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Chicard M, Iddir Y, Masliah Planchon J, Combaret V, Attignon V, Saint-Charles A, Frappaz D, Faure-Conter C, Beccaria K, Varlet P, Geoerger B, Baulande S, Pierron G, Bouchoucha Y, Doz F, Delattre O, Waterfall JJ, Bourdeaut F, Schleiermacher G. Cell-Free DNA Extracted from CSF for the Molecular Diagnosis of Pediatric Embryonal Brain Tumors. Cancers (Basel) 2023; 15:3532. [PMID: 37444642 DOI: 10.3390/cancers15133532] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Liquid biopsies are revolutionary tools used to detect tumor-specific genetic alterations in body fluids, including the use of cell-free DNA (cfDNA) for molecular diagnosis in cancer patients. In brain tumors, cerebrospinal fluid (CSF) cfDNA might be more informative than plasma cfDNA. Here, we assess the use of CSF cfDNA in pediatric embryonal brain tumors (EBT) for molecular diagnosis. METHODS The CSF cfDNA of pediatric patients with medulloblastoma (n = 18), ATRT (n = 3), ETMR (n = 1), CNS NB FOXR2 (n = 2) and pediatric EBT NOS (n = 1) (mean cfDNA concentration 48 ng/mL; range 4-442 ng/mL) and matched tumor genomic DNA were sequenced by WES and/or a targeted sequencing approach to determine single-nucleotide variations (SNVs) and copy number alterations (CNA). A specific capture covering transcription start sites (TSS) of genes of interest was also used for nucleosome footprinting in CSF cfDNA. RESULTS 15/25 CSF cfDNA samples yielded informative results, with informative CNA and SNVs in 11 and 15 cases, respectively. For cases with paired tumor and CSF cfDNA WES (n = 15), a mean of 83 (range 1-160) shared SNVs were observed, including SNVs in classical medulloblastoma genes such as SMO and KMT2D. Interestingly, tumor-specific SNVs (mean 18; range 1-62) or CSF-specific SNVs (mean 5; range 0-25) were also observed, suggesting clonal heterogeneity. The TSS panel resulted in differential coverage profiles across all 112 studied genes in 7 cases, indicating distinct promoter accessibility. CONCLUSION CSF cfDNA sequencing yielded informative results in 60% (15/25) of all cases, with informative results in 83% (15/18) of all cases analyzed by WES. These results pave the way for the implementation of these novel approaches for molecular diagnosis and minimal residual disease monitoring.
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Affiliation(s)
- Mathieu Chicard
- Recherche Translationelle en Oncologie Pédiatrique (RTOP), INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, Department of Translational Research, Institut Curie Research Center, PSL Research University, 75005 Paris, France
| | - Yasmine Iddir
- Recherche Translationelle en Oncologie Pédiatrique (RTOP), INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, Department of Translational Research, Institut Curie Research Center, PSL Research University, 75005 Paris, France
| | - Julien Masliah Planchon
- Unité de Génétique Somatique, Service de Génétique, Institut Curie Hospital Group, 75005 Paris, France
| | - Valérie Combaret
- Plateforme de Génomique des Cancers, Centre Léon Bérard, 69008 Lyon, France
- Laboratoire de Recherche Translationnelle, Centre Léon-Bérard, 69373 Lyon, France
| | - Valéry Attignon
- Plateforme de Génomique des Cancers, Centre Léon Bérard, 69008 Lyon, France
- Laboratoire de Recherche Translationnelle, Centre Léon-Bérard, 69373 Lyon, France
| | - Alexandra Saint-Charles
- Recherche Translationelle en Oncologie Pédiatrique (RTOP), INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, Department of Translational Research, Institut Curie Research Center, PSL Research University, 75005 Paris, France
| | - Didier Frappaz
- Department of Pediatric Clinical Trials and Department of Pediatric Neuro-Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, 69008 Lyon, France
| | - Cécile Faure-Conter
- Department of Pediatric Clinical Trials and Department of Pediatric Neuro-Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, 69008 Lyon, France
| | - Kévin Beccaria
- Department of Pediatric Neurosurgery, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris-Université Paris Cité, 75015 Paris, France
| | - Pascale Varlet
- GHU Psychiatrie et Neurosciences, Site Sainte-Anne, 75014 Paris, France
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, 94805 Villejuif, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, 75005 Paris, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service de Génétique, Institut Curie Hospital Group, 75005 Paris, France
| | - Yassine Bouchoucha
- SIREDO Integrated Pediatric Oncology Center, Institut Curie Hospital Group, 75005 Paris, France
| | - François Doz
- SIREDO Integrated Pediatric Oncology Center, Institut Curie Hospital Group, 75005 Paris, France
- Faculty of Medicine, Université Paris Cité, 75005 Paris, France
| | - Olivier Delattre
- SIREDO Integrated Pediatric Oncology Center, Institut Curie Hospital Group, 75005 Paris, France
- Diversity and Plasticity of Childhood Tumors Laboratory, INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, Institut Curie Research Center, PSL Research University, 75005 Paris, France
| | - Joshua J Waterfall
- Integrative Functional Genomics of Cancer Laboratory, INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, PSL Research University, 75005 Paris, France
- Department of Translational Research, Institut Curie Research Center, PSL Research University, 75005 Paris, France
| | - Franck Bourdeaut
- Recherche Translationelle en Oncologie Pédiatrique (RTOP), INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, Department of Translational Research, Institut Curie Research Center, PSL Research University, 75005 Paris, France
- SIREDO Integrated Pediatric Oncology Center, Institut Curie Hospital Group, 75005 Paris, France
| | - Gudrun Schleiermacher
- Recherche Translationelle en Oncologie Pédiatrique (RTOP), INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, Department of Translational Research, Institut Curie Research Center, PSL Research University, 75005 Paris, France
- SIREDO Integrated Pediatric Oncology Center, Institut Curie Hospital Group, 75005 Paris, France
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Gopisetty A, Federico A, Surdez D, Iddir Y, Zaidi S, Saint-Charles A, Waterfall J, Saberi-Ansari E, Wierzbinska J, Schlicker A, Mack N, Schwalm B, Previti C, Weiser L, Buchhalter I, Böttcher AL, Sill M, Autry R, Estermann F, Jones D, Volckmann R, Zwijnenburg D, Eggert A, Heidenreich O, Iradier F, Jeremias I, Kovar H, Klusmann JH, Debatin KM, Bomken S, Hamerlik P, Hattersley M, Witt O, Chesler L, Mackay A, Gojo J, Cairo S, Schueler J, Schulte J, Geoerger B, Molenaar JJ, Shields DJ, Caron HN, Vassal G, Stancato LF, Pfister SM, Jaeger N, Koster J, Kool M, Schleiermacher G. Abstract 234: ITCC-P4: Genomic profiling and analyses of pediatric patient tumor and patient-derived xenograft (PDX) models for high throughput in vivo testing. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-234] [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: 04/07/2023]
Abstract
Abstract
Advancements in state-of-the-art molecular profiling techniques have resulted in better understanding of pediatric cancers and driver events. It has become apparent that pediatric cancers are significantly more heterogeneous than previously thought as evidenced by the number of novel entities and subtypes that have been identified with distinct molecular and clinical characteristics. For most of these newly recognized entities there are extremely limited treatment options available. The ITCC-P4 consortium is an international collaboration between several European academic centers and pharmaceutical companies, with the overall aim to establish a sustainable platform of >400 molecularly well-characterized PDX models of high-risk pediatric cancers, their tumors and matching controls and to use the PDX models for in vivo testing of novel mechanism-of-action based treatments. Currently, 251 models are fully characterized, including 182 brain and 69 non-brain PDX models, representing 112 primary models, 92 relapse, 42 metastasis and 4 progressions under treatment models. Using low coverage whole-genome and whole exome sequencing, somatic mutation calling, DNA copy number and methylation analysis we aim to define genetic features in our PDX models and estimate the molecular fidelity of PDX models compared to their patient tumor. Based on DNA methylation profiling we identified 43 different tumor subgroups within 18 cancer entities. Mutational landscape analysis identified key somatic and germline oncogenic drivers. Ependymoma PDX models displayed the C11orf95-RELA fusion event, YAP1, C11orf95 and RELA structural variants. Medulloblastoma models were driven by MYCN, TP53, GLI2, SUFU and PTEN. High-grade glioma samples showed TP53, ATRX, MYCN and PIK3CA somatic SNVs, along with focal deletions in CDKN2A in chromosome 9. Neuroblastoma models were enriched for ALK SNVs and/or MYCN focal amplification, ATRX SNVs and CDKN2A/B deletions. Tumor mutational burden across entities and copy number analysis was performed to identify allele-specific copy number detection in tumor-normal pairs. Large chromosomal aberrations (deletions, duplications) detected in the PDX models were concurrent with molecular alterations frequently observed in each tumor type -isochromosome 17 was detected in 5 medulloblastoma models, while deletion of chromosome arm 1p or gain of parts of 17q in neuroblastomas which correlate with tumor progression. We observe clonal evolution of somatic variants not only in certain PDX-tumor pairs but also between disease states. The multi-omics approach in this study provides insight into the mutational landscape and patterns of the PDX models thus providing an overview of molecular mechanisms facilitating the identification and prioritization of oncogenic drivers and potential biomarkers for optimal treatment therapies.
Citation Format: Apurva Gopisetty, Aniello Federico, Didier Surdez, Yasmine Iddir, Sakina Zaidi, Alexandra Saint-Charles, Joshua Waterfall, Elnaz Saberi-Ansari, Justyna Wierzbinska, Andreas Schlicker, Norman Mack, Benjamin Schwalm, Christopher Previti, Lena Weiser, Ivo Buchhalter, Anna-Lisa Böttcher, Martin Sill, Robert Autry, Frank Estermann, David Jones, Richard Volckmann, Danny Zwijnenburg, Angelika Eggert, Olaf Heidenreich, Fatima Iradier, Irmela Jeremias, Heinrich Kovar, Jan-Henning Klusmann, Klaus-Michael Debatin, Simon Bomken, Petra Hamerlik, Maureen Hattersley, Olaf Witt, Louis Chesler, Alan Mackay, Johannes Gojo, Stefano Cairo, Julia Schueler, Johannes Schulte, Birgit Geoerger, Jan J. Molenaar, David J. Shields, Hubert N. Caron, Gilles Vassal, Louis F. Stancato, Stefan M. Pfister, Natalie Jaeger, Jan Koster, Marcel Kool, Gudrun Schleiermacher. ITCC-P4: Genomic profiling and analyses of pediatric patient tumor and patient-derived xenograft (PDX) models for high throughput in vivo testing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 234.
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Affiliation(s)
- Apurva Gopisetty
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Aniello Federico
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Didier Surdez
- 2INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Z, Paris, France
| | - Yasmine Iddir
- 2INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Z, Paris, France
| | - Sakina Zaidi
- 2INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Z, Paris, France
| | - Alexandra Saint-Charles
- 2INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Z, Paris, France
| | - Joshua Waterfall
- 2INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Z, Paris, France
| | - Elnaz Saberi-Ansari
- 2INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Z, Paris, France
| | - Justyna Wierzbinska
- 3Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany, Berlin, Germany
| | - Andreas Schlicker
- 3Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany, Berlin, Germany
| | - Norman Mack
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Benjamin Schwalm
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Christopher Previti
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Lena Weiser
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Ivo Buchhalter
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Anna-Lisa Böttcher
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Martin Sill
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Robert Autry
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Frank Estermann
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - David Jones
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Richard Volckmann
- 4Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands, Amsterdam, Netherlands
| | - Danny Zwijnenburg
- 4Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands, Amsterdam, Netherlands
| | - Angelika Eggert
- 5Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Berlin, Germany, Berlin, Germany
| | - Olaf Heidenreich
- 6Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Translational and Clinical Research Institute, Newcastle University and The Great North Children's Hospital, Newcastle upon Tyne, United Kingdom, Utrecht, Netherlands
| | - Fatima Iradier
- 7Eli Lilly and Company, Lilly SAU, Alcobendas, Spain., Alcobendas, Spain
| | - Irmela Jeremias
- 8Research 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), Muni, Munich, Germany
| | - Heinrich Kovar
- 9Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna, Austria, Vienna, Austria
| | - Jan-Henning Klusmann
- 10Department of Pediatrics I, Martin-Luther-University Halle-Wittenberg, Halle, Germany, Halle, Germany
| | - Klaus-Michael Debatin
- 11Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany, Ulm, Germany
| | - Simon Bomken
- 12Translational and Clinical Research Institute, Newcastle University and The Great North Children's Hospital, Newcastle upon Tyne, United Kingdom, Newcastle upon Tyne, United Kingdom
| | - Petra Hamerlik
- 13AstraZeneca, R&D, Cambridge, United Kingdom, Cambridge, United Kingdom
| | | | - Olaf Witt
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Louis Chesler
- 15Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom, London, United Kingdom
| | - Alan Mackay
- 15Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom, London, United Kingdom
| | - Johannes Gojo
- 16German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, 8. Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria, Vienna, Austria
| | - Stefano Cairo
- 17XenTech, 4 rue Pierre Fontaine, Evry-Courcouronnes, France, Evry-Courcouronnes, France
| | - Julia Schueler
- 18Charles River Germany, Freiburg, Germany, Freiburg, Germany
| | - Johannes Schulte
- 5Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Berlin, Germany, Berlin, Germany
| | - Birgit Geoerger
- 19INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, F-94805 France, Villejuif, France
| | - Jan J. Molenaar
- 20Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands, Utrecht, Netherlands
| | - David J. Shields
- 21Pfizer Centers for Therapeutic Innovation, Pfizer Inc., New York, USA, New York, NY
| | | | - Gilles Vassal
- 23Gustave Roussy Cancer Campus, INSERM U1015, Department of Pediatric and Adolescent Oncology, Université Paris-Saclay, Villejuif, France;22. European consortium for Innovative Therapies for Children with Cancer (ITCC), Paris, France, Paris, France
| | | | - Stefan M. Pfister
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Natalie Jaeger
- 1German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg, Germany
| | - Jan Koster
- 4Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands, Amsterdam, Netherlands
| | - Marcel Kool
- 25German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany; Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands, Heidelberg, Germany
| | - Gudrun Schleiermacher
- 2INSERM U830, Équipe Labellisée LNCC, Genetics and Biology of Pediatric Cancers, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Z, Paris, France
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Tucker ER, Jiménez I, Chen L, Bellini A, Gorrini C, Calton E, Gao Q, Che H, Poon E, Jamin Y, Martins Da Costa B, Barker K, Shrestha S, Hutchinson JC, Dhariwal S, Goodman A, Del Nery E, Gestraud P, Bhalshankar J, Iddir Y, Saberi-Ansari E, Saint-Charles A, Geoerger B, Marques Da Costa ME, Pierre-Eugene C, Janoueix-Lerosey I, Decaudin D, Némati F, Carcaboso AM, Surdez D, Delattre O, George SL, Chesler L, Tweddle DA, Schleiermacher G. Combination Therapies Targeting Alk-Aberrant Neuroblastoma in Preclinical Models. Clin Cancer Res 2023; 29:1317-1331. [PMID: 36602782 PMCID: PMC10068437 DOI: 10.1158/1078-0432.ccr-22-2274] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/31/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
BACKGROUND ALK activating mutations are identified in approximately 10% of newly diagnosed neuroblastomas and ALK amplifications in a further 1-2% of cases. Lorlatinib, a third generation ALK inhibitor, will soon be given alongside induction chemotherapy for children with ALK-aberrant neuroblastoma. However, resistance to single agent treatment has been reported and therapies that improve the response duration are urgently required. We studied the preclinical combination of lorlatinib with chemotherapy, or with the MDM2 inhibitor, idasanutlin, as recent data has suggested that ALK inhibitor resistance can be overcome through activation of the p53-MDM2 pathway. AIMS To study the preclinical activity of ALK inhibitors alone and combined with chemotherapy or idasanutlin. METHODS We compared different ALK inhibitors in preclinical models prior to evaluating lorlatinib in combination with chemotherapy or idasanutlin. We developed a triple chemotherapy (CAV: cyclophosphamide, doxorubicin and vincristine) in vivo dosing schedule and applied this to both neuroblastoma genetically engineered mouse models (GEMM) and patient derived xenografts (PDX). RESULTS Lorlatinib in combination with chemotherapy was synergistic in immunocompetent neuroblastoma GEMM. Significant growth inhibition in response to lorlatinib was only observed in the ALK-amplified PDX model with high ALK expression. In this PDX lorlatinib combined with idasanutlin resulted in complete tumor regression and significantly delayed tumor regrowth. CONCLUSION In our preclinical neuroblastoma models, high ALK expression was associated with lorlatinib response alone or in combination with either chemotherapy or idasanutlin. The synergy between MDM2 and ALK inhibition warrants further evaluation of this combination as a potential clinical approach for children with neuroblastoma.
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Affiliation(s)
| | | | - Lindi Chen
- Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | | | | | - Qiong Gao
- Institute of Cancer Research, London, United Kingdom
| | - Harvey Che
- Institute of Cancer Research, London, United Kingdom
| | - Evon Poon
- Institute of Cancer Research, London, United Kingdom
| | - Yann Jamin
- The Institute of Cancer Research, London, London, Surrey, United Kingdom
| | | | - Karen Barker
- The Institute of Cancer Research, London, Sutton, Surrey, United Kingdom
| | | | - J Ciaran Hutchinson
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | | | - Angharad Goodman
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | | | | | | | | | | | - Birgit Geoerger
- Gustave Roussy Cancer Institute, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | | | | | | | | | | | - Angel M Carcaboso
- Institut de Recerca Sant Joan de Deu, Esplugues de Llobregat, Barcelona, Spain
| | | | | | - Sally L George
- The Institute of Cancer Research and Marsden NHS Foundation Trust, Sutton, Surrey, United Kingdom
| | - Louis Chesler
- The Institute of Cancer Research, London, London, Greater London, United Kingdom
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4
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Gopisetty A, Federico A, Surdez D, Saberi-Ansari E, Iddir Y, Saint-Charles A, Waterfall J, Wierzbinska J, Schlicker A, Mack N, Schwalm B, Jones DT, Gojo J, Chesler L, Vassal G, Stancato L, Koster J, Molenaar JJ, Jaeger N, Schleiermacher G, Pfister S, Kool M. EPCO-47. ITCC-P4: GENOMIC PROFILING AND ANALYSES OF PEDIATRIC PATIENT TUMOR AND PATIENT-DERIVED XENOGRAFT (PDX) MODELS FOR HIGH THROUGHPUT IN VIVO TESTING. Neuro Oncol 2022. [PMCID: PMC9660314 DOI: 10.1093/neuonc/noac209.481] [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] Open
Abstract
Abstract
Advancements in state-of-the-art molecular profiling techniques has resulted in better understanding of pediatric cancers and their drivers. Conversely, it also became apparent 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 most newly recognized entities there is no specific treatment available yet. The ITCC-P4 consortium is a collaboration between many academic centers across Europe and several pharmaceutical companies involved in preclinical testing, 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 are fully established, including 87 brain and 253 non-brain tumor models, together representing different tumor types both from primary (113) and relapsed (92)/metastatic disease (42). 252 of these models have been fully molecularly characterized, representing 18 pediatric cancer entities and 43 different subtypes. Using low coverage whole-genome and whole exome sequencing, somatic mutation calling, DNA copy number, transcriptome analysis and methylation profiling we have observed that the molecular profile of most PDX models closely mimics their original tumors. Clonal evolution of somatic variants was only observed in some PDX-tumor pairs or so between disease states. Somatic copy number variant analysis highlights specific alterations for instance MYB, MYC, MYCN, NTRK3, PTEN loss differently distributed between PDX-patient tumor pairs in high-grade gliomas. Overall, our results show that we have established >250 PDX models of solid pediatric cancers, that well represents the disease spectrum and that is currently being used for in vivo testing of standard of care drugs and targeted small molecules. Treatment responses will be directly linked to molecular data to identify potential biomarkers for prioritization or deprioritization of individual, patient-specific specific drugs.
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Affiliation(s)
- Apurva Gopisetty
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg , Baden-Wurttemberg , Germany
| | - Aniello Federico
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany, Heidelberg , Baden-Wurttemberg , 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 , Paris , France
| | - 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 , 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 , 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 , 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 , Paris , France
| | - Justyna Wierzbinska
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany , Berlin , Germany
| | - Andreas Schlicker
- Bayer AG, Pharmaceuticals, Research and Development, Berlin, Germany , Berlin , Germany
| | - Norman Mack
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany , Heidelberg , Germany
| | - Benjamin Schwalm
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany , Heidelberg , Germany
| | - David T Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg University Hospital and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | | | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom , London , United Kingdom
| | - Gilles Vassal
- Department of Clinical Research, Gustave Roussy, Villejuif, France , Paris , France
| | | | - Jan Koster
- Department of Oncogenomics, Amsterdam University Medical Centre, Amsterdam, the Netherlands , Amsterdam , Netherlands
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands , Utrecht , Netherlands
| | - Natalie Jaeger
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany , Heidelberg , Germany
| | - 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 , Paris , France
| | - Stefan Pfister
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany , Heidelberg , Germany
| | - Marcel Kool
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany , Heidelberg , Germany
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5
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Ruhen O, Lak NS, Stutterheim J, Danielli SG, Chicard M, Iddir Y, Saint-Charles A, Di Paolo V, Tombolan L, Gatz SA, Aladowicz E, Proszek P, Jamal S, Stankunaite R, Hughes D, Carter P, Izquierdo E, Wasti A, Chisholm JC, George SL, Pace E, Chesler L, Aerts I, Pierron G, Zaidi S, Delattre O, Surdez D, Kelsey A, Hubank M, Bonvini P, Bisogno G, Di Giannatale A, Schleiermacher G, Schäfer BW, Tytgat GA, Shipley J. Molecular Characterization of Circulating Tumor DNA in Pediatric Rhabdomyosarcoma: A Feasibility Study. JCO Precis Oncol 2022; 6:e2100534. [PMID: 36265118 PMCID: PMC9616639 DOI: 10.1200/po.21.00534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/03/2021] [Revised: 05/17/2022] [Accepted: 08/26/2022] [Indexed: 05/24/2023] Open
Abstract
PURPOSE Rhabdomyosarcomas (RMS) are rare neoplasms affecting children and young adults. Efforts to improve patient survival have been undermined by a lack of suitable disease markers. Plasma circulating tumor DNA (ctDNA) has shown promise as a potential minimally invasive biomarker and monitoring tool in other cancers; however, it remains underexplored in RMS. We aimed to determine the feasibility of identifying and quantifying ctDNA in plasma as a marker of disease burden and/or treatment response using blood samples from RMS mouse models and patients. METHODS We established mouse models of RMS and applied quantitative polymerase chain reaction (PCR) and droplet digital PCR (ddPCR) to detect ctDNA within the mouse plasma. Potential driver mutations, copy-number alterations, and DNA breakpoints associated with PAX3/7-FOXO1 gene fusions were identified in the RMS samples collected at diagnosis. Patient-matched plasma samples collected from 28 patients with RMS before, during, and after treatment were analyzed for the presence of ctDNA via ddPCR, panel sequencing, and/or whole-exome sequencing. RESULTS Human tumor-derived DNA was detectable in plasma samples from mouse models of RMS and correlated with tumor burden. In patients, ctDNA was detected in 14/18 pretreatment plasma samples with ddPCR and 7/7 cases assessed by sequencing. Levels of ctDNA at diagnosis were significantly higher in patients with unfavorable tumor sites, positive nodal status, and metastasis. In patients with serial plasma samples (n = 18), fluctuations in ctDNA levels corresponded to treatment response. CONCLUSION Comprehensive ctDNA analysis combining high sensitivity and throughput can identify key molecular drivers in RMS models and patients, suggesting potential as a minimally invasive biomarker. Preclinical assessment of treatments using mouse models and further patient testing through prospective clinical trials are now warranted.
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Affiliation(s)
- Olivia Ruhen
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Nathalie S.M. Lak
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Experimental Immunohematology, Sanquin, Amsterdam, the Netherlands
| | - Janine Stutterheim
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Experimental Immunohematology, Sanquin, Amsterdam, the Netherlands
| | - Sara G. Danielli
- Department of Oncology and Children's Research Centre, University Children's Hospital, Zurich, Switzerland
| | - Mathieu Chicard
- SiRIC RTOP (Recherche Translationelle en Oncologie Pediatrique), Institut Curie, Paris, France
| | - Yasmine Iddir
- SiRIC RTOP (Recherche Translationelle en Oncologie Pediatrique), Institut Curie, Paris, France
| | - Alexandra Saint-Charles
- SiRIC RTOP (Recherche Translationelle en Oncologie Pediatrique), Institut Curie, Paris, France
| | - Virginia Di Paolo
- Department of Pediatric Haematology/Oncology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lucia Tombolan
- Institute of Pediatric Research, Fondazione Città della Speranza, Padova, Italy
| | - Susanne A. Gatz
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ewa Aladowicz
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Paula Proszek
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Sabri Jamal
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Reda Stankunaite
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Deborah Hughes
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Paul Carter
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Elisa Izquierdo
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Ajla Wasti
- Children & Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Julia C. Chisholm
- Children & Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Sally L. George
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Children & Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Erika Pace
- Children & Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Department of Diagnostic Radiology, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Louis Chesler
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Children & Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Isabelle Aerts
- SiRIC RTOP (Recherche Translationelle en Oncologie Pediatrique), Institut Curie, Paris, France
| | - Gaelle Pierron
- SiRIC RTOP (Recherche Translationelle en Oncologie Pediatrique), Institut Curie, Paris, France
| | - Sakina Zaidi
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, Paris, France
- Bone Sarcoma Research Laboratory, Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Anna Kelsey
- Department of Pediatric Histopathology, Manchester University Foundation Trust, Manchester, United Kingdom
| | - Michael Hubank
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Molecular Diagnostics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Paolo Bonvini
- Institute of Pediatric Research, Fondazione Città della Speranza, Padova, Italy
| | - Gianni Bisogno
- Department of Woman's and Children's Health, Hematology and Oncology Unit, University of Padova, Padova, Italy
| | - Angela Di Giannatale
- Department of Pediatric Haematology/Oncology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Gudrun Schleiermacher
- SiRIC RTOP (Recherche Translationelle en Oncologie Pediatrique), Institut Curie, Paris, France
- Department of Pediatric Oncology, Hospital Group, Institut Curie, Paris, France
| | - Beat W. Schäfer
- Department of Oncology and Children's Research Centre, University Children's Hospital, Zurich, Switzerland
| | - Godelieve A.M. Tytgat
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Experimental Immunohematology, Sanquin, Amsterdam, the Netherlands
| | - Janet Shipley
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
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6
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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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7
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Mathieu C, Iddir Y, Masliah-Planchon J, Combaret V, Saint-Charles A, Baulande S, Delattre O, Waterfall J, Bourdeaut F, Schleiermacher G. TBIO-06. Study of cell free DNA extracted from CSF enables molecular classification of embryonal brain tumors. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.688] [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: 11/14/2022] Open
Abstract
Abstract
Liquid biopsies are revolutionary tools to detect tumour-specific genetic alterations in body fluids. Here, we assess whether the circulating tumor DNA (ctDNA) in Cerebral Spinal Fluid (CSF) could be used for the tumor genetic profiling of pediatric embryonal brain tumors (EBT). Cell free DNA extracted from CSF from 4-5 lumbar puncture droplets from patients with Medulloblastoma (n=18), ATRT (n=3), ETMR(n=1), FOXR2 EBT (n=2) or other pediatric EBT (n=1) (cfDNA mean quantity 48 ng/ml ; range 5.6 - 442 ng/ml) and matched genomic DNA from primary tumors were sequenced by WES (Illumina 100PE) using Nimblegen Medexome Capture. SNVs/mutations were called using GATK-UnifiedGenotyper, GATK-HaplotypeCaller and Samtools. Copy Number profiles were generated with CNVkits. 10/13 cfDNA WES yielded satisfactory depth (>10x). A mean of 466 (range 93-945) SNVs were detected in the primary tumor and 474 (range 18-922) in the CSF. A mean of 416 (range 18-872) commons SNVs were observed between the cfDNA and the primary tumor, comprising classical medulloblastoma genes such as SMO or MLL2. Interestingly, several SNVs were observed either in the tumor only (mean 50 ; range 3-115) or in CSF only (mean 58 ; range 0-148) suggesting a clonal heterogeneity. For 5 cases, Copy Number profiles were also available, allowing the detection of MYCN amplification or 19q13 miRNA cluster amplification. Altogether, we demonstrate the feasibility of WES on CSF with a low input of ctDNA. These results may pave the way for new tumor monitoring tools.
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Alejevski F, Saint-Charles A, Michard-Vanhée C, Martin B, Galant S, Vasiliauskas D, Rouyer F. The HisCl1 histamine receptor acts in photoreceptors to synchronize Drosophila behavioral rhythms with light-dark cycles. Nat Commun 2019; 10:252. [PMID: 30651542 PMCID: PMC6335465 DOI: 10.1038/s41467-018-08116-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 02/27/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023] Open
Abstract
In Drosophila, the clock that controls rest-activity rhythms synchronizes with light-dark cycles through either the blue-light sensitive cryptochrome (Cry) located in most clock neurons, or rhodopsin-expressing histaminergic photoreceptors. Here we show that, in the absence of Cry, each of the two histamine receptors Ort and HisCl1 contribute to entrain the clock whereas no entrainment occurs in the absence of the two receptors. In contrast to Ort, HisCl1 does not restore entrainment when expressed in the optic lobe interneurons. Indeed, HisCl1 is expressed in wild-type photoreceptors and entrainment is strongly impaired in flies with photoreceptors mutant for HisCl1. Rescuing HisCl1 expression in the Rh6-expressing photoreceptors restores entrainment but it does not in other photoreceptors, which send histaminergic inputs to Rh6-expressing photoreceptors. Our results thus show that Rh6-expressing neurons contribute to circadian entrainment as both photoreceptors and interneurons, recalling the dual function of melanopsin-expressing ganglion cells in the mammalian retina.
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Affiliation(s)
- Faredin Alejevski
- Institut des Neurosciences Paris-Saclay, Univ. Paris Sud, CNRS, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Alexandra Saint-Charles
- Institut des Neurosciences Paris-Saclay, Univ. Paris Sud, CNRS, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
- Institut de la Vision, Univ. P. & M. Curie, INSERM, CNRS, Sorbonne Université, Paris, 75012, France
| | - Christine Michard-Vanhée
- Institut des Neurosciences Paris-Saclay, Univ. Paris Sud, CNRS, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Béatrice Martin
- Institut des Neurosciences Paris-Saclay, Univ. Paris Sud, CNRS, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Sonya Galant
- Institut des Neurosciences Paris-Saclay, Univ. Paris Sud, CNRS, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Daniel Vasiliauskas
- Institut des Neurosciences Paris-Saclay, Univ. Paris Sud, CNRS, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - François Rouyer
- Institut des Neurosciences Paris-Saclay, Univ. Paris Sud, CNRS, Université Paris-Saclay, 91190, Gif-sur-Yvette, France.
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Saint-Charles A, Michard-Vanhée C, Alejevski F, Chélot E, Boivin A, Rouyer F. Four of the six Drosophila rhodopsin-expressing photoreceptors can mediate circadian entrainment in low light. J Comp Neurol 2016; 524:2828-44. [PMID: 26972685 DOI: 10.1002/cne.23994] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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: 12/29/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 12/30/2022]
Abstract
Light is the major stimulus for the synchronization of circadian clocks with day-night cycles. The light-driven entrainment of the clock that controls rest-activity rhythms in Drosophila relies on different photoreceptive molecules. Cryptochrome (CRY) is expressed in most brain clock neurons, whereas six different rhodopsins (RH) are present in the light-sensing organs. The compound eye includes outer photoreceptors that express RH1 and inner photoreceptors that each express one of the four rhodopsins RH3-RH6. RH6 is also expressed in the extraretinal Hofbauer-Buchner eyelet, whereas RH2 is only found in the ocelli. In low light, the synchronization of behavioral rhythms relies on either CRY or the canonical rhodopsin phototransduction pathway, which requires the phospholipase C-β encoded by norpA (no receptor potential A). We used norpA(P24) cry(02) double mutants that are circadianly blind in low light and restored NORPA function in each of the six types of photoreceptors, defined as expressing a particular rhodopsin. We first show that the NORPA pathway is less efficient than CRY for synchronizing rest-activity rhythms with delayed light-dark cycles but is important for proper phasing, whereas the two light-sensing pathways can mediate efficient adjustments to phase advances. Four of the six rhodopsin-expressing photoreceptors can mediate circadian entrainment, and all are more efficient for advancing than for delaying the behavioral clock. In contrast, neither RH5-expressing retinal photoreceptors nor RH2-expressing ocellar photoreceptors are sufficient to mediate synchronization through the NORPA pathway. Our results thus reveal different contributions of rhodopsin-expressing photoreceptors and suggest the existence of several circuits for rhodopsin-dependent circadian entrainment. J. Comp. Neurol. 524:2828-2844, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Alexandra Saint-Charles
- Paris-Saclay Institute of Neuroscience, Université Paris Sud, Centre National de la Recherche Scientifque, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Christine Michard-Vanhée
- Paris-Saclay Institute of Neuroscience, Université Paris Sud, Centre National de la Recherche Scientifque, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Faredin Alejevski
- Paris-Saclay Institute of Neuroscience, Université Paris Sud, Centre National de la Recherche Scientifque, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Elisabeth Chélot
- Paris-Saclay Institute of Neuroscience, Université Paris Sud, Centre National de la Recherche Scientifque, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Antoine Boivin
- Paris-Saclay Institute of Neuroscience, Université Paris Sud, Centre National de la Recherche Scientifque, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - François Rouyer
- Paris-Saclay Institute of Neuroscience, Université Paris Sud, Centre National de la Recherche Scientifque, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
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10
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Terrien J, Ambid L, Nibbelink M, Saint-Charles A, Aujard F. Non-shivering thermogenesis activation and maintenance in the aging gray mouse lemur (Microcebus murinus). Exp Gerontol 2010; 45:442-8. [DOI: 10.1016/j.exger.2010.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 02/15/2010] [Accepted: 03/17/2010] [Indexed: 10/19/2022]
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