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Gilbertson RJ, Behjati S, Böttcher AL, Bronner ME, Burridge M, Clausing H, Clifford H, Danaher T, Donovan LK, Drost J, Eggermont AMM, Emerson C, Flores MG, Hamerlik P, Jabado N, Jones A, Kaessmann H, Kleinman CL, Kool M, Kutscher LM, Lindberg G, Linnane E, Marioni JC, Maris JM, Monje M, Macaskill A, Niederer S, Northcott PA, Peeters E, Plieger-van Solkema W, Preußner L, Rios AC, Rippe K, Sandford P, Sgourakis NG, Shlien A, Smith P, Straathof K, Sullivan PJ, Suvà ML, Taylor MD, Thompson E, Vento-Tormo R, Wainwright BJ, Wechsler-Reya RJ, Westermann F, Winslade S, Al-Lazikani B, Pfister SM. The Virtual Child. Cancer Discov 2024; 14:663-668. [PMID: 38571421 DOI: 10.1158/2159-8290.cd-23-1500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
SUMMARY We are building the world's first Virtual Child-a computer model of normal and cancerous human development at the level of each individual cell. The Virtual Child will "develop cancer" that we will subject to unlimited virtual clinical trials that pinpoint, predict, and prioritize potential new treatments, bringing forward the day when no child dies of cancer, giving each one the opportunity to lead a full and healthy life.
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Affiliation(s)
- Richard J Gilbertson
- CRUK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Anna-Lisa Böttcher
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | | | | | | | | | - Laura K Donovan
- University College London Great Ormond Street Institute of Child Health, United Kingdom
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | | | | | | | - Nada Jabado
- Department of Paediatrics, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Henrick Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Claudia L Kleinman
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Lena M Kutscher
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Emily Linnane
- CRUK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - John C Marioni
- CRUK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, California
| | | | - Steven Niederer
- Turing Research and Innovation Cluster in Digital Twins (TRIC: DT), The Alan Turing Institute, London, United Kingdom
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | | | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, Heidelberg, Germany
| | | | - Nikolaos G Sgourakis
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Adam Shlien
- Genetics and Genomics Program, The Hospital for Sick Children, Toronto, Canada
| | - Pete Smith
- Hula Therapeutics, Philadelphia, Pennsylvania
| | - Karin Straathof
- University College London Cancer Institute, London, United Kingdom
- Great Ormond Street Hospital for Children, London, United Kingdom
| | | | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Boston, Massachusetts
| | - Michael D Taylor
- Texas Children's Cancer Center, Hematology-Oncology Section and Department of Pediatrics - Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, Texas
| | | | | | - Brandon J Wainwright
- The University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Robert J Wechsler-Reya
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Frank Westermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Bissan Al-Lazikani
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
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2
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Mayakonda A, Westermann F. Trackplot: a fast and lightweight R script for epigenomic enrichment plots. Bioinform Adv 2024; 4:vbae031. [PMID: 38476298 PMCID: PMC10932608 DOI: 10.1093/bioadv/vbae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
Motivation BigWig files serve as essential inputs in epigenomic data visualization. However, current R packages for visualizing these files are limited, slow, and burdened by numerous dependencies. Results We introduce trackplot, a minimal R script designed for the rapid generation of integrative genomics viewer (IGV) style track plots, profile plots, and heatmaps from bigWig files. This script offers speed, owing to its reliance on bwtool, resulting in performance gains of several magnitudes compared to equivalent packages. The script is lightweight, requiring only the data.table and bwtool packages as primary dependencies. Notably, the plots are generated in base R graphics, eliminating the need for additional packages. trackplot queries the University of California Santa Cruz (UCSC) genome browser for gene models thereby enhancing the reproducibility of analyses. The script extends its support to general transfer format (GTF) further enhancing its versatility. This tool addresses the gaps in existing bigWig visualization approaches by offering speed, simplicity, and minimal dependencies, thereby presenting a valuable asset to researchers in the fields of epigenomics. Availability and implementation trackplot is implemented in R is made available under MIT license at https://github.com/PoisonAlien/trackplot.
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Affiliation(s)
- Anand Mayakonda
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Frank Westermann
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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3
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Bechmann N, Moskopp ML, Constantinescu G, Stell A, Ernst A, Berthold F, Westermann F, Jiang J, Lui L, Nowak E, Zopp S, Pacak K, Peitzsch M, Schedl A, Reincke M, Beuschlein F, Bornstein SR, Fassnacht M, Eisenhofer G. Asymmetric Adrenals: Sexual Dimorphism of Adrenal Tumors. J Clin Endocrinol Metab 2024; 109:471-482. [PMID: 37647861 PMCID: PMC11032253 DOI: 10.1210/clinem/dgad515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/03/2023] [Accepted: 08/28/2023] [Indexed: 09/01/2023]
Abstract
CONTEXT Sexual dimorphism has direct consequences on the incidence and survival of cancer. Early and accurate diagnosis is crucial to improve prognosis. OBJECTIVE This work aimed to characterized the influence of sex and adrenal asymmetry on the emergence of adrenal tumors. METHODS We conducted a multicenter, observational study involving 8037 patients with adrenal tumors, including adrenocortical carcinoma (ACC), aldosterone-producing adenoma (APA), cortisol-secreting adrenocortical adenomas (CSAs), non-aldosterone-producing adrenal cortical adenoma (NAPACA), pheochromocytoma (PCC), and neuroblastoma (NB), and investigated tumor lateralization according to sex. Human adrenal tissues (n = 20) were analyzed with a multiomics approach that allows determination of gene expression, catecholamine, and steroid contents in a single sample. In addition, we performed a literature review of computed tomography and magnetic resonance imaging-based studies examining adrenal gland size. RESULTS ACC (n = 1858); CSA (n = 68), NAPACA (n = 2174), and PCC (n = 1824) were more common in females than in males (female-to-male ratio: 1.1:1-3.8:1), whereas NBs (n = 2320) and APAs (n = 228) were less prevalent in females (0.8:1). ACC, APA, CSA, NAPACA, and NB occurred more frequently in the left than in the right adrenal (left-to-right ratio: 1.1:1-1.8:1), whereas PCC arose more often in the right than in the left adrenal (0.8:1). In both sexes, the left adrenal was larger than the right adrenal; females have smaller adrenals than males. CONCLUSION Adrenal asymmetry in both sexes may be related to the pathogenesis of adrenal tumors and should be considered during the diagnosis of these tumors.
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Affiliation(s)
- Nicole Bechmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Mats Leif Moskopp
- Department of Neurosurgery, Vivantes Friedrichshain Hospital, Charité Academic Teaching Hospital, 10249 Berlin, Germany
| | - Georgiana Constantinescu
- Department of Internal Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Anthony Stell
- School of Computing and Information Systems, University of Melbourne, 3052 Melbourne, Australia
| | - Angela Ernst
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, 50931 Cologne, Germany
| | - Frank Berthold
- Children's Hospital, University of Cologne, 50735 Cologne, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jingjing Jiang
- Department of Endocrinology and Metabolism, Zhongshan Hospital, 200031 Shanghai, China
| | - Longfei Lui
- Department of Urology, Xiangya Hospital, Central South University, 410017 Changsha, China
| | - Elisabeth Nowak
- Department of Medicine IV, University Hospital, Ludwig-Maximilians-Universität Munich, 80539 Munich, Germany
| | - Stephanie Zopp
- Department of Medicine IV, University Hospital, Ludwig-Maximilians-Universität Munich, 80539 Munich, Germany
| | - Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Rockville, MD 20892, USA
| | - Mirko Peitzsch
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Schedl
- Université Côte d’Azur, Inserm, CNRS, Institut de Biologie Valrose, 06108 Nice, France
| | - Martin Reincke
- Department of Medicine IV, University Hospital, Ludwig-Maximilians-Universität Munich, 80539 Munich, Germany
| | - Felix Beuschlein
- Department of Medicine IV, University Hospital, Ludwig-Maximilians-Universität Munich, 80539 Munich, Germany
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), 8091 Zurich, Switzerland
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Stefan R Bornstein
- Department of Internal Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Martin Fassnacht
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital of Würzburg, University of Würzburg, 97080 Würzburg, Germany
| | - Graeme Eisenhofer
- Department of Internal Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
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Bessonneau-Gaborit V, Cruard J, Guerin-Charbonnel C, Derrien J, Alberge JB, Douillard E, Devic M, Deshayes S, Campion L, Westermann F, Moreau P, Herrmann C, Bourdon J, Magrangeas F, Minvielle S. Exploring the impact of dexamethasone on gene regulation in myeloma cells. Life Sci Alliance 2023; 6:e202302195. [PMID: 37524526 PMCID: PMC10390781 DOI: 10.26508/lsa.202302195] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023] Open
Abstract
Among glucocorticoids (GCs), dexamethasone (Dex) is widely used in treatment of multiple myelomas. However, despite a definite benefit, all patients relapse. Moreover, the molecular basis of glucocorticoid efficacy remains elusive. To determine genomic response to Dex in myeloma cells, we generated bulk and single-cell multi-omics data and high-resolution contact maps of active enhancers and target genes. We show that a minority of glucocorticoid receptor-binding sites are associated with enhancer activity gains, increased interaction loops, and transcriptional activity. We identified and characterized a predominant enhancer enriched in cohesin (RAD21) and more accessible upon Dex exposure. Analysis of four gene-specific networks revealed the importance of the CTCF-cohesin couple and the synchronization of regulatory sequence openings for efficient transcription in response to Dex. Notably, these epigenomic changes are associated with cell-to-cell transcriptional heterogeneity, in particular, lineage-specific genes. As consequences, BCL2L11-encoding BIM critical for Dex-induced apoptosis and CXCR4 protective from chemotherapy-induced apoptosis are rather up-regulated in different cells. In summary, our work provides new insights into the molecular mechanisms involved in Dex escape.
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Affiliation(s)
- Victor Bessonneau-Gaborit
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Jonathan Cruard
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
| | - Catherine Guerin-Charbonnel
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Institut de Cancérologie de l'Ouest, Nantes, France
| | - Jennifer Derrien
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
| | - Jean-Baptiste Alberge
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
| | - Elise Douillard
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Magali Devic
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Sophie Deshayes
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
| | - Loïc Campion
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Institut de Cancérologie de l'Ouest, Nantes, France
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg, KITZ, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Phillipe Moreau
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Carl Herrmann
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany
| | | | - Florence Magrangeas
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Centre Hospitalier Universitaire, Nantes, France
| | - Stéphane Minvielle
- Université de Nantes, CNRS, INSERM, Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers, France
- Centre Hospitalier Universitaire, Nantes, France
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5
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Cobos FA, Panah MJN, Epps J, Long X, Man TK, Chiu HS, Chomsky E, Kiner E, Krueger MJ, di Bernardo D, Voloch L, Molenaar J, van Hooff SR, Westermann F, Jansky S, Redell ML, Mestdagh P, Sumazin P. Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes. Genome Biol 2023; 24:177. [PMID: 37528411 PMCID: PMC10394903 DOI: 10.1186/s13059-023-03016-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, scnRNA-seq for short), can help characterize the composition of tissues and reveal cells that influence key functions in both healthy and disease tissues. However, the use of these technologies is operationally challenging because of high costs and stringent sample-collection requirements. Computational deconvolution methods that infer the composition of bulk-profiled samples using scnRNA-seq-characterized cell types can broaden scnRNA-seq applications, but their effectiveness remains controversial. RESULTS We produced the first systematic evaluation of deconvolution methods on datasets with either known or scnRNA-seq-estimated compositions. Our analyses revealed biases that are common to scnRNA-seq 10X Genomics assays and illustrated the importance of accurate and properly controlled data preprocessing and method selection and optimization. Moreover, our results suggested that concurrent RNA-seq and scnRNA-seq profiles can help improve the accuracy of both scnRNA-seq preprocessing and the deconvolution methods that employ them. Indeed, our proposed method, Single-cell RNA Quantity Informed Deconvolution (SQUID), which combines RNA-seq transformation and dampened weighted least-squares deconvolution approaches, consistently outperformed other methods in predicting the composition of cell mixtures and tissue samples. CONCLUSIONS We showed that analysis of concurrent RNA-seq and scnRNA-seq profiles with SQUID can produce accurate cell-type abundance estimates and that this accuracy improvement was necessary for identifying outcomes-predictive cancer cell subclones in pediatric acute myeloid leukemia and neuroblastoma datasets. These results suggest that deconvolution accuracy improvements are vital to enabling its applications in the life sciences.
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Affiliation(s)
- Francisco Avila Cobos
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium
| | - Mohammad Javad Najaf Panah
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital Cancer Center, Houston, TX, USA
| | - Jessica Epps
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital Cancer Center, Houston, TX, USA
| | - Xiaochen Long
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital Cancer Center, Houston, TX, USA
- Department of Statistics, Rice University, Houston, TX, 77251, USA
| | - Tsz-Kwong Man
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital Cancer Center, Houston, TX, USA
| | - Hua-Sheng Chiu
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital Cancer Center, Houston, TX, USA
| | | | | | - Michael J Krueger
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital Cancer Center, Houston, TX, USA
| | - Diego di Bernardo
- Department Chemical, Materials and Industrial Engineering, Telethon Institute of Genetics and Medicine, University of Naples "Federico II", Via Campi Flegrei 34, 80078, Naples, Pozzuoli, Italy
| | | | - Jan Molenaar
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | | | - Selina Jansky
- German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Michele L Redell
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital Cancer Center, Houston, TX, USA
| | - Pieter Mestdagh
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium.
| | - Pavel Sumazin
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital Cancer Center, Houston, TX, USA.
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6
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Bechmann N, Westermann F, Eisenhofer G. HIF and MYC signaling in adrenal neoplasms of the neural crest: implications for pediatrics. Front Endocrinol (Lausanne) 2023; 14:1022192. [PMID: 37361539 PMCID: PMC10286580 DOI: 10.3389/fendo.2023.1022192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 05/09/2023] [Indexed: 06/28/2023] Open
Abstract
Pediatric neural crest-derived adrenal neoplasms include neuroblastoma and pheochromocytoma. Both entities are associated with a high degree of clinical heterogeneity, varying from spontaneous regression to malignant disease with poor outcome. Increased expression and stabilization of HIF2α appears to contribute to a more aggressive and undifferentiated phenotype in both adrenal neoplasms, whereas MYCN amplification is a valuable prognostic marker in neuroblastoma. The present review focuses on HIF- and MYC signaling in both neoplasms and discusses the interaction of associated pathways during neural crest and adrenal development as well as potential consequences on tumorigenesis. Emerging single-cell methods together with epigenetic and transcriptomic analyses provide further insights into the importance of a tight regulation of HIF and MYC signaling pathways during adrenal development and tumorigenesis. In this context, increased attention to HIF-MYC/MAX interactions may also provide new therapeutic options for these pediatric adrenal neoplasms.
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Affiliation(s)
- Nicole Bechmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Frank Westermann
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Graeme Eisenhofer
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Medicine III, University Hospital Carl Gustav Carus, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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7
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Körber V, Stainczyk SA, Kurilov R, Henrich KO, Hero B, Brors B, Westermann F, Höfer T. Neuroblastoma arises in early fetal development and its evolutionary duration predicts outcome. Nat Genet 2023; 55:619-630. [PMID: 36973454 PMCID: PMC10101850 DOI: 10.1038/s41588-023-01332-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 02/06/2023] [Indexed: 03/29/2023]
Abstract
AbstractNeuroblastoma, the most frequent solid tumor in infants, shows very diverse outcomes from spontaneous regression to fatal disease. When these different tumors originate and how they evolve are not known. Here we quantify the somatic evolution of neuroblastoma by deep whole-genome sequencing, molecular clock analysis and population-genetic modeling in a comprehensive cohort covering all subtypes. We find that tumors across the entire clinical spectrum begin to develop via aberrant mitoses as early as the first trimester of pregnancy. Neuroblastomas with favorable prognosis expand clonally after short evolution, whereas aggressive neuroblastomas show prolonged evolution during which they acquire telomere maintenance mechanisms. The initial aneuploidization events condition subsequent evolution, with aggressive neuroblastoma exhibiting early genomic instability. We find in the discovery cohort (n = 100), and validate in an independent cohort (n = 86), that the duration of evolution is an accurate predictor of outcome. Thus, insight into neuroblastoma evolution may prospectively guide treatment decisions.
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8
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Weichenhan D, Riedel A, Meinen C, Basic A, Toth R, Bähr M, Lutsik P, Hey J, Sollier E, Toprak UH, Kelekçi S, Lin YY, Hakobyan M, Touzart A, Goyal A, Wierzbinska JA, Schlesner M, Westermann F, Lipka DB, Plass C. Translocation t(6;7) in AML-M4 cell line GDM-1 results in MNX1 activation through enhancer-hijacking. Leukemia 2023; 37:1147-1150. [PMID: 36949154 PMCID: PMC10169647 DOI: 10.1038/s41375-023-01865-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 03/24/2023]
Affiliation(s)
- Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna Riedel
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
| | - Charlotte Meinen
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alisa Basic
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Reka Toth
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Marion Bähr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Oncology KU Leuven, Leuven, Belgium
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
| | - Etienne Sollier
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
| | - Umut H Toprak
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simge Kelekçi
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
| | - Yu-Yu Lin
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mariam Hakobyan
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Aurore Touzart
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Université de Paris Cité, Institut Necker Enfants-Malades (INEM), Institut National de la Santé et de la Recherche Médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, Paris, France
| | - Ashish Goyal
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Justyna A Wierzbinska
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
| | - Matthias Schlesner
- Faculty of Applied Informatics, University of Augsburg, Augsburg, Germany
| | - Frank Westermann
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Daniel B Lipka
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
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9
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Rosswog C, Fassunke J, Ernst A, Schömig-Markiefka B, Merkelbach-Bruse S, Bartenhagen C, Cartolano M, Ackermann S, Theissen J, Blattner-Johnson M, Jones B, Schramm K, Altmüller J, Nürnberg P, Ortmann M, Berthold F, Peifer M, Büttner R, Westermann F, Schulte JH, Simon T, Hero B, Fischer M. Genomic ALK alterations in primary and relapsed neuroblastoma. Br J Cancer 2023; 128:1559-1571. [PMID: 36807339 PMCID: PMC10070426 DOI: 10.1038/s41416-023-02208-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Genomic alterations of the anaplastic lymphoma kinase gene (ALK) occur recurrently in neuroblastoma, a pediatric malignancy of the sympathetic nervous system. However, information on their development over time has remained sparse. METHODS ALK alterations were assessed in neuroblastomas at diagnosis and/or relapse from a total of 943 patients, covering all stages of disease. Longitudinal information on diagnostic and relapsed samples from individual patients was available in 101 and 102 cases for mutation and amplification status, respectively. RESULTS At diagnosis, ALK point mutations occurred in 10.5% of all cases, with highest frequencies in stage 4 patients <18 months. At relapse, ALK alteration frequency increased by 70%, both in high-risk and non-high-risk cases. The increase was most likely due to de novo mutations, frequently leading to R1275Q substitutions, which are sensitive to pharmacological ALK inhibition. By contrast, the frequency of ALK amplifications did not change over the course of the disease. ALK amplifications, but not mutations, were associated with poor patient outcome. CONCLUSIONS The considerably increased frequency of ALK mutations at relapse and their high prevalence in young stage 4 patients suggest surveying the genomic ALK status regularly in these patient cohorts, and to evaluate ALK-targeted treatment also in intermediate-risk patients.
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Affiliation(s)
- Carolina Rosswog
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany.,Else Kröner Forschungskolleg Clonal Evolution in Cancer, University Hospital of Cologne, Cologne, Germany.,Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Jana Fassunke
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Angela Ernst
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | | | | | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany
| | - Maria Cartolano
- Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany
| | - Sandra Ackermann
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany
| | - Jessica Theissen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, Germany.,Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Barbara Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kathrin Schramm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Genomics, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Monika Ortmann
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Frank Berthold
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany.,Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Frank Westermann
- Division Neuroblastoma Genomics, B087, German Cancer Research Center and Hopp Children´s Cancer Center at the NCT (KiTZ), Heidelberg, Germany
| | - Johannes H Schulte
- Department of Paediatric Oncology and Haematology, Charité University Medical Centre Berlin, Berlin, Germany
| | - Thorsten Simon
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany. .,Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, Germany.
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10
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Fiaschetti G, Castelletti D, Zoller S, Schramm A, Schroeder C, Nagaishi M, Stearns D, Mittelbronn M, Eggert A, Westermann F, Ohgaki H, Shalaby T, Pruschy M, Arcaro A, Grotzer MA. Correction: Bone morphogenetic protein-7 is a MYC target with prosurvival functions in childhood medulloblastoma. Oncogene 2023; 42:168. [PMID: 36476835 DOI: 10.1038/s41388-022-02555-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- G Fiaschetti
- Department of Oncology, University Children's Hospital, Zurich, Switzerland
| | - D Castelletti
- Department of Oncology, University Children's Hospital, Zurich, Switzerland
| | - S Zoller
- Functional Genomics Center Zurich, UZH/ETH, Zurich, Switzerland
| | - A Schramm
- Division of Hematology/Oncology, University Children's Hospital Essen, Essen, Germany
| | - C Schroeder
- Department Tumor Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Nagaishi
- Section of Molecular Pathology, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - D Stearns
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - M Mittelbronn
- Institute of Neurology (Edinger Institute) Goethe-University Frankfurt, Frankfurt/Main, Germany
| | - A Eggert
- Division of Hematology/Oncology, University Children's Hospital Essen, Essen, Germany
| | - F Westermann
- Department Tumor Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - H Ohgaki
- Section of Molecular Pathology, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - T Shalaby
- Department of Oncology, University Children's Hospital, Zurich, Switzerland
| | - M Pruschy
- Department Radiation Oncology, University Hospital, Zurich, Switzerland
| | - A Arcaro
- Division of Pediatric Hematology/Oncology, Department of Clinical Research, University of Bern, Bern, Switzerland
| | - M A Grotzer
- Department of Oncology, University Children's Hospital, Zurich, Switzerland.
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11
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Peterziel H, Jamaladdin N, ElHarouni D, Gerloff XF, Herter S, Fiesel P, Berker Y, Blattner-Johnson M, Schramm K, Jones BC, Reuss D, Turunen L, Friedenauer A, Holland-Letz T, Sill M, Weiser L, Previti C, Balasubramanian G, Gerber NU, Gojo J, Hutter C, Øra I, Lohi O, Kattamis A, de Wilde B, Westermann F, Tippelt S, Graf N, Nathrath M, Sparber-Sauer M, Sehested A, Kramm CM, Dirksen U, Kallioniemi O, Pfister SM, van Tilburg CM, Jones DTW, Saarela J, Pietiäinen V, Jäger N, Schlesner M, Kopp-Schneider A, Oppermann S, Milde T, Witt O, Oehme I. Drug sensitivity profiling of 3D tumor tissue cultures in the pediatric precision oncology program INFORM. NPJ Precis Oncol 2022; 6:94. [PMID: 36575299 PMCID: PMC9794727 DOI: 10.1038/s41698-022-00335-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/29/2022] [Indexed: 12/28/2022] Open
Abstract
The international precision oncology program INFORM enrolls relapsed/refractory pediatric cancer patients for comprehensive molecular analysis. We report a two-year pilot study implementing ex vivo drug sensitivity profiling (DSP) using a library of 75-78 clinically relevant drugs. We included 132 viable tumor samples from 35 pediatric oncology centers in seven countries. DSP was conducted on multicellular fresh tumor tissue spheroid cultures in 384-well plates with an overall mean processing time of three weeks. In 89 cases (67%), sufficient viable tissue was received; 69 (78%) passed internal quality controls. The DSP results matched the identified molecular targets, including BRAF, ALK, MET, and TP53 status. Drug vulnerabilities were identified in 80% of cases lacking actionable (very) high-evidence molecular events, adding value to the molecular data. Striking parallels between clinical courses and the DSP results were observed in selected patients. Overall, DSP in clinical real-time is feasible in international multicenter precision oncology programs.
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Affiliation(s)
- Heike Peterziel
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Nora Jamaladdin
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Dina ElHarouni
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Xenia F. Gerloff
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Mathematics and Computer Science, Heidelberg University, 69120 Heidelberg, Germany
| | - Sonja Herter
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Petra Fiesel
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), 69120 Heidelberg, Germany
| | - Yannick Berker
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Mirjam Blattner-Johnson
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Kathrin Schramm
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Barbara C. Jones
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - David Reuss
- grid.5253.10000 0001 0328 4908Department Neuropathology at Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Present Address: Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), 69120 Heidelberg, Germany
| | - Laura Turunen
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
| | - Aileen Friedenauer
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Tim Holland-Letz
- grid.7497.d0000 0004 0492 0584Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Lena Weiser
- grid.7497.d0000 0004 0492 0584Core Facility Omics IT and Data Management (ODCF), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christopher Previti
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Core Facility Omics IT and Data Management (ODCF), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Gnanaprakash Balasubramanian
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Nicolas U. Gerber
- grid.412341.10000 0001 0726 4330Department of Oncology, University Children’s Hospital Zürich, CH-8032 Zürich, Switzerland
| | - Johannes Gojo
- grid.22937.3d0000 0000 9259 8492Department of Pediatrics and Adolescent Medicine, Comprehensive Cancer Center and Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Caroline Hutter
- grid.22937.3d0000 0000 9259 8492St. Anna Children’s Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria ,grid.416346.2St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Ingrid Øra
- grid.411843.b0000 0004 0623 9987Children’s Hospital, Pediatric Oncology, Skåne University Hospital, Lund & Karolinska University Hospital, Stockholm, Sweden
| | - Olli Lohi
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere Center for Child Health Research, Tampere University, Tampere, Finland, and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Antonis Kattamis
- grid.5216.00000 0001 2155 0800First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Bram de Wilde
- grid.5342.00000 0001 2069 7798Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Frank Westermann
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Stephan Tippelt
- grid.410718.b0000 0001 0262 7331Pediatrics III Pediatric Hematology, Oncology, Immunology, Cardiology, Pulmonology, West German Cancer Center; German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
| | - Norbert Graf
- grid.411937.9Department of Pediatric Oncology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Michaela Nathrath
- grid.419824.20000 0004 0625 3279Department of Pediatric Oncology, Klinikum Kassel, Kassel, Germany ,grid.6936.a0000000123222966Department of Pediatrics and Children’s Cancer Research Center, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Monika Sparber-Sauer
- grid.459687.10000 0004 0493 3975Klinikum der Landeshauptstadt Stuttgart gKAöR, Olgahospital, Stuttgart Cancer Center, Zentrum für Kinder-, Jugend- und Frauenmedizin, Pädiatrie 5 (Pädiatrische Onkologie, Hämatologie, Immunologie), Stuttgart, Germany ,University of Medicine Tübingen, Tübingen, Germany
| | - Astrid Sehested
- grid.475435.4Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen Denmark
| | - Christof M. Kramm
- grid.411984.10000 0001 0482 5331Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Uta Dirksen
- grid.410718.b0000 0001 0262 7331Pediatrics III Pediatric Hematology, Oncology, Immunology, Cardiology, Pulmonology, West German Cancer Center; German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
| | - Olli Kallioniemi
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, FI-00014 Finland
| | - Stefan M. Pfister
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Cornelis M. van Tilburg
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - David T. W. Jones
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Jani Saarela
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
| | - Vilja Pietiäinen
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, FI-00014 Finland
| | - Natalie Jäger
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany ,grid.7307.30000 0001 2108 9006Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Annette Kopp-Schneider
- grid.7497.d0000 0004 0492 0584Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sina Oppermann
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Till Milde
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Olaf Witt
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Ina Oehme
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
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12
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Bonfiglio F, Lasorsa VA, Cantalupo S, D'Alterio G, Aievola V, Boccia A, Ardito M, Furini S, Renieri A, Morini M, Stainczyk S, Westermann F, Paolella G, Eva A, Iolascon A, Capasso M. Inherited rare variants in homologous recombination and neurodevelopmental genes are associated with increased risk of neuroblastoma. EBioMedicine 2022; 87:104395. [PMID: 36493725 PMCID: PMC9732128 DOI: 10.1016/j.ebiom.2022.104395] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the most common solid extracranial paediatric tumour. Genome-wide association studies have driven the discovery of common risk variants, but no large study has investigated the contribution of rare variants to NB susceptibility. Here, we conducted a whole-exome sequencing (WES) of 664 NB cases and 822 controls and used independent validation datasets to identify genes with rare risk variants and involved pathways. METHODS WES was performed at 50× depth and variants were jointly called in cases and controls. We developed two models to identify mutations with high clinical impact (P/LP model) and to discover less penetrant risk mutations affecting non-canonical cancer pathways (RPV model). We performed a gene-level collapsing test using Firth's logistic regression in 242 selected cancer predisposition genes (CPGs) and a gene-sets burden analysis of biologically-informed pathways. FINDINGS Twelve percent of patients carried P/LP variants in CPGs and showed a significant enrichment (P = 2.3 × 10-4) compared to controls (6%). We identified P/LP variants in 45 CPGs enriched in homologous recombination (HR) pathway. The most P/LP enriched genes in NB were BRCA1, ALK and RAD51C. Additionally, we found higher RPV burden in gene-sets of neuron differentiation, neural tube development and synapse assembly, and in gene-sets associated with neurodevelopmental disorders (NDD). INTERPRETATION The high fraction of NB patients with P/LP variants indicates the need of genetic counselling. Furthermore, inherited rare variants predispose to NB development by affecting mechanisms related to HR and neurodevelopmental processes, and demonstrate that NDD genes are altered in NB at the germline level. FUNDING Associazione Italiana per la Ricerca sul Cancro, Fondazione Italiana per la Lotta al Neuroblastoma, Associazione Oncologia Pediatrica e Neuroblastoma, Regione Campania, Associazione Giulio Adelfio onlus, and Italian Health Ministry.
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Affiliation(s)
- Ferdinando Bonfiglio
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Chemical, Materials and Production Engineering, University of Naples Federico II, Naples, Italy
| | - Vito Alessandro Lasorsa
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Sueva Cantalupo
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Giuseppe D'Alterio
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,European School of Medical Medicine, University of Milan, Milan, Italy
| | - Vincenzo Aievola
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Angelo Boccia
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Martina Ardito
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessandra Renieri
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Martina Morini
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Sabine Stainczyk
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Frank Westermann
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Giovanni Paolella
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Alessandra Eva
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Achille Iolascon
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Mario Capasso
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy,Corresponding author. Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, Via Gaetano Salvatore 486, 80145 Napoli, Italy.
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13
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Wirth AK, Wange L, Vosberg S, Henrich KO, Rausch C, Özdemir E, Zeller CM, Richter D, Feuchtinger T, Kaller M, Hermeking H, Greif PA, Senft D, Jurinovic V, Bahrami E, Jayavelu AK, Westermann F, Mann M, Enard W, Herold T, Jeremias I. In vivo PDX CRISPR/Cas9 screens reveal mutual therapeutic targets to overcome heterogeneous acquired chemo-resistance. Leukemia 2022; 36:2863-2874. [PMID: 36333584 PMCID: PMC9712105 DOI: 10.1038/s41375-022-01726-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/30/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
Resistance towards cancer treatment represents a major clinical obstacle, preventing cure of cancer patients. To gain mechanistic insights, we developed a model for acquired resistance to chemotherapy by treating mice carrying patient derived xenografts (PDX) of acute lymphoblastic leukemia with widely-used cytotoxic drugs for 18 consecutive weeks. In two distinct PDX samples, tumors initially responded to treatment, until stable disease and eventually tumor re-growth evolved under therapy, at highly similar kinetics between replicate mice. Notably, replicate tumors developed different mutations in TP53 and individual sets of chromosomal alterations, suggesting independent parallel clonal evolution rather than selection, driven by a combination of stochastic and deterministic processes. Transcriptome and proteome showed shared dysregulations between replicate tumors providing putative targets to overcome resistance. In vivo CRISPR/Cas9 dropout screens in PDX revealed broad dependency on BCL2, BRIP1 and COPS2. Accordingly, venetoclax re-sensitized derivative tumors towards chemotherapy, despite genomic heterogeneity, demonstrating direct translatability of the approach. Hence, despite the presence of multiple resistance-associated genomic alterations, effective rescue treatment for polychemotherapy-resistant tumors can be identified using functional testing in preclinical models.
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Affiliation(s)
- Anna-Katharina Wirth
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
| | - Lucas Wange
- Anthropology and Human Genomics, Faculty of Biology, Ludwig Maximilian University (LMU), Martinsried, Germany
| | - Sebastian Vosberg
- Clinical Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Kai-Oliver Henrich
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Christian Rausch
- Department of Medicine III, and Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Erbey Özdemir
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
| | - Christina M Zeller
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
| | - Daniel Richter
- Anthropology and Human Genomics, Faculty of Biology, Ludwig Maximilian University (LMU), Martinsried, Germany
| | - Tobias Feuchtinger
- Department of Pediatrics, Dr. von Hauner Children´s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Markus Kaller
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig Maximilian University (LMU), Munich, Germany
| | - Heiko Hermeking
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig Maximilian University (LMU), Munich, Germany
| | - Philipp A Greif
- Department of Medicine III, and Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partnering Site Munich, Munich, Germany
| | - Daniela Senft
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
| | - Vindi Jurinovic
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
- Department of Medicine III, and Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Ehsan Bahrami
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
| | - Ashok Kumar Jayavelu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center, Heidelberg, Germany
| | - Frank Westermann
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig Maximilian University (LMU), Martinsried, Germany
| | - Tobias Herold
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
- Department of Medicine III, and Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany.
- Department of Pediatrics, Dr. von Hauner Children´s Hospital, University Hospital, LMU Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Partnering Site Munich, Munich, Germany.
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14
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Kool M, Federico A, Surdez D, Gopisetty A, Saberi-Ansari E, Saint-Charles A, Iddir Y, Waterfall J, Wierzbinska J, Schlicker A, Bhalsankar J, Mack N, Schwalm B, Böttcher AL, Sill M, Westermann F, Jones DTW, Volckmann R, Zwijnenburg D, Gürgen D, Inderise E, Schulte J, Eggert A, Molenaar JJ, Delattre O, Colombetti S, Heidenreich O, Jeremias I, Scotlandi K, Manara MC, Gojo J, Berger W, Iradier F, Geoerger B, Costa J, Schäfer B, Wachtel M, Chesler L, Jones C, Kovar H, Carcaboso ÁM, Klusmann JH, Debatin KM, Bomken S, Guttke C, Hamerlik P, Hattersley M, Garcia M, Colland F, Strougo A, Witt O, Vassal G, Caron H, Shields DJ, Stancato LF, Aviles PM, Hoffmann J, Cairo S, Schueler J, Jäger N, Koster J, Schleiermacher G, Pfister SM. INSP-15. ITCC-P4: A sustainable platform of molecularly well-characterized PDX models of pediatric cancers for high throughput in vivo testing. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Thanks to state-of-the-art molecular profiling techniques we by now have a much better understanding of pediatric cancers and what is driving them. On the other hand, we have also realized that pediatric cancers are much more heterogeneous than previously thought. Many new types and subtypes of pediatric cancers have been identified with distinct molecular and clinical characteristics. However, for many if not most of these new types and subtypes there is no specific treatment available, yet. In order to develop specific treatment protocols and to increase survival rates for pediatric cancer patients further, both at diagnosis and relapse/metastasis, we need a large collection of well-characterized preclinical models representing all the different types and subtypes. These models can be used for preclinical drug testing to prioritize the pediatric development of anticancer drugs that would be best targeting pediatric tumor biology. The ITCC-P4 consortium, which is a collaboration between many academic centers across Europe, several companies involved in in vivo preclinical testing, and ten pharmaceutical companies, started in 2017 with the overall aim to establish a sustainable platform of >400 molecularly well-characterized PDX models of high-risk pediatric cancers and to use them for in vivo testing of novel mechanism-of-action based treatments. Currently, 340 models have been fully established, including 87 brain tumor models and 253 non-brain tumor models, together representing many different tumor types both from primary and relapsed/metastatic disease. Out of these 340 models, 252 have been fully molecularly characterized, most of them together with their matching original tumors, and almost of all these models are currently being subjected to in vivo testing using three standard of care drugs and six novel mechanism-of-action based drugs. In this presentation, an update on the current status of the ITCC-P4 platform and the data we collectively have generated thus far will be presented.
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Affiliation(s)
- Marcel Kool
- Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - Aniello Federico
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre , Paris , France
| | - Apurva Gopisetty
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - Elnaz Saberi-Ansari
- INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre , Paris , France
| | - Alexandra Saint-Charles
- INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre , Paris , France
| | - Yasmine Iddir
- INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre , Paris , France
| | - Joshua Waterfall
- INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre , Paris , France
| | | | - Andreas Schlicker
- Bayer AG, Pharmaceuticals, Research and Development , Berlin , Germany
| | - Jaydutt Bhalsankar
- INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre , Paris , France
| | - Norman Mack
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - Benjamin Schwalm
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - Anna-Lisa Böttcher
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - Martin Sill
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - Frank Westermann
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - David T W Jones
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - Richard Volckmann
- Department of Oncogenomics, Amsterdam University Medical Centre , Amsterdam , Netherlands
| | - Danny Zwijnenburg
- Department of Oncogenomics, Amsterdam University Medical Centre , Amsterdam , Netherlands
| | - Dennis Gürgen
- Experimental Pharmacology and Oncology Berlin-Buch GmbH , Berlin , Germany
| | | | - Johannes Schulte
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin , Berlin , Germany
| | - Angelika Eggert
- Department of Oncogenomics, Amsterdam University Medical Centre , Berlin , Germany
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre , Paris , France
| | | | - Olaf Heidenreich
- Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
- Translational and Clinical Research Institute, Newcastle University and The Great North Children's Hospital, Newcastle upon Tyne, United Kingdom
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany; Department of Pediatrics, Dr. von Hauner Childrens Hospital, Ludwig Maximilian University of Munich (LMU) , Munich , Germany
- German Consortium for Translational Cancer Research (DKTK), Partnering Site Munich , Munich , Germany
| | - Katia Scotlandi
- IRCCS—Istituto Ortopedico Rizzoli, Experimental Oncology Laboratory , Bologna , Italy
| | - Maria Cristina Manara
- IRCCS—Istituto Ortopedico Rizzoli, Experimental Oncology Laboratory , Bologna , Italy
| | - Johannes Gojo
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna , Vienna , Austria
| | - Walter Berger
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin , Vienna , Austria
| | | | - Birgit Geoerger
- Department of Clinical Research, Gustave Roussy , Villejuif , France
| | - Jenny Costa
- Department of Clinical Research, Gustave Roussy , Villejuif , France
| | - Beat Schäfer
- University Children’s Hospital, Department of Oncology and Children’s Research Center , Zurich , Switzerland
| | - Marco Wachtel
- University Children’s Hospital, Department of Oncology and Children’s Research Center , Zurich , Switzerland
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research , London , United Kingdom
| | - Chris Jones
- Division of Molecular Pathology, Institute of Cancer Research , London , United Kingdom
| | - Heinrich Kovar
- Children's Cancer Research Institute, St Anna Kinderkrebsforschung , Vienna , Austria
| | | | - Jan-Henning Klusmann
- Department of Pediatrics I, Martin-Luther-University Halle-Wittenberg , Halle , Germany
| | - Klaus-Michael Debatin
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center , Ulm , Germany
| | - Simon Bomken
- Translational and Clinical Research Institute, Newcastle University and The Great North Children's Hospital, Newcastle upon Tyne, United Kingdom
| | - Christina Guttke
- Janssen Research & Development, LLC, Spring House , Pennsylvania , USA
| | | | | | | | | | - Ashley Strougo
- Sanofi-Aventis Deutschland GmbH, R&D , Frankfurt , Germany
| | - Olaf Witt
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - Gilles Vassal
- Department of Clinical Research, Gustave Roussy , Villejuif , France
- European consortium for Innovative Therapies for Children with Cancer (ITCC) , Paris , France
| | | | - David J Shields
- Pfizer Centers for Therapeutic Innovation, Pfizer Inc , New York , USA
| | | | - Pablo M Aviles
- Institut de Recerca Sant Joan de Deu , Barcelona , Spain
| | - Jens Hoffmann
- Experimental Pharmacology and Oncology Berlin-Buch GmbH , Berlin , Germany
| | | | - Julia Schueler
- Charles River Discovery Research Services Germany , Freiburg , Germany
| | - Natalie Jäger
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
| | - Jan Koster
- Department of Oncogenomics, Amsterdam University Medical Centre , Amsterdam , Netherlands
| | - Gudrun Schleiermacher
- INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre , Paris , France
| | - Stefan M Pfister
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) , Heidelberg , Germany
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15
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Khalid U, Simovic M, Hammann LA, Iskar M, Kl Wong J, Kumar R, Jugold M, Sill M, Bolkestein M, Kolb T, Hergt M, Devens F, Ecker J, Kool M, Milde T, Westermann F, Benner A, Lewis J, Dietrich S, Pfister SM, Lichter P, Zapatka M, Ernst A. A synergistic interaction between HDAC- and PARP inhibitors in childhood tumors with chromothripsis. Int J Cancer 2022; 151:590-606. [PMID: 35411591 DOI: 10.1002/ijc.34027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/15/2021] [Accepted: 01/25/2022] [Indexed: 11/06/2022]
Abstract
Chromothripsis is a form of genomic instability characterized by the occurrence of tens to hundreds of clustered DNA double-strand breaks in a one-off catastrophic event. Rearrangements associated with chromothripsis are detectable in numerous tumor entities and linked with poor prognosis in some of these, such as Sonic Hedgehog medulloblastoma, neuroblastoma and osteosarcoma. Hence, there is a need for therapeutic strategies eliminating tumor cells with chromothripsis. Defects in DNA double-strand break repair, and in particular homologous recombination repair, have been linked with chromothripsis. Targeting DNA repair deficiencies by synthetic lethality approaches, we performed a synergy screen using drug libraries (n = 375 compounds, 15 models) combined with either a PARP inhibitor or cisplatin. This revealed a synergistic interaction between the HDAC inhibitor romidepsin and PARP inhibition. Functional assays, transcriptome analyses, and in vivo validation in patient-derived xenograft mouse models confirmed the efficacy of the combinatorial treatment.
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Affiliation(s)
- Umar Khalid
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.,University of Heidelberg, Germany
| | - Milena Simovic
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.,University of Heidelberg, Germany
| | - Linda A Hammann
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.,University of Heidelberg, Germany
| | - Murat Iskar
- Division of Molecular Genetics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John Kl Wong
- Division of Molecular Genetics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rithu Kumar
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manfred Jugold
- Core Facility, Small Animal Imaging Center, DKFZ, Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michiel Bolkestein
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thorsten Kolb
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michaela Hergt
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frauke Devens
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jonas Ecker
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany; KiTZ Clinical Trial Unit.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joe Lewis
- European Molecular Biology Laboratory
| | - Sascha Dietrich
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aurélie Ernst
- Group Genome Instability in Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
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16
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Alborzinia H, Flórez AF, Kreth S, Brückner LM, Yildiz U, Gartlgruber M, Odoni DI, Poschet G, Garbowicz K, Shao C, Klein C, Meier J, Zeisberger P, Nadler-Holly M, Ziehm M, Paul F, Burhenne J, Bell E, Shaikhkarami M, Würth R, Stainczyk SA, Wecht EM, Kreth J, Büttner M, Ishaque N, Schlesner M, Nicke B, Stresemann C, Llamazares-Prada M, Reiling JH, Fischer M, Amit I, Selbach M, Herrmann C, Wölfl S, Henrich KO, Höfer T, Trumpp A, Westermann F. MYCN mediates cysteine addiction and sensitizes neuroblastoma to ferroptosis. Nat Cancer 2022; 3:471-485. [PMID: 35484422 PMCID: PMC9050595 DOI: 10.1038/s43018-022-00355-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/28/2022] [Indexed: 12/13/2022]
Abstract
Aberrant expression of MYC transcription factor family members predicts poor clinical outcome in many human cancers. Oncogenic MYC profoundly alters metabolism and mediates an antioxidant response to maintain redox balance. Here we show that MYCN induces massive lipid peroxidation on depletion of cysteine, the rate-limiting amino acid for glutathione (GSH) biosynthesis, and sensitizes cells to ferroptosis, an oxidative, non-apoptotic and iron-dependent type of cell death. The high cysteine demand of MYCN-amplified childhood neuroblastoma is met by uptake and transsulfuration. When uptake is limited, cysteine usage for protein synthesis is maintained at the expense of GSH triggering ferroptosis and potentially contributing to spontaneous tumor regression in low-risk neuroblastomas. Pharmacological inhibition of both cystine uptake and transsulfuration combined with GPX4 inactivation resulted in tumor remission in an orthotopic MYCN-amplified neuroblastoma model. These findings provide a proof of concept of combining multiple ferroptosis targets as a promising therapeutic strategy for aggressive MYCN-amplified tumors.
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Affiliation(s)
- Hamed Alborzinia
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany.
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
- Division of Stem Cells and Cancer German Cancer Research Center and Center for Molecular Biology of the University of Heidelberg Alliance, Heidelberg, Germany.
| | - Andrés F Flórez
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Sina Kreth
- Hopp Children's Cancer Center, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Lena M Brückner
- Hopp Children's Cancer Center, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Umut Yildiz
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- Division of Stem Cells and Cancer German Cancer Research Center and Center for Molecular Biology of the University of Heidelberg Alliance, Heidelberg, Germany
| | - Moritz Gartlgruber
- Hopp Children's Cancer Center, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Dorett I Odoni
- Bioinformatics and Omics Data Analytics, German Cancer Research Center, Heidelberg, Germany
- Biomedical Informatics, Data Mining and Data Analytics, Augsburg University, Augsburg, Germany
| | - Gernot Poschet
- Metabolomics Core Technology Platform, University of Heidelberg, Heidelberg, Germany
| | - Karolina Garbowicz
- Hopp Children's Cancer Center, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Chunxuan Shao
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany
| | - Corinna Klein
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- Division of Stem Cells and Cancer German Cancer Research Center and Center for Molecular Biology of the University of Heidelberg Alliance, Heidelberg, Germany
| | - Jasmin Meier
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- Division of Stem Cells and Cancer German Cancer Research Center and Center for Molecular Biology of the University of Heidelberg Alliance, Heidelberg, Germany
| | - Petra Zeisberger
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- Division of Stem Cells and Cancer German Cancer Research Center and Center for Molecular Biology of the University of Heidelberg Alliance, Heidelberg, Germany
| | - Michal Nadler-Holly
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Matthias Ziehm
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Franziska Paul
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Jürgen Burhenne
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Emma Bell
- Hopp Children's Cancer Center, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Marjan Shaikhkarami
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Roberto Würth
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- Division of Stem Cells and Cancer German Cancer Research Center and Center for Molecular Biology of the University of Heidelberg Alliance, Heidelberg, Germany
| | - Sabine A Stainczyk
- Hopp Children's Cancer Center, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Elisa M Wecht
- Hopp Children's Cancer Center, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Jochen Kreth
- Hopp Children's Cancer Center, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Michael Büttner
- Metabolomics Core Technology Platform, University of Heidelberg, Heidelberg, Germany
| | - Naveed Ishaque
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center, Heidelberg, Germany
- Biomedical Informatics, Data Mining and Data Analytics, Augsburg University, Augsburg, Germany
| | - Barbara Nicke
- Target Discovery Technologies, Bayer AG, Berlin, Germany
| | - Carlo Stresemann
- Research & Development, Pharmaceuticals Division, Bayer AG, Berlin, Germany
| | - María Llamazares-Prada
- Division of Cancer Epigenomics, German Cancer Research Center, Member of the German Center for Lung Research, Heidelberg, Germany
| | - Jan H Reiling
- Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthias Fischer
- Experimental Pediatric Oncology, Children's Hospital and Center for Molecular Medicine, Medical Faculty, University of Cologne, Cologne, Germany
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Carl Herrmann
- Bioinformatics and Omics Data Analytics, German Cancer Research Center, Heidelberg, Germany
- Health Data Science Unit, Medical Faculty University Heidelberg and BioQuant, Heidelberg, Germany
| | - Stefan Wölfl
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Kai-Oliver Henrich
- Hopp Children's Cancer Center, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- Division of Stem Cells and Cancer German Cancer Research Center and Center for Molecular Biology of the University of Heidelberg Alliance, Heidelberg, Germany
- German Cancer Consortium, Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center, Heidelberg, Germany.
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany.
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17
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Frank L, Rademacher A, Mücke N, Tirier SM, Koeleman E, Knotz C, Schumacher S, Stainczyk S, Westermann F, Fröhling S, Chudasama P, Rippe K. OUP accepted manuscript. Nucleic Acids Res 2022; 50:e61. [PMID: 35188570 PMCID: PMC9226501 DOI: 10.1093/nar/gkac113] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 11/14/2022] Open
Abstract
Alternative lengthening of telomeres (ALT) occurs in ∼10% of cancer entities. However, little is known about the heterogeneity of ALT activity since robust ALT detection assays with high-throughput in situ readouts are lacking. Here, we introduce ALT-FISH, a method to quantitate ALT activity in single cells from the accumulation of single-stranded telomeric DNA and RNA. It involves a one-step fluorescent in situ hybridization approach followed by fluorescence microscopy imaging. Our method reliably identified ALT in cancer cell lines from different tumor entities and was validated in three established models of ALT induction and suppression. Furthermore, we successfully applied ALT-FISH to spatially resolve ALT activity in primary tissue sections from leiomyosarcoma and neuroblastoma tumors. Thus, our assay provides insights into the heterogeneity of ALT tumors and is suited for high-throughput applications, which will facilitate screening for ALT-specific drugs.
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Affiliation(s)
- Lukas Frank
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Anne Rademacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Norbert Mücke
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Stephan M Tirier
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Emma Koeleman
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Caroline Knotz
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Sabrina Schumacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Sabine A Stainczyk
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Priya Chudasama
- Precision Sarcoma Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Karsten Rippe
- To whom correspondence should be addressed. Tel: +49 6221 5451450;
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18
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van Tilburg CM, Pfaff E, Pajtler KW, Langenberg KP, Fiesel P, Jones BC, Balasubramanian GP, Stark S, Johann PD, Blattner-Johnson M, Schramm K, Dikow N, Hirsch S, Sutter C, Grund K, von Stackelberg A, Kulozik AE, Lissat A, Borkhardt A, Meisel R, Reinhardt D, Klusmann JH, Fleischhack G, Tippelt S, von Schweinitz D, Schmid I, Kramm CM, von Bueren AO, Calaminus G, Vorwerk P, Graf N, Westermann F, Fischer M, Eggert A, Burkhardt B, Wößmann W, Nathrath M, Hecker-Nolting S, Frühwald MC, Schneider DT, Brecht IB, Ketteler P, Fulda S, Koscielniak E, Meister MT, Scheer M, Hettmer S, Schwab M, Tremmel R, Øra I, Hutter C, Gerber NU, Lohi O, Kazanowska B, Kattamis A, Filippidou M, Goemans B, Zwaan CM, Milde T, Jäger N, Wolf S, Reuss D, Sahm F, von Deimling A, Dirksen U, Freitag A, Witt R, Lichter P, Kopp-Schneider A, Jones DT, Molenaar JJ, Capper D, Pfister SM, Witt O. The Pediatric Precision Oncology INFORM Registry: Clinical Outcome and Benefit for Patients with Very High-Evidence Targets. Cancer Discov 2021; 11:2764-2779. [PMID: 34373263 PMCID: PMC9414287 DOI: 10.1158/2159-8290.cd-21-0094] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/26/2021] [Accepted: 07/28/2021] [Indexed: 01/26/2023]
Abstract
INFORM is a prospective, multinational registry gathering clinical and molecular data of relapsed, progressive, or high-risk pediatric patients with cancer. This report describes long-term follow-up of 519 patients in whom molecular alterations were evaluated according to a predefined seven-scale target prioritization algorithm. Mean turnaround time from sample receipt to report was 25.4 days. The highest target priority level was observed in 42 patients (8.1%). Of these, 20 patients received matched targeted treatment with a median progression-free survival of 204 days [95% confidence interval (CI), 99-not applicable], compared with 117 days (95% CI, 106-143; P = 0.011) in all other patients. The respective molecular targets were shown to be predictive for matched treatment response and not prognostic surrogates for improved outcome. Hereditary cancer predisposition syndromes were identified in 7.5% of patients, half of which were newly identified through the study. Integrated molecular analyses resulted in a change or refinement of diagnoses in 8.2% of cases. SIGNIFICANCE: The pediatric precision oncology INFORM registry prospectively tested a target prioritization algorithm in a real-world, multinational setting and identified subgroups of patients benefiting from matched targeted treatment with improved progression-free survival, refinement of diagnosis, and identification of hereditary cancer predisposition syndromes.See related commentary by Eggermont et al., p. 2677.This article is highlighted in the In This Issue feature, p. 2659.
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Affiliation(s)
- Cornelis M. van Tilburg
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Corresponding Author: Cornelis M. van Tilburg, Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ) and Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg 69120, Germany. Phone: 00-49-6221-56-36926; E-mail:
| | - Elke Pfaff
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristian W. Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Petra Fiesel
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Barbara C. Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gnana Prakash Balasubramanian
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Stark
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pascal D. Johann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Swabian Children's Cancer Center, Paediatric and Adolescent Medicine, University Medical Center Augsburg, Augsburg, Germany
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kathrin Schramm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Steffen Hirsch
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Sutter
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Kerstin Grund
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Arend von Stackelberg
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Oncology and Hematology Department, Charité–Campus Virchow Klinikum, Berlin, Germany
| | - Andreas E. Kulozik
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrej Lissat
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Oncology and Hematology Department, Charité–Campus Virchow Klinikum, Berlin, Germany
| | - Arndt Borkhardt
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Oncology and Hematology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Roland Meisel
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Pediatric Stem Cell Therapy, Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Dirk Reinhardt
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Jan-Henning Klusmann
- Department of Pediatric Hematology, Oncology and Hemostaseology, Clinic for Pediatrics, University Hospital of Frankfurt, Goethe-University Frankfurt, Frankfurt/Main, Germany
| | - Gudrun Fleischhack
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Stephan Tippelt
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Dietrich von Schweinitz
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Irene Schmid
- Department of Pediatric Oncology and Hematology, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Christof M. Kramm
- Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - André O. von Bueren
- Department of Pediatrics, Obstetrics and Gynecology, Division of Pediatric Hematology and Oncology, University Hospital Geneva, Geneva, Switzerland
| | - Gabriele Calaminus
- Department of Pediatric Oncology and Hematology, University Hospital Bonn, Bonn, Germany
| | - Peter Vorwerk
- Department of Pediatric Oncology and Hematology, University Hospital Magdeburg, Magdeburg, Germany
| | - Norbert Graf
- Department of Pediatric Oncology and Hematology, University Hospital Saarland, Saarland, Germany
| | - Frank Westermann
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Fischer
- National Center for Tumor Diseases (NCT) Network, Germany.,Department of Experimental Pediatric Oncology, University Hospital Köln, and Center for Molecular Medicine (CMMC), Medical Faculty, Cologne, Germany
| | - Angelika Eggert
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Oncology and Hematology Department, Charité–Campus Virchow Klinikum, Berlin, Germany
| | - Birgit Burkhardt
- Clinic of Pediatric Oncology and Hematology, University Hospital Münster, Muenster, Germany
| | - Wilhelm Wößmann
- Department of Pediatric Oncology and Hematology, University Hospital Hamburg, Hamburg, Germany
| | - Michaela Nathrath
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Klinikum Kassel, Kassel, Germany.,Department of Pediatrics, Technical University Munich, Munich, Germany
| | - Stefanie Hecker-Nolting
- National Center for Tumor Diseases (NCT) Network, Germany.,Department of Pediatric Oncology, Hematology and Immunology, Klinikum Stuttgart, Olgahospital, Stuttgart, Germany
| | - Michael C. Frühwald
- National Center for Tumor Diseases (NCT) Network, Germany.,Swabian Children's Cancer Center, Paediatric and Adolescent Medicine, University Medical Center Augsburg, Augsburg, Germany
| | | | - Ines B. Brecht
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Department of Pediatric Oncology and Hematology, University Hospital Tübingen, Tübingen, Germany
| | - Petra Ketteler
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Simone Fulda
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Institute for Experimental Cancer Research in Pediatrics, Goethe University Frankfurt, Frankfurt, Germany
| | - Ewa Koscielniak
- National Center for Tumor Diseases (NCT) Network, Germany.,Department of Pediatric Oncology, Hematology and Immunology, Klinikum Stuttgart, Olgahospital, Stuttgart, Germany
| | - Michael T. Meister
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Monika Scheer
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Oncology and Hematology Department, Charité–Campus Virchow Klinikum, Berlin, Germany
| | - Simone Hettmer
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Schwab
- German Cancer Consortium (DKTK), Heidelberg, Germany.,Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,Departments of Clinical Pharmacology, Pharmacy and Biochemistry, and Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tübingen, Tübingen, Germany
| | - Roman Tremmel
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Ingrid Øra
- Department of Pediatric Oncology and Hematology, Skane University Hospital Lund, and HOPE-ITCC Unit, Pediatric Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Hutter
- St. Anna Children's Hospital, Department of Pediatrics, Medical University of Vienna, and St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Nicolas U. Gerber
- Department of Oncology, University Children's Hospital, Zurich, Switzerland
| | - Olli Lohi
- Tampere Center for Child Health Research and Tays Cancer Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Bernarda Kazanowska
- Department of Pediatric Hematology/Oncology and BMT, Wroclaw Medical University, Wroclaw, Poland
| | - Antonis Kattamis
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Filippidou
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Bianca Goemans
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - C. Michel Zwaan
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephan Wolf
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Reuss
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Uta Dirksen
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Angelika Freitag
- NCT Trial Center, National Center for Tumor Diseases, Heidelberg, Germany, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ruth Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany
| | - Peter Lichter
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annette Kopp-Schneider
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Department Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T.W. Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan J. Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Utrecht University, Department of Pharmaceutical Sciences, Utrecht, the Netherlands
| | - David Capper
- German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
| | - Stefan M. Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT) Network, Germany
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19
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Stainczyk SA, Westermann F. Neuroblastoma-Telomere maintenance, deregulated signaling transduction and beyond. Int J Cancer 2021; 150:903-915. [PMID: 34636058 DOI: 10.1002/ijc.33839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/06/2021] [Accepted: 09/27/2021] [Indexed: 11/11/2022]
Abstract
The childhood malignancy neuroblastoma belongs to the group of embryonal tumors and originates from progenitor cells of the sympathoadrenal lineage. Treatment options for children with high-risk and relapsed disease are still very limited. In recent years, an ever-growing molecular diversity was identified using (epi)-genetic profiling of neuroblastoma tumors, indicating that molecularly targeted therapies could be a promising therapeutic option. In this review article, we summarize the various molecular subtypes and genetic events associated with neuroblastoma and describe recent advances in targeted therapies. We lay a strong emphasis on the importance of telomere maintenance mechanisms for understanding tumor progression and risk classification of neuroblastoma.
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Affiliation(s)
- Sabine A Stainczyk
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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20
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Dieter SM, Siegl C, Codó PL, Huerta M, Ostermann-Parucha AL, Schulz E, Zowada MK, Martin S, Laaber K, Nowrouzi A, Blatter M, Kreth S, Westermann F, Benner A, Uhrig U, Putzker K, Lewis J, Haegebarth A, Mumberg D, Holton SJ, Weiske J, Toepper LM, Scheib U, Siemeister G, Ball CR, Kuster B, Stoehr G, Hahne H, Johannes S, Lange M, Herbst F, Glimm H. Degradation of CCNK/CDK12 is a druggable vulnerability of colorectal cancer. Cell Rep 2021; 36:109394. [PMID: 34289372 DOI: 10.1016/j.celrep.2021.109394] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/08/2021] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
Novel treatment options for metastatic colorectal cancer (CRC) are urgently needed to improve patient outcome. Here, we screen a library of non-characterized small molecules against a heterogeneous collection of patient-derived CRC spheroids. By prioritizing compounds with inhibitory activity in a subset of-but not all-spheroid cultures, NCT02 is identified as a candidate with minimal risk of non-specific toxicity. Mechanistically, we show that NCT02 acts as molecular glue that induces ubiquitination of cyclin K (CCNK) and proteasomal degradation of CCNK and its complex partner CDK12. Knockout of CCNK or CDK12 decreases proliferation of CRC cells in vitro and tumor growth in vivo. Interestingly, sensitivity to pharmacological CCNK/CDK12 degradation is associated with TP53 deficiency and consensus molecular subtype 4 in vitro and in patient-derived xenografts. We thus demonstrate the efficacy of targeted CCNK/CDK12 degradation for a CRC subset, highlighting the potential of drug-induced proteolysis for difficult-to-treat types of cancer.
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Affiliation(s)
- Sebastian M Dieter
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany.
| | | | - Paula L Codó
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; CureVac AG, 60325 Frankfurt am Main, Germany
| | - Mario Huerta
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Anna L Ostermann-Parucha
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Erik Schulz
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Martina K Zowada
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Sylvia Martin
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Karin Laaber
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Ali Nowrouzi
- Division of Molecular and Translational Radiation Oncology, Heidelberg Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Mona Blatter
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Neuroblastoma Genomics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Sina Kreth
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Neuroblastoma Genomics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Neuroblastoma Genomics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Ulrike Uhrig
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, 69117 Heidelberg, Germany
| | - Kerstin Putzker
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, 69117 Heidelberg, Germany
| | - Joe Lewis
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, 69117 Heidelberg, Germany
| | - Andrea Haegebarth
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Dominik Mumberg
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Simon J Holton
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Joerg Weiske
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Lena-Marit Toepper
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Ulrike Scheib
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Gerhard Siemeister
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Claudia R Ball
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 01307 Dresden, Germany; Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden at TU Dresden, 01307 Dresden, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | | | | | - Sarah Johannes
- Bayer AG, Research & Development, Pharmaceuticals, 42117 Wuppertal, Germany
| | - Martin Lange
- Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany; Nuvisan Innovation Campus Berlin GmbH, 13353 Berlin, Germany
| | - Friederike Herbst
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), 01307 Dresden, Germany; Translational Functional Cancer Genomics, NCT and DKFZ Heidelberg, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 01307 Dresden, Germany; Center for Personalized Oncology, University Hospital Carl Gustav Carus Dresden at TU Dresden, 01307 Dresden, Germany.
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21
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Schmitt-Hoffner F, van Rijn S, Toprak UH, Mauermann M, Rosemann F, Heit-Mondrzyk A, Hübner JM, Camgöz A, Hartlieb S, Pfister SM, Henrich KO, Westermann F, Kool M. FOXR2 Stabilizes MYCN Protein and Identifies Non- MYCN-Amplified Neuroblastoma Patients With Unfavorable Outcome. J Clin Oncol 2021; 39:3217-3228. [PMID: 34110923 PMCID: PMC8500564 DOI: 10.1200/jco.20.02540] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clinical outcomes of patients with neuroblastoma range from spontaneous tumor regression to fatality. Hence, understanding the mechanisms that cause tumor progression is crucial for the treatment of patients. In this study, we show that FOXR2 activation identifies a subset of neuroblastoma tumors with unfavorable outcome and we investigate the mechanism how FOXR2 relates to poor outcome in patients.
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Affiliation(s)
- Felix Schmitt-Hoffner
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sjoerd van Rijn
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Umut H Toprak
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Monika Mauermann
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Felix Rosemann
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Anke Heit-Mondrzyk
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Jens-Martin Hübner
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Aylin Camgöz
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Sabine Hartlieb
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kai-Oliver Henrich
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Westermann
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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22
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Jansky S, Sharma AK, Körber V, Quintero A, Toprak UH, Wecht EM, Gartlgruber M, Greco A, Chomsky E, Grünewald TGP, Henrich KO, Tanay A, Herrmann C, Höfer T, Westermann F. Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma. Nat Genet 2021; 53:683-693. [PMID: 33767450 DOI: 10.1038/s41588-021-00806-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 01/29/2021] [Indexed: 01/31/2023]
Abstract
Neuroblastoma is a pediatric tumor of the developing sympathetic nervous system. However, the cellular origin of neuroblastoma has yet to be defined. Here we studied the single-cell transcriptomes of neuroblastomas and normal human developing adrenal glands at various stages of embryonic and fetal development. We defined normal differentiation trajectories from Schwann cell precursors over intermediate states to neuroblasts or chromaffin cells and showed that neuroblastomas transcriptionally resemble normal fetal adrenal neuroblasts. Importantly, neuroblastomas with varying clinical phenotypes matched different temporal states along normal neuroblast differentiation trajectories, with the degree of differentiation corresponding to clinical prognosis. Our work highlights the roles of oncogenic MYCN and loss of TFAP2B in blocking differentiation and may provide the basis for designing therapeutic interventions to overcome differentiation blocks.
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Affiliation(s)
- Selina Jansky
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Ashwini Kumar Sharma
- Health Data Science Unit, Medical Faculty University Heidelberg and BioQuant, Heidelberg, Germany
| | - Verena Körber
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrés Quintero
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Health Data Science Unit, Medical Faculty University Heidelberg and BioQuant, Heidelberg, Germany
| | - Umut H Toprak
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elisa M Wecht
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Moritz Gartlgruber
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alessandro Greco
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elad Chomsky
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Thomas G P Grünewald
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kai-Oliver Henrich
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Carl Herrmann
- Health Data Science Unit, Medical Faculty University Heidelberg and BioQuant, Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany. .,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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23
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Afanasyeva EA, Gartlgruber M, Ryl T, Decaesteker B, Denecker G, Mönke G, Toprak UH, Florez A, Torkov A, Dreidax D, Herrmann C, Okonechnikov K, Ek S, Sharma AK, Sagulenko V, Speleman F, Henrich KO, Westermann F. Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma. Life Sci Alliance 2021; 4:e201900332. [PMID: 33658318 PMCID: PMC8017594 DOI: 10.26508/lsa.201900332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
The migrational propensity of neuroblastoma is affected by cell identity, but the mechanisms behind the divergence remain unknown. Using RNAi and time-lapse imaging, we show that ADRN-type NB cells exhibit RAC1- and kalirin-dependent nucleokinetic (NUC) migration that relies on several integral components of neuronal migration. Inhibition of NUC migration by RAC1 and kalirin-GEF1 inhibitors occurs without hampering cell proliferation and ADRN identity. Using three clinically relevant expression dichotomies, we reveal that most of up-regulated mRNAs in RAC1- and kalirin-GEF1-suppressed ADRN-type NB cells are associated with low-risk characteristics. The computational analysis shows that, in a context of overall gene set poverty, the upregulomes in RAC1- and kalirin-GEF1-suppressed ADRN-type cells are a batch of AU-rich element-containing mRNAs, which suggests a link between NUC migration and mRNA stability. Gene set enrichment analysis-based search for vulnerabilities reveals prospective weak points in RAC1- and kalirin-GEF1-suppressed ADRN-type NB cells, including activities of H3K27- and DNA methyltransferases. Altogether, these data support the introduction of NUC inhibitors into cancer treatment research.
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Affiliation(s)
- Elena A Afanasyeva
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Moritz Gartlgruber
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Tatsiana Ryl
- Department of Neurosurgery, University of Duisburg Essen, Essen, Germany
| | - Bieke Decaesteker
- Center for Medical Genetics, Ghent University, and Cancer Research Institute Ghent, Ghent, Belgium
| | - Geertrui Denecker
- Center for Medical Genetics, Ghent University, and Cancer Research Institute Ghent, Ghent, Belgium
| | - Gregor Mönke
- European Molecular Biology Laboratories, Heidelberg, Germany
| | - Umut H Toprak
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Andres Florez
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
- Center for Systems Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Alica Torkov
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Daniel Dreidax
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Carl Herrmann
- Group of Cancer Regulatory Genomics B086, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Department of Pediatric Neurooncology, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Sara Ek
- Department of Immunotechnology, CREATE Health, Faculty of Engineering, Lund University, Lund, Sweden
| | - Ashwini Kumar Sharma
- Institute for Pharmacy and Molecular Biotechnology and BioQuant, Heidelberg University, Heidelberg, Germany
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vitaliya Sagulenko
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, and Cancer Research Institute Ghent, Ghent, Belgium
| | - Kai-Oliver Henrich
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Frank Westermann
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
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24
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Ecker J, Thatikonda V, Sigismondo G, Selt F, Valinciute G, Oehme I, Müller C, Buhl JL, Ridinger J, Usta D, Qin N, van Tilburg CM, Herold-Mende C, Remke M, Sahm F, Westermann F, Kool M, Wechsler-Reya RJ, Chavez L, Krijgsveld J, Jäger N, Pfister SM, Witt O, Milde T. Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified medulloblastoma. Neuro Oncol 2021; 23:226-239. [PMID: 32822486 DOI: 10.1093/neuonc/noaa191] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The sensitivity of myelocytomatosis oncogene (MYC) amplified medulloblastoma to class I histone deacetylase (HDAC) inhibition has been shown previously; however, understanding the underlying molecular mechanism is crucial for selection of effective HDAC inhibitors for clinical use. The aim of this study was to investigate the direct molecular interaction of MYC and class I HDAC2, and the impact of class I HDAC inhibition on MYC function. METHODS Co-immunoprecipitation and mass spectrometry were used to determine the co-localization of MYC and HDAC2. Chromatin immunoprecipitation (ChIP) sequencing and gene expression profiling were used to analyze the co-localization of MYC and HDAC2 on DNA and the impact on transcriptional activity in primary tumors and a MYC amplified cell line treated with the class I HDAC inhibitor entinostat. The effect on MYC was investigated by quantitative real-time PCR, western blot, and immunofluorescence. RESULTS HDAC2 is a cofactor of MYC in MYC amplified medulloblastoma. The MYC-HDAC2 complex is bound to genes defining the MYC-dependent transcriptional profile. Class I HDAC inhibition leads to stabilization and reduced DNA binding of MYC protein, inducing a downregulation of MYC activated genes (MAGs) and upregulation of MYC repressed genes (MRGs). MAGs and MRGs are characterized by opposing biological functions and by distinct enhancer-box distribution. CONCLUSIONS Our data elucidate the molecular interaction of MYC and HDAC2 and support a model in which inhibition of class I HDACs directly targets MYC's transactivating and transrepressing functions.
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Affiliation(s)
- Jonas Ecker
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Venu Thatikonda
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research, German Cancer Research Center, Heidelberg, Germany
| | - Gintvile Valinciute
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Ina Oehme
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Carina Müller
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Juliane L Buhl
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Johannes Ridinger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Diren Usta
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Nan Qin
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Germany.,Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
| | - Cornelis M van Tilburg
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | | | - Marc Remke
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Germany.,Department of Pediatric Neuro-Oncogenomics, German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany.,Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Lukas Chavez
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany.,Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Natalie Jäger
- Division of Pediatric Neurooncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,KiTZ Clinical Trial Unit, Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center and German Consortium for Translational Cancer Research, Heidelberg, Germany
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25
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Hartlieb SA, Sieverling L, Nadler-Holly M, Ziehm M, Toprak UH, Herrmann C, Ishaque N, Okonechnikov K, Gartlgruber M, Park YG, Wecht EM, Savelyeva L, Henrich KO, Rosswog C, Fischer M, Hero B, Jones DTW, Pfaff E, Witt O, Pfister SM, Volckmann R, Koster J, Kiesel K, Rippe K, Taschner-Mandl S, Ambros P, Brors B, Selbach M, Feuerbach L, Westermann F. Alternative lengthening of telomeres in childhood neuroblastoma from genome to proteome. Nat Commun 2021; 12:1269. [PMID: 33627664 PMCID: PMC7904810 DOI: 10.1038/s41467-021-21247-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 01/13/2021] [Indexed: 02/08/2023] Open
Abstract
Telomere maintenance by telomerase activation or alternative lengthening of telomeres (ALT) is a major determinant of poor outcome in neuroblastoma. Here, we screen for ALT in primary and relapsed neuroblastomas (n = 760) and characterize its features using multi-omics profiling. ALT-positive tumors are molecularly distinct from other neuroblastoma subtypes and enriched in a population-based clinical sequencing study cohort for relapsed cases. They display reduced ATRX/DAXX complex abundance, due to either ATRX mutations (55%) or low protein expression. The heterochromatic histone mark H3K9me3 recognized by ATRX is enriched at the telomeres of ALT-positive tumors. Notably, we find a high frequency of telomeric repeat loci with a neuroblastoma ALT-specific hotspot on chr1q42.2 and loss of the adjacent chromosomal segment forming a neo-telomere. ALT-positive neuroblastomas proliferate slowly, which is reflected by a protracted clinical course of disease. Nevertheless, children with an ALT-positive neuroblastoma have dismal outcome.
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Affiliation(s)
- Sabine A Hartlieb
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Lina Sieverling
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Applied Bioinformatics, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Michal Nadler-Holly
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Matthias Ziehm
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Umut H Toprak
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carl Herrmann
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany
| | - Naveed Ishaque
- Digital Health Centre, Berlin Institute of Health (BIH), Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Moritz Gartlgruber
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Young-Gyu Park
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elisa Maria Wecht
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Larissa Savelyeva
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolina Rosswog
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - David T W Jones
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elke Pfaff
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital, Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital, Heidelberg, Germany
| | - Richard Volckmann
- Department of Oncogenomics Amsterdam University Medical Centers (AUMC), Amsterdam, the Netherlands
| | - Jan Koster
- Department of Oncogenomics Amsterdam University Medical Centers (AUMC), Amsterdam, the Netherlands
| | - Katharina Kiesel
- Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Karsten Rippe
- Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | | | - Peter Ambros
- CCRI, St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Benedikt Brors
- Applied Bioinformatics, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lars Feuerbach
- Applied Bioinformatics, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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26
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Gartlgruber M, Sharma AK, Quintero A, Dreidax D, Jansky S, Park YG, Kreth S, Meder J, Doncevic D, Saary P, Toprak UH, Ishaque N, Afanasyeva E, Wecht E, Koster J, Versteeg R, Grünewald TGP, Jones DTW, Pfister SM, Henrich KO, van Nes J, Herrmann C, Westermann F. Super enhancers define regulatory subtypes and cell identity in neuroblastoma. Nat Cancer 2021; 2:114-128. [PMID: 35121888 DOI: 10.1038/s43018-020-00145-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/19/2020] [Indexed: 02/07/2023]
Abstract
Half of the children diagnosed with neuroblastoma (NB) have high-risk disease, disproportionately contributing to overall childhood cancer-related deaths. In addition to recurrent gene mutations, there is increasing evidence supporting the role of epigenetic deregulation in disease pathogenesis. Yet, comprehensive cis-regulatory network descriptions from NB are lacking. Here, using genome-wide H3K27ac profiles across 60 NBs, covering the different clinical and molecular subtypes, we identified four major super-enhancer-driven epigenetic subtypes and their underlying master regulatory networks. Three of these subtypes recapitulated known clinical groups; namely, MYCN-amplified, MYCN non-amplified high-risk and MYCN non-amplified low-risk NBs. The fourth subtype, exhibiting mesenchymal characteristics, shared cellular identity with multipotent Schwann cell precursors, was induced by RAS activation and was enriched in relapsed disease. Notably, CCND1, an essential gene in NB, was regulated by both mesenchymal and adrenergic regulatory networks converging on distinct super-enhancer modules. Overall, this study reveals subtype-specific super-enhancer regulation in NBs.
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Affiliation(s)
- Moritz Gartlgruber
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Ashwini Kumar Sharma
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany
| | - Andrés Quintero
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany
| | - Daniel Dreidax
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Selina Jansky
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Young-Gyu Park
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Sina Kreth
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Johanna Meder
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Daria Doncevic
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany
| | - Paul Saary
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany
| | - Umut H Toprak
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Naveed Ishaque
- Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Elena Afanasyeva
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Elisa Wecht
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Jan Koster
- Department of Oncogenomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Rogier Versteeg
- Department of Oncogenomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Thomas G P Grünewald
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital and Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Johan van Nes
- Department of Oncogenomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Carl Herrmann
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany.
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany.
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27
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Colmenero-Repiso A, Gómez-Muñoz MA, Rodríguez-Prieto I, Amador-Álvarez A, Henrich KO, Pascual-Vaca D, Okonechnikov K, Rivas E, Westermann F, Pardal R, Vega FM. Identification of VRK1 as a New Neuroblastoma Tumor Progression Marker Regulating Cell Proliferation. Cancers (Basel) 2020; 12:cancers12113465. [PMID: 33233777 PMCID: PMC7699843 DOI: 10.3390/cancers12113465] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 12/31/2022] Open
Abstract
Neuroblastoma (NB) is one of the most common pediatric cancers and presents a poor survival rate in affected children. Current pretreatment risk assessment relies on a few known molecular parameters, like the amplification of the oncogene MYCN. However, a better molecular knowledge about the aggressive progression of the disease is needed to provide new therapeutical targets and prognostic markers and to improve patients' outcomes. The human protein kinase VRK1 phosphorylates various signaling molecules and transcription factors to regulate cell cycle progression and other processes in physiological and pathological situations. Using neuroblastoma tumor expression data, tissue microarrays from fresh human samples and patient-derived xenografts (PDXs), we have determined that VRK1 kinase expression stratifies patients according to tumor aggressiveness and survival, allowing the identification of patients with worse outcome among intermediate risk. VRK1 associates with cell cycle signaling pathways in NB and its downregulation abrogates cell proliferation in vitro and in vivo. Through the analysis of ChIP-seq and methylation data from NB tumors, we show that VRK1 is a MYCN gene target, however VRK1 correlates with NB aggressiveness independently of MYCN gene amplification, synergizing with the oncogene to drive NB progression. Our study also suggests that VRK1 inhibition may constitute a novel cell-cycle-targeted strategy for anticancer therapy in neuroblastoma.
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Affiliation(s)
- Ana Colmenero-Repiso
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Seville, Spain; (A.C.-R.); (M.A.G.-M.); (I.R.-P.); (A.A.-Á.)
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, 41013 Seville, Spain
| | - María A. Gómez-Muñoz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Seville, Spain; (A.C.-R.); (M.A.G.-M.); (I.R.-P.); (A.A.-Á.)
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, 41013 Seville, Spain
| | - Ismael Rodríguez-Prieto
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Seville, Spain; (A.C.-R.); (M.A.G.-M.); (I.R.-P.); (A.A.-Á.)
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, 41013 Seville, Spain
| | - Aida Amador-Álvarez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Seville, Spain; (A.C.-R.); (M.A.G.-M.); (I.R.-P.); (A.A.-Á.)
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Kai-Oliver Henrich
- German Cancer Research Center (DKFZ), Division Neuroblastoma Genomics, 69120 Heidelberg, Germany; (K.-O.H.); (F.W.)
| | - Diego Pascual-Vaca
- Departamento de Anatomía Patológica, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain; (D.P.-V.); (E.R.)
| | | | - Eloy Rivas
- Departamento de Anatomía Patológica, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain; (D.P.-V.); (E.R.)
| | - Frank Westermann
- German Cancer Research Center (DKFZ), Division Neuroblastoma Genomics, 69120 Heidelberg, Germany; (K.-O.H.); (F.W.)
| | - Ricardo Pardal
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Seville, Spain; (A.C.-R.); (M.A.G.-M.); (I.R.-P.); (A.A.-Á.)
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, 41013 Seville, Spain
- Correspondence: (R.P.); (F.M.V.)
| | - Francisco M. Vega
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Seville, Spain; (A.C.-R.); (M.A.G.-M.); (I.R.-P.); (A.A.-Á.)
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
- Correspondence: (R.P.); (F.M.V.)
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28
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George SL, Lorenzi F, King D, Hartlieb S, Campbell J, Pemberton H, Toprak UH, Barker K, Tall J, da Costa BM, van den Boogaard ML, Dolman MEM, Molenaar JJ, Bryant HE, Westermann F, Lord CJ, Chesler L. Therapeutic vulnerabilities in the DNA damage response for the treatment of ATRX mutant neuroblastoma. EBioMedicine 2020; 59:102971. [PMID: 32846370 PMCID: PMC7452577 DOI: 10.1016/j.ebiom.2020.102971] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In neuroblastoma, genetic alterations in ATRX, define a distinct poor outcome patient subgroup. Despite the need for new therapies, there is a lack of available models and a dearth of pre-clinical research. METHODS To evaluate the impact of ATRX loss of function (LoF) in neuroblastoma, we utilized CRISPR-Cas9 gene editing to generate neuroblastoma cell lines isogenic for ATRX. We used these and other models to identify therapeutically exploitable synthetic lethal vulnerabilities associated with ATRX LoF. FINDINGS In isogenic cell lines, we found that ATRX inactivation results in increased DNA damage, homologous recombination repair (HRR) defects and impaired replication fork processivity. In keeping with this, high-throughput compound screening showed selective sensitivity in ATRX mutant cells to multiple PARP inhibitors and the ATM inhibitor KU60019. ATRX mutant cells also showed selective sensitivity to the DNA damaging agents, sapacitabine and irinotecan. HRR deficiency was also seen in the ATRX deleted CHLA-90 cell line, and significant sensitivity demonstrated to olaparib/irinotecan combination therapy in all ATRX LoF models. In-vivo sensitivity to olaparib/irinotecan was seen in ATRX mutant but not wild-type xenografts. Finally, sustained responses to olaparib/irinotecan therapy were seen in an ATRX deleted neuroblastoma patient derived xenograft. INTERPRETATION ATRX LoF results in specific DNA damage repair defects that can be therapeutically exploited. In ATRX LoF models, preclinical sensitivity is demonstrated to olaparib and irinotecan, a combination that can be rapidly translated into the clinic. FUNDING This work was supported by Christopher's Smile, Neuroblastoma UK, Cancer Research UK, and the Royal Marsden Hospital NIHR BRC.
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Affiliation(s)
- Sally L George
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT United Kingdom.
| | - Federica Lorenzi
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - David King
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, United Kingdom
| | - Sabine Hartlieb
- Neuroblastoma Genomics, Hopp Children`s Cancer Center Heidelberg (KiTZ) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - James Campbell
- Bioinformatics Core Facility, The Institute of Cancer Research, London, United Kingdom
| | - Helen Pemberton
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research London, SW3 6JB, United Kingdom
| | - Umut H Toprak
- Neuroblastoma Genomics, Hopp Children`s Cancer Center Heidelberg (KiTZ) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karen Barker
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Jennifer Tall
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | - Barbara Martins da Costa
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
| | | | - M Emmy M Dolman
- Princess Maxima Center for Pediatric Cancer, Utrecht, The Netherlands
| | - Jan J Molenaar
- Princess Maxima Center for Pediatric Cancer, Utrecht, The Netherlands
| | - Helen E Bryant
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, United Kingdom
| | - Frank Westermann
- Neuroblastoma Genomics, Hopp Children`s Cancer Center Heidelberg (KiTZ) & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christopher J Lord
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research London, SW3 6JB, United Kingdom
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT United Kingdom
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29
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Michaelis M, Voges Y, Rothweiler F, Weipert F, Zia-Ahmad A, Cinatl J, von Deimling A, Westermann F, Rödel F, Wass MN, Cinatl J. Testing of the Survivin Suppressant YM155 in a Large Panel of Drug-Resistant Neuroblastoma Cell Lines. Cancers (Basel) 2020; 12:cancers12030577. [PMID: 32131402 PMCID: PMC7139505 DOI: 10.3390/cancers12030577] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 12/11/2022] Open
Abstract
The survivin suppressant YM155 is a drug candidate for neuroblastoma. Here, we tested YM155 in 101 neuroblastoma cell lines (19 parental cell lines, 82 drug-adapted sublines). Seventy seven (77) cell lines displayed YM155 IC50s in the range of clinical YM155 concentrations. ABCB1 was an important determinant of YM155 resistance. The activity of the ABCB1 inhibitor zosuquidar ranged from being similar to that of the structurally different ABCB1 inhibitor verapamil to being 65-fold higher. ABCB1 sequence variations may be responsible for this, suggesting that the design of variant-specific ABCB1 inhibitors may be possible. Further, we showed that ABCC1 confers YM155 resistance. Previously, p53 depletion had resulted in decreased YM155 sensitivity. However, TP53-mutant cells were not generally less sensitive to YM155 than TP53 wild-type cells in this study. Finally, YM155 cross-resistance profiles differed between cells adapted to drugs as similar as cisplatin and carboplatin. In conclusion, the large cell line panel was necessary to reveal an unanticipated complexity of the YM155 response in neuroblastoma cell lines with acquired drug resistance. Novel findings include that ABCC1 mediates YM155 resistance and that YM155 cross-resistance profiles differ between cell lines adapted to drugs as similar as cisplatin and carboplatin.
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Affiliation(s)
- Martin Michaelis
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (M.M.); (M.N.W.)
| | - Yvonne Voges
- Institut für Medizinische Virologie, Goethe-Universität, 60596 Frankfurt am Main, Germany; (Y.V.); (F.R.); (A.Z.-A.); (J.C.)
| | - Florian Rothweiler
- Institut für Medizinische Virologie, Goethe-Universität, 60596 Frankfurt am Main, Germany; (Y.V.); (F.R.); (A.Z.-A.); (J.C.)
| | - Fabian Weipert
- Department of Radiotherapy and Oncology, Goethe-Universität, 60590 Frankfurt am Main, Germany; (F.W.); (F.R.)
| | - Amara Zia-Ahmad
- Institut für Medizinische Virologie, Goethe-Universität, 60596 Frankfurt am Main, Germany; (Y.V.); (F.R.); (A.Z.-A.); (J.C.)
| | - Jaroslav Cinatl
- Institut für Medizinische Virologie, Goethe-Universität, 60596 Frankfurt am Main, Germany; (Y.V.); (F.R.); (A.Z.-A.); (J.C.)
| | - Andreas von Deimling
- Department of Neuropathology, Ruprecht-Karls-University Heidelberg and Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany;
| | - Frank Westermann
- Division Neuroblastoma Genomics, B087, German Cancer Research Center and Hopp Children’s Cancer Center at the NCT (KiTZ), 69120 Heidelberg, Germany;
| | - Franz Rödel
- Department of Radiotherapy and Oncology, Goethe-Universität, 60590 Frankfurt am Main, Germany; (F.W.); (F.R.)
| | - Mark N. Wass
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (M.M.); (M.N.W.)
| | - Jindrich Cinatl
- Institut für Medizinische Virologie, Goethe-Universität, 60596 Frankfurt am Main, Germany; (Y.V.); (F.R.); (A.Z.-A.); (J.C.)
- Correspondence: ; Tel.: +49-69-6301-6409
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30
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Musa J, Cidre-Aranaz F, Aynaud MM, Orth MF, Knott MML, Mirabeau O, Mazor G, Varon M, Hölting TLB, Grossetête S, Gartlgruber M, Surdez D, Gerke JS, Ohmura S, Marchetto A, Dallmayer M, Baldauf MC, Stein S, Sannino G, Li J, Romero-Pérez L, Westermann F, Hartmann W, Dirksen U, Gymrek M, Anderson ND, Shlien A, Rotblat B, Kirchner T, Delattre O, Grünewald TGP. Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes. Nat Commun 2019; 10:4128. [PMID: 31511524 PMCID: PMC6739408 DOI: 10.1038/s41467-019-12071-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 08/16/2019] [Indexed: 12/02/2022] Open
Abstract
Pediatric malignancies including Ewing sarcoma (EwS) feature a paucity of somatic alterations except for pathognomonic driver-mutations that cannot explain overt variations in clinical outcome. Here, we demonstrate in EwS how cooperation of dominant oncogenes and regulatory germline variants determine tumor growth, patient survival and drug response. Binding of the oncogenic EWSR1-FLI1 fusion transcription factor to a polymorphic enhancer-like DNA element controls expression of the transcription factor MYBL2 mediating these phenotypes. Whole-genome and RNA sequencing reveals that variability at this locus is inherited via the germline and is associated with variable inter-tumoral MYBL2 expression. High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. Collectively, we establish cooperation of somatic mutations and regulatory germline variants as a major determinant of tumor progression and highlight the importance of integrating the regulatory genome in precision medicine.
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Affiliation(s)
- Julian Musa
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Florencia Cidre-Aranaz
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Marie-Ming Aynaud
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Maximilian M L Knott
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Olivier Mirabeau
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Gal Mazor
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Mor Varon
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tilman L B Hölting
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Sandrine Grossetête
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Moritz Gartlgruber
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Julia S Gerke
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Shunya Ohmura
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Aruna Marchetto
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Marlene Dallmayer
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Michaela C Baldauf
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Stefanie Stein
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Giuseppina Sannino
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Jing Li
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Frank Westermann
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk Institute of Pathology, University Hospital of Münster, Münster, Germany
| | - Uta Dirksen
- Department of Pediatric Hematology and Oncology, University Hospital of Essen, Essen, Germany
| | - Melissa Gymrek
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Nathaniel D Anderson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Barak Rotblat
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany.
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Partner site Munich, Munich, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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31
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Jones DTW, Banito A, Grünewald TGP, Haber M, Jäger N, Kool M, Milde T, Molenaar JJ, Nabbi A, Pugh TJ, Schleiermacher G, Smith MA, Westermann F, Pfister SM. Molecular characteristics and therapeutic vulnerabilities across paediatric solid tumours. Nat Rev Cancer 2019; 19:420-438. [PMID: 31300807 DOI: 10.1038/s41568-019-0169-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/12/2019] [Indexed: 02/06/2023]
Abstract
The spectrum of tumours arising in childhood is fundamentally different from that seen in adults, and they are known to be divergent from adult malignancies in terms of cellular origins, epidemiology, genetic complexity, driver mutations and underlying mutational processes. Despite the immense knowledge generated through sequencing efforts and functional characterization of identified (epi-)genetic alterations over the past decade, the clinical implications of this knowledge have so far been limited. Novel preclinical platforms such as the European Innovative Therapies for Children with Cancer-Paediatric Preclinical Proof-of-Concept Platform and the US-based Pediatric Preclinical Testing Consortium are being developed to try to change this by aiming to recapitulate the extensive heterogeneity of paediatric tumours and thereby, hopefully, improve the ability to predict clinical benefit. Numerous studies have also been established worldwide to provide patients with access to real-time molecular profiling and the possibility of more precise mechanism-of-action-based treatments. In addition to tumour-intrinsic findings and mechanisms, ongoing studies are investigating features such as the immune microenvironment of paediatric tumours in comparison with adult cancers - currently of very timely clinical relevance. However, there is an ongoing need for rigorous preclinical biomarker and target validation to feed into the next generation of molecularly stratified clinical trials. This Review aims to provide a comprehensive state-of-the-art overview of the molecular landscape of paediatric solid tumours, including their underlying genomic alterations and interactions with the microenvironment, complemented with our current understanding of potential therapeutic vulnerabilities and how these can be preclinically tested using more accurate predictive methods. Finally, we provide an outlook on the challenges and opportunities associated with translating this overwhelming scientific progress into real clinical benefit.
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Affiliation(s)
- David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ana Banito
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Soft Tissue Sarcoma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Australia, Randwick, NSW, Australia
- School of Women's & Children's Health, UNSW Australia, Randwick, NSW, Australia
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jan J Molenaar
- Princess Maxima Center for Pediatric Cancer, Utrecht, The Netherlands
| | - Arash Nabbi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Gudrun Schleiermacher
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, Paris, France
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Research Center, Institut Curie, Paris, France
| | - Malcolm A Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Rockville, MD, USA
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.
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32
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Savini C, Yang R, Savelyeva L, Göckel-Krzikalla E, Hotz-Wagenblatt A, Westermann F, Rösl F. Folate Repletion after Deficiency Induces Irreversible Genomic and Transcriptional Changes in Human Papillomavirus Type 16 (HPV16)-Immortalized Human Keratinocytes. Int J Mol Sci 2019; 20:ijms20051100. [PMID: 30836646 PMCID: PMC6429418 DOI: 10.3390/ijms20051100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/19/2019] [Accepted: 02/23/2019] [Indexed: 01/01/2023] Open
Abstract
Supplementation of micronutrients like folate is a double-edged sword in terms of their ambivalent role in cell metabolism. Although several epidemiological studies support a protective role of folate in carcinogenesis, there are also data arguing for an opposite effect. To address this issue in the context of human papillomavirus (HPV)-induced transformation, the molecular events of different folate availability on human keratinocytes immortalized by HPV16 E6 and E7 oncoproteins were examined. Several sublines were established: Control (4.5 µM folate), folate deficient (0.002 µM folate), and repleted cells (4.5 µM folate). Cells were analyzed in terms of oncogene expression, DNA damage and repair, karyotype changes, whole-genome sequencing, and transcriptomics. Here we show that folate depletion irreversibly induces DNA damage, impairment of DNA repair fidelity, and unique chromosomal alterations. Repleted cells additionally underwent growth advantage and enhanced clonogenicity, while the above mentioned impaired molecular properties became even more pronounced. Overall, it appears that a period of folate deficiency followed by repletion can shape immortalized cells toward an anomalous phenotype, thereby potentially contributing to carcinogenesis. These observations should elicit questions and inquiries for broader additional studies regarding folate fortification programs, especially in developing countries with micronutrient deficiencies and high HPV prevalence.
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Affiliation(s)
- Claudia Savini
- Division of Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Ruwen Yang
- Division of Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Larisa Savelyeva
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Elke Göckel-Krzikalla
- Division of Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Agnes Hotz-Wagenblatt
- Omics IT and Data Management, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Frank Westermann
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Frank Rösl
- Division of Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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33
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Ackermann S, Cartolano M, Hero B, Welte A, Kahlert Y, Roderwieser A, Bartenhagen C, Walter E, Gecht J, Kerschke L, Volland R, Menon R, Heuckmann JM, Gartlgruber M, Hartlieb S, Henrich KO, Okonechnikov K, Altmüller J, Nürnberg P, Lefever S, de Wilde B, Sand F, Ikram F, Rosswog C, Fischer J, Theissen J, Hertwig F, Singhi AD, Simon T, Vogel W, Perner S, Krug B, Schmidt M, Rahmann S, Achter V, Lang U, Vokuhl C, Ortmann M, Büttner R, Eggert A, Speleman F, O'Sullivan RJ, Thomas RK, Berthold F, Vandesompele J, Schramm A, Westermann F, Schulte JH, Peifer M, Fischer M. A mechanistic classification of clinical phenotypes in neuroblastoma. Science 2019; 362:1165-1170. [PMID: 30523111 DOI: 10.1126/science.aat6768] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/26/2018] [Accepted: 10/31/2018] [Indexed: 12/20/2022]
Abstract
Neuroblastoma is a pediatric tumor of the sympathetic nervous system. Its clinical course ranges from spontaneous tumor regression to fatal progression. To investigate the molecular features of the divergent tumor subtypes, we performed genome sequencing on 416 pretreatment neuroblastomas and assessed telomere maintenance mechanisms in 208 of these tumors. We found that patients whose tumors lacked telomere maintenance mechanisms had an excellent prognosis, whereas the prognosis of patients whose tumors harbored telomere maintenance mechanisms was substantially worse. Survival rates were lowest for neuroblastoma patients whose tumors harbored telomere maintenance mechanisms in combination with RAS and/or p53 pathway mutations. Spontaneous tumor regression occurred both in the presence and absence of these mutations in patients with telomere maintenance-negative tumors. On the basis of these data, we propose a mechanistic classification of neuroblastoma that may benefit the clinical management of patients.
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Affiliation(s)
- Sandra Ackermann
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Maria Cartolano
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Anne Welte
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Yvonne Kahlert
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Andrea Roderwieser
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Esther Walter
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Judith Gecht
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Laura Kerschke
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Ruth Volland
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | | | | | - Moritz Gartlgruber
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Sabine Hartlieb
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Division of Pediatric Neurooncology, German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Janine Altmüller
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Steve Lefever
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Bram de Wilde
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Frederik Sand
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Fakhera Ikram
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, Lahore, Pakistan
| | - Carolina Rosswog
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Janina Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Jessica Theissen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Falk Hertwig
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Aatur D Singhi
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Thorsten Simon
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Wenzel Vogel
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.,Research Center Borstel, Leibniz Center for Medicine and Biosciences, Borstel, Germany
| | - Sven Perner
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.,Research Center Borstel, Leibniz Center for Medicine and Biosciences, Borstel, Germany
| | - Barbara Krug
- Department of Diagnostic and Interventional Radiology, University Hospital of Cologne, Cologne, Germany
| | - Matthias Schmidt
- Department of Nuclear Medicine, University of Cologne, Cologne, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Computer Science, TU Dortmund, Dortmund, Germany
| | - Viktor Achter
- Computing Center, University of Cologne, Cologne, Germany
| | - Ulrich Lang
- Computing Center, University of Cologne, Cologne, Germany.,Department of Informatics, University of Cologne, Cologne, Germany
| | - Christian Vokuhl
- Kiel Pediatric Tumor Registry, Department of Pediatric Pathology, University of Kiel, Kiel, Germany
| | - Monika Ortmann
- Department of Pathology, University of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Department of Pathology, University of Cologne, Cologne, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute (UPCI), Hillman Cancer Center, Pittsburgh, PA, USA
| | - Roman K Thomas
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pathology, University of Cologne, Cologne, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Berthold
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Alexander Schramm
- Department of Medical Oncology, West German Cancer Center Essen, University of Duisburg-Essen, Essen, Germany
| | - Frank Westermann
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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34
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Soriano A, Masanas M, Boloix A, Masiá N, París-Coderch L, Piskareva O, Jiménez C, Henrich KO, Roma J, Westermann F, Stallings RL, Sábado C, de Toledo JS, Santamaria A, Gallego S, Segura MF. Functional high-throughput screening reveals miR-323a-5p and miR-342-5p as new tumor-suppressive microRNA for neuroblastoma. Cell Mol Life Sci 2019; 76:2231-2243. [PMID: 30770954 PMCID: PMC6502783 DOI: 10.1007/s00018-019-03041-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/28/2019] [Accepted: 02/04/2019] [Indexed: 01/13/2023]
Abstract
Current therapies for most non-infectious diseases are directed at or affect functionality of the human translated genome, barely 2% of all genetic information. By contrast, the therapeutic potential of targeting the transcriptome, ~ 70% of the genome, remains largely unexplored. RNA therapeutics is an emerging field that widens the range of druggable targets and includes elements such as microRNA. Here, we sought to screen for microRNA with tumor-suppressive functions in neuroblastoma, an aggressive pediatric tumor of the sympathetic nervous system that requires the development of new therapies. We found miR-323a-5p and miR-342-5p to be capable of reducing cell proliferation in multiple neuroblastoma cell lines in vitro and in vivo, thereby providing a proof of concept for miRNA-based therapies for neuroblastoma. Furthermore, the combined inhibition of the direct identified targets such as CCND1, CHAF1A, INCENP and BCL-XL could reveal new vulnerabilities of high-risk neuroblastoma.
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Affiliation(s)
- Aroa Soriano
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR)-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119-129, Collserola Building. Lab 207, 08035, Barcelona, Spain
| | - Marc Masanas
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR)-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119-129, Collserola Building. Lab 207, 08035, Barcelona, Spain
| | - Ariadna Boloix
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR)-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119-129, Collserola Building. Lab 207, 08035, Barcelona, Spain.,Institut de Ciència de Materials de Barcelona (ICMAB-CSIC) and Nanomol Technologies SA, Mòdul de Recerca B, Campus UAB, 08193, Bellaterra, Spain
| | - Núria Masiá
- Cell Cycle and Cancer Laboratory, Biomedical Research Group in Urology, Vall d'Hebron Research Institute (VHIR)-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119, 08035, Barcelona, Spain
| | - Laia París-Coderch
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR)-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119-129, Collserola Building. Lab 207, 08035, Barcelona, Spain
| | - Olga Piskareva
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland and National Children's Research Centre Our Lady's Children's Hospital, Dublin, Ireland
| | - Carlos Jiménez
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR)-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119-129, Collserola Building. Lab 207, 08035, Barcelona, Spain
| | - Kai-Oliver Henrich
- Neuroblastoma Genomics Group, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Josep Roma
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR)-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119-129, Collserola Building. Lab 207, 08035, Barcelona, Spain
| | - Frank Westermann
- Neuroblastoma Genomics Group, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Raymond L Stallings
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland and National Children's Research Centre Our Lady's Children's Hospital, Dublin, Ireland
| | - Constantino Sábado
- Pediatric Oncology and Hematology Department, Hospital Universitari Vall d'Hebron-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119, 08035, Barcelona, Spain
| | - Josep Sánchez de Toledo
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR)-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119-129, Collserola Building. Lab 207, 08035, Barcelona, Spain.,Pediatric Oncology and Hematology Department, Hospital Universitari Vall d'Hebron-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119, 08035, Barcelona, Spain
| | - Anna Santamaria
- Cell Cycle and Cancer Laboratory, Biomedical Research Group in Urology, Vall d'Hebron Research Institute (VHIR)-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119, 08035, Barcelona, Spain
| | - Soledad Gallego
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR)-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119-129, Collserola Building. Lab 207, 08035, Barcelona, Spain.,Pediatric Oncology and Hematology Department, Hospital Universitari Vall d'Hebron-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119, 08035, Barcelona, Spain
| | - Miguel F Segura
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR)-Universitat Autònoma de Barcelona (UAB), Passeig Vall d'Hebron 119-129, Collserola Building. Lab 207, 08035, Barcelona, Spain.
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35
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Gustafsson S, Westermann F, Hanrieder T, Jung L, Ruppach H, Mihranyan A. Comparative Analysis of Dry and Wet Porometry Methods for Characterization of Regular and Cross-Linked Virus Removal Filter Papers. Membranes (Basel) 2018; 9:E1. [PMID: 30577520 PMCID: PMC6359513 DOI: 10.3390/membranes9010001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/02/2018] [Accepted: 12/14/2018] [Indexed: 11/17/2022]
Abstract
Pore-size distribution (PSD) is the most critical parameter for size-exclusion virus removal filters. Yet, different dry- and wet-state porometry methods yield different pore-size values. The goal of this work is to conduct comparative analysis of nitrogen gas sorption (NGSP), liquid-liquid and cryoporometry with differential scanning calorimetry (CP-DSC) methods with respect to characterization of regular and cross-linked virus removal filter paper based on cellulose nanofibers, i.e. the mille-feuille filter. The filters were further characterized with atomic force and scanning electron microscopy. Finally, the removal of the worst-case model virus, i.e. minute virus of mice (MVM; 20 nm, nonenveloped parvovirus) was evaluated. The results revealed that there is no difference of the obtained PSDs between the wet methods, i.e. DSC and liquid-liquid porometry (LLP), as well as no difference between the regular and cross-linked filters regardless of method. MVM filtration at different trans membrane pressure (TMP) revealed strong dependence of the virus removal capability on applied pressure. It was further observed that cross-linking filters showed enhanced virus removal, especially at lower TMP. In all, the results of this study highlight the complex nature of virus capture in size-exclusion filters.
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Affiliation(s)
- Simon Gustafsson
- Division for Nanotechnology and Functional Materials, Department for Engineering Sciences, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden.
| | - Frank Westermann
- Charles River Biopharmaceutical Services, Gottfried Hagen Str. 20, 51105 Köln, Germany.
| | - Tobias Hanrieder
- Charles River Biopharmaceutical Services, Gottfried Hagen Str. 20, 51105 Köln, Germany.
| | - Laura Jung
- Charles River Biopharmaceutical Services, Gottfried Hagen Str. 20, 51105 Köln, Germany.
| | - Horst Ruppach
- Charles River Biopharmaceutical Services, Gottfried Hagen Str. 20, 51105 Köln, Germany.
| | - Albert Mihranyan
- Division for Nanotechnology and Functional Materials, Department for Engineering Sciences, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden.
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36
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Ogorodnikov A, Levin M, Tattikota S, Tokalov S, Hoque M, Scherzinger D, Marini F, Poetsch A, Binder H, Macher-Göppinger S, Probst HC, Tian B, Schaefer M, Lackner KJ, Westermann F, Danckwardt S. Transcriptome 3'end organization by PCF11 links alternative polyadenylation to formation and neuronal differentiation of neuroblastoma. Nat Commun 2018; 9:5331. [PMID: 30552333 PMCID: PMC6294251 DOI: 10.1038/s41467-018-07580-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 11/08/2018] [Indexed: 12/12/2022] Open
Abstract
Diversification at the transcriptome 3'end is an important and evolutionarily conserved layer of gene regulation associated with differentiation and dedifferentiation processes. Here, we identify extensive transcriptome 3'end-alterations in neuroblastoma, a tumour entity with a paucity of recurrent somatic mutations and an unusually high frequency of spontaneous regression. Utilising extensive RNAi-screening we reveal the landscape and drivers of transcriptome 3'end-diversification, discovering PCF11 as critical regulator, directing alternative polyadenylation (APA) of hundreds of transcripts including a differentiation RNA-operon. PCF11 shapes inputs converging on WNT-signalling, and governs cell cycle, proliferation, apoptosis and neurodifferentiation. Postnatal PCF11 down-regulation induces a neurodifferentiation program, and low-level PCF11 in neuroblastoma associates with favourable outcome and spontaneous tumour regression. Our findings document a critical role for APA in tumorigenesis and describe a novel mechanism for cell fate reprogramming in neuroblastoma with potentially important clinical implications. We provide an interactive data repository of transcriptome-wide APA covering > 170 RNAis, and an APA-network map with regulatory hubs.
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Affiliation(s)
- Anton Ogorodnikov
- Posttranscriptional Gene Regulation, Cancer Research and Experimental Haemostasis, University Medical Centre Mainz, Mainz, 55131, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, 55131, Germany
- Centre for Thrombosis and Haemostasis (CTH), University Medical Centre Mainz, Mainz, 55131, Germany
- McManus Laboratory, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Michal Levin
- Posttranscriptional Gene Regulation, Cancer Research and Experimental Haemostasis, University Medical Centre Mainz, Mainz, 55131, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, 55131, Germany
- Centre for Thrombosis and Haemostasis (CTH), University Medical Centre Mainz, Mainz, 55131, Germany
| | - Surendra Tattikota
- Posttranscriptional Gene Regulation, Cancer Research and Experimental Haemostasis, University Medical Centre Mainz, Mainz, 55131, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, 55131, Germany
- Centre for Thrombosis and Haemostasis (CTH), University Medical Centre Mainz, Mainz, 55131, Germany
| | - Sergey Tokalov
- Posttranscriptional Gene Regulation, Cancer Research and Experimental Haemostasis, University Medical Centre Mainz, Mainz, 55131, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, 55131, Germany
- Centre for Thrombosis and Haemostasis (CTH), University Medical Centre Mainz, Mainz, 55131, Germany
| | - Mainul Hoque
- Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Denise Scherzinger
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre Mainz, Mainz, 55131, Germany
| | - Federico Marini
- Centre for Thrombosis and Haemostasis (CTH), University Medical Centre Mainz, Mainz, 55131, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre Mainz, Mainz, 55131, Germany
| | - Ansgar Poetsch
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
- Institute for Plant Biochemistry, Ruhr-University Bochum, Bochum, 44801, Germany
- School of Biomedical & Healthcare Sciences, Plymouth University, Plymouth, PL4 8AA, United Kingdom
| | - Harald Binder
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, 79104, Germany
| | | | - Hans Christian Probst
- Institute for Immunology, University Medical Centre Mainz, Mainz, 55131, Germany
- Research Center for Immunotherapy (FZI), University Medical Centre Mainz, Mainz, 55131, Germany
| | - Bin Tian
- Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Michael Schaefer
- Department of Anaesthesiology and Research Centre Translational Neurosciences, University Medical Centre Mainz, Mainz, 55131, Germany
| | - Karl J Lackner
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, 55131, Germany
| | - Frank Westermann
- Division of Neuroblastoma Genomics, German Cancer Research Centre (DKFZ), Heidelberg, 69120, Germany
| | - Sven Danckwardt
- Posttranscriptional Gene Regulation, Cancer Research and Experimental Haemostasis, University Medical Centre Mainz, Mainz, 55131, Germany.
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, 55131, Germany.
- Centre for Thrombosis and Haemostasis (CTH), University Medical Centre Mainz, Mainz, 55131, Germany.
- German Centre for Cardiovascular Research (DZHK), Mainz, 55131, Germany.
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37
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Westermann F, Alborzinia H, Gogolin S, Flórez AF, Brückner LM, Gartlgruber M, Hartlieb S, Dreidax D, Nadler-Holly M, Ziehm M, Shao C, Selbach M, Stresemann C, Poschet G, Nicke B, Wölfl S, Henrich KO, Höfer T. Abstract 4973: MYCN mediates cysteine addiction and sensitizes to ferroptosis in cancer cells. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Aberrant expression of MYC family members predicts poor clinical outcome in many human cancers. Oncogenic MYC profoundly alters metabolism and mediates an antioxidant response to maintain redox balance. The purpose of the study was to analyze the interplay of oncogenic MYCN or c-MYC, referred to here as MYC(N), activity with cysteine metabolism and ferroptosis, an oxidative, non-apoptotic, and iron dependent form of regulated cell death caused by ROS-mediated massive lipid peroxidation (L-ROS), using MYC(N)-driven childhood neuroblastoma as a model.The intracellular amino acid levels at MYC(N)-high and MYC(N)-low cellular states were analyzed by HPLC. Effects on cell viability upon depletion of individual amino acids from the growth medium was tested in various cancer cell lines with regulable MYC(N). An unbiased high-throughput MYCN synthetic lethal siRNA screen was used to identify genes preferentially acting in the 'MYC(N)-high' state and protecting cells from ROS accumulation and ferroptosis. The capacity of cyst(e)ine uptake, intracellular cysteine synthesis via transsulfuration and glutathione biosynthesis was assessed in various neuroblastoma cell lines and tissues using metabolome, RNAseq, ChiP-seq and global proteome analyses. To investigate L-ROS formation at various conditions cells were stained with the lipid peroxidation sensor, C11-BODIPY, and flow cytometrically analyzed. Ferroptosis inducers (FINs) and inhibitors of transsulfuration were used to test their activity in various MYC(N)-dependent neuroblastoma cell lines and in vivo xenografts.We found that intracellular cysteine depletion in a 'MYC(N)-high' context induces cell death by ferroptosis and identified multiple points in glutathione synthesis and metabolism, particularly detoxification of L-ROS, that are vulnerable in the 'MYC(N)-high' state as compared to the 'MYC(N)-low' context. We could show that ferroptosis was dependent on MYC(N) expression and was enhanced by iron. We further demonstrated that both cystine import and intracellular cysteine synthesis via transulfuration achieved the intracellular state supportive of oncogenic MYC(N)-driven growth without endangering the cell to ferroptosis. We demonstrated the MYC(N) drives increased transsulfuration activity, rather than cysteine import, in tumor cells to maintain the cellular cysteine supply for glutathione synthesis. Our findings together with new descriptions of the ferroptotic process establish a novel functional link between oncogenic MYC(N) and ferroptosis, and imply regulation by cysteine-dependent glutathione availability. In MYCN-amplified childhood neuroblastoma, MYCN mediates resistance to ferroptosis by activating transsulfuration of methionine to cysteine. We identified enzymes and antiporter proteins crucial to ferroptotic escape, providing multiple previously unknown sites that may be acted on therapeutically.
Citation Format: Frank Westermann, Hamed Alborzinia, Sina Gogolin, Andrés F. Flórez, Lena M. Brückner, Moritz Gartlgruber, Sabine Hartlieb, Daniel Dreidax, Michal Nadler-Holly, Matthias Ziehm, Chunxuan Shao, Matthias Selbach, Carlo Stresemann, Gernot Poschet, Barbara Nicke, Stefan Wölfl, Kai O. Henrich, Thomas Höfer. MYCN mediates cysteine addiction and sensitizes to ferroptosis in cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4973.
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Affiliation(s)
| | | | - Sina Gogolin
- 1German Cancer Research Center, Heidelberg, Germany
| | | | | | | | | | | | | | - Matthias Ziehm
- 3Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | | | | | | | | | | | | | | | - Thomas Höfer
- 1German Cancer Research Center, Heidelberg, Germany
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38
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Kolbinger FR, Koeneke E, Ridinger J, Heimburg T, Müller M, Bayer T, Sippl W, Jung M, Gunkel N, Miller AK, Westermann F, Witt O, Oehme I. The HDAC6/8/10 inhibitor TH34 induces DNA damage-mediated cell death in human high-grade neuroblastoma cell lines. Arch Toxicol 2018; 92:2649-2664. [PMID: 29947893 PMCID: PMC6063332 DOI: 10.1007/s00204-018-2234-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/04/2018] [Indexed: 12/20/2022]
Abstract
High histone deacetylase (HDAC) 8 and HDAC10 expression levels have been identified as predictors of exceptionally poor outcomes in neuroblastoma, the most common extracranial solid tumor in childhood. HDAC8 inhibition synergizes with retinoic acid treatment to induce neuroblast maturation in vitro and to inhibit neuroblastoma xenograft growth in vivo. HDAC10 inhibition increases intracellular accumulation of chemotherapeutics through interference with lysosomal homeostasis, ultimately leading to cell death in cultured neuroblastoma cells. So far, no HDAC inhibitor covering HDAC8 and HDAC10 at micromolar concentrations without inhibiting HDACs 1, 2 and 3 has been described. Here, we introduce TH34 (3-(N-benzylamino)-4-methylbenzhydroxamic acid), a novel HDAC6/8/10 inhibitor for neuroblastoma therapy. TH34 is well-tolerated by non-transformed human skin fibroblasts at concentrations up to 25 µM and modestly impairs colony growth in medulloblastoma cell lines, but specifically induces caspase-dependent programmed cell death in a concentration-dependent manner in several human neuroblastoma cell lines. In addition to the induction of DNA double-strand breaks, HDAC6/8/10 inhibition also leads to mitotic aberrations and cell-cycle arrest. Neuroblastoma cells display elevated levels of neuronal differentiation markers, mirrored by formation of neurite-like outgrowths under maintained TH34 treatment. Eventually, after long-term treatment, all neuroblastoma cells undergo cell death. The combination of TH34 with plasma-achievable concentrations of retinoic acid, a drug applied in neuroblastoma therapy, synergistically inhibits colony growth (combination index (CI) < 0.1 for 10 µM of each). In summary, our study supports using selective HDAC inhibitors as targeted antineoplastic agents and underlines the therapeutic potential of selective HDAC6/8/10 inhibition in high-grade neuroblastoma.
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Affiliation(s)
- Fiona R Kolbinger
- Preclinical Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Emily Koeneke
- Preclinical Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Johannes Ridinger
- Preclinical Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Tino Heimburg
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Michael Müller
- Preclinical Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Theresa Bayer
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104, Freiburg, Germany
| | - Nikolas Gunkel
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Aubry K Miller
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Frank Westermann
- Research Group Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Olaf Witt
- Preclinical Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Ina Oehme
- Preclinical Program, Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), 69120, Heidelberg, Germany. .,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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39
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Marcone S, Iljin K, Dempsey E, Fey D, Duffy D, Westermann F, Kolch W, Halasz M. PO-461 Mitochondria-mediated anticancer effect of diphenyleneiodonium chloride (DPI) in aggressive neuroblastoma is regulated by MYCN. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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40
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Duffy DJ, Krstic A, Schwarzl T, Halasz M, Iljin K, Fey D, Haley B, Whilde J, Haapa-Paananen S, Fey V, Fischer M, Westermann F, Henrich KO, Bannert S, Higgins DG, Kolch W. Wnt signalling is a bi-directional vulnerability of cancer cells. Oncotarget 2018; 7:60310-60331. [PMID: 27531891 PMCID: PMC5312386 DOI: 10.18632/oncotarget.11203] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 07/26/2016] [Indexed: 12/30/2022] Open
Abstract
Wnt signalling is involved in the formation, metastasis and relapse of a wide array of cancers. However, there is ongoing debate as to whether activation or inhibition of the pathway holds the most promise as a therapeutic treatment for cancer, with conflicting evidence from a variety of tumour types. We show that Wnt/β-catenin signalling is a bi-directional vulnerability of neuroblastoma, malignant melanoma and colorectal cancer, with hyper-activation or repression of the pathway both representing a promising therapeutic strategy, even within the same cancer type. Hyper-activation directs cancer cells to undergo apoptosis, even in cells oncogenically driven by β-catenin. Wnt inhibition blocks proliferation of cancer cells and promotes neuroblastoma differentiation. Wnt and retinoic acid co-treatments synergise, representing a promising combination treatment for MYCN-amplified neuroblastoma. Additionally, we report novel cross-talks between MYCN and β-catenin signalling, which repress normal β-catenin mediated transcriptional regulation. A β-catenin target gene signature could predict patient outcome, as could the expression level of its DNA binding partners, the TCF/LEFs. This β-catenin signature provides a tool to identify neuroblastoma patients likely to benefit from Wnt-directed therapy. Taken together, we show that Wnt/β-catenin signalling is a bi-directional vulnerability of a number of cancer entities, and potentially a more broadly conserved feature of malignant cells.
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Affiliation(s)
- David J Duffy
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Current address: The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, USA
| | - Aleksandar Krstic
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Thomas Schwarzl
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Current address: European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Melinda Halasz
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | | | - Dirk Fey
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Bridget Haley
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Jenny Whilde
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | | | - Vidal Fey
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Matthias Fischer
- Department of Paediatric Haematology and Oncology and Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Frank Westermann
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Bannert
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Desmond G Higgins
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.,School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.,School of Medicine, University College Dublin, Belfield, Dublin, Ireland
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41
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Ryl T, Kuchen EE, Bell E, Shao C, Flórez AF, Mönke G, Gogolin S, Friedrich M, Lamprecht F, Westermann F, Höfer T. Cell-Cycle Position of Single MYC-Driven Cancer Cells Dictates Their Susceptibility to a Chemotherapeutic Drug. Cell Syst 2017; 5:237-250.e8. [PMID: 28843484 DOI: 10.1016/j.cels.2017.07.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/25/2017] [Accepted: 07/24/2017] [Indexed: 12/26/2022]
Abstract
While many tumors initially respond to chemotherapy, regrowth of surviving cells compromises treatment efficacy in the long term. The cell-biological basis of this regrowth is not understood. Here, we characterize the response of individual, patient-derived neuroblastoma cells driven by the prominent oncogene MYC to the first-line chemotherapy, doxorubicin. Combining live-cell imaging, cell-cycle-resolved transcriptomics, and mathematical modeling, we demonstrate that a cell's treatment response is dictated by its expression level of MYC and its cell-cycle position prior to treatment. All low-MYC cells enter therapy-induced senescence. High-MYC cells, by contrast, disable their cell-cycle checkpoints, forcing renewed proliferation despite treatment-induced DNA damage. After treatment, the viability of high-MYC cells depends on their cell-cycle position during treatment: newborn cells promptly halt in G1 phase, repair DNA damage, and form re-growing clones; all other cells show protracted DNA repair and ultimately die. These findings demonstrate that fast-proliferating tumor cells may resist cytotoxic treatment non-genetically, by arresting within a favorable window of the cell cycle.
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Affiliation(s)
- Tatsiana Ryl
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Erika E Kuchen
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Emma Bell
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Chunxuan Shao
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Andrés F Flórez
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Gregor Mönke
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Sina Gogolin
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mona Friedrich
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Florian Lamprecht
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Frank Westermann
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany.
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Gartlgruber M, Dreidax D, Doncevic D, Steinhauser S, Gröschel S, Henrich KO, Park YG, Herrmann C, Westermann F. Abstract LB-083: Core transcriptional regulatory circuitries in neuroblastoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Neuroblastoma (NB) is a pediatric tumor derived from precursor cells of the sympathetic nervous system. NB accounts for 12% of all childhood cancer deaths with ~50% high-risk cases which frequently harbor amplified proto-oncogene MYCN. Evidence accumulates that epigenetic deregulation, including aberrant DNA methylation in high-risk disease or oncogene activation by enhancer hijacking, plays a prominent role in NB. The present study applies a comprehensive approach integrating chromatin modification data with genomic and expression data to elucidate NB subtype specific super-enhancer (SE) landscapes and core regulatory circuitries (CRCs) consisting of lineage-specific interconnected loops of SE-driven, auto-regulatory master transcription factors.
Methods
Chromatin immunoprecipitation sequencing (ChIP-seq) of histone 3 lysine 27 acetylation (H3K27ac) was used to identify active enhancer elements in 23 primary NBs. A validation cohort consisting of 16 NB cell lines and two human neural crest cell lines was used. ChIPmentation was applied to validate predicted transcription factor (TF) binding events. Circular chromatin conformation capture sequencing (4C-seq) was used to assay physical promoter-enhancer interactions.
Results
Unsupervised clustering of 23 primary NBs according to H3K27ac signal intensity at the most variable SEs (genome-wide) revealed two main subgroups, MYCN-amplified (n = 8) and MYCN single copy tumors (n = 15), with distinctive activity patterns. Calling of CRCs in the 23 primary NBs yielded a core set of NB master TFs (CRC TFs). Amongst the top ten of them are HAND2, PHOX2B and MYCN, all of which are implicated in NB biology and playing essential roles in the development of the sympathetic nervous system. In line with this, gene ontology analyses of the top 50 CRC TFs converge on biological processes like development of neural crest cells, sympathetic nervous system and peripheral nervous system neurons. ChIPmentation analyses of selected CRC TFs confirmed auto-binding to their assigned SEs and those of other CRC TFs in their respective network. Interactions between promoters and SEs of selected CRC TFs were verified via 4C-seq. Intriguingly, expression analysis of the top 50 CRC TFs in a cohort of 498 primary NBs revealed that less than 20% of the CRC TFs are up-regulated in MYCN-amplified tumors while the remaining 80% are down-regulated in that subgroup. This suggests a superordinate role of MYCN in differentially orchestrating NB master TFs.
Conclusion
The study identifies the core set of NB master transcription factors and assigns established NB regulators like HAND2, PHOX2B and MYCN to well-defined CRCs. It reveals an association of MYCN amplification with the global SE landscape of primary NBs and suggests a role for MYCN in differentially controlling subsets of CRC TFs and their networks. Specific targeting of the SE-dependent CRC networks may open a therapeutic window for epigenetic drugs, including BET inhibitors, CDK7 or EZH2 inhibition, in NB.
Citation Format: Moritz Gartlgruber, Daniel Dreidax, Daria Doncevic, Sebastian Steinhauser, Stefan Gröschel, Kai Oliver Henrich, Young-Gyu Park, Carl Herrmann, Frank Westermann. Core transcriptional regulatory circuitries in neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-083. doi:10.1158/1538-7445.AM2017-LB-083
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Affiliation(s)
| | - Daniel Dreidax
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daria Doncevic
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | | | - Young-Gyu Park
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carl Herrmann
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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Torkov A, Henrich KO, Shao C, Gartlgruber M, Westermann F. Abstract 1426: Blinding the CYCLOPS - Cancer vulnerabilities unveiled by genomic loss. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background:
Heterozygous deletions within distal 1p are observed in 30% of neuroblastomas. So far, several potential 1p tumor suppressor genes have been identified. However, in this study we are focussing on 1p genes whose inactivation is not necessarily linked to tumor development but which mediate cell-essential functions, rendering cells with copy number loss vulnerable to further impairment. These genes are candidate therapeutic targets according to the concept of CYCLOPS (copy number alterations yielding cancer liabilities owing to partial loss).
Methods:
To identify a subset of 1p genes for which heterozygous loss may be tolerated but further reduction leads to cell death, we performed siRNA screens mediating the systematic knock-down of distal 1p genes in five 1p-deleted versus five non-1p-deleted neuroblastoma cell lines. We used 3 different siRNAs per gene in a liquid forward approach. After 96h Hoechst stained nuclei were count. Among others, a neuron-related candidate gene has been identified as a potential CYCLOPS. The candidate gene was validated by viability assays, immunocytochemistry and cell cycle analysis via FACS.
Results:
We identified many potential CYCLOPS genes mapping on the distal end of chromosome arm 1p. One of these genes is involved in neuronal and embryonic development and has been further validated. Knock-down of the gene impaired cell viability in 1p-deleted cell lines but did not in 1p-non-deleted cells. G1/G0 phase arrest with corresponding S phase decrease was observed in both 1p-deleted and 1p-non-deleted cells. Additionally, neurite-like outgrowth could be observed in 1p-non-deleted cells indicating an induction of differentiation.
Conclusion:
This study identified a candidate CYCLOPS gene in neuroblastoma. Heterozygous deletions of chromosome arm 1p are also frequently observed in other cancers including melanoma, colorectal and breast cancer. We hypothesize that this proof-of-principle opens a new therapeutic window for tumors harbouring a heterozygous deletion of our candidate gene or other cell essential genes on chromosome arm 1p.
Citation Format: Alica Torkov, Kai-Oliver Henrich, Chunxuan Shao, Moritz Gartlgruber, Frank Westermann. Blinding the CYCLOPS - Cancer vulnerabilities unveiled by genomic loss [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1426. doi:10.1158/1538-7445.AM2017-1426
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Denecker G, Claeys S, Lambertz I, Janssens E, Vanhauwaert S, Decaesteker B, Maerken TV, Wilde BD, Laureys G, Althoff K, Schulte J, Demoulin JB, Roberts SS, Bate-Eya L, Molenaar JJ, Westermann F, Preter KD, Speleman F. Abstract 5815: The HBP1 tumor suppressor is a negative epigenetic regulator of MYCN driven neuroblastoma through interaction with the PRC2 complex. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
MYCN is a key driver in initiation and progression of neuroblastoma (NB) and represents a major target for novel drug strategies. We previously reported that the MYC repressor gene HBP1 was down regulated by mutant ALK via the PI3K-AKT-FOXO3 signaling axis1. Here, we further demonstrate that HBP1 upregulation suppresses proliferation of neuroblastoma cells by decreasing the MYCN signaling pathway. HBP1 levels were also shown to be repressed in neuroblastoma cells through MYC/MYCN driven upregulation of the miR-17~92 cluster, indicating that MYCN and mutant ALK both act to inhibit HBP1 expression in NB. Next, we tested the green tea polyphenol epigallocatechin gallate (EGCG), known to upregulate HBP1, and the BET inhibitor JQ1, which represses MYCN activity in neuroblastoma cells, and showed in vitro and in vivo synergistic effects on cell viability and tumor growth. Treatment with the PI3K/mTOR dual inhibitor BEZ-235 together with JQ1 also showed very strong synergistic effects. Further dissection of the HBP1 regulome using Gene Set Enrichment Analysis (GSEA) and iRegulon analysis (http://iregulon.aertslab.org) allowed identification of the PRC2 component SUZ12 as a central node in HBP1 regulated signaling, mainly through controlling the repression of MYCN regulated genes. In keeping with this finding, GSEA analysis of our HBP1 overexpression data set revealed also strong enrichment for genes that are differentially expressed upon EZH2 inhibition in neuroblastoma cells. Because HBP1 has previously been shown to interact with HDAC, we tested the effects of the HDAC inhibitors vorinostat and panobinostat as single agents and in combination with BEZ-235. Both combinations showed a strong synergistic effect on cell viability. The molecular mechanism of this synergism will be explored through RNAseq expression analysis. We conclude that HBP1 is a crucial component in MYCN controlled repression of gene activity through PRC2 interaction and demonstrate novel opportunities for precision drugging of MYCN overexpressing NB cells. 1Lambertz et al. Clin Cancer Res. (2015)
Citation Format: Geertrui Denecker, Shana Claeys, Irina Lambertz, Els Janssens, Suzanne Vanhauwaert, Bieke Decaesteker, Tom Van Maerken, Bram De Wilde, Genevieve Laureys, Kristina Althoff, Johannes Schulte, Jean-Baptiste Demoulin, Stephen S. Roberts, Laurel Bate-Eya, Jan J. Molenaar, Frank Westermann, Katleen De Preter, Frank Speleman. The HBP1 tumor suppressor is a negative epigenetic regulator of MYCN driven neuroblastoma through interaction with the PRC2 complex [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5815. doi:10.1158/1538-7445.AM2017-5815
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Affiliation(s)
| | - Shana Claeys
- 1Center for Medical Genetics Ghent, Ghent, Belgium
| | | | - Els Janssens
- 1Center for Medical Genetics Ghent, Ghent, Belgium
| | | | | | | | | | | | | | | | | | | | - Laurel Bate-Eya
- 6Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Jan J. Molenaar
- 6Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
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Dreidax D, Gartlgruber M, Steinhauser S, Savelyeva L, Schwessinger R, Toprak U, Ha N, Juraeva D, Peifer M, Fischer M, Gröschel S, Henrich KO, Park YG, Brors B, Schlesner M, Herrmann C, Westermann F. Abstract 1023: Activation of proto-oncogenes by enhancer-hijacking in high-risk neuroblastoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Neuroblastoma (NB), a neural crest-derived tumor of the sympathetic nervous system, is the most common extracranial solid tumor in children. We have previously shown that genomic rearrangements activate proto-oncogenic telomerase by juxtaposing active enhancer elements to the TERT gene in a large fraction of high-risk NBs. In the present study, we applied a global approach integrating whole genome sequencing (WGS), Chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) data of NB cells and tumors to identify further key oncogenes activated by enhancer-hijacking in NB.
Methods: WGS was applied to search for structural rearrangements in 120 NB tumors and five NB cell lines. Corresponding RNA-seq data were used to discover mono-allelic and/or outlier expression of candidate genes potentially involved in enhancer hijacking events. ChIP-seq of 34 NB tumors and 17 NB cell lines was applied to identify active enhancer elements in NB. Circular chromatin conformation capture sequencing (4C-seq) was used to confirm physical promoter-enhancer interactions in NB cell lines.
Results: WGS analyses revealed that chromosomal rearrangements are common events in NB tumors and cell lines and frequently affect regions harboring proto-oncogenes and lineage specific enhancers. ChIP-seq analyses of the chromatin mark histone 3 lysine 27 acetylation (H3K27ac), surrogate for enhancer activity, confirmed that these rearrangements recurrently juxtapose active enhancer elements to oncogenes including MYCN and MYC in NB. Intriguingly, quantification of H3K27ac ChIP-seq profiles uncovered that the enhancer elements translocated to MYC were among the most active ones within the respective epigenomes. 4C-seq analyses proofed physical interactions between translocated enhancer elements and promoters of the respective oncogenes, which is in line with their elevated expression in rearranged cases.
Conclusions: Our study reveals that structural rearrangements in high-risk neuroblastoma frequently juxtapose strong enhancers to key oncogenes, including MYCN and MYC, leading to physical promoter-enhancer interactions which likely drive overexpression of the oncogenes observed in rearranged cases. The common mechanism of oncogene activation by enhancer-hijacking may open a therapeutic window for epigenetic drugs including BET or CDK7 inhibitors in high-risk NBs.
Citation Format: Daniel Dreidax, Moritz Gartlgruber, Sebastian Steinhauser, Larisa Savelyeva, Ron Schwessinger, Umut Toprak, Nati Ha, Dilafruz Juraeva, Martin Peifer, Matthias Fischer, Stefan Gröschel, Kai-Oliver Henrich, Young-Gyu Park, Benedikt Brors, Matthias Schlesner, Carl Herrmann, Frank Westermann. Activation of proto-oncogenes by enhancer-hijacking in high-risk neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1023. doi:10.1158/1538-7445.AM2017-1023
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Affiliation(s)
- Daniel Dreidax
- 1German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | | | | | - Umut Toprak
- 1German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nati Ha
- 1German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | | | | | | | - Young-Gyu Park
- 1German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benedikt Brors
- 1German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Carl Herrmann
- 1German Cancer Research Center (DKFZ), Heidelberg, Germany
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Layer JP, Kronmüller MT, Quast T, van den Boorn-Konijnenberg D, Effern M, Hinze D, Althoff K, Schramm A, Westermann F, Peifer M, Hartmann G, Tüting T, Kolanus W, Fischer M, Schulte J, Hölzel M. Amplification of N-Myc is associated with a T-cell-poor microenvironment in metastatic neuroblastoma restraining interferon pathway activity and chemokine expression. Oncoimmunology 2017; 6:e1320626. [PMID: 28680756 DOI: 10.1080/2162402x.2017.1320626] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/26/2017] [Accepted: 04/13/2017] [Indexed: 01/05/2023] Open
Abstract
Immune checkpoint inhibitors have significantly improved the treatment of several cancers. T-cell infiltration and the number of neoantigens caused by tumor-specific mutations are correlated to favorable responses in cancers with a high mutation load. Accordingly, checkpoint immunotherapy is thought to be less effective in tumors with low mutation frequencies such as neuroblastoma, a neuroendocrine tumor of early childhood with poor outcome of the high-risk disease group. However, spontaneous regressions and paraneoplastic syndromes seen in neuroblastoma patients suggest substantial immunogenicity. Using an integrative transcriptomic approach, we investigated the molecular characteristics of T-cell infiltration in primary neuroblastomas as an indicator of pre-existing immune responses and potential responsiveness to checkpoint inhibition. Here, we report that a T-cell-poor microenvironment in primary metastatic neuroblastomas is associated with genomic amplification of the MYCN (N-Myc) proto-oncogene. These tumors exhibited lower interferon pathway activity and chemokine expression in line with reduced immune cell infiltration. Importantly, we identified a global role for N-Myc in the suppression of interferon and pro-inflammatory pathways in human and murine neuroblastoma cell lines. N-Myc depletion potently enhanced targeted interferon pathway activation by a small molecule agonist of the cGAS-STING innate immune pathway. This promoted chemokine expression including Cxcl10 and T-cell recruitment in microfluidics migration assays. Hence, our data suggest N-Myc inhibition plus targeted IFN activation as adjuvant strategy to enforce cytotoxic T-cell recruitment in MYCN-amplified neuroblastomas.
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Affiliation(s)
- Julian P Layer
- Unit for RNA Biology, Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Marie T Kronmüller
- Division of Molecular Immunology and Cell Biology, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Thomas Quast
- Division of Molecular Immunology and Cell Biology, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | | | - Maike Effern
- Unit for RNA Biology, Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany.,Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Hinze
- Unit for RNA Biology, Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Kristina Althoff
- Pediatric Oncology and Hematology, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Alexander Schramm
- Pediatric Oncology and Hematology, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Molecular Oncology, Internal Medicine/Cancer Research Unit, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Frank Westermann
- Neuroblastoma Genomics B087, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Peifer
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Gunther Hartmann
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Thomas Tüting
- Laboratory of Experimental Dermatology, Department of Dermatology, University of Magdeburg, Magdeburg, Germany.,Laboratory of Experimental Dermatology, Department of Dermatology, University of Bonn, Bonn, Germany
| | - Waldemar Kolanus
- Division of Molecular Immunology and Cell Biology, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Matthias Fischer
- Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany.,Department of Experimental Pediatric Hematology and Oncology, University of Cologne, Cologne, Germany.,Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Johannes Schulte
- Department of Pediatric Hematology, Oncology and SCT, Charité - University Hospital Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | - Michael Hölzel
- Unit for RNA Biology, Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
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Bulashevska S, Priest C, Speicher D, Zimmermann J, Westermann F, Cremers AB. SwitchFinder - a novel method and query facility for discovering dynamic gene expression patterns. BMC Bioinformatics 2016; 17:532. [PMID: 27978814 PMCID: PMC5160026 DOI: 10.1186/s12859-016-1391-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 11/29/2016] [Indexed: 12/20/2022] Open
Abstract
Background Biological systems and processes are highly dynamic. To gain insights into their functioning time-resolved measurements are necessary. Time-resolved gene expression data captures temporal behaviour of the genes genome-wide under various biological conditions: in response to stimuli, during cell cycle, differentiation or developmental programs. Dissecting dynamic gene expression patterns from this data may shed light on the functioning of the gene regulatory system. The present approach facilitates this discovery. The fundamental idea behind it is the following: there are change-points (switches) in the gene behaviour separating intervals of increasing and decreasing activity, whereas the intervals may have different durations. Elucidating the switch-points is important for the identification of biologically meanigfull features and patterns of the gene dynamics. Results We developed a statistical method, called SwitchFinder, for the analysis of time-series data, in particular gene expression data, based on a change-point model. Fitting the model to the gene expression time-courses indicates switch-points between increasing and decreasing activities of each gene. Two types of the model - based on linear and on generalized logistic function - were used to capture the data between the switch-points. Model inference was facilitated with the Bayesian methodology using Markov chain Monte Carlo (MCMC) technique Gibbs sampling. Further on, we introduced features of the switch-points: growth, decay, spike and cleft, which reflect important dynamic aspects. With this, the gene expression profiles are represented in a qualitative manner - as sets of the dynamic features at their onset-times. We developed a Web application of the approach, enabling to put queries to the gene expression time-courses and to deduce groups of genes with common dynamic patterns. SwitchFinder was applied to our original data - the gene expression time-series measured in neuroblastoma cell line upon treatment with all-trans retinoic acid (ATRA). The analysis revealed eight patterns of the gene expression responses to ATRA, indicating the induction of the BMP, WNT, Notch, FGF and NTRK-receptor signaling pathways involved in cell differentiation, as well as the repression of the cell-cycle related genes. Conclusions SwitchFinder is a novel approach to the analysis of biological time-series data, supporting inference and interactive exploration of its inherent dynamic patterns, hence facilitating biological discovery process. SwitchFinder is freely available at https://newbioinformatics.eu/switchfinder. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1391-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Svetlana Bulashevska
- B-IT Bonn-Aachen International Center for Information Technology, University of Bonn, Dahlmannstr. 2, Bonn, 53113, Germany.
| | - Colin Priest
- Sigma Plus Consulting Pty Ltd, Crows Nest, 2065, NSW, Australia
| | - Daniel Speicher
- B-IT Bonn-Aachen International Center for Information Technology, University of Bonn, Dahlmannstr. 2, Bonn, 53113, Germany.,Institute of Computer Science, University of Bonn, Roemerstr. 164, Bonn, 53117, Germany
| | - Jörg Zimmermann
- B-IT Bonn-Aachen International Center for Information Technology, University of Bonn, Dahlmannstr. 2, Bonn, 53113, Germany.,Institute of Computer Science, University of Bonn, Roemerstr. 164, Bonn, 53117, Germany
| | - Frank Westermann
- Neuroblastoma Genomics Group, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Armin B Cremers
- B-IT Bonn-Aachen International Center for Information Technology, University of Bonn, Dahlmannstr. 2, Bonn, 53113, Germany.,Institute of Computer Science, University of Bonn, Roemerstr. 164, Bonn, 53117, Germany
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Michaelis M, Agha B, Rothweiler F, Loeschmann N, Voges Y, Westermann F, Wass M, Cinatl J. Flubendazole as potential anti-neuroblastoma therapy option. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)32725-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Duffy DJ, Krstic A, Halasz M, Schwarzl T, Fey D, Iljin K, Mehta JP, Killick K, Whilde J, Turriziani B, Haapa-Paananen S, Fey V, Fischer M, Westermann F, Henrich KO, Bannert S, Higgins DG, Kolch W. Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma. Oncotarget 2016; 6:43182-201. [PMID: 26673823 PMCID: PMC4791225 DOI: 10.18632/oncotarget.6568] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 11/23/2015] [Indexed: 12/12/2022] Open
Abstract
Despite intensive study, many mysteries remain about the MYCN oncogene's functions. Here we focus on MYCN's role in neuroblastoma, the most common extracranial childhood cancer. MYCN gene amplification occurs in 20% of cases, but other recurrent somatic mutations are rare. This scarcity of tractable targets has hampered efforts to develop new therapeutic options. We employed a multi-level omics approach to examine MYCN functioning and identify novel therapeutic targets for this largely un-druggable oncogene. We used systems medicine based computational network reconstruction and analysis to integrate a range of omic techniques: sequencing-based transcriptomics, genome-wide chromatin immunoprecipitation, siRNA screening and interaction proteomics, revealing that MYCN controls highly connected networks, with MYCN primarily supressing the activity of network components. MYCN's oncogenic functions are likely independent of its classical heterodimerisation partner, MAX. In particular, MYCN controls its own protein interaction network by transcriptionally regulating its binding partners. Our network-based approach identified vulnerable therapeutically targetable nodes that function as critical regulators or effectors of MYCN in neuroblastoma. These were validated by siRNA knockdown screens, functional studies and patient data. We identified β-estradiol and MAPK/ERK as having functional cross-talk with MYCN and being novel targetable vulnerabilities of MYCN-amplified neuroblastoma. These results reveal surprising differences between the functioning of endogenous, overexpressed and amplified MYCN, and rationalise how different MYCN dosages can orchestrate cell fate decisions and cancerous outcomes. Importantly, this work describes a systems-level approach to systematically uncovering network based vulnerabilities and therapeutic targets for multifactorial diseases by integrating disparate omic data types.
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Affiliation(s)
- David J Duffy
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, USA
| | - Aleksandar Krstic
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Melinda Halasz
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Thomas Schwarzl
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,European Molecular Biology Laboratory (EMBL), Meyerhofstraße, Heidelberg, Germany
| | - Dirk Fey
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | | | - Jai Prakash Mehta
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Kate Killick
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Jenny Whilde
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | | | | | - Vidal Fey
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Matthias Fischer
- Department of Paediatric Haematology and Oncology and Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Frank Westermann
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Bannert
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Desmond G Higgins
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
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50
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Henrich KO, Bender S, Saadati M, Dreidax D, Gartlgruber M, Shao C, Herrmann C, Wiesenfarth M, Parzonka M, Wehrmann L, Fischer M, Duffy DJ, Bell E, Torkov A, Schmezer P, Plass C, Höfer T, Benner A, Pfister SM, Westermann F. Integrative Genome-Scale Analysis Identifies Epigenetic Mechanisms of Transcriptional Deregulation in Unfavorable Neuroblastomas. Cancer Res 2016; 76:5523-37. [PMID: 27635046 DOI: 10.1158/0008-5472.can-15-2507] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 05/29/2016] [Indexed: 11/16/2022]
Abstract
The broad clinical spectrum of neuroblastoma ranges from spontaneous regression to rapid progression despite intensive multimodal therapy. This diversity is not fully explained by known genetic aberrations, suggesting the possibility of epigenetic involvement in pathogenesis. In pursuit of this hypothesis, we took an integrative approach to analyze the methylomes, transcriptomes, and copy number variations in 105 cases of neuroblastoma, complemented by primary tumor- and cell line-derived global histone modification analyses and epigenetic drug treatment in vitro We found that DNA methylation patterns identify divergent patient subgroups with respect to survival and clinicobiologic variables, including amplified MYCN Transcriptome integration and histone modification-based definition of enhancer elements revealed intragenic enhancer methylation as a mechanism for high-risk-associated transcriptional deregulation. Furthermore, in high-risk neuroblastomas, we obtained evidence for cooperation between PRC2 activity and DNA methylation in blocking tumor-suppressive differentiation programs. Notably, these programs could be re-activated by combination treatments, which targeted both PRC2 and DNA methylation. Overall, our results illuminate how epigenetic deregulation contributes to neuroblastoma pathogenesis, with novel implications for its diagnosis and therapy. Cancer Res; 76(18); 5523-37. ©2016 AACR.
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Affiliation(s)
- Kai-Oliver Henrich
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany. k.henrich@dkfz
| | - Sebastian Bender
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany & Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Germany
| | - Maral Saadati
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Daniel Dreidax
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Moritz Gartlgruber
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Chunxuan Shao
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany
| | - Carl Herrmann
- Division of Theoretical Bioinformatics, German Cancer Research Center, Institute of Pharmacy and Molecular Biotechnology, Bioquant, University of Heidelberg, Germany
| | - Manuel Wiesenfarth
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Martha Parzonka
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Lea Wehrmann
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Matthias Fischer
- Department of Pediatric Oncology, University Children's Hospital, and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - David J Duffy
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Emma Bell
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Alica Torkov
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany
| | - Peter Schmezer
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany & Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Germany
| | - Frank Westermann
- Neuroblastoma Genomics B087, German Cancer Research Center, Heidelberg, Germany. k.henrich@dkfz
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