoma, endometrial stromal sarcoma and histologically heterogeneous CNS neoplasms group with similar genomic methylation patterns known as CNS-HGNET-BCOR. Furthermore, other BCOR alterations (often loss of function mutations) recur in a large variety of mesenchymal, epithelial, neural and hematological tumors, suggesting a central role in cancer evolution.
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Affiliation(s)
- Annalisa Astolfi
- 'Giorgio Prodi' Cancer Research Center, University of Bologna, 40138 Bologna, Italy
| | - Michele Fiore
- Pediatric Oncology & Hematology Unit 'Lalla Seràgnoli', S Orsola-Malpighi Hospital, 40138 Bologna, Italy
| | - Fraia Melchionda
- Pediatric Oncology & Hematology Unit 'Lalla Seràgnoli', S Orsola-Malpighi Hospital, 40138 Bologna, Italy
| | - Valentina Indio
- 'Giorgio Prodi' Cancer Research Center, University of Bologna, 40138 Bologna, Italy
| | - Salvatore N Bertuccio
- Pediatric Oncology & Hematology Unit 'Lalla Seràgnoli', S Orsola-Malpighi Hospital, 40138 Bologna, Italy
| | - Andrea Pession
- Pediatric Oncology & Hematology Unit 'Lalla Seràgnoli', S Orsola-Malpighi Hospital, 40138 Bologna, Italy.,Department of Medical & Surgical Sciences, University of Bologna, S Orsola-Malpighi Hospital, 40138 Bologna, Italy
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203
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Feuerbach L, Sieverling L, Deeg KI, Ginsbach P, Hutter B, Buchhalter I, Northcott PA, Mughal SS, Chudasama P, Glimm H, Scholl C, Lichter P, Fröhling S, Pfister SM, Jones DTW, Rippe K, Brors B. TelomereHunter - in silico estimation of telomere content and composition from cancer genomes. BMC Bioinformatics 2019; 20:272. [PMID: 31138115 PMCID: PMC6540518 DOI: 10.1186/s12859-019-2851-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/26/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Establishment of telomere maintenance mechanisms is a universal step in tumor development to achieve replicative immortality. These processes leave molecular footprints in cancer genomes in the form of altered telomere content and aberrations in telomere composition. To retrieve these telomere characteristics from high-throughput sequencing data the available computational approaches need to be extended and optimized to fully exploit the information provided by large scale cancer genome data sets. RESULTS We here present TelomereHunter, a software for the detailed characterization of telomere maintenance mechanism footprints in the genome. The tool is implemented for the analysis of large cancer genome cohorts and provides a variety of diagnostic diagrams as well as machine-readable output for subsequent analysis. A novel key feature is the extraction of singleton telomere variant repeats, which improves the identification and subclassification of the alternative lengthening of telomeres phenotype. We find that whole genome sequencing-derived telomere content estimates strongly correlate with telomere qPCR measurements (r = 0.94). For the first time, we determine the correlation of in silico telomere content quantification from whole genome sequencing and whole genome bisulfite sequencing data derived from the same tumor sample (r = 0.78). An analogous comparison of whole exome sequencing data and whole genome sequencing data measured slightly lower correlation (r = 0.79). However, this is considerably improved by normalization with matched controls (r = 0.91). CONCLUSIONS TelomereHunter provides new functionality for the analysis of the footprints of telomere maintenance mechanisms in cancer genomes. Besides whole genome sequencing, whole exome sequencing and whole genome bisulfite sequencing are suited for in silico telomere content quantification, especially if matched control samples are available. The software runs under a GPL license and is available at https://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html .
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Affiliation(s)
- Lars Feuerbach
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lina Sieverling
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Katharina I. Deeg
- Research Group Genome Organization & Function/Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant Center, 69120 Heidelberg, Germany
| | - Philip Ginsbach
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Barbara Hutter
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ivo Buchhalter
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Paul A. Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sadaf S. Mughal
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Priya Chudasama
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Hanno Glimm
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden, University Hospital Carl Gustav Carus, Dresden and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Claudia Scholl
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Division of Applied Functional Genomics, DKFZ, 69120 Heidelberg, Germany
| | - Peter Lichter
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Stefan M. Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - David T. W. Jones
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Karsten Rippe
- Research Group Genome Organization & Function/Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant Center, 69120 Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
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204
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Hellwig M, Merk DJ, Lutz B, Schüller U. Preferential sensitivity to HDAC inhibitors in tumors with CREBBP mutation. Cancer Gene Ther 2019; 27:294-300. [PMID: 31068675 DOI: 10.1038/s41417-019-0099-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 04/27/2019] [Indexed: 11/09/2022]
Abstract
Mutations in the gene encoding for the histone acetyltransferase (HAT) CREBBP are common driver events in multiple types of human cancer, such as small cell lung cancer (SCLC) or Sonic Hedgehog medulloblastoma (SHH MB). Therefore, therapeutic options targeting such alterations are highly desired. We used human cell lines from SCLC as well as primary mouse tumor cells and genetically engineered mouse models for SHH MB to test treatment options with histone deacetylase inhibitors (HDACi) in CREBBP wild-type and mutated tumors. In contrast to CREBBP wild-type SCLC cells, CREBBP-mutated SCLC cells showed significantly lower IC50 values after treatment with HDACi. In addition, both in vitro and in vivo, HDACi had significant effects on cell proliferation of SHH-driven tumor MB cells harboring a CREBBP-mutation as compared to CREBBP wild-type controls. These data suggest that HDACi may serve as an additional therapeutic option for patients suffering from tumors driven by CREBBP mutations.
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Affiliation(s)
- Malte Hellwig
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute, Children's Cancer Center Hamburg, Hamburg, Germany
| | - Daniel J Merk
- Center for Neuropathology, Ludwig-Maximilians-University of Munich, Munich, Germany.,Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - Beat Lutz
- Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. .,Research Institute, Children's Cancer Center Hamburg, Hamburg, Germany. .,Center for Neuropathology, Ludwig-Maximilians-University of Munich, Munich, Germany. .,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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205
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Wu B, Pan X, Chen X, Chen M, Shi K, Xu J, Zheng J, Niu T, Chen C, Shuai X, Liu Y. Epigenetic drug library screening identified an LSD1 inhibitor to target UTX-deficient cells for differentiation therapy. Signal Transduct Target Ther 2019; 4:11. [PMID: 31044091 PMCID: PMC6483994 DOI: 10.1038/s41392-019-0040-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 02/22/2019] [Accepted: 02/24/2019] [Indexed: 02/05/2023] Open
Abstract
UTX (also known as KDM6A), a histone 3 lysine 27 demethylase, is among the most frequently mutated epigenetic regulators in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Recent studies have suggested that UTX mutations promote MDS and AML by blocking the differentiation of hematopoietic stem and progenitor cells (HSPCs). Here, we performed an epigenetic drug library screening for small molecules able to release the differentiation block on HSPCs induced by UTX deficiency. We found that SP2509, a selective inhibitor of LSD1, specifically promoted the differentiation of Utx-null HSPCs while sparing wild-type HSPCs. Transcriptome profiling showed that Utx loss reduced the expression of differentiation-related and tumor suppressor genes, correlating with their potential roles in HSPC self-renewal and leukemogenesis. In contrast, SP2509 treatment reversed these changes in gene expression in Utx-null HSPCs. Accordingly, Utx loss decreased H3K4 methylation level probably through the COMPASS-like complex, while LSD1 inhibition by SP2509 partially reversed the reduction of H3K4 methylation in Utx-deficient HSPCs. Further, SP2509 promoted the differentiation of Utx-null AML cells in vitro and in vivo and, therefore, extended the survival of these leukemic mice. Thus, our study identified a novel strategy to specifically target both premalignant and malignant cells with Utx deficiency for differentiation therapy and provided insights into the molecular mechanisms underlying the role of Utx in regulating HSPCs and related diseases.
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Affiliation(s)
- Baohong Wu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Xiangyu Pan
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Xuelan Chen
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Mei Chen
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Kaidou Shi
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Jing Xu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Jianan Zheng
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Ting Niu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Chong Chen
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Xiao Shuai
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
| | - Yu Liu
- Department of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, 610041 Chengdu, Sichuan China
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206
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Lesch BJ, Tothova Z, Morgan EA, Liao Z, Bronson RT, Ebert BL, Page DC. Intergenerational epigenetic inheritance of cancer susceptibility in mammals. eLife 2019; 8:e39380. [PMID: 30963999 PMCID: PMC6456297 DOI: 10.7554/elife.39380] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 03/03/2019] [Indexed: 12/11/2022] Open
Abstract
Susceptibility to cancer is heritable, but much of this heritability remains unexplained. Some 'missing' heritability may be mediated by epigenetic changes in the parental germ line that do not involve transmission of genetic variants from parent to offspring. We report that deletion of the chromatin regulator Kdm6a (Utx) in the paternal germ line results in elevated tumor incidence in genetically wild type mice. This effect increases following passage through two successive generations of Kdm6a male germline deletion, but is lost following passage through a wild type germ line. The H3K27me3 mark is redistributed in sperm of Kdm6a mutants, and we define approximately 200 H3K27me3-marked regions that exhibit increased DNA methylation, both in sperm of Kdm6a mutants and in somatic tissue of progeny. Hypermethylated regions in enhancers may alter regulation of genes involved in cancer initiation or progression. Epigenetic changes in male gametes may therefore impact cancer susceptibility in adult offspring.
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Affiliation(s)
| | - Zuzana Tothova
- Department of Medicine, Division of HematologyBrigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Elizabeth A Morgan
- Department of PathologyBrigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Zhicong Liao
- Department of GeneticsYale School of MedicineNew HavenUnited States
- Yale Cancer CenterYale School of MedicineNew HavenUnited States
| | - Roderick T Bronson
- Department of PathologyTufts University School of Medicine and Veterinary MedicineNorth GraftonUnited States
| | - Benjamin L Ebert
- Department of Medicine, Division of HematologyBrigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - David C Page
- Whitehead InstituteCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Whitehead InstituteCambridgeUnited States
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207
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Defective homologous recombination DNA repair as therapeutic target in advanced chordoma. Nat Commun 2019; 10:1635. [PMID: 30967556 PMCID: PMC6456501 DOI: 10.1038/s41467-019-09633-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 03/19/2019] [Indexed: 12/21/2022] Open
Abstract
Chordomas are rare bone tumors with few therapeutic options. Here we show, using whole-exome and genome sequencing within a precision oncology program, that advanced chordomas (n = 11) may be characterized by genomic patterns indicative of defective homologous recombination (HR) DNA repair and alterations affecting HR-related genes, including, for example, deletions and pathogenic germline variants of BRCA2, NBN, and CHEK2. A mutational signature associated with HR deficiency was significantly enriched in 72.7% of samples and co-occurred with genomic instability. The poly(ADP-ribose) polymerase (PARP) inhibitor olaparib, which is preferentially toxic to HR-incompetent cells, led to prolonged clinical benefit in a patient with refractory chordoma, and whole-genome analysis at progression revealed a PARP1 p.T910A mutation predicted to disrupt the autoinhibitory PARP1 helical domain. These findings uncover a therapeutic opportunity in chordoma that warrants further exploration, and provide insight into the mechanisms underlying PARP inhibitor resistance. Chordomas are rare bone tumors with limited therapeutic options. Here, the authors identify molecular alterations associated with defective homologous recombination DNA repair in advanced chordomas and report prolonged response in a patient treated with a PARP inhibitor, which later acquired resistance due to a newly gained PARP1 mutation.
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208
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Lu QR, Qian L, Zhou X. Developmental origins and oncogenic pathways in malignant brain tumors. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2019; 8:e342. [PMID: 30945456 DOI: 10.1002/wdev.342] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/20/2019] [Accepted: 03/08/2019] [Indexed: 12/21/2022]
Abstract
Brain tumors such as adult glioblastomas and pediatric high-grade gliomas or medulloblastomas are among the leading causes of cancer-related deaths, exhibiting poor prognoses with little improvement in outcomes in the past several decades. These tumors are heterogeneous and can be initiated from various neural cell types, contributing to therapy resistance. How such heterogeneity arises is linked to the tumor cell of origin and their genetic alterations. Brain tumorigenesis and progression recapitulate key features associated with normal neurogenesis; however, the underlying mechanisms are quite dysregulated as tumor cells grow and divide in an uncontrolled manner. Recent comprehensive genomic, transcriptomic, and epigenomic studies at single-cell resolution have shed new light onto diverse tumor-driving events, cellular heterogeneity, and cells of origin in different brain tumors. Primary and secondary glioblastomas develop through different genetic alterations and pathways, such as EGFR amplification and IDH1/2 or TP53 mutation, respectively. Mutations such as histone H3K27M impacting epigenetic modifications define a distinct group of pediatric high-grade gliomas such as diffuse intrinsic pontine glioma. The identification of distinct genetic, epigenomic profiles and cellular heterogeneity has led to new classifications of adult and pediatric brain tumor subtypes, affording insights into molecular and lineage-specific vulnerabilities for treatment stratification. This review discusses our current understanding of tumor cells of origin, heterogeneity, recurring genetic and epigenetic alterations, oncogenic drivers and signaling pathways for adult glioblastomas, pediatric high-grade gliomas, and medulloblastomas, the genetically heterogeneous groups of malignant brain tumors. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cell Differentiation and Reversion Signaling Pathways > Cell Fate Signaling.
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Affiliation(s)
- Q Richard Lu
- Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Lily Qian
- Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Xianyao Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Sichuan University, Chengdu, China.,Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
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209
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Menyhárt O, Győrffy B. Principles of tumorigenesis and emerging molecular drivers of SHH-activated medulloblastomas. Ann Clin Transl Neurol 2019; 6:990-1005. [PMID: 31139698 PMCID: PMC6529984 DOI: 10.1002/acn3.762] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
SHH-activated medulloblastomas (SHH-MB) account for 25-30% of all medulloblastomas (MB) and occur with a bimodal age distribution, encompassing many infant and adult, but fewer childhood cases. Different age groups are characterized by distinct survival outcomes and age-specific alterations of regulatory pathways. Here, we review SHH-specific genetic aberrations and signaling pathways. Over 95% of SHH-MBs contain at least one driver event - the activating mutations frequently affect sonic hedgehog signaling (PTCH1, SMO, SUFU), genome maintenance (TP53), and chromatin modulation (KMT2D, KMT2C, HAT complexes), while genes responsible for transcriptional regulation (MYCN) are recurrently amplified. SHH-MBs have the highest prevalence of damaging germline mutations among all MBs. TP53-mutant MBs are enriched among older children and have the worst prognosis among all SHH-MBs. Numerous genetic aberrations, including mutations of TERT, DDX3X, and the PI3K/AKT/mTOR pathway are almost exclusive to adult patients. We elaborate on the newest development within the evolution of molecular subclassification, and compare proposed risk categories across emerging classification systems. We discuss discoveries based on preclinical models and elaborate on the applicability of potential new therapies, including BET bromodomain inhibitors, statins, inhibitors of SMO, AURK, PLK, cMET, targeting stem-like cells, and emerging immunotherapeutic strategies. An enormous amount of data on the genetic background of SHH-MB have accumulated, nevertheless, subgroup affiliation does not provide reliable prediction about response to therapy. Emerging subtypes within SHH-MB offer more layered risk stratifications. Rational clinical trial designs with the incorporation of available molecular knowledge are inevitable. Improved collaboration across the scientific community will be imperative for therapeutic breakthroughs.
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Affiliation(s)
- Otília Menyhárt
- 2nd Department of Pediatrics Semmelweis University H-1094 Budapest Hungary.,MTA TTK Lendület Cancer Biomarker Research Group Institute of Enzymology Hungarian Academy of Sciences Magyar tudósok körútja 2 Budapest Hungary
| | - Balázs Győrffy
- 2nd Department of Pediatrics Semmelweis University H-1094 Budapest Hungary.,MTA TTK Lendület Cancer Biomarker Research Group Institute of Enzymology Hungarian Academy of Sciences Magyar tudósok körútja 2 Budapest Hungary
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210
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Woolman M, Kuzan-Fischer CM, Ferry I, Kiyota T, Luu B, Wu M, Munoz DG, Das S, Aman A, Taylor MD, Rutka JT, Ginsberg HJ, Zarrine-Afsar A. Picosecond Infrared Laser Desorption Mass Spectrometry Identifies Medulloblastoma Subgroups on Intrasurgical Timescales. Cancer Res 2019; 79:2426-2434. [DOI: 10.1158/0008-5472.can-18-3411] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/13/2019] [Accepted: 03/14/2019] [Indexed: 11/16/2022]
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211
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Menyhárt O, Giangaspero F, Győrffy B. Molecular markers and potential therapeutic targets in non-WNT/non-SHH (group 3 and group 4) medulloblastomas. J Hematol Oncol 2019; 12:29. [PMID: 30876441 PMCID: PMC6420757 DOI: 10.1186/s13045-019-0712-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/26/2019] [Indexed: 12/31/2022] Open
Abstract
Childhood medulloblastomas (MB) are heterogeneous and are divided into four molecular subgroups. The provisional non-wingless-activated (WNT)/non-sonic hedgehog-activated (SHH) category combining group 3 and group 4 represents over two thirds of all MBs, coupled with the highest rates of metastases and least understood pathology. The molecular era expanded our knowledge about molecular aberrations involved in MB tumorigenesis, and here, we review processes leading to non-WNT/non-SHH MB formations. The heterogeneous group 3 and group 4 MBs frequently harbor rare individual genetic alterations, yet the emerging profiles suggest that infrequent events converge on common, potentially targetable signaling pathways. A mutual theme is the altered epigenetic regulation, and in vitro approaches targeting epigenetic machinery are promising. Growing evidence indicates the presence of an intermediate, mixed signature group along group 3 and group 4, and future clarifications are imperative for concordant classification, as misidentifying patient samples has serious implications for therapy and clinical trials. To subdue the high MB mortality, we need to discern mechanisms of disease spread and recurrence. Current preclinical models do not represent the full scale of group 3 and group 4 heterogeneity: all of existing group 3 cell lines are MYC-amplified and most mouse models resemble MYC-activated MBs. Clinical samples provide a wealth of information about the genetic divergence between primary tumors and metastatic clones, but recurrent MBs are rarely resected. Molecularly stratified treatment options are limited, and targeted therapies are still in preclinical development. Attacking these aggressive tumors at multiple frontiers will be needed to improve stagnant survival rates.
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Affiliation(s)
- Otília Menyhárt
- 2nd Department of Pediatrics, Semmelweis University, Tűzoltó u. 7-9, Budapest, H-1094, Hungary.,MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Hungarian Academy of Sciences, Magyar tudósok körútja 2, Budapest, H-1117, Hungary
| | - Felice Giangaspero
- Department of Radiological, Oncological, and Anatomo-Pathological Sciences, University Sapienza of Rome, Rome, Italy.,IRCCS Neuromed, Pozzilli (Is), Italy
| | - Balázs Győrffy
- 2nd Department of Pediatrics, Semmelweis University, Tűzoltó u. 7-9, Budapest, H-1094, Hungary. .,MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Hungarian Academy of Sciences, Magyar tudósok körútja 2, Budapest, H-1117, Hungary.
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212
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Sahu AD, S Lee J, Wang Z, Zhang G, Iglesias-Bartolome R, Tian T, Wei Z, Miao B, Nair NU, Ponomarova O, Friedman AA, Amzallag A, Moll T, Kasumova G, Greninger P, Egan RK, Damon LJ, Frederick DT, Jerby-Arnon L, Wagner A, Cheng K, Park SG, Robinson W, Gardner K, Boland G, Hannenhalli S, Herlyn M, Benes C, Flaherty K, Luo J, Gutkind JS, Ruppin E. Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy. Mol Syst Biol 2019; 15:e8323. [PMID: 30858180 PMCID: PMC6413886 DOI: 10.15252/msb.20188323] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 12/31/2018] [Accepted: 01/21/2019] [Indexed: 01/09/2023] Open
Abstract
Most patients with advanced cancer eventually acquire resistance to targeted therapies, spurring extensive efforts to identify molecular events mediating therapy resistance. Many of these events involve synthetic rescue (SR) interactions, where the reduction in cancer cell viability caused by targeted gene inactivation is rescued by an adaptive alteration of another gene (the rescuer). Here, we perform a genome-wide in silico prediction of SR rescuer genes by analyzing tumor transcriptomics and survival data of 10,000 TCGA cancer patients. Predicted SR interactions are validated in new experimental screens. We show that SR interactions can successfully predict cancer patients' response and emerging resistance. Inhibiting predicted rescuer genes sensitizes resistant cancer cells to therapies synergistically, providing initial leads for developing combinatorial approaches to overcome resistance proactively. Finally, we show that the SR analysis of melanoma patients successfully identifies known mediators of resistance to immunotherapy and predicts novel rescuers.
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Affiliation(s)
- Avinash Das Sahu
- Department of Biostatistics and Computational Biology, Harvard School of Public Health, Boston, MA, USA
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Joo S Lee
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhiyong Wang
- Department of Pharmacology & Moores Cancer Center, University of California, San Diego La Jolla, CA, USA
| | - Gao Zhang
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
- Department of Neurosurgery and The Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC, USA
| | | | - Tian Tian
- New Jersey Institute of Technology, Newark, NJ, USA
| | - Zhi Wei
- New Jersey Institute of Technology, Newark, NJ, USA
| | - Benchun Miao
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Nishanth Ulhas Nair
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olga Ponomarova
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Adam A Friedman
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Arnaud Amzallag
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Tabea Moll
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Gyulnara Kasumova
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Patricia Greninger
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Regina K Egan
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Leah J Damon
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Dennie T Frederick
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Livnat Jerby-Arnon
- Schools of Computer Science & Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Allon Wagner
- Department of Electrical Engineering and Computer Science, the Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Kuoyuan Cheng
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Seung Gu Park
- Department of Biostatistics and Computational Biology, Harvard School of Public Health, Boston, MA, USA
| | - Welles Robinson
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Kevin Gardner
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Genevieve Boland
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Sridhar Hannenhalli
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - Cyril Benes
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Keith Flaherty
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Ji Luo
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - J Silvio Gutkind
- Department of Pharmacology & Moores Cancer Center, University of California, San Diego La Jolla, CA, USA
| | - Eytan Ruppin
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Schools of Computer Science & Medicine, Tel-Aviv University, Tel-Aviv, Israel
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213
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Targeting epigenetic modifications in cancer therapy: erasing the roadmap to cancer. Nat Med 2019; 25:403-418. [PMID: 30842676 DOI: 10.1038/s41591-019-0376-8] [Citation(s) in RCA: 247] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 01/25/2019] [Indexed: 12/31/2022]
Abstract
Epigenetic dysregulation is a common feature of most cancers, often occurring directly through alteration of epigenetic machinery. Over the last several years, a new generation of drugs directed at epigenetic modulators have entered clinical development, and results from these trials are now being disclosed. Unlike first-generation epigenetic therapies, these new agents are selective, and many are targeted to proteins which are mutated or translocated in cancer. This review will provide a summary of the epigenetic modulatory agents currently in clinical development and discuss the opportunities and challenges in their development. As these drugs advance in the clinic, drug discovery has continued with a focus on both novel and existing epigenetic targets. We will provide an overview of these efforts and the strategies being employed.
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214
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Fremd C, Hlevnjak M, Zapatka M, Zoernig I, Halama N, Fejzibegovic N, Thewes V, Lichter P, Schirmacher P, Kloor M, Marmé F, Schütz F, Kosaloglu Z, Sinn HP, Jäger D, Schneeweiss A. Mismatch Repair Deficiency Drives Durable Complete Remission by Targeting Programmed Death Receptor 1 in a Metastatic Luminal Breast Cancer Patient. Breast Care (Basel) 2019; 14:53-59. [PMID: 31019444 PMCID: PMC6465703 DOI: 10.1159/000492580] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In the field of breast cancer tumor biology, triple-negative breast cancer patients are the main focus of current clinical trials exploring the use of immune checkpoint inhibitors due to higher frequencies of somatic mutations, neoantigens, and resulting tumor-specific T-cell reactivity. CASE REPORT Here, we present the case of a 66-year-old woman with metastatic luminal breast cancer that rapidly responded to monotherapy with pembrolizumab, a monoclonal anti-PD-1 antibody. This patient obtained a partial clinical response within the first cycle of treatment and an ongoing durable complete remission after 12 weeks. Except for a transient immune-related thyreoiditis, there were no side effects observed offering remarkable quality of life to the patient. To evaluate the underlying mechanisms, we performed immunohistochemistry, explored the mutational landscape by whole-exome sequencing, and identified potential T-cell epitopes by prediction of neoantigens with high affinity binding to one of the patient's HLA. Briefly, we found a strong infiltration of CD8+ T cells without staining for PD-L1 in the tumor stroma. Exome sequencing revealed an enormous frequency of somatic and tumor-specific alterations, mainly C>T/G>A transitions. The mutational pattern was further linked to genome instability and deficient mismatch repair supported by the loss of MSH6 protein expression and therefore leading to susceptibility to immune checkpoint blockade. CONCLUSION Within the overall goal to establish operating procedures for breast cancer immunotherapy, we propose to re-evaluate testing for deficient mismatch repair and to further intensify the search for biomarkers predictive for the success of immune checkpoint modulation including all tumor biologic subtypes of breast cancer.
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Affiliation(s)
- Carlo Fremd
- National Center for Tumor Diseases, Department of Medical Oncology, University of Heidelberg, Heidelberg, Germany
| | - Mario Hlevnjak
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Inka Zoernig
- National Center for Tumor Diseases, Department of Medical Oncology, University of Heidelberg, Heidelberg, Germany
| | - Niels Halama
- National Center for Tumor Diseases, Department of Medical Oncology, University of Heidelberg, Heidelberg, Germany
| | - Nino Fejzibegovic
- National Center for Tumor Diseases, Department of Medical Oncology, University of Heidelberg, Heidelberg, Germany
| | - Verena Thewes
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Peter Schirmacher
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Frederik Marmé
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Florian Schütz
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Zeynep Kosaloglu
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Hans Peter Sinn
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Dirk Jäger
- National Center for Tumor Diseases, Department of Medical Oncology, University of Heidelberg, Heidelberg, Germany
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, Department of Medical Oncology, University of Heidelberg, Heidelberg, Germany
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215
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Abstract
Epigenetics is the process by which gene expression is regulated by events other than alterations of the genome. This includes DNA methylation, histone modifications, chromatin remodeling, microRNAs, and long non-coding RNAs. Methylation of DNA, chromatin remodeling, and histone modifications regulate the chromatin and access of transcription factors to DNA and in turn gene transcription. Alteration of chromatin is now recognized to be deregulated in many cancers. Medulloblastoma is an embryonal tumor of the cerebellum and the most common malignant brain tumor in children, that occurs only rarely in adults. Medulloblastoma is characterized by four major molecularly and histopathologically distinct groups, wingless (WNT), sonic hedgehog (SHH), group 3 (G3), and group 4 (G4), that, except for WNT, are each now subdivided in several subgroups. Gene expression array, next-generation sequencing, and methylation profiling of several hundred primary tumors by several consortia and independent groups revealed that medulloblastomas harbor a paucity of mutations most of which occur in epigenetic regulators, genetic alterations in oncogenes and tumor suppressors, in addition to copy number alterations and chromosome gains and losses. Remarkably, some tumors have no reported mutations, suggesting that some genes required for oncogenesis might be regulated by epigenetic mechanisms which are still to be uncovered and validated. This review will highlight several epigenetic regulators focusing mainly on histone modifiers identified in medulloblastoma.
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Affiliation(s)
- Martine F Roussel
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Jennifer L Stripay
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
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216
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Abstract
Medulloblastoma (MB) comprises a biologically heterogeneous group of embryonal tumours of the cerebellum. Four subgroups of MB have been described (WNT, sonic hedgehog (SHH), Group 3 and Group 4), each of which is associated with different genetic alterations, age at onset and prognosis. These subgroups have broadly been incorporated into the WHO classification of central nervous system tumours but still need to be accounted for to appropriately tailor disease risk to therapy intensity and to target therapy to disease biology. In this Primer, the epidemiology (including MB predisposition), molecular pathogenesis and integrative diagnosis taking histomorphology, molecular genetics and imaging into account are reviewed. In addition, management strategies, which encompass surgical resection of the tumour, cranio-spinal irradiation and chemotherapy, are discussed, together with the possibility of focusing more on disease biology and robust molecularly driven patient stratification in future clinical trials.
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217
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Nicola P, Blackburn PR, Rasmussen KJ, Bertsch NL, Klee EW, Hasadsri L, Pichurin PN, Rankin J, Raymond FL, Clayton-Smith J. De novo DDX3X missense variants in males appear viable and contribute to syndromic intellectual disability. Am J Med Genet A 2019; 179:570-578. [PMID: 30734472 DOI: 10.1002/ajmg.a.61061] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/12/2018] [Accepted: 01/04/2019] [Indexed: 12/23/2022]
Abstract
DDX3X (Xp11.4) encodes a DEAD-box RNA helicase that escapes X chromosome inactivation. Pathogenic variants in DDX3X have been shown to cause X-linked intellectual disability (ID) (MRX102, MIM: 300958). The phenotypes associated with DDX3X variants are heterogeneous and include brain and behavioral abnormalities, microcephaly, hypotonia, and movement disorders and/or spasticity. The majority of DDX3X variants described are de novo mutations in females with ID. In contrast, most male DDX3X variants are inherited from an unaffected mother, with one documented exception being a recently identified de novo splice site variant. It has been suggested, therefore, that DDX3X exerts its effects through haploinsufficiency in females, and that affected males carry hypomorphic alleles that retain partial function. Given the lack of male de novo DDX3X variants, loss-of-function variants in this gene are suspected to be male lethal. Through whole-exome sequencing, we identified three unrelated males with hemizygous missense DDX3X variants and ID. All three variants were confirmed by Sanger sequencing, with two established as de novo. In silico analyses were supportive of pathogenicity. We report the male phenotypes and compare them to phenotypes observed in previously reported male and female patients. In conclusion, we propose that de novo DDX3X variants are not necessarily male lethal and should be considered as a cause of syndromic ID in both males and females.
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Affiliation(s)
- Pantelis Nicola
- University Hospital of South Manchester NHS Foundation Trust, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, Manchester, United Kingdom
| | - Patrick R Blackburn
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kristen J Rasmussen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Nicole L Bertsch
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Julia Rankin
- Clinical Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - F Lucy Raymond
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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- Deciphering Developmental Disorders Study (DDD), Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Manchester, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
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218
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Endris V, Buchhalter I, Allgäuer M, Rempel E, Lier A, Volckmar AL, Kirchner M, von Winterfeld M, Leichsenring J, Neumann O, Penzel R, Weichert W, Glimm H, Fröhling S, Winter H, Herth F, Thomas M, Schirmacher P, Budczies J, Stenzinger A. Measurement of tumor mutational burden (TMB) in routine molecular diagnostics: in silico and real-life analysis of three larger gene panels. Int J Cancer 2019; 144:2303-2312. [PMID: 30446996 DOI: 10.1002/ijc.32002] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/03/2018] [Accepted: 10/29/2018] [Indexed: 12/19/2022]
Abstract
Assessment of Tumor Mutational Burden (TMB) for response stratification of cancer patients treated with immune checkpoint inhibitors is emerging as a new biomarker. Commonly defined as the total number of exonic somatic mutations, TMB approximates the amount of neoantigens that potentially are recognized by the immune system. While whole exome sequencing (WES) is an unbiased approach to quantify TMB, implementation in diagnostics is hampered by tissue availability as well as time and cost constrains. Conversely, panel-based targeted sequencing is nowadays widely used in routine molecular diagnostics, but only very limited data are available on its performance for TMB estimation. Here, we evaluated three commercially available larger gene panels with covered genomic regions of 0.39 Megabase pairs (Mbp), 0.53 Mbp and 1.7 Mbp using i) in silico analysis of TCGA (The Cancer Genome Atlas) data and ii) wet-lab sequencing of a total of 92 formalin-fixed and paraffin-embedded (FFPE) cancer samples grouped in three independent cohorts (non-small cell lung cancer, NSCLC; colorectal cancer, CRC; and mixed cancer types) for which matching WES data were available. We observed a strong correlation of the panel data with WES mutation counts especially for the gene panel >1Mbp. Sensitivity and specificity related to TMB cutpoints for checkpoint inhibitor response in NSCLC determined by wet-lab experiments well reflected the in silico data. Additionally, we highlight potential pitfalls in bioinformatics pipelines and provide recommendations for variant filtering. In summary, our study is a valuable data source for researchers working in the field of immuno-oncology as well as for diagnostic laboratories planning TMB testing.
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Affiliation(s)
- Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ivo Buchhalter
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Allgäuer
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Eugen Rempel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Amelie Lier
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Martina Kirchner
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Jonas Leichsenring
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Olaf Neumann
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich partner site, Germany
| | - Hanno Glimm
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany
| | - Stefan Fröhling
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Translational Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Hauke Winter
- Department of Thoracic Surgery, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany
| | - Felix Herth
- Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany.,Department of Pneumology and Critical Care Medicine, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Thomas
- Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany.,Department of Thoracic Oncology, Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg partner site, Germany
| | - Jan Budczies
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg partner site, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg partner site, Germany
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219
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Defective Epstein-Barr virus in chronic active infection and haematological malignancy. Nat Microbiol 2019; 4:404-413. [PMID: 30664667 DOI: 10.1038/s41564-018-0334-0] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 12/04/2018] [Indexed: 01/01/2023]
Abstract
Epstein-Barr virus (EBV) infection is highly prevalent in humans and is implicated in various diseases, including cancer1,2. Chronic active EBV infection (CAEBV) is an intractable disease classified as a lymphoproliferative disorder in the 2016 World Health Organization lymphoma classification1,2. CAEBV is characterized by EBV-infected T/natural killer (NK) cells and recurrent/persistent infectious mononucleosis-like symptoms3. Here, we show that CAEBV originates from an EBV-infected lymphoid progenitor that acquires DDX3X and other mutations, causing clonal evolution comprising multiple cell lineages. Conspicuously, the EBV genome in CAEBV patients harboured frequent intragenic deletions (27/77) that were also common in various EBV-associated neoplastic disorders (28/61), including extranodal NK/T-cell lymphoma and EBV-positive diffuse large B-cell lymphoma, but were not detected in infectious mononucleosis or post-transplant lymphoproliferative disorders (0/47), which suggests a unique role of these mutations in neoplastic proliferation of EBV-infected cells. These deletions frequently affected BamHI A rightward transcript microRNA clusters (31 cases) and several genes that are essential for producing viral particles (20 cases). The deletions observed in our study are thought to reactivate the lytic cycle by upregulating the expression of two immediate early genes, BZLF1 and BRLF14-7, while averting viral production and subsequent cell lysis. In fact, the deletion of one of the essential genes, BALF5, resulted in upregulation of the lytic cycle and the promotion of lymphomagenesis in a xenograft model. Our findings highlight a pathogenic link between intragenic EBV deletions and EBV-associated neoplastic proliferations.
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220
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Haller F, Bieg M, Will R, Körner C, Weichenhan D, Bott A, Ishaque N, Lutsik P, Moskalev EA, Mueller SK, Bähr M, Woerner A, Kaiser B, Scherl C, Haderlein M, Kleinheinz K, Fietkau R, Iro H, Eils R, Hartmann A, Plass C, Wiemann S, Agaimy A. Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands. Nat Commun 2019; 10:368. [PMID: 30664630 PMCID: PMC6341107 DOI: 10.1038/s41467-018-08069-x] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 12/12/2018] [Indexed: 02/06/2023] Open
Abstract
The molecular pathogenesis of salivary gland acinic cell carcinoma (AciCC) is poorly understood. The secretory Ca-binding phosphoprotein (SCPP) gene cluster at 4q13 encodes structurally related phosphoproteins of which some are specifically expressed at high levels in the salivary glands and constitute major components of saliva. Here we report on recurrent rearrangements [t(4;9)(q13;q31)] in AciCC that translocate active enhancer regions from the SCPP gene cluster to the region upstream of Nuclear Receptor Subfamily 4 Group A Member 3 (NR4A3) at 9q31. We show that NR4A3 is specifically upregulated in AciCCs, and that active chromatin regions and gene expression signatures in AciCCs are highly correlated with the NR4A3 transcription factor binding motif. Overexpression of NR4A3 in mouse salivary gland cells increases expression of known NR4A3 target genes and has a stimulatory functional effect on cell proliferation. We conclude that NR4A3 is upregulated through enhancer hijacking and has important oncogenic functions in AciCC.
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MESH Headings
- Acinar Cells/metabolism
- Acinar Cells/pathology
- Animals
- Carcinoma, Acinar Cell/genetics
- Carcinoma, Acinar Cell/metabolism
- Carcinoma, Acinar Cell/pathology
- Cell Proliferation
- Chromatin/chemistry
- Chromatin/metabolism
- Chromosomes, Human, Pair 4/chemistry
- Chromosomes, Human, Pair 4/metabolism
- Chromosomes, Human, Pair 9/chemistry
- Chromosomes, Human, Pair 9/metabolism
- Cohort Studies
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Enhancer Elements, Genetic
- Epigenesis, Genetic
- Female
- Gene Expression Regulation, Neoplastic
- Genetic Loci
- Humans
- Male
- Mice
- Multigene Family
- Primary Cell Culture
- Receptors, Steroid/genetics
- Receptors, Steroid/metabolism
- Receptors, Thyroid Hormone/genetics
- Receptors, Thyroid Hormone/metabolism
- Salivary Gland Neoplasms/genetics
- Salivary Gland Neoplasms/metabolism
- Salivary Gland Neoplasms/pathology
- Salivary Glands/metabolism
- Salivary Glands/pathology
- Salivary Proteins and Peptides/genetics
- Salivary Proteins and Peptides/metabolism
- Translocation, Genetic
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Affiliation(s)
- Florian Haller
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstr. 8-10, 91054, Erlangen, Germany.
| | - Matthias Bieg
- Center for Digital Health, Berlin Institute of Health and Charité - Universitätsmedizin Berlin, Kapelle-Ufer 2, 10117, Berlin, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Rainer Will
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Cindy Körner
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Alexander Bott
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Naveed Ishaque
- Center for Digital Health, Berlin Institute of Health and Charité - Universitätsmedizin Berlin, Kapelle-Ufer 2, 10117, Berlin, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Evgeny A Moskalev
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstr. 8-10, 91054, Erlangen, Germany
| | - Sarina K Mueller
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Waldstrasse 1, 91054, Erlangen, Germany
| | - Marion Bähr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Angelika Woerner
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Birgit Kaiser
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Claudia Scherl
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Waldstrasse 1, 91054, Erlangen, Germany
| | - Marlen Haderlein
- Department of Radiation Therapy, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Universitätsstrasse 27, 91054, Erlangen, Germany
| | - Kortine Kleinheinz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Rainer Fietkau
- Department of Radiation Therapy, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Universitätsstrasse 27, 91054, Erlangen, Germany
| | - Heinrich Iro
- Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Waldstrasse 1, 91054, Erlangen, Germany
| | - Roland Eils
- Center for Digital Health, Berlin Institute of Health and Charité - Universitätsmedizin Berlin, Kapelle-Ufer 2, 10117, Berlin, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Health Data Science Unit, University Hospital Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg, German Center for Lung Research, University of Heidelberg, Im Neuenheimer Feld 156, 69120 Heidelberg, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstr. 8-10, 91054, Erlangen, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Stefan Wiemann
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstr. 8-10, 91054, Erlangen, Germany
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Breckwoldt MO, Bode J, Sahm F, Krüwel T, Solecki G, Hahn A, Wirthschaft P, Berghoff AS, Haas M, Venkataramani V, von Deimling A, Wick W, Herold-Mende C, Heiland S, Platten M, Bendszus M, Kurz FT, Winkler F, Tews B. Correlated MRI and Ultramicroscopy (MR-UM) of Brain Tumors Reveals Vast Heterogeneity of Tumor Infiltration and Neoangiogenesis in Preclinical Models and Human Disease. Front Neurosci 2019; 12:1004. [PMID: 30686972 PMCID: PMC6335617 DOI: 10.3389/fnins.2018.01004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 12/13/2018] [Indexed: 12/11/2022] Open
Abstract
Diffuse tumor infiltration into the adjacent parenchyma is an effective dissemination mechanism of brain tumors. We have previously developed correlated high field magnetic resonance imaging and ultramicroscopy (MR-UM) to study neonangiogenesis in a glioma model. In the present study we used MR-UM to investigate tumor infiltration and neoangiogenesis in a translational approach. We compare infiltration and neoangiogenesis patterns in four brain tumor models and the human disease: whereas the U87MG glioma model resembles brain metastases with an encapsulated growth and extensive neoangiogenesis, S24 experimental gliomas mimic IDH1 wildtype glioblastomas, exhibiting infiltration into the adjacent parenchyma and along white matter tracts to the contralateral hemisphere. MR-UM resolves tumor infiltration and neoangiogenesis longitudinally based on the expression of fluorescent proteins, intravital dyes or endogenous contrasts. Our study demonstrates the huge morphological diversity of brain tumor models regarding their infiltrative and neoangiogenic capacities and further establishes MR-UM as a platform for translational neuroimaging.
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Affiliation(s)
- Michael O Breckwoldt
- Neuroradiology Department, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julia Bode
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Krüwel
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
| | - Gergely Solecki
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK) Within the DKFZ, Heidelberg, Germany
| | - Artur Hahn
- Neuroradiology Department, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Wirthschaft
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
| | - Anna S Berghoff
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK) Within the DKFZ, Heidelberg, Germany
| | - Maximilian Haas
- Neuroradiology Department, Heidelberg University Hospital, Heidelberg, Germany
| | - Varun Venkataramani
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK) Within the DKFZ, Heidelberg, Germany.,Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK) Within the DKFZ, Heidelberg, Germany.,Neurology Clinic and National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University of Heidelberg, Heidelberg, Germany
| | - Sabine Heiland
- Neuroradiology Department, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Martin Bendszus
- Neuroradiology Department, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix T Kurz
- Neuroradiology Department, Heidelberg University Hospital, Heidelberg, Germany
| | - Frank Winkler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK) Within the DKFZ, Heidelberg, Germany.,Neurology Clinic and National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Björn Tews
- Schaller Research Group at the University of Heidelberg and the German Cancer Research Center (DKFZ), Molecular Mechanisms of Tumor Invasion, Heidelberg, Germany
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222
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Ramaswamy V, Taylor MD. Bioinformatic Strategies for the Genomic and Epigenomic Characterization of Brain Tumors. Methods Mol Biol 2019; 1869:37-56. [PMID: 30324512 DOI: 10.1007/978-1-4939-8805-1_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genomics has significantly advanced our knowledge of the biology of brain tumors, and refined our classification over the past 10 years. These advances have relied on the unbiased analysis of large cohorts of brain tumors, where they are clustered in an unbiased manner prior to ascribing clinical and biological features. Indeed, this has resulted in the identification of several layers of heterogeneity not previously appreciated by morphology alone. As such, the classification of unknown samples into known biological subgroups can be performed robustly using either gene expression or DNA methylation profiling.
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Affiliation(s)
- Vijay Ramaswamy
- Division of Haematology/Oncology, Hospital for Sick Children, Toronto, ON, Canada.
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada.
| | - Michael D Taylor
- Division of Neurosurgery, Hospital for Sick Children, Toronto, ON, Canada
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada
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223
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Galluzzi L, Spranger S, Fuchs E, López-Soto A. WNT Signaling in Cancer Immunosurveillance. Trends Cell Biol 2019; 29:44-65. [PMID: 30220580 PMCID: PMC7001864 DOI: 10.1016/j.tcb.2018.08.005] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 08/23/2018] [Indexed: 12/25/2022]
Abstract
Deregulated WNT signaling has been shown to favor malignant transformation, tumor progression, and resistance to conventional cancer therapy in a variety of preclinical and clinical settings. Accumulating evidence suggests that aberrant WNT signaling may also subvert cancer immunosurveillance, hence promoting immunoevasion and resistance to multiple immunotherapeutics, including immune checkpoint blockers. Here, we discuss the molecular and cellular mechanisms through which WNT signaling influences cancer immunosurveillance and present potential therapeutic avenues to harness currently available WNT modulators for cancer immunotherapy.
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Affiliation(s)
- Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, New York, NY 10065, USA; Université Paris Descartes/Paris V, 75006 Paris, France.
| | - Stefani Spranger
- The Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elaine Fuchs
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Alejandro López-Soto
- Departamento de Biología Funcional, Área de Inmunología, Universidad de Oviedo. Instituto Universitario de Oncología del Principado de Asturias (IUOPA), 33006 Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (IISPA), 33011 Oviedo, Asturias, Spain.
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224
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Pietrobono S, Stecca B. Targeting the Oncoprotein Smoothened by Small Molecules: Focus on Novel Acylguanidine Derivatives as Potent Smoothened Inhibitors. Cells 2018; 7:cells7120272. [PMID: 30558232 PMCID: PMC6316656 DOI: 10.3390/cells7120272] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/30/2018] [Accepted: 12/10/2018] [Indexed: 12/13/2022] Open
Abstract
Hedgehog-GLI (HH) signaling was originally identified as a critical morphogenetic pathway in embryonic development. Since its discovery, a multitude of studies have reported that HH signaling also plays key roles in a variety of cancer types and in maintaining tumor-initiating cells. Smoothened (SMO) is the main transducer of HH signaling, and in the last few years, it has emerged as a promising therapeutic target for anticancer therapy. Although vismodegib and sonidegib have demonstrated effectiveness for the treatment of basal cell carcinoma (BCC), their clinical use has been hampered by severe side effects, low selectivity against cancer stem cells, and the onset of mutation-driven drug resistance. Moreover, SMO antagonists are not effective in cancers where HH activation is due to mutations of pathway components downstream of SMO, or in the case of noncanonical, SMO-independent activation of the GLI transcription factors, the final mediators of HH signaling. Here, we review the current and rapidly expanding field of SMO small-molecule inhibitors in experimental and clinical settings, focusing on a class of acylguanidine derivatives. We also discuss various aspects of SMO, including mechanisms of resistance to SMO antagonists.
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Affiliation(s)
- Silvia Pietrobono
- Tumor Cell Biology Unit⁻Core Research Laboratory, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy.
| | - Barbara Stecca
- Tumor Cell Biology Unit⁻Core Research Laboratory, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139 Florence, Italy.
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225
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Medulloblastomas in adolescents and adults - Can the pediatric experience be extrapolated? Neurochirurgie 2018; 67:76-82. [PMID: 30554773 DOI: 10.1016/j.neuchi.2018.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 08/27/2018] [Accepted: 10/06/2018] [Indexed: 01/07/2023]
Abstract
Adult medulloblastomas are orphan diseases that differ from their pediatric counterpart. Most are classified as classic or desmoplastic and fall in the SHH subgroup, mainly with loss-of-function mutations in PTCH1 and some by TP53-mutation due to underlying germline mutation. Activation of the WNT pathway is sporadic, although underlying Turcot syndrome may be present. One-third of tumors are issued from group 4. Most adult studies are small non-randomized retrospective heterogeneous studies performed at a single center with short follow-up. Standard craniospinal irradiation followed by maintenance chemotherapy (CCNU, cisplatin-vincristine) results in a 4-year event-free survival (EFS) and overall survival (OS) of 68% and 89% respectively in standard-risk adults, and in a 4-year EFS and OS of 50% and 90%, respectively in high-risk adults. Several pooled analyses point out the potential role of chemotherapy in adults. The feasibility of pediatric protocols in adults is sometimes hampered because of blood and peripheral nerve toxicity. In the near future, subgroups of medulloblastomas may be treated by personalized therapies. With prolonged follow-up, adults fare worse. Long-term sequelae and second line treatment are not well defined in adults. Prospective studies are ongoing to define optimal first-line and relapse treatments.
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226
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Extensive cellular heterogeneity of X inactivation revealed by single-cell allele-specific expression in human fibroblasts. Proc Natl Acad Sci U S A 2018; 115:13015-13020. [PMID: 30510006 DOI: 10.1073/pnas.1806811115] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
X-chromosome inactivation (XCI) provides a dosage compensation mechanism where, in each female cell, one of the two X chromosomes is randomly silenced. However, some genes on the inactive X chromosome and outside the pseudoautosomal regions escape from XCI and are expressed from both alleles (escapees). We investigated XCI at single-cell resolution combining deep single-cell RNA sequencing with whole-genome sequencing to examine allelic-specific expression in 935 primary fibroblast and 48 lymphoblastoid single cells from five female individuals. In this framework we integrated an original method to identify and exclude doublets of cells. In fibroblast cells, we have identified 55 genes as escapees including five undescribed escapee genes. Moreover, we observed that all genes exhibit a variable propensity to escape XCI in each cell and cell type and that each cell displays a distinct expression profile of the escapee genes. A metric, the Inactivation Score-defined as the mean of the allelic expression profiles of the escapees per cell-enables us to discover a heterogeneous and continuous degree of cellular XCI with extremes represented by "inactive" cells, i.e., cells exclusively expressing the escaping genes from the active X chromosome and "escaping" cells expressing the escapees from both alleles. We found that this effect is associated with cell-cycle phases and, independently, with the XIST expression level, which is higher in the quiescent phase (G0). Single-cell allele-specific expression is a powerful tool to identify novel escapees in different tissues and provide evidence of an unexpected cellular heterogeneity of XCI.
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227
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Martirosian V, Neman J. Medulloblastoma: Challenges and advances in treatment and research. Cancer Rep (Hoboken) 2018; 2:e1146. [PMCID: PMC7941576 DOI: 10.1002/cnr2.1146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/03/2023] Open
Abstract
Background Medulloblastoma (MB) is a pediatric brain tumor occurring in the posterior fossa. MB is a highly heterogeneous tumor, which can be grouped into four main subgroups: WNT, SHH, Group 3, and Group 4. Each subgroup is different both in its implicated pathways and pathology, as well as how they are treated in the clinic. Recent Findings Standard protocol for MB treatment consists of maximal safe resection, followed by craniospinal radiation (in patients 3 years and older) and adjuvant chemotherapy. Advances in clinical stratification of this tumor have allowed establishment of treatment de‐escalation trials aimed at reducing long‐term side effects. However, there have been few advances in identifying novel therapeutic strategies for MB patients due to difficulties in creating chemotherapeutics that can bypass the blood‐brain‐barrier—among other factors. On the other hand, with the help of whole genome sequencing technologies, molecular pathways involved in MB pathogenesis have become clearer and have helped drive MB research. Regardless, this advance in research has yet to translate to the clinic, which may be due to the inability of current in vivo and in vitro models to accurately recapitulate this heterogeneous tumor in humans. Conclusions There have been significant advances in knowledge and treatment of medulloblastoma over the last few decades. Whole genome sequencing has helped elucidate clear differences between the subgroups of MB, allowing physicians to better tailor treatments to each patient in an effort to reduce long‐term sequelae. However, there are still many more obstacles to overcome, including less cytotoxic therapies in the clinic and better modeling systems to accurately replicate this disease in the laboratory. Scientists and physicians must work in a more cohesive manner to create translatable results from the laboratory to the clinic—helping improve therapies for medulloblastoma patients.
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Affiliation(s)
- Vahan Martirosian
- Department of Neurological Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Josh Neman
- Department of Neurological Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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228
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Robbins CJ, Bou-Dargham MJ, Sanchez K, Rosen MC, Sang QXA. Decoding Somatic Driver Gene Mutations and Affected Signaling Pathways in Human Medulloblastoma Subgroups. J Cancer 2018; 9:4596-4610. [PMID: 30588243 PMCID: PMC6299398 DOI: 10.7150/jca.27993] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/08/2018] [Indexed: 01/02/2023] Open
Abstract
Medulloblastoma is the most common malignant pediatric brain tumor. Prior studies have concentrated their efforts studying the four molecular subgroups: SHH, Wnt, group 3, and group 4. SHH and Wnt are driven by their canonical pathways. Groups 3 and 4 are highly metastatic and associated with aberrations in epigenetic regulators. Recent developments in the field have revealed that these subgroups are not as homogenous as previously believed. The objective of this study is to investigate the involvement of somatic driver gene mutations in these medulloblastoma subgroups. We obtained medulloblastoma data from the Catalogue of Somatic Mutations in Cancer (COSMIC), which contains distinct samples that were not previously studied in a large cohort. We identified somatic driver gene mutations and the signaling pathways affected by these driver genes for medulloblastoma subgroups using bioinformatics tools. We have revealed novel infrequent drivers in these subgroups that contribute to our understanding of tumor heterogeneity in medulloblastoma. Normally SHH signaling is activated in the SHH subgroup, however, we determined gain-of-function mutations in ubiquitin ligase (CUL1) that inhibit Gli-mediated transcription. This suggests a potential hindrance in SHH signaling for some patients. For group 3, gain-of-function in the inhibitor of proinflammatory cytokines (HIVEP3) suggests an immunosuppressive phenotype and thus a more hostile tumor microenvironment. Surprisingly, group 4 tumors possess mutations that may prompt the activation of Wnt signaling through gain-of-function mutations in MUC16 and PCDH9. These infrequent mutations detected in this study could be due to subclonal or spatially restricted alterations. The investigation of aberrant driver gene mutations can lead to the identification of new drug targets and a greater understanding of human medulloblastoma heterogeneity.
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Affiliation(s)
- Charles J Robbins
- Department of Chemistry & Biochemistry, Institute of Molecular Biophysics, Florida State University
| | - Mayassa J Bou-Dargham
- Department of Chemistry & Biochemistry, Institute of Molecular Biophysics, Florida State University
| | - Kevin Sanchez
- Department of Chemistry & Biochemistry, Institute of Molecular Biophysics, Florida State University
| | - Matthew C Rosen
- Department of Chemistry & Biochemistry, Institute of Molecular Biophysics, Florida State University
| | - Qing-Xiang Amy Sang
- Department of Chemistry & Biochemistry, Institute of Molecular Biophysics, Florida State University
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229
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Korshunov A, Casalini B, Chavez L, Hielscher T, Sill M, Ryzhova M, Sharma T, Schrimpf D, Stichel D, Capper D, Reuss DE, Sturm D, Absalyamova O, Golanov A, Lambo S, Bewerunge-Hudler M, Lichter P, Herold-Mende C, Wick W, Pfister SM, Kool M, Jones DTW, von Deimling A, Sahm F. Integrated molecular characterization of IDH-mutant glioblastomas. Neuropathol Appl Neurobiol 2018; 45:108-118. [PMID: 30326163 DOI: 10.1111/nan.12523] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 09/02/2018] [Indexed: 01/14/2023]
Abstract
AIMS Mutations of isocitrate dehydrogenase (IDH)1/2 affect almost all astrocytomas of WHO grade II and III. A subset of IDH-mutant astrocytic tumours progresses to IDH-mutant glioblastoma or presents with the histology of a glioblastoma at first presentation. We set out here to assess the molecular spectrum of IDH-mutant glioblastomas. METHODS We performed an integrated molecular analysis of a mono-centric cohort (n = 97); assessed through genome-wide DNA methylation analysis, copy-number profiling and targeted next generation sequencing using a neurooncology-tailored gene panel. RESULTS Of these 97 IDH-mutant glioblastomas, 68 had a glioblastoma at first presentation ('de novo' IDH-mutant glioblastoma) and 29 emerged from a prior low-grade lesion ('evolved' IDH-mutant glioblastoma). Unsupervised hierarchical clustering of DNA methylation data disclosed that IDH-mutant glioblastoma ('de novo' and 'evolved') formed a distinct group separate from other diffuse glioma subtypes. Homozygous deletions of CDKN2A/B were found to be associated with shorter survival. CONCLUSIONS This study demonstrates DNA methylation patterns in IDH-mutant glioblastoma to be distinct from lower-grade astrocytic counterparts but homogeneous within de novo and evolved IDH-mutant glioblastomas, and identifies CDKN2A as a marker for possible genetic sub-stratification.
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Affiliation(s)
- A Korshunov
- Department of Neuropathology, University Hospital Heidelberg, Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - B Casalini
- Department of Neuropathology, University Hospital Heidelberg, Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - L Chavez
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - T Hielscher
- Department of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Sill
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - M Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - T Sharma
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - D Schrimpf
- Department of Neuropathology, University Hospital Heidelberg, Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - D Stichel
- Department of Neuropathology, University Hospital Heidelberg, Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - D Capper
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Neuropathology, Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - D E Reuss
- Department of Neuropathology, University Hospital Heidelberg, Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - D Sturm
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University Hospital, Heidelberg, Germany
| | - O Absalyamova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - A Golanov
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - S Lambo
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - M Bewerunge-Hudler
- Genomics and Proteomics Core Facility, Microarray Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - P Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - C Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - W Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - S M Pfister
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University Hospital, Heidelberg, Germany
| | - M Kool
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - D T W Jones
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - A von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - F Sahm
- Department of Neuropathology, University Hospital Heidelberg, Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
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230
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Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer. Nat Commun 2018; 9:4782. [PMID: 30429477 PMCID: PMC6235880 DOI: 10.1038/s41467-018-07041-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/15/2018] [Indexed: 12/23/2022] Open
Abstract
Incomplete understanding of the metastatic process hinders personalized therapy. Here we report the most comprehensive whole-genome study of colorectal metastases vs. matched primary tumors. 65% of somatic mutations originate from a common progenitor, with 15% being tumor- and 19% metastasis-specific, implicating a higher mutation rate in metastases. Tumor- and metastasis-specific mutations harbor elevated levels of BRCAness. We confirm multistage progression with new components ARHGEF7/ARHGEF33. Recurrently mutated non-coding elements include ncRNAs RP11-594N15.3, AC010091, SNHG14, 3’ UTRs of FOXP2, DACH2, TRPM3, XKR4, ANO5, CBL, CBLB, the latter four potentially dual protagonists in metastasis and efferocytosis-/PD-L1 mediated immunosuppression. Actionable metastasis-specific lesions include FAT1, FGF1, BRCA2, KDR, and AKT2-, AKT3-, and PDGFRA-3’ UTRs. Metastasis specific mutations are enriched in PI3K-Akt signaling, cell adhesion, ECM and hepatic stellate activation genes, suggesting genetic programs for site-specific colonization. Our results put forward hypotheses on tumor and metastasis evolution, and evidence for metastasis-specific events relevant for personalized therapy. The evolution and genetic nature of metastatic lesions is not completely characterized. Here the authors perform a comprehensive whole-genome study of colorectal metastases in comparison to matched primary tumors and define a multistage progression model and metastasis-specific changes that, in part, are therapeutically actionable.
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231
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Viaene AN, Santi M, Rosenbaum J, Li MM, Surrey LF, Nasrallah MP. SETD2 mutations in primary central nervous system tumors. Acta Neuropathol Commun 2018; 6:123. [PMID: 30419952 PMCID: PMC6231273 DOI: 10.1186/s40478-018-0623-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 10/21/2018] [Indexed: 02/07/2023] Open
Abstract
Mutations in SETD2 are found in many tumors, including central nervous system (CNS) tumors. Previous work has shown these mutations occur specifically in high grade gliomas of the cerebral hemispheres in pediatric and young adult patients. We investigated SETD2 mutations in a cohort of approximately 640 CNS tumors via next generation sequencing; 23 mutations were detected across 19 primary CNS tumors. Mutations were found in a wide variety of tumors and locations at a broad range of allele frequencies. SETD2 mutations were seen in both low and high grade gliomas as well as non-glial tumors, and occurred in patients greater than 55 years of age, in addition to pediatric and young adult patients. High grade gliomas at first occurrence demonstrated either frameshift/truncating mutations or point mutations at high allele frequencies, whereas recurrent high grade gliomas frequently harbored subclones with point mutations in SETD2 at lower allele frequencies in the setting of higher mutational burdens. Comparison with the TCGA dataset demonstrated consistent findings. Finally, immunohistochemistry showed decreased staining for H3K36me3 in our cohort of SETD2 mutant tumors compared to wildtype controls. Our data further describe the spectrum of tumors in which SETD2 mutations are found and provide a context for interpretation of these mutations in the clinical setting.
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232
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Ratnaparkhe M, Wong JKL, Wei PC, Hlevnjak M, Kolb T, Simovic M, Haag D, Paul Y, Devens F, Northcott P, Jones DTW, Kool M, Jauch A, Pastorczak A, Mlynarski W, Korshunov A, Kumar R, Downing SM, Pfister SM, Zapatka M, McKinnon PJ, Alt FW, Lichter P, Ernst A. Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors. Nat Commun 2018; 9:4760. [PMID: 30420702 PMCID: PMC6232171 DOI: 10.1038/s41467-018-06925-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 10/08/2018] [Indexed: 12/22/2022] Open
Abstract
Chromothripsis and chromoanasynthesis are catastrophic events leading to clustered genomic rearrangements. Whole-genome sequencing revealed frequent complex genomic rearrangements (n = 16/26) in brain tumors developing in mice deficient for factors involved in homologous-recombination-repair or non-homologous-end-joining. Catastrophic events were tightly linked to Myc/Mycn amplification, with increased DNA damage and inefficient apoptotic response already observable at early postnatal stages. Inhibition of repair processes and comparison of the mouse tumors with human medulloblastomas (n = 68) and glioblastomas (n = 32) identified chromothripsis as associated with MYC/MYCN gains and with DNA repair deficiencies, pointing towards therapeutic opportunities to target DNA repair defects in tumors with complex genomic rearrangements. Chromothripsis and chromoanasynthesis lead to locally clustered rearrangements affecting one or a few chromosomes, but their impact on cancer development and progression is unclear. Here the authors analyse the role of DNA repair factors in brain tumors by whole-genome sequencing of tumors from mouse models of medulloblastoma or high grade gliomas.
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Affiliation(s)
- Manasi Ratnaparkhe
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ); Faculty of Biosciences, Heidelberg University Germany, Heidelberg, 69120, Germany
| | - John K L Wong
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Pei-Chi Wei
- Boston Children's Hospital, Howard Hughes Medical Institute and Department of Genetics, Harvard Medical School, Boston, 02115, MA, USA
| | - Mario Hlevnjak
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Thorsten Kolb
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Milena Simovic
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ); Faculty of Biosciences, Heidelberg University Germany, Heidelberg, 69120, Germany
| | - Daniel Haag
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, 69120, Germany
| | - Yashna Paul
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Frauke Devens
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Paul Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.,Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, United States
| | - David T W Jones
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, 69120, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, 69120, Germany
| | - Anna Jauch
- Institute of Human Genetics, University of Heidelberg, Heidelberg, 69120, Germany
| | - Agata Pastorczak
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, 91-738, Poland
| | - Wojciech Mlynarski
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, 91-738, Poland
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Department of Neuropathology, Heidelberg University Hospital and German Cancer Consortium (DKTK), Heidelberg, 69120, Germany
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology; German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center, Heidelberg, 69120, Germany
| | - Susanna M Downing
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, 38105-3678, TN, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, 69120, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Peter J McKinnon
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, 38105-3678, TN, USA
| | - Frederick W Alt
- Boston Children's Hospital, Howard Hughes Medical Institute and Department of Genetics, Harvard Medical School, Boston, 02115, MA, USA
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Aurélie Ernst
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
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233
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Kumar R, Liu AP, Orr BA, Northcott PA, Robinson GW. Advances in the classification of pediatric brain tumors through DNA methylation profiling: From research tool to frontline diagnostic. Cancer 2018; 124:4168-4180. [PMID: 30255939 PMCID: PMC6263826 DOI: 10.1002/cncr.31583] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/16/2018] [Accepted: 04/23/2018] [Indexed: 12/22/2022]
Abstract
Despite significant improvements in pediatric brain tumor therapy and outcome, too many children still die of disease, and too many survivors experience significant sequelae as a result of conventional therapies. The molecular characterization of pediatric brain tumors has afforded tremendous insight into the basic biology and clinical management of these deadly childhood diseases. Genomic, epigenomic, and transcriptional profiling have facilitated the identification of significant heterogeneity among previously uniform disease entities. In particular, DNA methylation profiling has emerged as a robust tool for identifying key disease-specific subgroups that can exhibit distinct clinical outcomes. These approaches, which also complement classic histologic techniques, can suggest key mechanistic underpinnings of tumorigenesis and open the door for better informed and more tailored therapy. By leveraging the results of large-scale classifications of disease cohorts, novel driver mutations and pathways can be uncovered, enabling the generation of faithful animal models, promoting targeted drug design, informing developmental biology, and ultimately translating into improved clinical management. In this review, progress in the epigenetic classification of common malignant pediatric brain tumors, namely medulloblastoma, ependymoma, high-grade glioma, atypical teratoid/rhabdoid tumor, and central nervous system embryonal tumors, will be discussed, and the potential role of DNA methylation profiling as a frontline diagnostic modality will be emphasized.
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Affiliation(s)
- Rahul Kumar
- Division of Brain Tumor Research, Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN
| | - Anthony P.Y. Liu
- Division of Neuro-Oncology, Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Brent A. Orr
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Paul A. Northcott
- Division of Brain Tumor Research, Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Giles W. Robinson
- Division of Neuro-Oncology, Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN
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234
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Prognostic effect of whole chromosomal aberration signatures in standard-risk, non-WNT/non-SHH medulloblastoma: a retrospective, molecular analysis of the HIT-SIOP PNET 4 trial. Lancet Oncol 2018; 19:1602-1616. [PMID: 30392813 PMCID: PMC6262170 DOI: 10.1016/s1470-2045(18)30532-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/06/2018] [Accepted: 07/11/2018] [Indexed: 12/18/2022]
Abstract
Background Most children with medulloblastoma fall within the standard-risk clinical disease group defined by absence of high-risk features (metastatic disease, large-cell/anaplastic histology, and MYC amplification), which includes 50–60% of patients and has a 5-year event-free survival of 75–85%. Within standard-risk medulloblastoma, patients in the WNT subgroup are established as having a favourable prognosis; however, outcome prediction for the remaining majority of patients is imprecise. We sought to identify novel prognostic biomarkers to enable improved risk-adapted therapies. Methods The HIT-SIOP PNET 4 trial recruited 338 patients aged 4–21 years with medulloblastoma between Jan 1, 2001, and Dec 31, 2006, in 120 treatment institutions in seven European countries to investigate hyperfractionated radiotherapy versus standard radiotherapy. In this retrospective analysis, we assessed the remaining tumour samples from patients in the HIT-SIOP PNET 4 trial (n=136). We assessed the clinical behaviour of the molecularly defined WNT and SHH subgroups, and identified novel independent prognostic markers and models for standard-risk patients with non-WNT/non-SHH disease. Because of the scarcity and low quality of available genomic material, we used a mass spectrometry-minimal methylation classifier assay (MS-MIMIC) to assess methylation subgroup and a molecular inversion probe array to detect genome-wide copy number aberrations. Prognostic biomarkers and models identified were validated in an independent, demographically matched cohort (n=70) of medulloblastoma patients with non-WNT/non-SHH standard-risk disease treated with conventional therapies (maximal surgical resection followed by adjuvant craniospinal irradiation [all patients] and chemotherapy [65 of 70 patients], at UK Children's Cancer and Leukaemia Group and European Society for Paediatric Oncology (SIOPE) associated treatment centres between 1990 and 2014. These samples were analysed by Illumina 450k DNA methylation microarray. HIT-SIOP PNET 4 is registered with ClinicalTrials.gov, number NCT01351870. Findings We analysed methylation subgroup, genome-wide copy number aberrations, and mutational features in 136 assessable tumour samples from the HIT-SIOP PNET 4 cohort, representing 40% of the 338 patients in the trial cohort. This cohort of 136 samples consisted of 28 (21%) classified as WNT, 17 (13%) as SHH, and 91 (67%) as non-WNT/non-SHH (we considered Group3 and Group4 medulloblastoma together in our analysis because of their similar molecular and clinical features). Favourable outcomes for WNT tumours were confirmed in patients younger than 16 years, and all relapse events in SHH (four [24%] of 17) occurred in patients with TP53 mutation (TP53mut) or chromosome 17p loss. A novel whole chromosomal aberration signature associated with increased ploidy and multiple non-random whole chromosomal aberrations was identified in 38 (42%) of the 91 samples from patients with non-WNT/non-SHH medulloblastoma in the HIT-SIOP PNET 4 cohort. Biomarkers associated with this whole chromosomal aberration signature (at least two of chromosome 7 gain, chromosome 8 loss, and chromosome 11 loss) predicted favourable prognosis. Patients with non-WNT/non-SHH medulloblastoma could be reclassified by these markers as having favourable-risk or high-risk disease. In patients in the HIT-SIOP PNET4 cohort with non-WNT/non-SHH medulloblastoma, with a median follow-up of 6·7 years (IQR 5·8–8·2), 5-year event-free survival was 100% in the favourable-risk group and 68% (95% CI 57·5–82·7; p=0·00014) in the high-risk group. In the validation cohort, with a median follow-up of 5·6 years (IQR 3·1–8·1), 5-year event-free survival was 94·7% (95% CI 85·2–100) in the favourable-risk group and 58·6% (95% CI 45·1–76·1) in the high-risk group (hazard ratio 9·41, 95% CI 1·25–70·57; p=0·029). Our comprehensive molecular investigation identified subgroup-specific risk models which allowed 69 (51%) of 134 accessible patients from the standard-risk medulloblastoma HIT-SIOP PNET 4 cohort to be assigned to a favourable-risk group. Interpretation We define a whole chromosomal signature that allows the assignment of non-WNT/non-SHH medulloblastoma patients normally classified as standard-risk into favourable-risk and high-risk categories. In addition to patients younger than 16 years with WNT tumours, patients with non-WNT/non-SHH tumours with our defined whole chromosomal aberration signature and patients with SHH-TP53wild-type tumours should be considered for therapy de-escalation in future biomarker-driven, risk-adapted clinical trials. The remaining subgroups of patients with high-risk medulloblastoma might benefit from more intensive therapies. Funding Cancer Research UK, Swedish Childhood Cancer Foundation, French Ministry of Health/French National Cancer Institute, and the German Children's Cancer Foundation.
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235
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Khatua S, Song A, Citla Sridhar D, Mack SC. Childhood Medulloblastoma: Current Therapies, Emerging Molecular Landscape and Newer Therapeutic Insights. Curr Neuropharmacol 2018; 16:1045-1058. [PMID: 29189165 PMCID: PMC6120114 DOI: 10.2174/1570159x15666171129111324] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 11/06/2017] [Accepted: 11/27/2017] [Indexed: 12/21/2022] Open
Abstract
Background: Medulloblastoma is the most common malignant brain tumor in children, currently treated uniformly based on histopathology and clinico-radiological risk stratification leading to unpredictable relapses and therapeutic failures. Identification of molecular subgroups have thrown light on the reasons for these and now reveals clues to profile molecularly based personalized therapy against these tumors. Methods: Research and online contents were evaluated for pediatric medulloblastoma which included latest information on the molecular subgroups and their clinical relevance and update on efforts to translate them into clinics. Results: Scientific endeavors over the last decade have clearly identified four molecular variants (WNT, SHH, Group 3, and Group 4) and their demographic, genomic, and epigenetic profile. Latest revelations include significant heterogeneity within these subgroups and 12 different subtypes of MB are now identified with disparate outcomes and biology. These findings have important implications for stratification and profiling future clinical trials against these formidable tumors. Conclusion: With the continued outpouring of genomic/epigenomic data of these molecular subgroups and evolution of further subtypes in each subgroup, the challenge lies in comprehensive evaluation of these informations. Current and future endeavors are now needed to profile personalized therapy for each child based on the molecular risk stratification of medulloblastoma, with a hope to improve survival outcome and reduce relapses.
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Affiliation(s)
- Soumen Khatua
- Department of Pediatrics, MD Anderson Cancer Center, The University of Texas Health Science Center at Houston, Pediatrics Houston, Texas, United States
| | - Anne Song
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, The University of Texas Health Science Center at Houston, Pediatrics Houston, Texas, United States
| | - Divyaswathi Citla Sridhar
- Department of Pediatrics, The University of Texas Health Science Center at Houston, Pediatrics Houston, Texas, United States
| | - Stephen C Mack
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, The University of Texas Health Science Center at Houston, Pediatrics Houston, Texas, United States
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Henssen AG, Kentsis A. Emerging functions of DNA transposases and oncogenic mutators in childhood cancer development. JCI Insight 2018; 3:123172. [PMID: 30333322 DOI: 10.1172/jci.insight.123172] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Our understanding of the molecular pathogenesis of childhood cancers has advanced substantially, but their fundamental causes remain poorly understood. Recently, multiple mechanisms of DNA damage and repair have been associated with mutations observed in human cancers. Here, we review the physiologic functions and oncogenic activities of transposable genetic elements. In particular, we focus on the recent studies implicating DNA transposases RAG1/2 and PGBD5 as oncogenic mutators that promote genomic rearrangements in childhood leukemias and solid tumors. We outline future studies that will be needed to define the contributions of transposons to mutational processes that become dysregulated in cancer cells. In addition, we discuss translational approaches, including synthetic lethal strategies, for identifying and developing improved clinical therapies to target oncogenic transposons and transposases.
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Affiliation(s)
- Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin, Berlin, Germany.,German Cancer Consortium, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Alex Kentsis
- Departments of Pediatrics, Pharmacology, and Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York, USA.,Sloan Kettering Institute, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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237
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Miranda-Gonçalves V, Lameirinhas A, Henrique R, Jerónimo C. Metabolism and Epigenetic Interplay in Cancer: Regulation and Putative Therapeutic Targets. Front Genet 2018; 9:427. [PMID: 30356832 PMCID: PMC6190739 DOI: 10.3389/fgene.2018.00427] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/10/2018] [Indexed: 12/31/2022] Open
Abstract
Alterations in the epigenome and metabolism affect molecular rewiring of cancer cells facilitating cancer development and progression. Modulation of histone and DNA modification enzymes occurs owing to metabolic reprogramming driven by oncogenes and expression of metabolism-associated genes is, in turn, epigenetically regulated, promoting the well-known metabolic reprogramming of cancer cells and, consequently, altering the metabolome. Thus, several malignant traits are supported by the interplay between metabolomics and epigenetics, promoting neoplastic transformation. In this review we emphasize the importance of tumour metabolites in the activity of most chromatin-modifying enzymes and implication in neoplastic transformation. Furthermore, candidate targets deriving from metabolism of cancer cells and altered epigenetic factors is emphasized, focusing on compounds that counteract the epigenomic-metabolic interplay in cancer.
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Affiliation(s)
- Vera Miranda-Gonçalves
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Ana Lameirinhas
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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Targeting DDX3 in Medulloblastoma Using the Small Molecule Inhibitor RK-33. Transl Oncol 2018; 12:96-105. [PMID: 30292066 PMCID: PMC6171097 DOI: 10.1016/j.tranon.2018.09.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/31/2018] [Accepted: 09/07/2018] [Indexed: 02/08/2023] Open
Abstract
Medulloblastoma is the most common malignant tumor that arises from the cerebellum of the central nervous system. Clinically, medulloblastomas are treated by surgery, radiation, and chemotherapy, all of which result in toxicity and morbidity. Recent reports have identified that DDX3, a member of the RNA helicase family, is mutated in medulloblastoma. In this study, we demonstrate the role of DDX3 in driving medulloblastoma. With the use of a small molecule inhibitor of DDX3, RK-33, we could inhibit growth and promote cell death in two medulloblastoma cell lines, DAOY and UW228, with IC50 values of 2.5 μM and 3.5 μM, respectively. Treatment of DAOY and UW228 cells with RK-33 caused a G1 arrest, resulted in reduced TCF reporter activity, and reduced mRNA expression levels of downstream target genes of the WNT pathway, such as Axin2, CCND1, MYC, and Survivin. In addition, treatment of DAOY and UW228 cells with a combination of RK-33 and radiation exhibited a synergistic effect. Importantly, the combination of RK-33 and 5 Gy radiation caused tumor regression in a mouse xenograft model of medulloblastoma. Using immunohistochemistry, we observed DDX3 expression in both pediatric (55%) and adult (66%) medulloblastoma patients. Based on these results, we conclude that RK-33 is a promising radiosensitizing agent that inhibits DDX3 activity and down-regulates WNT/β-catenin signaling and could be used as a frontline therapeutic strategy for DDX3-expressing medulloblastomas in combination with radiation.
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239
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Testa U, Castelli G, Pelosi E. Genetic Abnormalities, Clonal Evolution, and Cancer Stem Cells of Brain Tumors. Med Sci (Basel) 2018; 6:E85. [PMID: 30279357 PMCID: PMC6313628 DOI: 10.3390/medsci6040085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 02/06/2023] Open
Abstract
Brain tumors are highly heterogeneous and have been classified by the World Health Organization in various histological and molecular subtypes. Gliomas have been classified as ranging from low-grade astrocytomas and oligodendrogliomas to high-grade astrocytomas or glioblastomas. These tumors are characterized by a peculiar pattern of genetic alterations. Pediatric high-grade gliomas are histologically indistinguishable from adult glioblastomas, but they are considered distinct from adult glioblastomas because they possess a different spectrum of driver mutations (genes encoding histones H3.3 and H3.1). Medulloblastomas, the most frequent pediatric brain tumors, are considered to be of embryonic derivation and are currently subdivided into distinct subgroups depending on histological features and genetic profiling. There is emerging evidence that brain tumors are maintained by a special neural or glial stem cell-like population that self-renews and gives rise to differentiated progeny. In many instances, the prognosis of the majority of brain tumors remains negative and there is hope that the new acquisition of information on the molecular and cellular bases of these tumors will be translated in the development of new, more active treatments.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
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240
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Embryonal Tumors of the Central Nervous System in Children: The Era of Targeted Therapeutics. Bioengineering (Basel) 2018; 5:bioengineering5040078. [PMID: 30249036 PMCID: PMC6315657 DOI: 10.3390/bioengineering5040078] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/12/2018] [Accepted: 09/12/2018] [Indexed: 02/07/2023] Open
Abstract
Embryonal tumors (ET) of the central nervous system (CNS) in children encompass a wide clinical spectrum of aggressive malignancies. Until recently, the overlapping morphological features of these lesions posed a diagnostic challenge and undermined discovery of optimal treatment strategies. However, with the advances in genomic technology and the outpouring of biological data over the last decade, clear insights into the molecular heterogeneity of these tumors are now well delineated. The major subtypes of ETs of the CNS in children include medulloblastoma, atypical teratoid rhabdoid tumor (ATRT), and embryonal tumors with multilayered rosettes (ETMR), which are now biologically and clinically characterized as different entities. These important developments have paved the way for treatments guided by risk stratification as well as novel targeted therapies in efforts to improve survival and reduce treatment burden.
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Abstract
PURPOSE OF REVIEW This article describes the most common pediatric brain tumors and highlights recent developments in their diagnosis and treatment strategies. RECENT FINDINGS We are in the midst of a molecular era for pediatric brain tumors. Genetic and epigenetic profiling of tumors has impacted their diagnosis, allowing for the subgrouping of heterogeneous tumor groups and leading to the complete renaming of some tumor types. These advances are reflected in the new 2016 World Health Organization classification. For example, primitive neuroectodermal tumors have been completely eliminated and replaced by subgroups defined by the absence or presence of specific chromosomal amplification. Medulloblastomas, diffuse astrocytomas, and ependymomas now have specific subtypes that are based on defining molecular features. More recent epigenetic-based subgrouping of atypical teratoid/rhabdoid tumors have not yet made it into the official classification system, but will surely have an impact on how these tumors are regarded in future preclinical and clinical trials. SUMMARY Genetic and epigenetic data are changing how pediatric brain tumors are diagnosed, are leading to new guidelines for how treatment outcome analyses can be organized, and are offering molecular targets that can be used for the development of novel therapies.
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Abstract
Although tumours initiate from oncogenic changes in a cancer cell, subsequent tumour progression and therapeutic response depend on interactions between the cancer cells and the tumour microenvironment (TME). The primary monocilium, or cilium, provides a spatially localized platform for signalling by Hedgehog, Notch, WNT and some receptor tyrosine kinase pathways and mechanosensation. Changes in ciliation of cancer cells and/or cells of the TME during tumour development enforce asymmetric intercellular signalling in the TME. Growing evidence indicates that some oncogenic signalling pathways as well as some targeted anticancer therapies induce ciliation, while others repress it. The links between the genomic profile of cancer cells, drug treatment and ciliary signalling in the TME likely affect tumour growth and therapeutic response.
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Affiliation(s)
- Hanqing Liu
- School of Pharmacy, Jiangsu University, Jiangsu, China
| | - Anna A Kiseleva
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
- Kazan Federal University, Kazan, Russia
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA.
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Abstract
INTRODUCTION Integrated genomics has significantly advanced our understanding of medulloblastoma heterogeneity. It is now clear that it actually comprises at least four distinct molecular subgroups termed Wnt/Wingless (WNT), Sonic Hedgehog (SHH), Group 3, and Group 4 with stark clinical and biological differences. Areas covered: This paper reviews advances in the classification and risk stratification of medulloblastoma, specifically integrating subgroup with clinical and cytogenetic risk factors, with a summary of the potential to lead to more precise therapies. Moreover, the current state of preclinical modeling is summarized with respect to their utility in generating new treatments and correlation with genomic discoveries. Opportunities and challenges in developing new treatment paradigms are summarized and discussed, specifically new therapies for very high-risk metastatic/MYC-amplified Group 3 and TP53-mutant SHH and reductions in therapy for lower risk groups. Expert commentary: Survival across medulloblastoma has been stagnant for over 30 years, and new treatment paradigms are urgently required. Current therapy significantly over treats a high proportion of patients leaving them with lifelong side effects; while many patients still succumb to their disease. Applying biological advances could improve quality of life for a significant proportion of patients while offering new upfront approaches to the highest risk patients.
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Affiliation(s)
- Carolina Nör
- a Programme in Developmental and Stem Cell Biology , Hospital for Sick Children , Toronto , ON , Canada.,b Labatt Brain Tumour Research Centre , Hospital for Sick Children , Toronto , ON , Canada
| | - Vijay Ramaswamy
- b Labatt Brain Tumour Research Centre , Hospital for Sick Children , Toronto , ON , Canada.,c Division of Haematology/Oncology , Hospital for Sick Children , Toronto , ON , Canada
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Goyal A, Cajigas I, Ibrahim GM, Brathwaite CD, Khatib Z, Niazi T, Bhatia S, Ragheb J. Surgical Treatment of Intramedullary Spinal Metastasis in Medulloblastoma: Case Report and Review of the Literature. World Neurosurg 2018; 118:42-46. [PMID: 29990605 DOI: 10.1016/j.wneu.2018.06.250] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 11/30/2022]
Abstract
BACKGROUND Medulloblastomas are common childhood central nervous system tumors that are prone to leptomeningeal spread. Intramedullary dissemination is rare with very few case reports existing in the available literature. CASE DESCRIPTION The authors here present a case of a 14-year-old boy with Li-Fraumeni syndrome and medulloblastoma who underwent surgical resection of spinal intramedullary spread. Histopathology revealed the tumor to be anaplastic medulloblastoma, same as the intracranial lesions. Genetic testing of the metastatic deposit revealed loss of functions mutations in SUFU, NOTCH3, and TP53 and TERC amplification. An improvement in ambulatory function at short-term follow-up was noted before the patient died of disseminated disease. CONCLUSIONS Intramedullary metastasis of medulloblastoma remains a rare disease. Surgical resection might play a possible role in management in addition to radiation and chemotherapy.
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Affiliation(s)
- Anshit Goyal
- Mayo Clinic Neuro-Informatics Laboratory, Mayo Clinic, Rochester, Minnesota, USA
| | - Iahn Cajigas
- Department of Neurosurgery, Nicklaus Children's Hospital, Miami, Florida, USA; Department of Neurosurgery, University of Miami Miller School of Medicine, Miami, Florida, USA.
| | - George M Ibrahim
- Department of Neurosurgery, Nicklaus Children's Hospital, Miami, Florida, USA
| | | | - Ziad Khatib
- Department of Pediatric Hematology-Oncology, Nicklaus Children's Hospital, Miami, Florida, USA
| | - Toba Niazi
- Department of Neurosurgery, Nicklaus Children's Hospital, Miami, Florida, USA; Department of Neurosurgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Sanjiv Bhatia
- Department of Neurosurgery, Nicklaus Children's Hospital, Miami, Florida, USA; Department of Neurosurgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - John Ragheb
- Department of Neurosurgery, Nicklaus Children's Hospital, Miami, Florida, USA; Department of Neurosurgery, University of Miami Miller School of Medicine, Miami, Florida, USA
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245
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Guerrini-Rousseau L, Dufour C, Varlet P, Masliah-Planchon J, Bourdeaut F, Guillaud-Bataille M, Abbas R, Bertozzi AI, Fouyssac F, Huybrechts S, Puget S, Bressac-De Paillerets B, Caron O, Sevenet N, Dimaria M, Villebasse S, Delattre O, Valteau-Couanet D, Grill J, Brugières L. Germline SUFU mutation carriers and medulloblastoma: clinical characteristics, cancer risk, and prognosis. Neuro Oncol 2018; 20:1122-1132. [PMID: 29186568 PMCID: PMC6280147 DOI: 10.1093/neuonc/nox228] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background Germline mutations of suppressor of fused homolog (SUFU) predispose to sonic hedgehog (SHH) medulloblastoma. Germline SUFU mutations have been reported in nevoid basal cell carcinoma syndrome (NBCCS), but little is known about the cancer risk and clinical spectrum. Methods We performed a retrospective review of all patients with medulloblastoma and a germline SUFU mutation in France. Results Twenty-two patients from 17 families were identified with medulloblastoma and a germline SUFU mutation (median age at diagnosis: 16.5 mo). Macrocrania was present in 20 patients, but only 5 met the diagnostic criteria for NBCCS. Despite treatment with surgery and chemotherapy, to avoid radiotherapy in all patients except one, the outcome was worse than expected for SHH medulloblastoma, due to the high incidence of local relapses (8/22 patients) and second malignancies (n = 6 in 4/22 patients). The 5-year progression-free survival and overall survival rates were 42% and 66%. Mutations were inherited in 79% of patients, and 34 additional SUFU mutation carriers were identified within 14 families. Medulloblastoma penetrance was incomplete, but higher than in Patched 1 (PTCH1) mutation carriers. Besides medulloblastoma, 19 other tumors were recorded among the 56 SUFU mutation carriers, including basal cell carcinoma (BCC) in 2 patients and meningioma in 3 patients. Conclusion Germline SUFU mutations strongly predispose to medulloblastoma in the first years of life, with worse prognosis than usually observed for SHH medulloblastoma. The clinical spectrum differs between SUFU and PTCH1 mutation carriers, and BCC incidence is much lower in SUFU mutation carriers. The optimal treatment of SUFU mutation-associated medulloblastoma has not been defined.
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Affiliation(s)
- Léa Guerrini-Rousseau
- Département de Cancérologie de l’Enfant et de l’Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France,Corresponding author: Léa Guerrini-Rousseau, Gustave Roussy, Département de Cancérologie de l’Enfant et de l’Adolescent, 114 rue Edouard Vaillant, 94805 Villejuif, France ()
| | - Christelle Dufour
- Département de Cancérologie de l’Enfant et de l’Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Pascale Varlet
- Service de neuropathologie, Hôpital Sainte-Anne, Université Paris Descartes, Paris, France
| | - Julien Masliah-Planchon
- PSL Research University, INSERM U830 Génétique et Biologie des Cancers Institut Curie, Paris, France,Unité de génétique somatique, SIREDO pediatric oncology center, Institut Curie, Paris, France
| | - Franck Bourdeaut
- PSL Research University, INSERM U830 Génétique et Biologie des Cancers Institut Curie, Paris, France,Département d’oncologie Pédiatrique adolescents Jeunes Adultes, Institut Curie, Paris, France, SIREDO pediatric oncology center, Institut Curie, Paris, France,Institut Curie SIRIC - Laboratoire de Recherche Translationnelle en Oncologie Pédiatrique, Institut Curie, Paris, France
| | - Marine Guillaud-Bataille
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Rachid Abbas
- INSERM U1018, CESP, Université Paris-Sud, Université Paris-Saclay, Villejuif, France,Service de Biostatistique et d’Epidémiologie, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | | | - Fanny Fouyssac
- Onco-hématologie pédiatrique, Hôpital d’Enfants, CHU Nancy, Nancy, France
| | - Sophie Huybrechts
- Hematology-Oncology Unit, Hôpital Universitaire des Enfants Reine Fabiola, ULB Université libre de Bruxelles, Brussels, Belgium
| | - Stéphanie Puget
- Service de neurochirurgie pédiatrique, Hôpital Necker-Enfants malades, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | | | - Olivier Caron
- PSL Research University, INSERM U830 Génétique et Biologie des Cancers Institut Curie, Paris, France,Unité de génétique somatique, SIREDO pediatric oncology center, Institut Curie, Paris, France,Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Nicolas Sevenet
- Laboratoire de génétique moléculaire, Département de bio-pathologie, Institut Bergonié, Bordeaux, France,INSERM U1218, Université de Bordeaux, Bordeaux, France,UFR des Sciences Pharmaceutiques, Université de Bordeaux, Bordeaux, France
| | - Marina Dimaria
- Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Sophie Villebasse
- Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Olivier Delattre
- Département de Cancérologie de l’Enfant et de l’Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Dominique Valteau-Couanet
- Département de Cancérologie de l’Enfant et de l’Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Jacques Grill
- Unité Mixte de Recherche 8203 du Centre National de la Recherche Scientifique, Université Paris-Saclay, Villejuif, France
| | - Laurence Brugières
- Département de Cancérologie de l’Enfant et de l’Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France
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Pallavicini G, Sgrò F, Garello F, Falcone M, Bitonto V, Berto GE, Bianchi FT, Gai M, Chiotto AM, Filippi M, Cutrin JC, Ala U, Terreno E, Turco E, Cunto FD. Inactivation of Citron Kinase Inhibits Medulloblastoma Progression by Inducing Apoptosis and Cell Senescence. Cancer Res 2018; 78:4599-4612. [DOI: 10.1158/0008-5472.can-17-4060] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 05/01/2018] [Accepted: 06/07/2018] [Indexed: 11/16/2022]
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Impact of miRNA-mRNA Profiling and Their Correlation on Medulloblastoma Tumorigenesis. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:490-503. [PMID: 30195786 PMCID: PMC6070673 DOI: 10.1016/j.omtn.2018.06.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 02/06/2023]
Abstract
Medulloblastoma (MB) is a clinically challenging, childhood brain tumor with a diverse genetic makeup and differential miRNA profile. Aiming to identify deregulated miRNAs in MB, the miRNA expression profile of human MB samples was compared to that of normal cerebellar tissues. As a result, 8 upregulated and 64 downregulated miRNAs were identified in MB samples. Although various algorithms have been developed to predict the interaction between miRNA-mRNA pairs, the complexity and fidelity of miRNA-mRNA remain a concern. Therefore, to identify the signatures of miRNA-mRNA interactions essential for MB pathogenesis, miRNA profiling, RNA sequencing, and ingenuity pathway analysis (IPA) were performed in the same primary human MB samples. Further, when miR-217 was inhibited, a significant upregulation of predicted target genes SIRT1, ROBO1, FOXO3, and SMAD7 in HDMB03 cells was observed, confirming the validity of our approach. Functional analysis revealed that the inhibition of miR-217 in HDMB03 cells suppresses colony formation, migration, invasion, promoted apoptosis, and arrested cell population in S phase, indicating that manipulation of miR-217 may have a therapeutic potential for MB patients. Therefore, our study provides an essential platform for future investigations of specific miRNAs responsible for MB pathogenesis.
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El-Ayadi M, Egervari K, Merkler D, McKee TA, Gumy-Pause F, Stichel D, Capper D, Pietsch T, Ansari M, von Bueren AO. Concurrent IDH1 and SMARCB1 Mutations in Pediatric Medulloblastoma: A Case Report. Front Neurol 2018; 9:398. [PMID: 29971034 PMCID: PMC6018091 DOI: 10.3389/fneur.2018.00398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/15/2018] [Indexed: 01/22/2023] Open
Abstract
Isocitrate Dehydrogenase-1 (IDH1) is a driver gene in several cancers including brain tumors such as low-grade and high-grade gliomas. Mutations of SMARCB1 were described in atypical teratoid rhabdoid tumors and to date have not been associated with the pathogenesis of medulloblastoma. We report concurrent IDH1 and SMARCB1 mutations in a medulloblastoma patient. We searched the catalog of somatic mutations in cancer (COSMIC) database and other mutation databases and -to our knowledge- this is the first reported case of medulloblastoma harboring both mutations together. Our patient is a 13-year-old male presenting with headache and vomiting at diagnosis. MRI revealed left cerebellar expansive lesion with no evidence of metastasis. A histopathological diagnosis of desmoplastic/nodular medulloblastoma was made after complete resection of the tumor. Immunophenotypic characterization and methylation profiling suggested a medulloblastoma with SHH activation. Next generation sequencing of a panel of 400 genes revealed heterozygous somatic IDH1(p.R132C), SMARCB1(p.R201Q), and CDH11(p.L625T) mutations. The patient was treated according to the HIT-SIOP PNET 4 protocol. He is in complete remission more than 2 years after diagnosis. In conclusion, increasing use of high throughput sequencing will certainly increase the frequency with which rare mutations or mutation combinations are identified. The exact frequency of this mutation combination and whether it has any particular therapeutic implications or prognostic relevance requires further investigation.
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Affiliation(s)
- Moatasem El-Ayadi
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
- CANSEARCH Research Laboratory, Department of Pediatrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Pediatric Oncology, National Cancer Institute, Cairo University, Cairo, Egypt
- Department of Pediatric Oncology, Children Cancer Hospital of Egypt, Cairo, Egypt
| | - Kristof Egervari
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Clinical Pathology, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Doron Merkler
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Clinical Pathology, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Thomas A. McKee
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Clinical Pathology, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Fabienne Gumy-Pause
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
- CANSEARCH Research Laboratory, Department of Pediatrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Charité — Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Partner Site Berlin, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Torsten Pietsch
- Institute of Neuropathology, Brain Tumor Reference Center, Deutsche Gesellschaft für Neuropathologie und Neuroanatomie, University of Bonn Medical Center, Bonn, Germany
| | - Marc Ansari
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
- CANSEARCH Research Laboratory, Department of Pediatrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - André O. von Bueren
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
- CANSEARCH Research Laboratory, Department of Pediatrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Colafati GS, Voicu IP, Carducci C, Miele E, Carai A, Di Loreto S, Marrazzo A, Cacchione A, Cecinati V, Tornesello A, Mastronuzzi A. MRI features as a helpful tool to predict the molecular subgroups of medulloblastoma: state of the art. Ther Adv Neurol Disord 2018; 11:1756286418775375. [PMID: 29977341 PMCID: PMC6024494 DOI: 10.1177/1756286418775375] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/28/2018] [Indexed: 12/20/2022] Open
Abstract
Medulloblastoma is the most common malignant pediatric brain tumor. Medulloblastoma should not be viewed as a single disease, but as a heterogeneous mixture of various subgroups with distinct characteristics. Based on genomic profiles, four distinct molecular subgroups are identified: Wingless (WNT), Sonic Hedgehog (SHH), Group 3 and Group 4. Each of these subgroups are associated with specific genetic aberrations, typical age of onset as well as survival prognosis. Magnetic resonance imaging (MRI) is performed for all patients with brain tumors, and has a key role in the diagnosis, surgical guidance and follow up of patients with medulloblastoma. Several studies indicate MRI as a promising tool for early detection of medulloblastoma subgroups. The early identification of the subgroup can influence the extent of surgical resection, radiotherapy and chemotherapy targeted treatments. In this article, we review the state of the art in MRI-facilitated medulloblastoma subgrouping, with a summary of the main MRI features in medulloblastoma and a brief discussion on molecular characterization of medulloblastoma subgroups. The main focus of the article is MRI features that correlate with medulloblastoma subtypes, as well as features suggestive of molecular subgroups. Finally, we briefly discuss the latest trends in MRI studies and latest developments in molecular characterization.
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Affiliation(s)
| | - Ioan Paul Voicu
- Department of Imaging, Neuroradiology Unit and Department of Hematology/Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, Rome, Italy
| | - Chiara Carducci
- Department of Imaging, Neuroradiology Unit, Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Evelina Miele
- Department of Hematology/Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, Rome, Italy
| | - Andrea Carai
- Department of Neuroscience and Neurorehabilitation, Neurosurgery Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - Simona Di Loreto
- Dipartimento di Pediatria, Università degli studi di Chieti, Chieti, Italy
| | - Antonio Marrazzo
- Department of Hematology/Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, Rome, Italy
| | - Antonella Cacchione
- Department of Hematology/Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, Rome, Italy
| | - Valerio Cecinati
- Pediatric Hematology and Oncology Unit, Department of Hematology, Transfusion Medicine and Biotechnology, Pescara, Italy
| | | | - Angela Mastronuzzi
- Department of Hematology/Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, Rome, Italy
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250
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Ezponda T, Dupéré-Richer D, Will CM, Small EC, Varghese N, Patel T, Nabet B, Popovic R, Oyer J, Bulic M, Zheng Y, Huang X, Shah MY, Maji S, Riva A, Occhionorelli M, Tonon G, Kelleher N, Keats J, Licht JD. UTX/KDM6A Loss Enhances the Malignant Phenotype of Multiple Myeloma and Sensitizes Cells to EZH2 inhibition. Cell Rep 2018; 21:628-640. [PMID: 29045832 DOI: 10.1016/j.celrep.2017.09.078] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 07/16/2017] [Accepted: 09/24/2017] [Indexed: 12/30/2022] Open
Abstract
Loss or inactivation of the histone H3K27 demethylase UTX occurs in several malignancies, including multiple myeloma (MM). Using an isogenic cell system, we found that loss of UTX leads to deactivation of gene expression ultimately promoting the proliferation, clonogenicity, adhesion, and tumorigenicity of MM cells. Moreover, UTX mutant cells showed increased in vitro and in vivo sensitivity to inhibition of EZH2, a histone methyltransferase that generates H3K27me3. Such sensitivity was related to a decrease in the levels of IRF4 and c-MYC and an activation of repressors of IRF4 characteristic of germinal center B cells such as BCL6 and IRF1. Rebalance of H3K27me3 levels at specific genes through EZH2 inhibitors may be a therapeutic strategy in MM cases harboring UTX mutations.
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Affiliation(s)
- Teresa Ezponda
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Daphné Dupéré-Richer
- Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, FL 2033, USA
| | - Christine M Will
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Eliza C Small
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nobish Varghese
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Tej Patel
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Behnam Nabet
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Relja Popovic
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jon Oyer
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marinka Bulic
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yupeng Zheng
- Department of Chemistry, Department of Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA
| | - Xiaoxiao Huang
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Chemistry, Department of Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA
| | - Mrinal Y Shah
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sayantan Maji
- Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, FL 2033, USA
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 2033, USA
| | - Manuela Occhionorelli
- Functional Genomics of Cancer Unit, Division of Molecular Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan 70126, Italy
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Molecular Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan 70126, Italy
| | - Neil Kelleher
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Chemistry, Department of Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA
| | - Jonathan Keats
- Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Jonathan D Licht
- Division of Hematology/Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, FL 2033, USA.
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