1
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Hermann AL, Lemelle L, Pierron G, Gauthier A, Nicolas N, Cardoen L, Moalla S, Petit P, Morel B, Ducou Le Pointe H, Hassani A, Fréneaux P, Guillemot D, Carton M, Corradini N, Rome A, Castex MP, Defachelles AS, Schleiermacher G, Berlanga P, Delattre O, Orbach D, Brisse HJ. Imaging characterization of paediatric tumours with the neurotrophic tyrosine receptor kinase fusion transcript. Br J Radiol 2024; 97:734-743. [PMID: 38327010 PMCID: PMC11027258 DOI: 10.1093/bjr/tqae016] [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] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 12/12/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
OBJECTIVES The neurotrophic tyrosine receptor kinase (NTRK) fusion transcript (FT) is a major genetic landmark of infantile fibrosarcoma (IFS) and cellular congenital mesoblastic nephroma (cCMN) but is also described in other tumours. The recent availability of NTRK-targeted drugs enhances the need for better identification. We aimed to describe the anatomic locations and imaging features of tumours with NTRK-FT in children. CASE SERIES Imaging characteristics of NTRK-FT tumours of 41 children (median age: 4 months; 63% <1 year old; range: 0-188) managed between 2001 and 2019 were retrospectively analysed. The tumours were located in the soft tissues (n = 24, including 19 IFS), kidneys (n = 9, including 8 cCMN), central nervous system (CNS) (n = 5), lung (n = 2), and bone (n = 1). The tumours were frequently deep-located (93%) and heterogeneous (71%) with necrotic (53%) or haemorrhagic components (29%). Although inconstant, enlarged intratumoural vessels were a recurrent finding (70%) with an irregular distribution (63%) in the most frequent anatomical locations. CONCLUSION Paediatric NTRK-FT tumours mainly occur in infants with very variable histotypes and locations. Rich and irregular intra-tumoural vascularization are recurrent findings. ADVANCES IN KNOWLEDGE Apart from IFS of soft tissues and cCMN of the kidneys, others NTRK-FT tumours locations have to be known, as CNS tumours. Better knowledge of the imaging characteristics may help guide the pathological and biological identification.
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Affiliation(s)
- Anne-Laure Hermann
- Department of Imaging, Institut Curie, PSL University, Paris, 75005, France
| | - Lauriane Lemelle
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL University, Paris, 75005, France
| | - Gaëlle Pierron
- Department of Somatic Genetics, Institut Curie, PSL University, Paris, 75005, France
| | - Arnaud Gauthier
- Department of Pathology, Institut Curie, PSL University, Paris, 75005, France
| | - Nayla Nicolas
- Department of Imaging, Institut Curie, PSL University, Paris, 75005, France
| | - Liesbeth Cardoen
- Department of Imaging, Institut Curie, PSL University, Paris, 75005, France
| | - Salma Moalla
- Department of Imaging, Gustave Roussy Cancer Center, Villejuif, 94805, France
| | - Philippe Petit
- Department of Imaging, Assistance Publique des Hôpitaux de Marseille, Hôpital de La Timone, Marseille, 13005, France
| | - Baptiste Morel
- Department of Pediatric Radiology, CHRU Hôpitaux de Tours, Tours, 37000, France
| | - Hubert Ducou Le Pointe
- Department of Pediatric Radiology, Assistance Publique des Hôpitaux de Paris, Hôpital Armand Trousseau, Paris, 75012, France
| | - Adnan Hassani
- Department of Pediatric Radiology, CHU Rouen, Rouen, 76000, France
| | - Paul Fréneaux
- Department of Pathology, Institut Curie, PSL University, Paris, 75005, France
| | - Delphine Guillemot
- Department of Somatic Genetics, Institut Curie, PSL University, Paris, 75005, France
| | - Matthieu Carton
- Department of Biostatistics, Institut Curie, PSL University, Paris, 75005, France
| | - Nadège Corradini
- Department of Pediatric Oncology and Hematology, Centre Léon Bérard, Lyon, 69008, France
| | - Angélique Rome
- Department of Pediatric Oncology, Assistance Publique des Hôpitaux de Marseille, Hôpital de la Timone, Marseille, 13005, France
| | - Marie-Pierre Castex
- Department of Pediatric Oncology and Hematology, CHU Toulouse, Toulouse, 31300, France
| | | | - Gudrun Schleiermacher
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL University, Paris, 75005, France
| | - Pablo Berlanga
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Center, INSERM U1015, Université Paris-Saclay, Villejuif, 94805, France
| | - Olivier Delattre
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL University, Paris, 75005, France
- Department of Somatic Genetics, Institut Curie, PSL University, Paris, 75005, France
| | - Daniel Orbach
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL University, Paris, 75005, France
| | - Hervé J Brisse
- Department of Imaging, Institut Curie, PSL University, Paris, 75005, France
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2
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Ruzanov P, Evdokimova V, Pachva MC, Minkovich A, Zhang Z, Langman S, Gassmann H, Thiel U, Orlic-Milacic M, Zaidi SH, Peltekova V, Heisler LE, Sharma M, Cox ME, McKee TD, Zaidi M, Lapouble E, McPherson JD, Delattre O, Radvanyi L, Burdach SE, Stein LD, Sorensen PH. Oncogenic ETS fusions promote DNA damage and proinflammatory responses via pericentromeric RNAs in extracellular vesicles. J Clin Invest 2024; 134:e169470. [PMID: 38530366 PMCID: PMC11060741 DOI: 10.1172/jci169470] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
Aberrant expression of the E26 transformation-specific (ETS) transcription factors characterizes numerous human malignancies. Many of these proteins, including EWS:FLI1 and EWS:ERG fusions in Ewing sarcoma (EwS) and TMPRSS2:ERG in prostate cancer (PCa), drive oncogenic programs via binding to GGAA repeats. We report here that both EWS:FLI1 and ERG bind and transcriptionally activate GGAA-rich pericentromeric heterochromatin. The respective pathogen-like HSAT2 and HSAT3 RNAs, together with LINE, SINE, ERV, and other repeat transcripts, are expressed in EwS and PCa tumors, secreted in extracellular vesicles (EVs), and are highly elevated in plasma of patients with EwS with metastatic disease. High human satellite 2 and 3 (HSAT2,3) levels in EWS:FLI1- or ERG-expressing cells and tumors were associated with induction of G2/M checkpoint, mitotic spindle, and DNA damage programs. These programs were also activated in EwS EV-treated fibroblasts, coincident with accumulation of HSAT2,3 RNAs, proinflammatory responses, mitotic defects, and senescence. Mechanistically, HSAT2,3-enriched cancer EVs induced cGAS-TBK1 innate immune signaling and formation of cytosolic granules positive for double-strand RNAs, RNA-DNA, and cGAS. Hence, aberrantly expressed ETS proteins derepress pericentromeric heterochromatin, yielding pathogenic RNAs that transmit genotoxic stress and inflammation to local and distant sites. Monitoring HSAT2,3 plasma levels and preventing their dissemination may thus improve therapeutic strategies and blood-based diagnostics.
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Affiliation(s)
- Peter Ruzanov
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Manideep C. Pachva
- Department of Molecular Oncology, British Columbia Cancer Research Centre and
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alon Minkovich
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Zhenbo Zhang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sofya Langman
- Department of Molecular Oncology, British Columbia Cancer Research Centre and
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hendrik Gassmann
- Department of Pediatrics, Children’s Cancer Research Center, Kinderklinik München Schwabing, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Uwe Thiel
- Department of Pediatrics, Children’s Cancer Research Center, Kinderklinik München Schwabing, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | | | - Syed H. Zaidi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vanya Peltekova
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Manju Sharma
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Michael E. Cox
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Trevor D. McKee
- STTARR Innovation Centre, Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Pathomics Inc., Toronto, Ontario, Canada
| | - Mark Zaidi
- Pathomics Inc., Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Eve Lapouble
- Unité Génétique Somatique (UGS), Institut Curie, Centre Hospitalier Paris, France
| | - John D. McPherson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Olivier Delattre
- Unité Génétique Somatique (UGS), Institut Curie, Centre Hospitalier Paris, France
- Diversity and Plasticity of Childhood tumors, INSERM U830, Institut Curie Research Center, PSL Research University, Paris, France
| | - Laszlo Radvanyi
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Stefan E.G. Burdach
- Department of Molecular Oncology, British Columbia Cancer Research Centre and
- Department of Pediatrics, Children’s Cancer Research Center, Kinderklinik München Schwabing, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- CCC München Comprehensive Cancer Center, DKTK German Cancer Consortium, Munich, Germany
- Institute of Pathology, Translation Pediatric Cancer Research Action, School of Medicine, Technical University of Munich, Munich, Germany
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Poul H. Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre and
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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3
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Sivori M, Dempsey B, Chettouh Z, Boismoreau F, Ayerdi M, Eymael A, Baulande S, Lameiras S, Coulpier F, Delattre O, Rohrer H, Mirabeau O, Brunet JF. The pelvic organs receive no parasympathetic innervation. eLife 2024; 12:RP91576. [PMID: 38488657 PMCID: PMC10942786 DOI: 10.7554/elife.91576] [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] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
The pelvic organs (bladder, rectum, and sex organs) have been represented for a century as receiving autonomic innervation from two pathways - lumbar sympathetic and sacral parasympathetic - by way of a shared relay, the pelvic ganglion, conceived as an assemblage of sympathetic and parasympathetic neurons. Using single-cell RNA sequencing, we find that the mouse pelvic ganglion is made of four classes of neurons, distinct from both sympathetic and parasympathetic ones, albeit with a kinship to the former, but not the latter, through a complex genetic signature. We also show that spinal lumbar preganglionic neurons synapse in the pelvic ganglion onto equal numbers of noradrenergic and cholinergic cells, both of which therefore serve as sympathetic relays. Thus, the pelvic viscera receive no innervation from parasympathetic or typical sympathetic neurons, but instead from a divergent tail end of the sympathetic chains, in charge of its idiosyncratic functions.
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Affiliation(s)
- Margaux Sivori
- Institut de Biologie de l’ENS (IBENS), Inserm, CNRS, École normale supérieure, PSL Research UniversityParisFrance
| | - Bowen Dempsey
- Faculty of Medicine, Health & Human Sciences, Macquarie University, Macquarie ParkSydneyAustralia
| | - Zoubida Chettouh
- Institut de Biologie de l’ENS (IBENS), Inserm, CNRS, École normale supérieure, PSL Research UniversityParisFrance
| | - Franck Boismoreau
- Institut de Biologie de l’ENS (IBENS), Inserm, CNRS, École normale supérieure, PSL Research UniversityParisFrance
| | - Maïlys Ayerdi
- Institut de Biologie de l’ENS (IBENS), Inserm, CNRS, École normale supérieure, PSL Research UniversityParisFrance
| | - Annaliese Eymael
- Faculty of Medicine, Health & Human Sciences, Macquarie University, Macquarie ParkSydneyAustralia
| | - Sylvain Baulande
- Institut Curie, PSL University, ICGex Next-Generation Sequencing PlatformParisFrance
| | - Sonia Lameiras
- Institut Curie, PSL University, ICGex Next-Generation Sequencing PlatformParisFrance
| | - Fanny Coulpier
- GenomiqueENS, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSLParisFrance
- Inserm U955, Mondor Institute for Biomedical Research (IMRB)CreteilFrance
| | - Olivier Delattre
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors LabParisFrance
| | - Hermann Rohrer
- Institute of Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Neuroscience Center, Goethe UniversityFrankfurt am MainGermany
| | - Olivier Mirabeau
- Institut de Biologie de l’ENS (IBENS), Inserm, CNRS, École normale supérieure, PSL Research UniversityParisFrance
| | - Jean-François Brunet
- Institut de Biologie de l’ENS (IBENS), Inserm, CNRS, École normale supérieure, PSL Research UniversityParisFrance
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4
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Danielli SG, Wurth J, Morice S, Kisele S, Surdez D, Delattre O, Bode PK, Wachtel M, Schafer BW. Evaluation of the role of AXL in fusion-positive pediatric rhabdomyosarcoma identifies the small-molecule inhibitor bemcentinib (BGB324) as potent chemosensitizer. Mol Cancer Ther 2024:735131. [PMID: 38471796 DOI: 10.1158/1535-7163.mct-23-0285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 12/16/2023] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
Rhabdomyosarcoma (RMS) is a highly aggressive pediatric cancer with features of skeletal muscle differentiation. Over 80% of the high-risk patients ultimately fail to respond to chemotherapy treatment, leading to limited therapeutic options and dismal prognostic rates. The lack of response - and subsequent tumor recurrence - is driven in part by stem cell-like cells, the tumor subpopulation that is enriched after treatment, and characterized by expression of the AXL receptor tyrosine kinase (AXL). AXL mediates survival, migration and therapy resistance in several cancer types; however, its function in RMS remains unclear. In this study, we investigated the role of AXL in RMS tumorigenesis, migration and chemotherapy response, and whether targeting of AXL with small molecule inhibitors could potentiate the efficacy of chemotherapy. We show that AXL is expressed in a heterogeneous manner in patient-derived xenografts (PDXs), primary cultures and cell line models of RMS, consistent with its stem-cell-state selectivity. By generating a CRISPR/Cas9 AXL knock-out and overexpressing models, we show that AXL contributes to the migratory phenotype of RMS, but not to chemotherapy resistance. Instead, pharmacological blockade with the AXL inhibitors bemcentinib (BGB324), cabozantinib and NPS-1034 rapidly killed RMS cells in an AXL-independent manner, and augmented the efficacy of the chemotherapeutics vincristine and cyclophosphamide. In vivo administration of the combination of bemcentinib and vincristine exerted strong anti-tumoral activity in a rapidly progressing PDX mouse model, significantly reducing tumor bruden compared to single-agent treatment. Collectively, our data identify bemcentinib as a promising drug to improve chemotherapy efficacy in RMS patients.
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Affiliation(s)
| | - Jakob Wurth
- University Children's Hospital Zurich, Zurich, Zurich, Switzerland
| | | | - Samanta Kisele
- Children's Clinical University Hospital, Zürich, Switzerland
| | | | | | - Peter K Bode
- Kantonsspital Winterthur, Winterthur, Switzerland
| | - Marco Wachtel
- Children's Clinical University Hospital, Zurich, Switzerland
| | - Beat W Schafer
- Children's Clinical University Hospital, Zurich, Switzerland
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5
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Savary C, Luciana L, Huchedé P, Tourbez A, Coquet C, Broustal M, Lopez Gonzalez A, Deligne C, Diot T, Naret O, Costa M, Meynard N, Barbet V, Müller K, Tonon L, Gadot N, Degletagne C, Attignon V, Léon S, Vanbelle C, Bomane A, Rochet I, Mournetas V, Oliveira L, Rinaudo P, Bergeron C, Dutour A, Cordier-Bussat M, Roch A, Brandenberg N, El Zein S, Watson S, Orbach D, Delattre O, Dijoud F, Corradini N, Picard C, Maucort-Boulch D, Le Grand M, Pasquier E, Blay JY, Castets M, Broutier L. Fusion-negative rhabdomyosarcoma 3D organoids to predict effective drug combinations: A proof-of-concept on cell death inducers. Cell Rep Med 2023; 4:101339. [PMID: 38118405 PMCID: PMC10772578 DOI: 10.1016/j.xcrm.2023.101339] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/29/2023] [Accepted: 11/22/2023] [Indexed: 12/22/2023]
Abstract
Rhabdomyosarcoma (RMS) is the main form of pediatric soft-tissue sarcoma. Its cure rate has not notably improved in the last 20 years following relapse, and the lack of reliable preclinical models has hampered the design of new therapies. This is particularly true for highly heterogeneous fusion-negative RMS (FNRMS). Although methods have been proposed to establish FNRMS organoids, their efficiency remains limited to date, both in terms of derivation rate and ability to accurately mimic the original tumor. Here, we present the development of a next-generation 3D organoid model derived from relapsed adult and pediatric FNRMS. This model preserves the molecular features of the patients' tumors and is expandable for several months in 3D, reinforcing its interest to drug combination screening with longitudinal efficacy monitoring. As a proof-of-concept, we demonstrate its preclinical relevance by reevaluating the therapeutic opportunities of targeting apoptosis in FNRMS from a streamlined approach based on transcriptomic data exploitation.
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Affiliation(s)
- Clara Savary
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Léa Luciana
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Paul Huchedé
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Arthur Tourbez
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Claire Coquet
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Maëlle Broustal
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Alejandro Lopez Gonzalez
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Clémence Deligne
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Thomas Diot
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Olivier Naret
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Mariana Costa
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Nina Meynard
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Virginie Barbet
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Kevin Müller
- Université Aix-Marseille, CNRS 7258, INSERM 1068, Institute Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), 13009 Marseille, France
| | - Laurie Tonon
- Synergie Lyon Cancer, Gilles Thomas' Bioinformatics Platform, Centre Léon Bérard, 69008 Lyon, France
| | - Nicolas Gadot
- Anatomopathology Research Platform, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Cyril Degletagne
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Valéry Attignon
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Sophie Léon
- EX-VIVO Platform, Centre de recherche en cancérologie de Lyon (CRCL), Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Christophe Vanbelle
- Plateforme d'Imagerie cellulaire, Centre de recherche en cancérologie de Lyon (CRCL), Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Alexandra Bomane
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Isabelle Rochet
- Multisite Institute of Pathology, Groupement Hospitalier Est du CHU de Lyon, Hôpital Femme-Mère-Enfant, 69677 Bron, France; Department of Pediatric Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, Centre Léon Bérard, 69008 Lyon, France
| | | | | | | | - Christophe Bergeron
- Department of Pediatric Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, Centre Léon Bérard, 69008 Lyon, France
| | - Aurélie Dutour
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Martine Cordier-Bussat
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Aline Roch
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Nathalie Brandenberg
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Sophie El Zein
- Department of Biopathology, Institut Curie, Paris, France
| | - Sarah Watson
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France; INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie, PSL Research University, Paris, France; Medical Oncology Department, Institut Curie, PSL Research University, Paris, France
| | - Daniel Orbach
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France
| | - Olivier Delattre
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France; INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie, PSL Research University, Paris, France
| | - Frédérique Dijoud
- Multisite Institute of Pathology, Groupement Hospitalier Est du CHU de Lyon, Hôpital Femme-Mère-Enfant, 69677 Bron, France
| | - Nadège Corradini
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Pediatric Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, Centre Léon Bérard, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France
| | - Cécile Picard
- Multisite Institute of Pathology, Groupement Hospitalier Est du CHU de Lyon, Hôpital Femme-Mère-Enfant, 69677 Bron, France
| | - Delphine Maucort-Boulch
- Université Lyon 1, 69100 Villeurbanne, France; Hospices Civils de Lyon, Pôle Santé Publique, Service de Biostatistique et Bioinformatique, 69003 Lyon, France; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, Équipe Biostatistique-Santé, 69100 Villeurbanne, France
| | - Marion Le Grand
- Université Aix-Marseille, CNRS 7258, INSERM 1068, Institute Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), 13009 Marseille, France
| | - Eddy Pasquier
- Université Aix-Marseille, CNRS 7258, INSERM 1068, Institute Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), 13009 Marseille, France
| | - Jean-Yves Blay
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France
| | - Marie Castets
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France.
| | - Laura Broutier
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France.
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6
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Asante Y, Benischke K, Osman I, Ngo QA, Wurth J, Laubscher D, Kim H, Udhayakumar B, Khan MIH, Chin DH, Porch J, Chakraborty M, Sallari R, Delattre O, Zaidi S, Morice S, Surdez D, Danielli SG, Schäfer BW, Gryder BE, Wachtel M. PAX3-FOXO1 uses its activation domain to recruit CBP/P300 and shape RNA Pol2 cluster distribution. Nat Commun 2023; 14:8361. [PMID: 38102136 PMCID: PMC10724205 DOI: 10.1038/s41467-023-43780-4] [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] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
Activation of oncogenic gene expression from long-range enhancers is initiated by the assembly of DNA-binding transcription factors (TF), leading to recruitment of co-activators such as CBP/p300 to modify the local genomic context and facilitate RNA-Polymerase 2 (Pol2) binding. Yet, most TF-to-coactivator recruitment relationships remain unmapped. Here, studying the oncogenic fusion TF PAX3-FOXO1 (P3F) from alveolar rhabdomyosarcoma (aRMS), we show that a single cysteine in the activation domain (AD) of P3F is important for a small alpha helical coil that recruits CBP/p300 to chromatin. P3F driven transcription requires both this single cysteine and CBP/p300. Mutants of the cysteine reduce aRMS cell proliferation and induce cellular differentiation. Furthermore, we discover a profound dependence on CBP/p300 for clustering of Pol2 loops that connect P3F to its target genes. In the absence of CBP/p300, Pol2 long range enhancer loops collapse, Pol2 accumulates in CpG islands and fails to exit the gene body. These results reveal a potential novel axis for therapeutic interference with P3F in aRMS and clarify the molecular relationship of P3F and CBP/p300 in sustaining active Pol2 clusters essential for oncogenic transcription.
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Affiliation(s)
- Yaw Asante
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Katharina Benischke
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland
| | - Issra Osman
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Quy A Ngo
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland
| | - Jakob Wurth
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland
| | - Dominik Laubscher
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland
| | - Hyunmin Kim
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Md Imdadul H Khan
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Diana H Chin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Jadon Porch
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | | | - Olivier Delattre
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Sakina Zaidi
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Sarah Morice
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Didier Surdez
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Sara G Danielli
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland
| | - Beat W Schäfer
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland.
| | - Berkley E Gryder
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | - Marco Wachtel
- University Children's Hospital, Children's Research Center and Department of Oncology, Steinwiesstrasse 75, CH-8032, Zürich, Switzerland.
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7
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Parent C, Raj Melayil K, Zhou Y, Aubert V, Surdez D, Delattre O, Wilhelm C, Viovy JL. Simple droplet microfluidics platform for drug screening on cancer spheroids. Lab Chip 2023; 23:5139-5150. [PMID: 37942508 DOI: 10.1039/d3lc00417a] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
3D in vitro biological systems are progressively replacing 2D systems to increase the physiological relevance of cellular studies. Microfluidics-based approaches can be powerful tools towards such biomimetic systems, but often require high-end complicated and expensive processes and equipment for microfabrication. Herein, a drug screening platform is proposed, minimizing technicality and manufacturing steps. It provides an alternate way of spheroid generation in droplets in tubes. Droplet microfluidics then elicit multiple droplets merging events at programmable times, to submit sequentially the spheroids to chemotherapy and to reagents for cytotoxicity screening. After a comprehensive study of tumorogenesis within the droplets, the system is validated for drug screening (IC50) with chemotherapies in cancer cell lines as well as cells from a patient-derived-xenografts (PDX). As compared to microtiter plates methods, our system reduces the initial number of cells up to 10 times and opens new avenues towards primary tumors drug screening approaches.
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Affiliation(s)
- Caroline Parent
- Laboratoire Physico Chimie Curie, Institut Curie, CNRS, PSL Research University, 75005 Paris, France.
| | - Kiran Raj Melayil
- Laboratoire Physico Chimie Curie, Institut Curie, CNRS, PSL Research University, 75005 Paris, France.
| | - Ya Zhou
- Laboratoire Physico Chimie Curie, Institut Curie, CNRS, PSL Research University, 75005 Paris, France.
| | - Vivian Aubert
- Laboratoire Physico Chimie Curie, Institut Curie, CNRS, PSL Research University, 75005 Paris, France.
| | - Didier Surdez
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Olivier Delattre
- INSERM U830, Institut Curie, PSL Research University, 75005 Paris, France
| | - Claire Wilhelm
- Laboratoire Physico Chimie Curie, Institut Curie, CNRS, PSL Research University, 75005 Paris, France.
| | - Jean-Louis Viovy
- Laboratoire Physico Chimie Curie, Institut Curie, CNRS, PSL Research University, 75005 Paris, France.
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8
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Filser M, Schwartz M, Merchadou K, Hamza A, Villy MC, Decees A, Frouin E, Girard E, Caputo SM, Renault V, Becette V, Golmard L, Servant N, Stoppa-Lyonnet D, Delattre O, Colas C, Masliah-Planchon J. Adaptive nanopore sequencing to determine pathogenicity of BRCA1 exonic duplication. J Med Genet 2023; 60:1206-1209. [PMID: 37263769 DOI: 10.1136/jmg-2023-109155] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/30/2023] [Indexed: 06/03/2023]
Abstract
BRCA1 and BRCA2 are tumour suppressor genes that have been characterised as predisposition genes for the development of hereditary breast and ovarian cancers among other malignancies. The molecular diagnosis of this predisposition syndrome is based on the detection of inactivating variants of any type in those genes. But in the case of structural variants, functional consequences can be difficult to assess using standard molecular methods, as the precise resolution of their sequence is often impossible with short-read next generation sequencing techniques. It has been recently demonstrated that Oxford Nanopore long-read sequencing technology can accurately and rapidly provide genetic diagnoses of Mendelian diseases, including those linked to pathogenic structural variants. Here, we report the accurate resolution of a germline duplication event of exons 18-20 of BRCA1 using Nanopore sequencing with adaptive sampling target enrichment. This allowed us to classify this variant as pathogenic within a short timeframe of 10 days. This study provides a proof-of-concept that nanopore adaptive sampling is a highly efficient technique for the investigation of structural variants of tumour suppressor genes in a clinical context.
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Affiliation(s)
- Mathilde Filser
- Genetics Department, Institut Curie, Paris, France
- PSL Research University, Paris, France
| | - Mathias Schwartz
- Genetics Department, Institut Curie, Paris, France
- PSL Research University, Paris, France
| | - Kevin Merchadou
- PSL Research University, Paris, France
- Clinical Bioinformatics Unit, Institut Curie, Paris, France
| | - Abderaouf Hamza
- Genetics Department, Institut Curie, Paris, France
- PSL Research University, Paris, France
| | - Marie-Charlotte Villy
- Oncogenetic Clinic Unit, Institut Curie, Paris, France
- SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Antoine Decees
- Genetics Department, Institut Curie, Paris, France
- PSL Research University, Paris, France
| | - Eléonore Frouin
- PSL Research University, Paris, France
- Clinical Bioinformatics Unit, Institut Curie, Paris, France
| | - Elodie Girard
- PSL Research University, Paris, France
- INSERM U900, Institut Curie, Paris, France
| | - Sandrine M Caputo
- Genetics Department, Institut Curie, Paris, France
- PSL Research University, Paris, France
| | - Victor Renault
- PSL Research University, Paris, France
- Clinical Bioinformatics Unit, Institut Curie, Paris, France
| | - Véronique Becette
- PSL Research University, Paris, France
- Anatomo- and Cyto-pathology, Institut Curie, Saint-Cloud, France
| | - Lisa Golmard
- Genetics Department, Institut Curie, Paris, France
- PSL Research University, Paris, France
| | - Nicolas Servant
- PSL Research University, Paris, France
- INSERM U900, Institut Curie, Paris, France
| | - Dominique Stoppa-Lyonnet
- Genetics Department, Institut Curie, Paris, France
- SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Olivier Delattre
- Genetics Department, Institut Curie, Paris, France
- Inserm U830, PSL University, Research Center, Institut Curie, Paris, France
| | - Chrystelle Colas
- PSL Research University, Paris, France
- Oncogenetic Clinic Unit, Institut Curie, Paris, France
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9
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Lobón-Iglesias MJ, Andrianteranagna M, Han ZY, Chauvin C, Masliah-Planchon J, Manriquez V, Tauziede-Espariat A, Turczynski S, Bouarich-Bourimi R, Frah M, Dufour C, Blauwblomme T, Cardoen L, Pierron G, Maillot L, Guillemot D, Reynaud S, Bourneix C, Pouponnot C, Surdez D, Bohec M, Baulande S, Delattre O, Piaggio E, Ayrault O, Waterfall JJ, Servant N, Beccaria K, Dangouloff-Ros V, Bourdeaut F. Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups. Nat Commun 2023; 14:6669. [PMID: 37863903 PMCID: PMC10589300 DOI: 10.1038/s41467-023-42371-7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/09/2023] [Indexed: 10/22/2023] Open
Abstract
Atypical teratoid rhabdoid tumors (ATRT) are divided into MYC, TYR and SHH subgroups, suggesting diverse lineages of origin. Here, we investigate the imaging of human ATRT at diagnosis and the precise anatomic origin of brain tumors in the Rosa26-CreERT2::Smarcb1flox/flox model. This cross-species analysis points to an extra-cerebral origin for MYC tumors. Additionally, we clearly distinguish SHH ATRT emerging from the cerebellar anterior lobe (CAL) from those emerging from the basal ganglia (BG) and intra-ventricular (IV) regions. Molecular characteristics point to the midbrain-hindbrain boundary as the origin of CAL SHH ATRT, and to the ganglionic eminence as the origin of BG/IV SHH ATRT. Single-cell RNA sequencing on SHH ATRT supports these hypotheses. Trajectory analyses suggest that SMARCB1 loss induces a de-differentiation process mediated by repressors of the neuronal program such as REST, ID and the NOTCH pathway.
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Affiliation(s)
- María-Jesús Lobón-Iglesias
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Mamy Andrianteranagna
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
- INSERM U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, Mines Paris Tech, PSL Research University, Institut Curie Research Center, Paris, France
| | - Zhi-Yan Han
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Céline Chauvin
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Julien Masliah-Planchon
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Valeria Manriquez
- INSERM U932, Immunity and Cancer, PSL Research University, Institut Curie Research Center, Paris, France
| | - Arnault Tauziede-Espariat
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
- Paris Psychiatry and Neurosciences Institute (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Sandrina Turczynski
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Rachida Bouarich-Bourimi
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Magali Frah
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Christelle Dufour
- Department of Children and Adolescents Oncology, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Thomas Blauwblomme
- Department of Pediatric Neurosurgery-AP-HP, Necker Sick Kids Hospital, Université de Paris, Paris, France
| | | | - Gaelle Pierron
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Laetitia Maillot
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Delphine Guillemot
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Stéphanie Reynaud
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Christine Bourneix
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Célio Pouponnot
- CNRS UMR 3347, INSERM U1021, Institut Curie, PSL Research University, Université Paris-Saclay, Orsay, France
| | - Didier Surdez
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Mylene Bohec
- Institut Curie, PSL University, Single Cell Initiative, ICGex Next-Generation Sequencing Platform, PSL University, 75005, Paris, France
| | - Sylvain Baulande
- Institut Curie, PSL University, Single Cell Initiative, ICGex Next-Generation Sequencing Platform, PSL University, 75005, Paris, France
| | - Olivier Delattre
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Eliane Piaggio
- INSERM U932, Immunity and Cancer, PSL Research University, Institut Curie Research Center, Paris, France
| | - Olivier Ayrault
- CNRS UMR 3347, INSERM U1021, Institut Curie, PSL Research University, Université Paris-Saclay, Orsay, France
| | - Joshua J Waterfall
- INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Nicolas Servant
- INSERM U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, Mines Paris Tech, PSL Research University, Institut Curie Research Center, Paris, France
| | - Kevin Beccaria
- Department of Pediatric Neurosurgery-AP-HP, Necker Sick Kids Hospital, Université de Paris, Paris, France
| | - Volodia Dangouloff-Ros
- Pediatric Radiology Department, AP-HP, Necker Sick Kids Hospital and Paris Cite Universiy INSERM 1299 and UMR 1163, Institut Imagine, Paris, France
| | - Franck Bourdeaut
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France.
- Department of Pediatric Oncology, SIREDO Oncology Center, Institut Curie Hospital, Paris, and Université de Paris, Paris, France.
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10
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de Traux de Wardin H, Dermawan JK, Merlin MS, Wexler LH, Orbach D, Vanoli F, Schleiermacher G, Geoerger B, Ballet S, Guillemot D, Frouin E, Cyrille S, Delattre O, Pierron G, Antonescu CR. Sequential genomic analysis using a multisample/multiplatform approach to better define rhabdomyosarcoma progression and relapse. NPJ Precis Oncol 2023; 7:96. [PMID: 37730754 PMCID: PMC10511463 DOI: 10.1038/s41698-023-00445-1] [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: 03/07/2023] [Accepted: 08/30/2023] [Indexed: 09/22/2023] Open
Abstract
The genomic spectrum of rhabdomyosarcoma (RMS) progression from primary to relapse is not fully understood. In this pilot study, we explore the sensitivity of various targeted and whole-genome NGS platforms in order to assess the best genomic approach of using liquid biopsy in future prospective clinical trials. Moreover, we investigate 35 paired primary/relapsed RMS from two contributing institutions, 18 fusion-positive (FP-RMS) and 17 fusion-negative RMS (FN-RMS) by either targeted DNA or whole exome sequencing (WES). In 10 cases, circulating tumor DNA (ctDNA) from multiple timepoints through clinical care and progression was analyzed for feasibility of liquid biopsy in monitoring treatment response/relapse. ctDNA alterations were evaluated using a targeted 36-gene custom RMS panel at high coverage for single-nucleotide variation and fusion detection, and a shallow whole-genome sequencing for copy number variation. FP-RMS have a stable genome with relapse, with common secondary alterations CDKN2A/B, MYCN, and CDK4 present at diagnosis and impacting survival. FP-RMS lacking major secondary events at baseline acquire recurrent MYCN and AKT1 alterations. FN-RMS acquire a higher number of new alterations, most commonly SMARCA2 missense mutations. ctDNA analyses detect pathognomonic variants in all RMS patients within our collection at diagnosis, regardless of type of alterations, and confirmed at relapse in 86% of FP-RMS and 100% FN-RMS. Moreover, a higher number of fusion reads is detected with increased disease burden and at relapse in patients following a fatal outcome. These results underscore patterns of tumor progression and provide rationale for using liquid biopsy to monitor treatment response.
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Affiliation(s)
- Henry de Traux de Wardin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Unit of Somatic Genetics, Institut Curie, Paris, France
| | - Josephine K Dermawan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marie-Sophie Merlin
- University of Lorraine, Centre Hospitalier Régional Universitaire (CHRU), Childrens' Hospital, Department of Pediatric Oncology, Vandoeuvre-lès-Nancy, France
| | - Leonard H Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Orbach
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), PSL University, Institut Curie, Paris, France
| | - Fabio Vanoli
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gudrun Schleiermacher
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), PSL University, Institut Curie, Paris, France
- U830 INSERM, Paris, France
| | - Birgit Geoerger
- Gustave Roussy Cancer Center, Department of Pediatric and Adolescent Oncology, Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Université Paris-Saclay, Villejuif, 94805, France
| | - Stelly Ballet
- Unit of Somatic Genetics, Institut Curie, Paris, France
| | | | | | - Stacy Cyrille
- Department of Biometrics, Institut Curie, Paris, France
| | - Olivier Delattre
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), PSL University, Institut Curie, Paris, France
- U830 INSERM, Paris, France
| | - Gaelle Pierron
- Unit of Somatic Genetics, Institut Curie, Paris, France.
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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11
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Marques Da Costa ME, Zaidi S, Scoazec JY, Droit R, Lim WC, Marchais A, Salmon J, Cherkaoui S, Morscher RJ, Laurent A, Malinge S, Mercher T, Tabone-Eglinger S, Goddard I, Pflumio F, Calvo J, Redini F, Entz-Werlé N, Soriano A, Villanueva A, Cairo S, Chastagner P, Moro M, Owens C, Casanova M, Hladun-Alvaro R, Berlanga P, Daudigeos-Dubus E, Dessen P, Zitvogel L, Lacroix L, Pierron G, Delattre O, Schleiermacher G, Surdez D, Geoerger B. A biobank of pediatric patient-derived-xenograft models in cancer precision medicine trial MAPPYACTS for relapsed and refractory tumors. Commun Biol 2023; 6:949. [PMID: 37723198 PMCID: PMC10507044 DOI: 10.1038/s42003-023-05320-0] [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] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/04/2023] [Indexed: 09/20/2023] Open
Abstract
Pediatric patients with recurrent and refractory cancers are in most need for new treatments. This study developed patient-derived-xenograft (PDX) models within the European MAPPYACTS cancer precision medicine trial (NCT02613962). To date, 131 PDX models were established following heterotopical and/or orthotopical implantation in immunocompromised mice: 76 sarcomas, 25 other solid tumors, 12 central nervous system tumors, 15 acute leukemias, and 3 lymphomas. PDX establishment rate was 43%. Histology, whole exome and RNA sequencing revealed a high concordance with the primary patient's tumor profile, human leukocyte-antigen characteristics and specific metabolic pathway signatures. A detailed patient molecular characterization, including specific mutations prioritized in the clinical molecular tumor boards are provided. Ninety models were shared with the IMI2 ITCC Pediatric Preclinical Proof-of-concept Platform (IMI2 ITCC-P4) for further exploitation. This PDX biobank of unique recurrent childhood cancers provides an essential support for basic and translational research and treatments development in advanced pediatric malignancies.
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Grants
- This work was supported by grants from Fondation Gustave Roussy; Fédération Enfants Cancers et Santé, Société Française de lutte contre les Cancers et les leucémies de l’Enfant et l’adolescent (SFCE), Association AREMIG and Thibault BRIET; Parrainage médecin-chercheur of Gustave Roussy; INSERM; Canceropôle Ile-de-France; Ligue Nationale Contre le Cancer (Equipe labellisée); Fondation ARC for the European projects ERA-NET on Translational Cancer Research (TRANSCAN 2) Joint Transnational Call 2014 (JTC 2014) ‘Targeting Of Resistance in PEDiatric Oncology (TORPEDO)’, ERA-NET TRANSCAN JTC 2014 (TRAN201501238), and TRANSCAN JTC 2017 (TRANS201801292); Agence Nationale de la Recherche (ANR-10-EQPX-03, Institut Curie Génomique d’Excellence (ICGex); IMI ITCC-P4 ; The Child Cancer Research Foundation (CCRF), Cancer Council Western Australia (CCWA); PAIR-Pédiatrie/CONECT-AML (INCa-ARC-LIGUE_11905 and Association Laurette Fugain), Ligue contre le cancer (Equipe labellisée, since 2016), OPALE Carnot institute; Dell; Fondation Bristol-Myers Squibb; Association Imagine for Margo; Association Manon Hope; L’Etoile de Martin; La Course de l’Espoir; M la vie avec Lisa; ADAM; Couleur Jade; Dans les pas du Géant; Courir pour Mathieu; Marabout de Ficelle; Olivier Chape; Les Bagouz à Manon; Association Hubert Gouin Enfance et Cancer; Les Amis de Claire; Kurt-und Senta Hermann Stiftung; Holcim Stiftung Wissen; Gertrud-Hagmann-Stiftung für Malignom-Forschung; Heidi Ras Grant Forschungszentrum fürs Kind; Children’s Liver Tumour European Research Network (ChiLTERN) EU H2020 projet (668596); Fundación FERO and the Rotary Clubs Barcelona Eixample, Barcelona Diagonal, Santa Coloma de Gramanet, München-Blutenburg, Sassella-Stiftung, Berger-Janser Stiftung and Krebsliga Zürich, Deutschland Gemeindienst e.V. and others from Barcelona and province, and No Limits Contra el Cáncer Infantil Association.
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Affiliation(s)
- Maria Eugénia Marques Da Costa
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Sakina Zaidi
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Jean-Yves Scoazec
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Robin Droit
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Gustave Roussy Cancer Campus, Bioinformatics Platform, AMMICA, INSERM US23/CNRS, UAR3655, Villejuif, France
| | - Wan Ching Lim
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Jerome Salmon
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Sarah Cherkaoui
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Raphael J Morscher
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anouchka Laurent
- Gustave Roussy Cancer Campus, INSERM U1170, Université Paris-Saclay, Equipe labellisée Ligue Nationale Contre le Cancer, PEDIAC program, Villejuif, France
| | - Sébastien Malinge
- Gustave Roussy Cancer Campus, INSERM U1170, Université Paris-Saclay, Equipe labellisée Ligue Nationale Contre le Cancer, PEDIAC program, Villejuif, France
- Telethon Kids Institute - Cancer Centre, Perth Children's Hospital, Nedlands, WA, Australia
| | - Thomas Mercher
- Gustave Roussy Cancer Campus, INSERM U1170, Université Paris-Saclay, Equipe labellisée Ligue Nationale Contre le Cancer, PEDIAC program, Villejuif, France
| | | | - Isabelle Goddard
- Small Animal Platform, Cancer Research Center of Lyon, INSERM U1052, CNRS UMR 5286, Centre Léon Bérard, Claude Bernard Université Lyon 1, Lyon, France
| | - Francoise Pflumio
- UMR-E008 Stabilité Génétique, Cellules Souches et Radiations, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université de Paris-Université Paris-Saclay, 92260, Fontenay-aux-Roses, France
| | - Julien Calvo
- UMR-E008 Stabilité Génétique, Cellules Souches et Radiations, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université de Paris-Université Paris-Saclay, 92260, Fontenay-aux-Roses, France
| | | | - Natacha Entz-Werlé
- Pediatric Onco-Hematology Unit, University Hospital of Strasbourg, Strasbourg, UMR CNRS 7021, team tumoral signaling and therapeutic targets, University of Strasbourg, Faculty of Pharmacy, Illkirch, France
| | - Aroa Soriano
- Vall d'Hebron Research Institute (VHIR), Childhood Cancer and Blood Disorders Research Group, Division of Pediatric Hematology and Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Alberto Villanueva
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Xenopat SL, Parc Cientific de Barcelona (PCB), Barcelona, Spain
| | | | - Pascal Chastagner
- Children University Hospital, Vandoeuvre‑lès‑Nancy, University of Nancy, Nancy, France
| | - Massimo Moro
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Cormac Owens
- Paediatric Haematology/Oncology, Children's Health Ireland, Crumlin, Dublin, Republic of Ireland
| | | | - Raquel Hladun-Alvaro
- Vall d'Hebron Research Institute (VHIR), Childhood Cancer and Blood Disorders Research Group, Division of Pediatric Hematology and Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Pablo Berlanga
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | | | - Philippe Dessen
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Gustave Roussy Cancer Campus, Bioinformatics Platform, AMMICA, INSERM US23/CNRS, UAR3655, Villejuif, France
| | - Laurence Zitvogel
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Ludovic Lacroix
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Paris, France
| | - Olivier Delattre
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Paris, France
- SiRIC RTOP (Recherche Translationnelle en Oncologie Pédiatrique); Translational Research Department, Institut Curie Research Center, PSL Research University, Institut Curie, Paris, France
| | - Gudrun Schleiermacher
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- SiRIC RTOP (Recherche Translationnelle en Oncologie Pédiatrique); Translational Research Department, Institut Curie Research Center, PSL Research University, Institut Curie, Paris, France
| | - Didier Surdez
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Birgit Geoerger
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France.
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12
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Fouché A, Chadoutaud L, Delattre O, Zinovyev A. Transmorph: a unifying computational framework for modular single-cell RNA-seq data integration. NAR Genom Bioinform 2023; 5:lqad069. [PMID: 37448589 PMCID: PMC10336778 DOI: 10.1093/nargab/lqad069] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/02/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023] Open
Abstract
Data integration of single-cell RNA-seq (scRNA-seq) data describes the task of embedding datasets gathered from different sources or experiments into a common representation so that cells with similar types or states are embedded close to one another independently from their dataset of origin. Data integration is a crucial step in most scRNA-seq data analysis pipelines involving multiple batches. It improves data visualization, batch effect reduction, clustering, label transfer, and cell type inference. Many data integration tools have been proposed during the last decade, but a surge in the number of these methods has made it difficult to pick one for a given use case. Furthermore, these tools are provided as rigid pieces of software, making it hard to adapt them to various specific scenarios. In order to address both of these issues at once, we introduce the transmorph framework. It allows the user to engineer powerful data integration pipelines and is supported by a rich software ecosystem. We demonstrate transmorph usefulness by solving a variety of practical challenges on scRNA-seq datasets including joint datasets embedding, gene space integration, and transfer of cycle phase annotations. transmorph is provided as an open source python package.
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Affiliation(s)
- Aziz Fouché
- To whom correspondence should be addressed. Tel: +33 156246989;
| | - Loïc Chadoutaud
- Institut Curie, PSL Research University, 75005 Paris, France
- INSERM, 75005 Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75005 Paris, France
| | - Olivier Delattre
- INSERM U830, Equipe Labellisée LNCC, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Andrei Zinovyev
- Correspondence may also be addressed to Andrei Zinovyev. Tel: +33 156246989;
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13
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Tauziède-Espariat A, Masliah-Planchon J, Andrianteranagna M, Sievers P, Sahm F, von Deimling A, Hasty L, Delattre O, Beccaria K, Métais A, Chrétien F, Varlet P, Bourdeaut F. Diagnostic accuracy of a minimal immunohistochemical panel in at/rt molecular subtyping, correlated to dna-methylation profiling. Acta Neuropathol Commun 2023; 11:136. [PMID: 37605249 PMCID: PMC10440909 DOI: 10.1186/s40478-023-01630-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Affiliation(s)
- Arnault Tauziède-Espariat
- Department of Neuropathology, GHU Paris - Psychiatry and Neuroscience, Sainte-Anne Hospital, 1, rue Cabanis, Paris, 75014, France.
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France.
- Université de Paris Cité, Paris, France.
| | - Julien Masliah-Planchon
- Laboratory of Somatic Genetics, Institut Curie, PMDT, Paris Sciences Lettres Research University, Paris, France
| | - Mamy Andrianteranagna
- Research In Pediatric, Adolescent and Young Adult Oncology, Laboratory of Translationnal Research in Pediatric Oncology, Institut Curie Institute, SIREDO Center Care, INSERM U830, Paris Sciences Lettres Research University, Innovation, Paris, France
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center DKFZ, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center DKFZ, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center DKFZ, Heidelberg, Germany
| | - Lauren Hasty
- Department of Neuropathology, GHU Paris - Psychiatry and Neuroscience, Sainte-Anne Hospital, 1, rue Cabanis, Paris, 75014, France
| | | | - Kévin Beccaria
- Department of Pediatric Neurosurgery, APHP, Necker Hospital, Université Paris Descartes, Sorbonne Paris Cite, Paris, 75015, France
| | - Alice Métais
- Department of Neuropathology, GHU Paris - Psychiatry and Neuroscience, Sainte-Anne Hospital, 1, rue Cabanis, Paris, 75014, France
| | - Fabrice Chrétien
- Department of Neuropathology, GHU Paris - Psychiatry and Neuroscience, Sainte-Anne Hospital, 1, rue Cabanis, Paris, 75014, France
- Université de Paris Cité, Paris, France
| | - Pascale Varlet
- Department of Neuropathology, GHU Paris - Psychiatry and Neuroscience, Sainte-Anne Hospital, 1, rue Cabanis, Paris, 75014, France
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
- Université de Paris Cité, Paris, France
| | - Franck Bourdeaut
- Research In Pediatric, Adolescent and Young Adult Oncology, Laboratory of Translationnal Research in Pediatric Oncology, Institut Curie Institute, SIREDO Center Care, INSERM U830, Paris Sciences Lettres Research University, Innovation, Paris, France
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14
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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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15
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Lemelle L, Guillemot D, Hermann AL, Gauthier A, Carton M, Corradini N, Rome A, Berlanga P, Jourdain A, Marie Cardine A, Jannier S, Boutroux H, Defachelles AS, Aerts I, Geoerger B, Karanian M, Doz F, Brisse HJ, Schleiermacher G, Delattre O, Pierron G, Orbach D. Neurotrophic tropomyosin receptor kinase (NTRK) fusion positive tumors: a historical cohort analysis. Expert Rev Anticancer Ther 2023; 23:865-874. [PMID: 37434345 DOI: 10.1080/14737140.2023.2236305] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/10/2023] [Indexed: 07/13/2023]
Abstract
BACKGROUND NTRK gene fusions have been identified in various tumors; some requiring aggressive therapy and sometimes new TRK inhibitors (TRKi). We aimed to describe a national, unselected, retrospective, multicenter cohort. RESEARCH DESIGN AND METHODS Patients were identified through the French sarcoma diagnostic laboratory at Institut Curie through samples analyzed by RT-qPCR or whole-transcriptome sequencing. RESULTS From 2001 to 2019, 65 NTRK fusion tumors were identified within 2120 analyses (3.1%): 58 by RNA sequencing (including 20 after RT-qPCR analysis) and 7 exclusively by RT-qPCR. Of the 61 patients identified, 37 patients had infantile soft tissue or kidney fibrosarcomas (IFS), 15 other mesenchymal (Other-MT) and nine central nervous system (CNS) tumors. They encompassed 14 different tumor types with variable behaviors. Overall, 53 patients had surgery (3 mutilating), 38 chemotherapy (20 alkylating agents/anthracycline), 11 radiotherapy, two 'observation strategy' and 13 received TRKi. After a median follow-up of 61.0 months [range, 2.5-226.0], 10 patients died. Five-year overall survival is, respectively, 91.9% [95%CI, 83.5-100.0], 61.1% [95%CI, 34.2-100.0] and 64.8% [95%CI, 39.3-100.0] for IFS, Other-MT, and CNS groups. CONCLUSIONS NTRK-fusion positive tumors are rare but detection is improved through RNA sequencing. TRKi could be considered at diagnosis for CNS NTRK-fusion positive tumors, some IFS, and Other-MT. TRIAL REGISTRATION Not adapted.
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Affiliation(s)
- Lauriane Lemelle
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, Paris, France
| | | | | | | | - Matthieu Carton
- Department of Biostatistics, Institut Curie, PSL University, Paris, France
| | - Nadège Corradini
- Institut d'Hematologie Et d'Oncologie Pédiatrique, Centre Léon Bérard, Lyon, France
| | - Angélique Rome
- Department of Pediatric Oncology, Assistance Publique des Hopitaux de Marseille, Marseille, France
| | - Pablo Berlanga
- Department of Pediatric and Adolescent Oncology, Gustave Roussy, Villejuif, France
| | - Anne Jourdain
- Department of Pediatric Oncology and Haematology, University Hospital of Tours, Tours, France
| | - Aude Marie Cardine
- Pediatric Immuno-Hematology-Oncology Unit, University Hospital of Rouen, Rouen, France
| | - Sarah Jannier
- Pediatric Oncology Department, University Hospital of Strasbourg, Strasbourg, France
| | - Hélène Boutroux
- Department of Pediatric Onco-Hematology, Armand Trousseau Hospital, Paris, France
| | | | - Isabelle Aerts
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, Paris, France
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy, Villejuif, France
| | - Marie Karanian
- Department of Pathology, Centre Leon Bérard, Lyon, France
| | - François Doz
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, Paris, France
- Université Paris-Cité, Paris, France
| | | | - Gudrun Schleiermacher
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, Paris, France
| | - Olivier Delattre
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, Paris, France
- Department of Somatic Genetics, Institut Curie, Paris, France
| | - Gaëlle Pierron
- Department of Somatic Genetics, Institut Curie, Paris, France
| | - Daniel Orbach
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, Paris, France
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16
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Desandes E, Lapouble E, Lacour B, Guissou S, Goujon S, Defachelles AS, Marechal V, Gaspar N, Gomez-Mascard A, Karanian M, Marec-Berard P, Minard-Colin V, Orbach D, Tabone MD, Delattre O, Pierron G. Impact of age on survival according to molecular tumor findings in children and adolescents with soft-tissue and bone sarcoma: The BIOSCA project. Cancer Epidemiol 2023:102398. [PMID: 37357067 DOI: 10.1016/j.canep.2023.102398] [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: 04/03/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/27/2023]
Abstract
BACKGROUND Adolescents (15-19 years) with sarcoma are known to have significantly worse survival than children (0-14 years). One possible reason may be that the adolescent sarcomas exhibit specific biological characteristics resulting in differences in clinical presentation and treatment resistance behaviors. The BIOSCA project aims to further explore these age-related differences in survival accounting for molecular tumor characteristic in children and adolescents with sarcoma. METHODS A retrospective national population-based observational study with documented somatic genetic analyses was conducted between 2011 and 2016 of all patients aged from 0 to 17 years with a diagnosis of sarcoma using the National Registry of Childhood Cancers Database. RESULTS A total of 1637 children (0-9years: 40%), preadolescents (10-14years: 35%) and adolescents (15-17 years: 25%) with a diagnosis of bone (N = 845) or soft-tissue (N = 792) sarcoma were included. Adolescents had significantly worse outcome for undifferentiated small round cell sarcoma (USRCS), alveolar rhabdomyosarcoma (ARMS), and epithelioid sarcoma. Five-year overall survivals were worse among CIC-rearranged USRCS cases (47% [95%CI:21-69]) as compared to other USRCS, and PAX3::FOXO1 ARMS patients (44% [95%CI:32-55]) as compared to other ARMS. Adjusting for stage and genomic-profiling status, adolescents with USRCS were 1.6-fold more likely to die than children (P = 0.05), while the difference in survival between age of ARMS patients was weaken. Indeed, the prevalence of PAX3::FOXO1 increased significantly with age. CONCLUSION Age was an independent prognostic factor of outcome only in patients with USRCS, while the association between age and survival of patients with ARMS could be partly explained by differences in prevalence of PAX3::FOXO1.
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Affiliation(s)
- Emmanuel Desandes
- Registre National des cancers de l'Enfant, Registre National des Tumeurs Solides de l'Enfant, CHRU Nancy, Vandœuvre-lès-Nancy, France; Epidemiology of childhood and adolescent cancers, CRESS, INSERM, UMR1153, Université Paris-Cité, Paris, France.
| | - Eve Lapouble
- Unité de Génétique Somatique, Département de génétique, Institut Curie, Paris, France
| | - Brigitte Lacour
- Registre National des cancers de l'Enfant, Registre National des Tumeurs Solides de l'Enfant, CHRU Nancy, Vandœuvre-lès-Nancy, France; Epidemiology of childhood and adolescent cancers, CRESS, INSERM, UMR1153, Université Paris-Cité, Paris, France
| | - Sandra Guissou
- Registre National des cancers de l'Enfant, Registre National des Tumeurs Solides de l'Enfant, CHRU Nancy, Vandœuvre-lès-Nancy, France; Epidemiology of childhood and adolescent cancers, CRESS, INSERM, UMR1153, Université Paris-Cité, Paris, France
| | - Stéphanie Goujon
- Epidemiology of childhood and adolescent cancers, CRESS, INSERM, UMR1153, Université Paris-Cité, Paris, France; Registre National des Cancers de l'Enfant, Hôpital Paul Brousse, Groupe Hospitalier Universitaire Paris-Sud, Assistance Publique Hôpitaux de Paris (AP-HP), Villejuif, and Centre Hospitalier Régional Universitaire de Nancy, Vandœuvre-lès-Nancy, France
| | - Anne-Sophie Defachelles
- Department of Pediatric, Adolescents and Young Adults Oncology, Centre Oscar Lambret, Lille, France
| | - Valérie Marechal
- Unité de Génétique Somatique, Département de génétique, Institut Curie, Paris, France
| | - Nathalie Gaspar
- Department of Oncology for Child and Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Anne Gomez-Mascard
- Laboratoire d'anatomie et cytologie pathologiques, Institut Universitaire du Cancer de Toulouse-Oncopole, Toulouse, France
| | - Marie Karanian
- Departments of Biopathology, Centre Léon Bérard, Lyon, France; Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Cancer Research of Lyon, Lyon, France
| | - Perrine Marec-Berard
- Département d'hémato-oncologie pédiatrique, IHOPe/Centre Leon Berard, Lyon, France
| | - Véronique Minard-Colin
- Department of Oncology for Child and Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Daniel Orbach
- SIREDO oncology center (Care, Innovation and Research for Children, Adolescents and young Adults with Cancer), Institut Curie, PSL University, Paris, France
| | - Marie-Dominique Tabone
- Department of Pediatric Hemato-Oncology, Armand-Trousseau Sorbonne University Hospital, AP-HP, Paris, France
| | - Olivier Delattre
- Unité de Génétique Somatique, Département de génétique, Institut Curie, Paris, France; INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Département de génétique, Institut Curie, Paris, France
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17
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Sturtzel C, Grissenberger S, Bozatzi P, Scheuringer E, Wenninger-Weinzierl A, Zajec Z, Dernovšek J, Pascoal S, Gehl V, Kutsch A, Granig A, Rifatbegovic F, Carre M, Lang A, Valtingojer I, Moll J, Lötsch D, Erhart F, Widhalm G, Surdez D, Delattre O, André N, Stampfl J, Tomašič T, Taschner-Mandl S, Distel M. Refined high-content imaging-based phenotypic drug screening in zebrafish xenografts. NPJ Precis Oncol 2023; 7:44. [PMID: 37202469 DOI: 10.1038/s41698-023-00386-9] [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: 12/07/2022] [Accepted: 05/03/2023] [Indexed: 05/20/2023] Open
Abstract
Zebrafish xenotransplantation models are increasingly applied for phenotypic drug screening to identify small compounds for precision oncology. Larval zebrafish xenografts offer the opportunity to perform drug screens at high-throughput in a complex in vivo environment. However, the full potential of the larval zebrafish xenograft model has not yet been realized and several steps of the drug screening workflow still await automation to increase throughput. Here, we present a robust workflow for drug screening in zebrafish xenografts using high-content imaging. We established embedding methods for high-content imaging of xenografts in 96-well format over consecutive days. In addition, we provide strategies for automated imaging and analysis of zebrafish xenografts including automated tumor cell detection and tumor size analysis over time. We also compared commonly used injection sites and cell labeling dyes and show specific site requirements for tumor cells from different entities. We demonstrate that our setup allows us to investigate proliferation and response to small compounds in several zebrafish xenografts ranging from pediatric sarcomas and neuroblastoma to glioblastoma and leukemia. This fast and cost-efficient assay enables the quantification of anti-tumor efficacy of small compounds in large cohorts of a vertebrate model system in vivo. Our assay may aid in prioritizing compounds or compound combinations for further preclinical and clinical investigations.
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Affiliation(s)
- C Sturtzel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - S Grissenberger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - P Bozatzi
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - E Scheuringer
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - A Wenninger-Weinzierl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - Z Zajec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - J Dernovšek
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - S Pascoal
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - V Gehl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - A Kutsch
- Christian Doppler Laboratory for Advanced Polymers for Biomaterials and 3D Printing, TU Wien, Vienna, Austria
| | - A Granig
- Christian Doppler Laboratory for Advanced Polymers for Biomaterials and 3D Printing, TU Wien, Vienna, Austria
| | - F Rifatbegovic
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - M Carre
- Service d'Hématologie & Oncologie Pédiatrique, Timone Hospital, AP-HM, Marseille, France
- Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, CNRS, Inserm, Institut Paoli Calmettes, Marseille, France
| | - A Lang
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
- Central Nervous System Tumors Unit, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - I Valtingojer
- Department of Molecular Oncology, Sanofi Research Center, Vitry-sur-Seine, France
| | - J Moll
- Department of Molecular Oncology, Sanofi Research Center, Vitry-sur-Seine, France
- Renon Biotech and Pharma Consulting, Unterinn am Ritten (Bz), Italy
| | - D Lötsch
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
- Central Nervous System Tumors Unit, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - F Erhart
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
- Central Nervous System Tumors Unit, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - G Widhalm
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
- Central Nervous System Tumors Unit, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - D Surdez
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - O Delattre
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - N André
- Service d'Hématologie & Oncologie Pédiatrique, Timone Hospital, AP-HM, Marseille, France
- Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, CNRS, Inserm, Institut Paoli Calmettes, Marseille, France
| | - J Stampfl
- Christian Doppler Laboratory for Advanced Polymers for Biomaterials and 3D Printing, TU Wien, Vienna, Austria
| | - T Tomašič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - S Taschner-Mandl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
| | - M Distel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
- Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria.
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18
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Thirant C, Peltier A, Durand S, Kramdi A, Louis-Brennetot C, Pierre-Eugène C, Gautier M, Costa A, Grelier A, Zaïdi S, Gruel N, Jimenez I, Lapouble E, Pierron G, Sitbon D, Brisse HJ, Gauthier A, Fréneaux P, Grossetête S, Baudrin LG, Raynal V, Baulande S, Bellini A, Bhalshankar J, Carcaboso AM, Geoerger B, Rohrer H, Surdez D, Boeva V, Schleiermacher G, Delattre O, Janoueix-Lerosey I. Reversible transitions between noradrenergic and mesenchymal tumor identities define cell plasticity in neuroblastoma. Nat Commun 2023; 14:2575. [PMID: 37142597 PMCID: PMC10160107 DOI: 10.1038/s41467-023-38239-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/21/2023] [Indexed: 05/06/2023] Open
Abstract
Noradrenergic and mesenchymal identities have been characterized in neuroblastoma cell lines according to their epigenetic landscapes and core regulatory circuitries. However, their relationship and relative contribution in patient tumors remain poorly defined. We now document spontaneous and reversible plasticity between the two identities, associated with epigenetic reprogramming, in several neuroblastoma models. Interestingly, xenografts with cells from each identity eventually harbor a noradrenergic phenotype suggesting that the microenvironment provides a powerful pressure towards this phenotype. Accordingly, such a noradrenergic cell identity is systematically observed in single-cell RNA-seq of 18 tumor biopsies and 15 PDX models. Yet, a subpopulation of these noradrenergic tumor cells presents with mesenchymal features that are shared with plasticity models, indicating that the plasticity described in these models has relevance in neuroblastoma patients. This work therefore emphasizes that intrinsic plasticity properties of neuroblastoma cells are dependent upon external cues of the environment to drive cell identity.
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Affiliation(s)
- Cécile Thirant
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Agathe Peltier
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Simon Durand
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Amira Kramdi
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Caroline Louis-Brennetot
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Cécile Pierre-Eugène
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Margot Gautier
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Ana Costa
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Amandine Grelier
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Sakina Zaïdi
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Nadège Gruel
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- Institut Curie, Department of Translational Research, Paris, France
| | - Irène Jimenez
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
- Institut Curie, Department of Translational Research, Paris, France
- Institut Curie, Laboratoire Recherche Translationnelle en Oncologie Pédiatrique (RTOP), Laboratoire "Gilles Thomas", Paris, France
| | - Eve Lapouble
- Institut Curie, Unité de Génétique Somatique, Paris, France
| | - Gaëlle Pierron
- Institut Curie, Unité de Génétique Somatique, Paris, France
| | - Déborah Sitbon
- Institut Curie, Unité de Génétique Somatique, Paris, France
| | - Hervé J Brisse
- Institut Curie, Department of Imaging, PSL Research University, Paris, France
| | | | - Paul Fréneaux
- Institut Curie, Department of Biopathology, Paris, France
| | - Sandrine Grossetête
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Laura G Baudrin
- Institut Curie, Genomics of Excellence (ICGex) Platform, Paris, France. Institut Curie, Single Cell Initiative, Paris, France
| | - Virginie Raynal
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- Institut Curie, Genomics of Excellence (ICGex) Platform, Paris, France. Institut Curie, Single Cell Initiative, Paris, France
| | - Sylvain Baulande
- Institut Curie, Genomics of Excellence (ICGex) Platform, Paris, France. Institut Curie, Single Cell Initiative, Paris, France
| | - Angela Bellini
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
- Institut Curie, Department of Translational Research, Paris, France
- Institut Curie, Laboratoire Recherche Translationnelle en Oncologie Pédiatrique (RTOP), Laboratoire "Gilles Thomas", Paris, France
| | - Jaydutt Bhalshankar
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
- Institut Curie, Department of Translational Research, Paris, France
- Institut Curie, Laboratoire Recherche Translationnelle en Oncologie Pédiatrique (RTOP), Laboratoire "Gilles Thomas", Paris, France
| | - Angel M Carcaboso
- SJD Pediatric Cancer Center Barcelona, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Birgit Geoerger
- Gustave Roussy Cancer Campus, INSERM U1015, Department of Pediatric and Adolescent Oncology, Université Paris-Saclay, Villejuif, France
| | - Hermann Rohrer
- Institute of Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Neuroscience Center, Goethe University, Frankfurt/M, Germany
| | - Didier Surdez
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Valentina Boeva
- Inserm, U1016, Cochin Institute, CNRS UMR8104, Paris University, Paris, France
- ETH Zürich, Department of Computer Science, Institute for Machine Learning, Zürich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Zürich, Switzerland
| | - Gudrun Schleiermacher
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
- Institut Curie, Department of Translational Research, Paris, France
- Institut Curie, Laboratoire Recherche Translationnelle en Oncologie Pédiatrique (RTOP), Laboratoire "Gilles Thomas", Paris, France
| | - Olivier Delattre
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
- Institut Curie, Unité de Génétique Somatique, Paris, France
| | - Isabelle Janoueix-Lerosey
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France.
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.
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Watson S, LaVigne CA, Xu L, Surdez D, Cyrta J, Calderon D, Cannon MV, Kent MR, Silvius KM, Kucinski JP, Harrison EN, Murchison W, Rakheja D, Tirode F, Delattre O, Amatruda JF, Kendall GC. Abstract 3525: VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3525] [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
Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that have not been functionally validated for their transformation capacity and biological activity. An example is the new fusion of transcriptional coactivators, VGLL2-NCOA2, found in infantile rhabdomyosarcoma. To delineate VGLL2-NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities, we implemented a cross-species comparative oncology approach with zebrafish, mouse allograft, and patient samples. We found that in our transgenic zebrafish and mouse allograft models, VGLL2-NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle. Zebrafish and mouse VGLL2-NCOA2 tumors are consistent with the human disease histologically and transcriptionally, and express diagnostic rhabdomyosarcoma markers. We found a shared molecular feature of these tumors was a suppression of myogenic differentiation pathways and reactivation of developmental programs. To identify impacted developmental programs, we transcriptionally clustered zebrafish VGLL2-NCOA2 tumors with the trajectory of early zebrafish development. A subset of VGLL2-NCOA2 zebrafish tumors cluster with embryonic somitogenesis and pinpoint VGLL2-NCOA2 developmental targets, including a RAS family GTPase, ARF6. In VGLL2-NCOA2 zebrafish, mouse allograft, and patient tumors, ARF6 is highly expressed and is absent from mature skeletal muscle. ARF6 knockout in our C2C12-VGLL2-NCOA2 cell culture model suppresses VGLL2-NCOA2 soft agar colony formation capacity, suggesting a genetic cooperating event in the disease. Our data indicate that VGLL2-NCOA2 is an oncogene which leverages developmental programs for tumorigenesis, and that the reactivation or persistence of ARF6 could represent a therapeutic opportunity.
Citation Format: Sarah Watson, Collette A. LaVigne, Lin Xu, Didier Surdez, Joanna Cyrta, Delia Calderon, Matthew V. Cannon, Matthew R. Kent, Katherine M. Silvius, Jack P. Kucinski, Emma N. Harrison, Whitney Murchison, Dinesh Rakheja, Franck Tirode, Olivier Delattre, James F. Amatruda, Genevieve C. Kendall. VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis. [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 3525.
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Affiliation(s)
- Sarah Watson
- 1Paris Sciences et Lettres (PSL) Research University, Paris, France
| | | | - Lin Xu
- 2UT Southwestern Medical Center, Dallas, TX
| | | | - Joanna Cyrta
- 1Paris Sciences et Lettres (PSL) Research University, Paris, France
| | | | | | | | | | | | | | | | | | | | - Olivier Delattre
- 1Paris Sciences et Lettres (PSL) Research University, Paris, France
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Gruel N, Quignot C, Vibert J, Bonvalot S, Zein SE, Tzanis D, Baulande S, Mariani O, Waterfall J, Delattre O, Watson S. Abstract 96: Integrated molecular analysis of human dedifferentiated liposarcoma identifies a population of liposarcoma progenitors vulnerable to TGF beta inhibition. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-96] [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
Introduction: Dedifferentiated liposarcomas (DDLPS) are the most frequent high-grade soft tissue sarcoma in adults. From a pathological point of view, these tumors are composed of high-grade undifferentiated tumor cells (DD), often showing an abrupt transition from a compartment of well-differentiated adipocytic tumor cells (WD). Tumor cells from both WD and DD compartments are characterized by recurrent MDM2 amplification, but their cellular origin and the molecular mechanisms associated with dedifferentiation are poorly understood.
Methods: We performed an integrated molecular analysis of tumors collected from 11 patients undergoing surgery for primary untreated DDLPS. DDLPS tumors were analyzed by single-cell RNA sequencing (scRNAseq) and bulk RNA sequencing on paired WD and DD samples from the same tumors. Results were validated in vitro and in vivo in an additional cohort of human tumors, patient-derived xenografts and DDLPS cell lines.
Results: Through RNA-sequencing of 102,753 individual cells from 11 primary DDLPS lesions, major cell clusters were identified based on unsupervised clustering of gene expression profiles and canonical markers. They include 31 tumor microenvironment clusters and 11 tumor cell clusters. A cluster of tumor cells from the WD compartment is characterized by signatures of early adipocytic progenitors, previously identified as TGFβ-dependent, DPP4-positive stromal progenitors. We show that these cells harbor specifically the truncal genomic alterations of the cancer, with further subclonal mutations identifiable in both WD and DD compartments of DDLPS. Furthermore, these cells have multipotent properties and their differentiation towards the adipocytic lineage is inhibited by TGFβ. Treatment of DD tumor cells with TGFβ inhibitors restores their adipocytic phenotype in vitro and in vivo.
Conclusion: We provide the first single-cell atlas of human DDLPS tumor and microenvironment and identify a population of adipocytic tumor progenitors at the origin of both WD and DD compartments. This study provides rationale for the development of therapeutic strategies based on TGFβ inhibition in advanced DDLPS.
Citation Format: Nadège Gruel, Chloé Quignot, Julien Vibert, Sylvie Bonvalot, Sophie El Zein, Dimitri Tzanis, Sylvain Baulande, Odette Mariani, Joshua Waterfall, Olivier Delattre, Sarah Watson. Integrated molecular analysis of human dedifferentiated liposarcoma identifies a population of liposarcoma progenitors vulnerable to TGF beta inhibition [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 96.
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21
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Raze T, Lapouble E, Lacour B, Guissou S, Defachelles AS, Gaspar N, Delattre O, Pierron G, Desandes E. PAX-FOXO1 fusion status in children and adolescents with alveolar rhabdomyosarcoma: Impact on clinical, pathological, and survival features. Pediatr Blood Cancer 2023; 70:e30228. [PMID: 36722003 DOI: 10.1002/pbc.30228] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 02/02/2023]
Abstract
BACKGROUND Alveolar rhabdomyosarcoma (ARMS) is an aggressive pediatric cancer and cases with fusion PAX3-FOXO1 and PAX7-FOXO1 seem to have a poor prognosis. The aim is to evaluate whether PAX-FOXO1 alterations influence clinical outcome in childhood and adolescence population with ARMS. PROCEDURE A population-based study was conducted between 2011 and 2016 in patients less than 17 years with a diagnosis of ARMS. Overall survival (OS) depending on fusion status with clinical factors was analyzed. RESULTS Out of 111 ARMS patients recorded in the French National Childhood Cancer Registry during the 2011-2016 period, 61% expressed PAX3-FOXO1, 15% expressed PAX7-FOXO1, 13% were FOXO1 fusion-positive without PAX specification, and 7% were PAX-FOXO1 negative (n = 4 missing data). Compared to patients with PAX7-FOXO1 positive ARMS, those with PAX3-FOXO1 positive tumor were significantly older (10-17 years: 57.4% vs. 29.4%), and had more often a metastatic disease (54.4% vs. 23.5%). Poorer 5-year OS for patients with PAX3-FOXO1 and PAX not specified FOXO1-positive tumor were observed (44.0% [32.0-55.4] and 35.7% [13.1-59.4], respectively). After adjustment for stage at diagnosis, patients with positive tumor for PAX3-FOXO1 were 3.6-fold more likely to die than those with positive tumor for PAX7-FOXO1. CONCLUSION At the population level, PAX3-FOXO1 was associated with a significant higher risk of death compared to PAX7-FOXO1-positive and PAX-FOXO1-negative tumors, and could explain poorer 5-year OS observed in adolescence population diagnosed with ARMS. A continuous risk score derived from the combination of clinical parameters with PAX3-FOXO1 fusion status represents a robust approach to improving current risk-adapted therapy for ARMS.
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Affiliation(s)
- Thomas Raze
- Registre National des cancers de l'Enfant, Registre National des Tumeurs Solides de l'Enfant, CHRU Nancy, Vandœuvre-lès-Nancy, France
| | - Eve Lapouble
- Département de génétique, Unité de Génétique Somatique, Institut Curie, Paris, France
| | - Brigitte Lacour
- Registre National des cancers de l'Enfant, Registre National des Tumeurs Solides de l'Enfant, CHRU Nancy, Vandœuvre-lès-Nancy, France
- Epidémiologie des Cancers des Enfants et des Adolescents (EPICEA), Centre de Recherche en Epidémiologie et Statistiques (CRESS), INSERM, UMR 1153, Université Paris-Cité, Paris, France
| | - Sandra Guissou
- Registre National des cancers de l'Enfant, Registre National des Tumeurs Solides de l'Enfant, CHRU Nancy, Vandœuvre-lès-Nancy, France
- Epidémiologie des Cancers des Enfants et des Adolescents (EPICEA), Centre de Recherche en Epidémiologie et Statistiques (CRESS), INSERM, UMR 1153, Université Paris-Cité, Paris, France
| | | | - Nathalie Gaspar
- Département d'Oncologie Enfants et Adolescents, Centre du Cancer Gustave Roussy, Université Paris Saclay, Villejuif, France
| | - Olivier Delattre
- Département de génétique, Unité de Génétique Somatique, Institut Curie, Paris, France
- Diversity and Plasticity of Childhood Tumors Lab, INSERM U830, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Gaelle Pierron
- Département de génétique, Unité de Génétique Somatique, Institut Curie, Paris, France
| | - Emmanuel Desandes
- Registre National des cancers de l'Enfant, Registre National des Tumeurs Solides de l'Enfant, CHRU Nancy, Vandœuvre-lès-Nancy, France
- Epidémiologie des Cancers des Enfants et des Adolescents (EPICEA), Centre de Recherche en Epidémiologie et Statistiques (CRESS), INSERM, UMR 1153, Université Paris-Cité, Paris, France
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22
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Lee OW, Rodrigues C, Lin SH, Luo W, Jones K, Brown DW, Zhou W, Karlins E, Khan SM, Baulande S, Raynal V, Surdez D, Reynaud S, Rubio RA, Zaidi S, Grossetête S, Ballet S, Lapouble E, Laurence V, Pierron G, Gaspar N, Corradini N, Marec-Bérard P, Rothman N, Dagnall CL, Burdett L, Manning M, Wyatt K, Yeager M, Chari R, Leisenring WM, Kulozik AE, Kriebel J, Meitinger T, Strauch K, Kirchner T, Dirksen U, Mirabello L, Tucker MA, Tirode F, Armstrong GT, Bhatia S, Robison LL, Yasui Y, Romero-Pérez L, Hartmann W, Metzler M, Diver WR, Lori A, Freedman ND, Hoover RN, Morton LM, Chanock SJ, Grünewald TGP, Delattre O, Machiela MJ. Targeted long-read sequencing of the Ewing sarcoma 6p25.1 susceptibility locus identifies germline-somatic interactions with EWSR1-FLI1 binding. Am J Hum Genet 2023; 110:427-441. [PMID: 36787739 PMCID: PMC10027473 DOI: 10.1016/j.ajhg.2023.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Ewing sarcoma (EwS) is a rare bone and soft tissue malignancy driven by chromosomal translocations encoding chimeric transcription factors, such as EWSR1-FLI1, that bind GGAA motifs forming novel enhancers that alter nearby expression. We propose that germline microsatellite variation at the 6p25.1 EwS susceptibility locus could impact downstream gene expression and EwS biology. We performed targeted long-read sequencing of EwS blood DNA to characterize variation and genomic features important for EWSR1-FLI1 binding. We identified 50 microsatellite alleles at 6p25.1 and observed that EwS-affected individuals had longer alleles (>135 bp) with more GGAA repeats. The 6p25.1 GGAA microsatellite showed chromatin features of an EWSR1-FLI1 enhancer and regulated expression of RREB1, a transcription factor associated with RAS/MAPK signaling. RREB1 knockdown reduced proliferation and clonogenic potential and reduced expression of cell cycle and DNA replication genes. Our integrative analysis at 6p25.1 details increased binding of longer GGAA microsatellite alleles with acquired EWSR-FLI1 to promote Ewing sarcomagenesis by RREB1-mediated proliferation.
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Affiliation(s)
- Olivia W Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Calvin Rodrigues
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Wen Luo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Sairah M Khan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sylvain Baulande
- ICGex Next-Generation Sequencing Platform, PSL Université, Research Center, Institut Curie, 75005 Paris, France
| | - Virginie Raynal
- ICGex Next-Generation Sequencing Platform, PSL Université, Research Center, Institut Curie, 75005 Paris, France
| | - Didier Surdez
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Stephanie Reynaud
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Rebeca Alba Rubio
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany
| | - Sakina Zaidi
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Sandrine Grossetête
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Stelly Ballet
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Eve Lapouble
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | | | - Gaelle Pierron
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Nathalie Gaspar
- Department of Oncology for Child and Adolescent, Institut Gustave Roussy, 94800 Villejuif, France
| | - Nadège Corradini
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, 69008 Lyon, France
| | - Perrine Marec-Bérard
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, 69008 Lyon, France
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Michelle Manning
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Kathleen Wyatt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Raj Chari
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Genome Modification Core Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Wendy M Leisenring
- Cancer Prevention and Clinical Statistics Programs, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Andreas E Kulozik
- University Children's Hospital of Heidelberg, 69120 Heidelberg, Germany
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 80333 Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU, 80539 Munich, Germany
| | - Thomas Kirchner
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany
| | - Uta Dirksen
- University Children's Hospital of Essen, 45147 Essen, Germany
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Franck Tirode
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama, Birmingham, AL 35294, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Wolfgang Hartmann
- Gerhard- Domagk Institute of Pathology, University Hospital of Münster, 48149 Münster, Germany
| | - Markus Metzler
- University Children's Hospital of Erlangen, 91054 Erlangen, Germany
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Adriana Lori
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olivier Delattre
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
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23
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Watson S, Gruel N, Quignot C, Vibert J, Bonvalot S, El Zein S, Tzanis D, Baulande S, Mariani O, Waterfall J, Delattre O. 46O Integrated molecular analysis of human dedifferentiated liposarcoma identifies a population of tumoral progenitors vulnerable to TGF beta inhibition. ESMO Open 2023. [DOI: 10.1016/j.esmoop.2023.101083] [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: 04/05/2023] Open
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24
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Danielli SG, Porpiglia E, De Micheli AJ, Navarro N, Zellinger MJ, Bechtold I, Kisele S, Volken L, Marques JG, Kasper S, Bode PK, Henssen AG, Gürgen D, Delattre O, Surdez D, Roma J, Bühlmann P, Blau HM, Wachtel M, Schäfer BW. Single-cell profiling of alveolar rhabdomyosarcoma reveals RAS pathway inhibitors as cell-fate hijackers with therapeutic relevance. Sci Adv 2023; 9:eade9238. [PMID: 36753540 PMCID: PMC9908029 DOI: 10.1126/sciadv.ade9238] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Rhabdomyosarcoma (RMS) is a group of pediatric cancers with features of developing skeletal muscle. The cellular hierarchy and mechanisms leading to developmental arrest remain elusive. Here, we combined single-cell RNA sequencing, mass cytometry, and high-content imaging to resolve intratumoral heterogeneity of patient-derived primary RMS cultures. We show that the aggressive alveolar RMS (aRMS) subtype contains plastic muscle stem-like cells and cycling progenitors that drive tumor growth, and a subpopulation of differentiated cells that lost its proliferative potential and correlates with better outcomes. While chemotherapy eliminates cycling progenitors, it enriches aRMS for muscle stem-like cells. We screened for drugs hijacking aRMS toward clinically favorable subpopulations and identified a combination of RAF and MEK inhibitors that potently induces myogenic differentiation and inhibits tumor growth. Overall, our work provides insights into the developmental states underlying aRMS aggressiveness, chemoresistance, and progression and identifies the RAS pathway as a promising therapeutic target.
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Affiliation(s)
- Sara G. Danielli
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Ermelinda Porpiglia
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biomedicine, Aarhus University, Aarhus C 8000, Denmark
- Corresponding author. (B.W.S.); (M.W.); (E.P.)
| | - Andrea J. De Micheli
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Natalia Navarro
- Laboratory of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | | | - Ingrid Bechtold
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Samanta Kisele
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Larissa Volken
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Joana G. Marques
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Stephanie Kasper
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Peter K. Bode
- Department of Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Anton G. Henssen
- Department of Pediatric Oncology/Hematology, Charité–Universitätsmedizin Berlin, Berlin 13353, Germany
| | - Dennis Gürgen
- EPO Experimental Pharmacology and Oncology Berlin-Buch GmbH Berlin 13125, Germany
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris 75005, France
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris 75005, France
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Josep Roma
- Laboratory of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Peter Bühlmann
- Seminar for Statistics, ETH Zürich, Zürich 8092, Switzerland
| | - Helen M. Blau
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marco Wachtel
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
- Corresponding author. (B.W.S.); (M.W.); (E.P.)
| | - Beat W. Schäfer
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
- Corresponding author. (B.W.S.); (M.W.); (E.P.)
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25
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Grissenberger S, Sturtzel C, Wenninger-Weinzierl A, Radic-Sarikas B, Scheuringer E, Bierbaumer L, Etienne V, Némati F, Pascoal S, Tötzl M, Tomazou EM, Metzelder M, Putz EM, Decaudin D, Delattre O, Surdez D, Kovar H, Halbritter F, Distel M. High-content drug screening in zebrafish xenografts reveals high efficacy of dual MCL-1/BCL-X L inhibition against Ewing sarcoma. Cancer Lett 2023; 554:216028. [PMID: 36462556 DOI: 10.1016/j.canlet.2022.216028] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
Ewing sarcoma is a pediatric bone and soft tissue cancer with an urgent need for new therapies to improve disease outcome. To identify effective drugs, phenotypic drug screening has proven to be a powerful method, but achievable throughput in mouse xenografts, the preclinical Ewing sarcoma standard model, is limited. Here, we explored the use of xenografts in zebrafish for high-throughput drug screening to discover new combination therapies for Ewing sarcoma. We subjected xenografts in zebrafish larvae to high-content imaging and subsequent automated tumor size analysis to screen single agents and compound combinations. We identified three drug combinations effective against Ewing sarcoma cells: Irinotecan combined with either an MCL-1 or an BCL-XL inhibitor and in particular dual inhibition of the anti-apoptotic proteins MCL-1 and BCL-XL, which efficiently eradicated tumor cells in zebrafish xenografts. We confirmed enhanced efficacy of dual MCL-1/BCL-XL inhibition compared to single agents in a mouse PDX model. In conclusion, high-content screening of small compounds on Ewing sarcoma zebrafish xenografts identified dual MCL-1/BCL-XL targeting as a specific vulnerability and promising therapeutic strategy for Ewing sarcoma, which warrants further investigation towards clinical application.
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Affiliation(s)
| | - Caterina Sturtzel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - Andrea Wenninger-Weinzierl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - Branka Radic-Sarikas
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Department of Pediatric Surgery, Medical University of Vienna, Vienna, Austria
| | - Eva Scheuringer
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - Lisa Bierbaumer
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Vesnie Etienne
- Laboratory of Preclinical Investigation, Department of Translational Research, Institut Curie, PSL University, Paris, France
| | - Fariba Némati
- Laboratory of Preclinical Investigation, Department of Translational Research, Institut Curie, PSL University, Paris, France
| | - Susana Pascoal
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria
| | - Marcus Tötzl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Eleni M Tomazou
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Martin Metzelder
- Department of Pediatric Surgery, Medical University of Vienna, Vienna, Austria
| | - Eva M Putz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Didier Decaudin
- Laboratory of Preclinical Investigation, Department of Translational Research, Institut Curie, PSL University, Paris, France; Department of Medical Oncology, Institut Curie Research Centre, Paris, France
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Heinrich Kovar
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Dept. Pediatrics, Medical University Vienna, Vienna, Austria
| | | | - Martin Distel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Zebrafish Platform Austria for Preclinical Drug Screening (ZANDR), Vienna, Austria.
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26
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Sillam-Dussès D, Jandák V, Stiblik P, Delattre O, Chouvenc T, Balvín O, Cvačka J, Soulet D, Synek J, Brothánek M, Jiříček O, Engel MS, Bourguignon T, Šobotník J. Alarm communication predates eusociality in termites. Commun Biol 2023; 6:83. [PMID: 36681783 PMCID: PMC9867704 DOI: 10.1038/s42003-023-04438-5] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/06/2023] [Indexed: 01/22/2023] Open
Abstract
Termites (Blattodea: Isoptera) have evolved specialized defensive strategies for colony protection. Alarm communication enables workers to escape threats while soldiers are recruited to the source of disturbance. Here, we study the vibroacoustic and chemical alarm communication in the wood roach Cryptocercus and in 20 termite species including seven of the nine termite families, all life-types, and all feeding and nesting habits. Our multidisciplinary approach shows that vibratory alarm signals represent an ethological synapomorphy of termites and Cryptocercus. In contrast, chemical alarms have evolved independently in several cockroach groups and at least twice in termites. Vibroacoustic alarm signaling patterns are the most complex in Neoisoptera, in which they are often combined with chemical signals. The alarm characters correlate to phylogenetic position, food type and hardness, foraging area size, and nesting habits. Overall, species of Neoisoptera have developed the most sophisticated communication system amongst termites, potentially contributing to their ecological success.
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Affiliation(s)
- David Sillam-Dussès
- University Sorbonne Paris Nord, Laboratory of Experimental and Comparative Ethology UR4443, 93430, Villetaneuse, France
| | - Vojtěch Jandák
- Czech Technical University in Prague, Faculty of Electrical Engineering, 166 27, Prague 6, Czech Republic
| | - Petr Stiblik
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, 165 21, Prague 6 - Suchdol, Czech Republic
| | - Olivier Delattre
- University Sorbonne Paris Nord, Laboratory of Experimental and Comparative Ethology UR4443, 93430, Villetaneuse, France
| | - Thomas Chouvenc
- Entomology and Nematology Department, Fort Lauderdale Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences, Fort Lauderdale, Florida, 33314, USA
| | - Ondřej Balvín
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, 165 21, Prague 6 - Suchdol, Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10, Prague, Czech Republic
| | - Delphine Soulet
- University Sorbonne Paris Nord, Laboratory of Experimental and Comparative Ethology UR4443, 93430, Villetaneuse, France
| | - Jiří Synek
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, 165 21, Prague 6 - Suchdol, Czech Republic
| | - Marek Brothánek
- Czech Technical University in Prague, Faculty of Electrical Engineering, 166 27, Prague 6, Czech Republic
| | - Ondřej Jiříček
- Czech Technical University in Prague, Faculty of Electrical Engineering, 166 27, Prague 6, Czech Republic
| | - Michael S Engel
- Division of Entomology, Natural History Museum, and Department of Ecology & Evolutionary Biology, 1501 Crestline Drive-Suite 140, University of Kansas, Lawrence, Kansas, 66045, USA.
| | - Thomas Bourguignon
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, 165 21, Prague 6 - Suchdol, Czech Republic
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, 165 21, Prague 6 - Suchdol, Czech Republic.
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27
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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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Guinot A, Tabone-Eglinger S, Isnardi V, Bahri H, Surdez D, Delattre O, Pierron G, Villemeur M, Lapouble E, Brahmi M, Bouhamama A, Corradini N, Marec-Bérard P. Staging of newly diagnosed Ewing sarcoma: Results of bone marrow aspiration and biopsy versus (18)FDG-PET/CT imaging for bone marrow involvement. Eur J Cancer 2023; 179:56-64. [PMID: 36502618 DOI: 10.1016/j.ejca.2022.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Ewing sarcoma (ES) is an aggressive bone or extraosseous tumour with an unfavourable prognosis when bone marrow metastases are present at diagnosis. The gold standard diagnosis for bone marrow (BM) involvement is cytological and pathological analysis through bone marrow aspiration and biopsy (BMAB). Several recent studies suggest that these invasive and painful procedures could be replaced by 18F-fluorodeoxyglucose-positron emission tomography/computed tomography ((18)FDG-PET/CT), as this nuclear imaging technique is highly sensitive at detecting bone and extraosseous metastases of ES. METHODS In order to study the precision of (18)FDG-PET/CT in the evaluation of bone marrow metastases at diagnosis, we compared the imaging results with cytological/histological analyses performed on BM samples. We retrospectively studied 180 patients with ES recorded at the Léon Bérard Centre over the past 10 years, who were evaluated by (18)FDG-PET/CT and BMAB at diagnosis. RESULTS Of the 180 patients, 13 displayed marrow metastases by cytological/histological examination, and only one of these did not have (18)FDG-PET/CT signs of bone marrow involvement, whereas the 167 remaining patients without marrow metastasis all had a negative (18)FDG-PET/CT, except for one. Hence, the sensitivity and specificity of (18)FDG-PET/CT in these patients was 92.3% and 99.4%, respectively. The overall survival at five years of all patients was 67.4% but decrease to 38.5% in the group with bone marrow metastases. CONCLUSION Given the results presented herein the bone sarcoma group of the French Sarcoma Group suggests that invasive BMAB no longer be systematically performed for the staging at the diagnosis of ES.
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Affiliation(s)
- A Guinot
- Department of Tumor Pediatrics, Centre Leon Berard, Lyon, France.
| | | | - V Isnardi
- Department of Nuclear Medicine, Centre Léon Bérard, Lyon, France
| | - H Bahri
- Department of Nuclear Medicine, Centre Léon Bérard, Lyon, France
| | - D Surdez
- PSL Research University, Institut Curie Research Center, INSERM U830, Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France; Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - O Delattre
- PSL Research University, Institut Curie Research Center, INSERM U830, Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France; Department of Genetics, Institut Curie, Paris, France
| | - G Pierron
- Department of Genetics, Institut Curie, Paris, France
| | - M Villemeur
- PSL Research University, Institut Curie Research Center, INSERM U830, Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France; Department of Genetics, Institut Curie, Paris, France
| | - E Lapouble
- Department of Genetics, Institut Curie, Paris, France
| | - M Brahmi
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - A Bouhamama
- Department of Interventional Radiology, Centre Léon Bérard, Lyon, France
| | - N Corradini
- Department of Tumor Pediatrics, Centre Leon Berard, Lyon, France
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29
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Orth MF, Surdez D, Faehling T, Ehlers AC, Marchetto A, Grossetête S, Volckmann R, Zwijnenburg DA, Gerke JS, Zaidi S, Alonso J, Sastre A, Baulande S, Sill M, Cidre-Aranaz F, Ohmura S, Kirchner T, Hauck SM, Reischl E, Gymrek M, Pfister SM, Strauch K, Koster J, Delattre O, Grünewald TGP. Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation. Cell Rep 2022; 41:111761. [PMID: 36476851 DOI: 10.1016/j.celrep.2022.111761] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/25/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Ewing sarcoma (EwS) is characterized by EWSR1-ETS fusion transcription factors converting polymorphic GGAA microsatellites (mSats) into potent neo-enhancers. Although the paucity of additional mutations makes EwS a genuine model to study principles of cooperation between dominant fusion oncogenes and neo-enhancers, this is impeded by the limited number of well-characterized models. Here we present the Ewing Sarcoma Cell Line Atlas (ESCLA), comprising whole-genome, DNA methylation, transcriptome, proteome, and chromatin immunoprecipitation sequencing (ChIP-seq) data of 18 cell lines with inducible EWSR1-ETS knockdown. The ESCLA shows hundreds of EWSR1-ETS-targets, the nature of EWSR1-ETS-preferred GGAA mSats, and putative indirect modes of EWSR1-ETS-mediated gene regulation, converging in the duality of a specific but plastic EwS signature. We identify heterogeneously regulated EWSR1-ETS-targets as potential prognostic EwS biomarkers. Our freely available ESCLA (http://r2platform.com/escla/) is a rich resource for EwS research and highlights the power of comprehensive datasets to unravel principles of heterogeneous gene regulation by chimeric transcription factors.
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Affiliation(s)
- Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany
| | - Didier Surdez
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zürich, 8008 Zürich, Switzerland
| | - Tobias Faehling
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Anna C Ehlers
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Aruna Marchetto
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany
| | - Sandrine Grossetête
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France
| | - Richard Volckmann
- Department of Oncogenomics, Amsterdam University Medical Centers (AUMC), 1105 Amsterdam, the Netherlands
| | - Danny A Zwijnenburg
- Department of Oncogenomics, Amsterdam University Medical Centers (AUMC), 1105 Amsterdam, the Netherlands
| | - Julia S Gerke
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany
| | - Sakina Zaidi
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, 28029 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CB06/07/1009, CIBERER-ISCIII), 28029 Madrid, Spain
| | - Ana Sastre
- Unidad Hemato-oncología Pediátrica, Hospital Infantil Universitario La Paz, 28029 Madrid, Spain
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, 75005 Paris, France
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Florencia Cidre-Aranaz
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Shunya Ohmura
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich, 80337 Munich, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Eva Reischl
- Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Melissa Gymrek
- Division of Genetics, Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Department of Pediatric Hematology & Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Konstantin Strauch
- Institute of Medical Biometry, Epidemiology, and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Faculty of Medicine, LMU Munich, 81377 Munich, Germany
| | - Jan Koster
- Department of Oncogenomics, Amsterdam University Medical Centers (AUMC), 1105 Amsterdam, the Netherlands
| | - Olivier Delattre
- INSERM Unit 830 "Genetics and Biology of Cancers," Institut Curie Research Center, 75005 Paris, France
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany; Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
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30
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Hendrikse LD, Haldipur P, Saulnier O, Millman J, Sjoboen AH, Erickson AW, Ong W, Gordon V, Coudière-Morrison L, Mercier AL, Shokouhian M, Suárez RA, Ly M, Borlase S, Scott DS, Vladoiu MC, Farooq H, Sirbu O, Nakashima T, Nambu S, Funakoshi Y, Bahcheli A, Diaz-Mejia JJ, Golser J, Bach K, Phuong-Bao T, Skowron P, Wang EY, Kumar SA, Balin P, Visvanathan A, Lee JJY, Ayoub R, Chen X, Chen X, Mungall KL, Luu B, Bérubé P, Wang YC, Pfister SM, Kim SK, Delattre O, Bourdeaut F, Doz F, Masliah-Planchon J, Grajkowska WA, Loukides J, Dirks P, Fèvre-Montange M, Jouvet A, French PJ, Kros JM, Zitterbart K, Bailey SD, Eberhart CG, Rao AAN, Giannini C, Olson JM, Garami M, Hauser P, Phillips JJ, Ra YS, de Torres C, Mora J, Li KKW, Ng HK, Poon WS, Pollack IF, López-Aguilar E, Gillespie GY, Van Meter TE, Shofuda T, Vibhakar R, Thompson RC, Cooper MK, Rubin JB, Kumabe T, Jung S, Lach B, Iolascon A, Ferrucci V, de Antonellis P, Zollo M, Cinalli G, Robinson S, Stearns DS, Van Meir EG, Porrati P, Finocchiaro G, Massimino M, Carlotti CG, Faria CC, Roussel MF, Boop F, Chan JA, Aldinger KA, Razavi F, Silvestri E, McLendon RE, Thompson EM, Ansari M, Garre ML, Chico F, Eguía P, Pérezpeña M, Morrissy AS, Cavalli FMG, Wu X, Daniels C, Rich JN, Jones SJM, Moore RA, Marra MA, Huang X, Reimand J, Sorensen PH, Wechsler-Reya RJ, Weiss WA, Pugh TJ, Garzia L, Kleinman CL, Stein LD, Jabado N, Malkin D, Ayrault O, Golden JA, Ellison DW, Doble B, Ramaswamy V, Werbowetski-Ogilvie TE, Suzuki H, Millen KJ, Taylor MD. Author Correction: Failure of human rhombic lip differentiation underlies medulloblastoma formation. Nature 2022; 612:E12. [PMID: 36446943 PMCID: PMC10729707 DOI: 10.1038/s41586-022-05578-0] [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: 11/30/2022]
Affiliation(s)
- Liam D Hendrikse
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Parthiv Haldipur
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Olivier Saulnier
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jake Millman
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Alexandria H Sjoboen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Anders W Erickson
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Winnie Ong
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Victor Gordon
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Audrey L Mercier
- PSL Research University, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Institut Curie, Orsay, France
| | - Mohammad Shokouhian
- Department of Pediatrics and Child Health and Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Raúl A Suárez
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle Ly
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Borlase
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - David S Scott
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maria C Vladoiu
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Hamza Farooq
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Olga Sirbu
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Takuma Nakashima
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Shohei Nambu
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Yusuke Funakoshi
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Alec Bahcheli
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - J Javier Diaz-Mejia
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Joseph Golser
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Kathleen Bach
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Tram Phuong-Bao
- Department of Pediatrics and Child Health and Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Patryk Skowron
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Evan Y Wang
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Sachin A Kumar
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Polina Balin
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Abhirami Visvanathan
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - John J Y Lee
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ramy Ayoub
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Xin Chen
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xiaodi Chen
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Betty Luu
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pierre Bérubé
- McGill University Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Yu C Wang
- McGill University Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Seung-Ki Kim
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea
| | - Olivier Delattre
- SIREDO Oncology Center (Pediatric, Adolescent and Young Adults Oncology), Institut Curie, Paris, France
- INSERM U830, Institut Curie, Paris, France
| | - Franck Bourdeaut
- SIREDO Oncology Center (Pediatric, Adolescent and Young Adults Oncology), Institut Curie, Paris, France
- INSERM U830, Institut Curie, Paris, France
| | - François Doz
- SIREDO Oncology Center (Pediatric, Adolescent and Young Adults Oncology), Institut Curie, Paris, France
- Université Paris Cité, Paris, France
| | | | | | - James Loukides
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Dirks
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle Fèvre-Montange
- INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences, Université de Lyon, Lyon, France
- Centre de Pathologie EST, Groupement Hospitalier EST, Université de Lyon, Bron, France
| | - Anne Jouvet
- Centre de Pathologie EST, Groupement Hospitalier EST, Université de Lyon, Bron, France
| | - Pim J French
- Department of Neurology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Karel Zitterbart
- Department of Pediatric Oncology, Masaryk University School of Medicine, Brno, Czech Republic
| | - Swneke D Bailey
- Department of Surgery, Division of Thoracic and Upper Gastrointestinal Surgery, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Charles G Eberhart
- Departments of Pathology, Ophthalmology and Oncology, John Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amulya A N Rao
- Division of Pediatric Hematology/Oncology, Mayo Clinic, Rochester, MN, USA
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Miklós Garami
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Peter Hauser
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Young S Ra
- Department of Neurosurgery, University of Ulsan, Asan Medical Center, Seoul, South Korea
| | - Carmen de Torres
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Kay K W Li
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wai S Poon
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ian F Pollack
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Enrique López-Aguilar
- Division of Pediatric Hematology/Oncology, Hospital Pediatría Centro Médico Nacional century XXI, Mexico City, Mexico
| | - G Yancey Gillespie
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Timothy E Van Meter
- Pediatrics, Virginia Commonwealthy University, School of Medicine, Richmond, VA, USA
| | - Tomoko Shofuda
- Division of Stem Cell Research, Institute for Clinical Research, Osaka National Hospital, Osaka, Japan
| | - Rajeev Vibhakar
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, USA
| | - Reid C Thompson
- Department of Neurological Surgery, Vanderbilt Medical Center, Nashville, TN, USA
| | - Michael K Cooper
- Department of Neurology, Vanderbilt Medical Center, Nashville, TN, USA
| | - Joshua B Rubin
- Departments of Neuroscience, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Toshihiro Kumabe
- Department of Neurosurgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Shin Jung
- Department of Neurosurgery, Chonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical School, Hwasun-gun, South Korea
| | - Boleslaw Lach
- Department of Pathology and Molecular Medicine, Division of Anatomical Pathology, McMaster University, Hamilton, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Hamilton General Hospital, Hamilton, Ontario, Canada
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Veronica Ferrucci
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Pasqualino de Antonellis
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Massimo Zollo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Giuseppe Cinalli
- Department of Pediatric Neurosurgery, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Shenandoah Robinson
- Division of Pediatric Neurosurgery, Case Western Reserve, Cleveland, OH, USA
| | - Duncan S Stearns
- Department of Pediatrics-Hematology and Oncology, Case Western Reserve, Cleveland, OH, USA
| | - Erwin G Van Meir
- Department of Hematology and Medical Oncology, Emory University School of Medicine and Winship Cancer Institute, Atlanta, GA, USA
| | - Paola Porrati
- Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | | | | | - Carlos G Carlotti
- Department of Surgery and Anatomy, Faculty of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Claudia C Faria
- Division of Neurosurgery, Centro Hospitalar Lisboa Norte (CHULN), Hospital de Santa Maria, Lisbon, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Martine F Roussel
- Department of Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Frederick Boop
- Department of Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jennifer A Chan
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Ferechte Razavi
- Assistance Publique Hôpitaux de Paris, Hôpital Necker-Enfants Malades, Paris, France
| | - Evelina Silvestri
- Surgical Pathology Unit, San Camillo Forlanini Hospital, Rome, Italy
| | - Roger E McLendon
- Department of Pathology, Duke University, Durham, NC, USA
- Department of Neurosurgery, Duke University, Durham, NC, USA
| | - Eric M Thompson
- Department of Neurosurgery, Duke University, Durham, NC, USA
| | - Marc Ansari
- Cansearch Research Platform for Pediatric Oncology and Hematology, Faculty of Medicine, Department of Pediatrics, Gynecology and Obstetrics, University of Geneva, Geneva, Switzerland
- Division of Pediatric Oncology and Hematology, Department of Women, Child and Adolescent, University Geneva Hospitals, Geneva, Switzerland
| | - Maria L Garre
- U.O. Neurochirurgia, Istituto Giannina Gaslini, Genova, Italy
| | - Fernando Chico
- Department of Neurosurgery, Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico
| | - Pilar Eguía
- Department of Neurosurgery, Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico
| | - Mario Pérezpeña
- Instituto Nacional De Pediatría de México, Mexico City, Mexico
| | - A Sorana Morrissy
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Florence M G Cavalli
- INSERM U900, Institut Curie, Paris, France
- PSL Research University, Institut Curie, Paris, France
- CBIO-Centre for Computational Biology, PSL Research University, MINES ParisTech, Paris, France
| | - Xiaochong Wu
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Craig Daniels
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xi Huang
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jüri Reimand
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - William A Weiss
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Livia Garzia
- Cancer Research Program, McGill University Health Centre Research Institute, Montreal, Quebec, Canada
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Lincoln D Stein
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Adaptive Oncology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Nada Jabado
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Quebec, Canada
- The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - David Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Division of Haematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Olivier Ayrault
- PSL Research University, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Institut Curie, Orsay, France
| | - Jeffrey A Golden
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Brad Doble
- Department of Pediatrics and Child Health and Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Division of Haematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tamra E Werbowetski-Ogilvie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
| | - Hiromichi Suzuki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Kathleen J Millen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada.
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31
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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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32
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Delattre O, Vibert J, Saulnier O, Waterfall J. Abstract IA009: Oncogenic transcription factors drive highly tumor-specific LincRNA. Clin Cancer Res 2022. [DOI: 10.1158/1557-3265.sarcomas22-ia009] [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
Many cancers are characterized by gene fusions encoding oncogenic chimeric transcription factors (TFs) such as EWS::FLI1 in Ewing sarcoma (EwS). EWS::FLI1 induces a complete reprogramming of mesenchymal stem cells, the putative cell of origin of Ewing sarcoma, through binding and subsequent generation of thousands of neoenhancers at GGAA microsatellite repeats. We show that EWS::FLI1 induces the robust expression of a specific set of novel spliced and polyadenylated transcripts within otherwise transcriptionally silent regions of the genome. These neo-genes (NGs) are virtually undetectable in large collections of normal tissues or non-EwS tumors and can be silenced by CRISPR interference at regulatory EWS::FLI1-bound microsatellites. Ribosome profiling and proteomics further show that some NGs are translated into highly EwS-specific peptides. More generally, hundreds of NGs can be detected in diverse cancers characterized by chimeric TFs. Altogether, we identify the transcription, processing, and translation of novel, specific, highly expressed multi-exonic transcripts from otherwise silent regions of the genome as a new activity of aberrant TFs in cancer. These neotranscripts, which can be classified as LincRNAs, or neopeptides may have specific functions in the tumor cells. The latter may also constitute ideal neoepitopes as they are tumor-specific, clonally expressed in sarcoma cells, induced by the driver genetic alterations and public for a given sarcoma.
Citation Format: Olivier Delattre, Julien Vibert, Olivier Saulnier, Joshua Waterfall. Oncogenic transcription factors drive highly tumor-specific LincRNA [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr IA009.
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33
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Hendrikse LD, Haldipur P, Saulnier O, Millman J, Sjoboen AH, Erickson AW, Ong W, Gordon V, Coudière-Morrison L, Mercier AL, Shokouhian M, Suárez RA, Ly M, Borlase S, Scott DS, Vladoiu MC, Farooq H, Sirbu O, Nakashima T, Nambu S, Funakoshi Y, Bahcheli A, Diaz-Mejia JJ, Golser J, Bach K, Phuong-Bao T, Skowron P, Wang EY, Kumar SA, Balin P, Visvanathan A, Lee JJY, Ayoub R, Chen X, Chen X, Mungall KL, Luu B, Bérubé P, Wang YC, Pfister SM, Kim SK, Delattre O, Bourdeaut F, Doz F, Masliah-Planchon J, Grajkowska WA, Loukides J, Dirks P, Fèvre-Montange M, Jouvet A, French PJ, Kros JM, Zitterbart K, Bailey SD, Eberhart CG, Rao AAN, Giannini C, Olson JM, Garami M, Hauser P, Phillips JJ, Ra YS, de Torres C, Mora J, Li KKW, Ng HK, Poon WS, Pollack IF, López-Aguilar E, Gillespie GY, Van Meter TE, Shofuda T, Vibhakar R, Thompson RC, Cooper MK, Rubin JB, Kumabe T, Jung S, Lach B, Iolascon A, Ferrucci V, de Antonellis P, Zollo M, Cinalli G, Robinson S, Stearns DS, Van Meir EG, Porrati P, Finocchiaro G, Massimino M, Carlotti CG, Faria CC, Roussel MF, Boop F, Chan JA, Aldinger KA, Razavi F, Silvestri E, McLendon RE, Thompson EM, Ansari M, Garre ML, Chico F, Eguía P, Pérezpeña M, Morrissy AS, Cavalli FMG, Wu X, Daniels C, Rich JN, Jones SJM, Moore RA, Marra MA, Huang X, Reimand J, Sorensen PH, Wechsler-Reya RJ, Weiss WA, Pugh TJ, Garzia L, Kleinman CL, Stein LD, Jabado N, Malkin D, Ayrault O, Golden JA, Ellison DW, Doble B, Ramaswamy V, Werbowetski-Ogilvie TE, Suzuki H, Millen KJ, Taylor MD. Failure of human rhombic lip differentiation underlies medulloblastoma formation. Nature 2022; 609:1021-1028. [PMID: 36131014 PMCID: PMC10026724 DOI: 10.1038/s41586-022-05215-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/09/2022] [Indexed: 02/08/2023]
Abstract
Medulloblastoma (MB) comprises a group of heterogeneous paediatric embryonal neoplasms of the hindbrain with strong links to early development of the hindbrain1-4. Mutations that activate Sonic hedgehog signalling lead to Sonic hedgehog MB in the upper rhombic lip (RL) granule cell lineage5-8. By contrast, mutations that activate WNT signalling lead to WNT MB in the lower RL9,10. However, little is known about the more commonly occurring group 4 (G4) MB, which is thought to arise in the unipolar brush cell lineage3,4. Here we demonstrate that somatic mutations that cause G4 MB converge on the core binding factor alpha (CBFA) complex and mutually exclusive alterations that affect CBFA2T2, CBFA2T3, PRDM6, UTX and OTX2. CBFA2T2 is expressed early in the progenitor cells of the cerebellar RL subventricular zone in Homo sapiens, and G4 MB transcriptionally resembles these progenitors but are stalled in developmental time. Knockdown of OTX2 in model systems relieves this differentiation blockade, which allows MB cells to spontaneously proceed along normal developmental differentiation trajectories. The specific nature of the split human RL, which is destined to generate most of the neurons in the human brain, and its high level of susceptible EOMES+KI67+ unipolar brush cell progenitor cells probably predisposes our species to the development of G4 MB.
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Affiliation(s)
- Liam D Hendrikse
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Parthiv Haldipur
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Olivier Saulnier
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jake Millman
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Alexandria H Sjoboen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Anders W Erickson
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Winnie Ong
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Victor Gordon
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Audrey L Mercier
- PSL Research University, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Institut Curie, Orsay, France
| | - Mohammad Shokouhian
- Department of Pediatrics and Child Health and Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Raúl A Suárez
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle Ly
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Borlase
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - David S Scott
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maria C Vladoiu
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Hamza Farooq
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Olga Sirbu
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Takuma Nakashima
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Shohei Nambu
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Yusuke Funakoshi
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Alec Bahcheli
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - J Javier Diaz-Mejia
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Joseph Golser
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Kathleen Bach
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Tram Phuong-Bao
- Department of Pediatrics and Child Health and Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Patryk Skowron
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Evan Y Wang
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Sachin A Kumar
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Polina Balin
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Abhirami Visvanathan
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - John J Y Lee
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ramy Ayoub
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Xin Chen
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xiaodi Chen
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Betty Luu
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pierre Bérubé
- McGill University Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Yu C Wang
- McGill University Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Seung-Ki Kim
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea
| | - Olivier Delattre
- SIREDO Oncology Center (Pediatric, Adolescent and Young Adults Oncology), Institut Curie, Paris, France
- INSERM U830, Institut Curie, Paris, France
| | - Franck Bourdeaut
- SIREDO Oncology Center (Pediatric, Adolescent and Young Adults Oncology), Institut Curie, Paris, France
- INSERM U830, Institut Curie, Paris, France
| | - François Doz
- SIREDO Oncology Center (Pediatric, Adolescent and Young Adults Oncology), Institut Curie, Paris, France
- Université Paris Cité, Paris, France
| | | | | | - James Loukides
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Dirks
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle Fèvre-Montange
- INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences, Université de Lyon, Lyon, France
- Centre de Pathologie EST, Groupement Hospitalier EST, Université de Lyon, Bron, France
| | - Anne Jouvet
- Centre de Pathologie EST, Groupement Hospitalier EST, Université de Lyon, Bron, France
| | - Pim J French
- Department of Neurology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Karel Zitterbart
- Department of Pediatric Oncology, Masaryk University School of Medicine, Brno, Czech Republic
| | - Swneke D Bailey
- Department of Surgery, Division of Thoracic and Upper Gastrointestinal Surgery, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Charles G Eberhart
- Departments of Pathology, Ophthalmology and Oncology, John Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amulya A N Rao
- Division of Pediatric Hematology/Oncology, Mayo Clinic, Rochester, MN, USA
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Miklós Garami
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Peter Hauser
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Young S Ra
- Department of Neurosurgery, University of Ulsan, Asan Medical Center, Seoul, South Korea
| | - Carmen de Torres
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Kay K W Li
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wai S Poon
- Department of Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ian F Pollack
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Enrique López-Aguilar
- Division of Pediatric Hematology/Oncology, Hospital Pediatría Centro Médico Nacional century XXI, Mexico City, Mexico
| | - G Yancey Gillespie
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Timothy E Van Meter
- Pediatrics, Virginia Commonwealthy University, School of Medicine, Richmond, VA, USA
| | - Tomoko Shofuda
- Division of Stem Cell Research, Institute for Clinical Research, Osaka National Hospital, Osaka, Japan
| | - Rajeev Vibhakar
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, USA
| | - Reid C Thompson
- Department of Neurological Surgery, Vanderbilt Medical Center, Nashville, TN, USA
| | - Michael K Cooper
- Department of Neurology, Vanderbilt Medical Center, Nashville, TN, USA
| | - Joshua B Rubin
- Departments of Neuroscience, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Toshihiro Kumabe
- Department of Neurosurgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Shin Jung
- Department of Neurosurgery, Chonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical School, Hwasun-gun, South Korea
| | - Boleslaw Lach
- Department of Pathology and Molecular Medicine, Division of Anatomical Pathology, McMaster University, Hamilton, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Hamilton General Hospital, Hamilton, Ontario, Canada
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Veronica Ferrucci
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Pasqualino de Antonellis
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Massimo Zollo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche (DMMBM), University of Naples Federico II, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Giuseppe Cinalli
- Department of Pediatric Neurosurgery, Santobono-Pausilipon Children's Hospital, Naples, Italy
| | - Shenandoah Robinson
- Division of Pediatric Neurosurgery, Case Western Reserve, Cleveland, OH, USA
| | - Duncan S Stearns
- Department of Pediatrics-Hematology and Oncology, Case Western Reserve, Cleveland, OH, USA
| | - Erwin G Van Meir
- Department of Hematology and Medical Oncology, Emory University School of Medicine and Winship Cancer Institute, Atlanta, GA, USA
| | - Paola Porrati
- Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | | | | | - Carlos G Carlotti
- Department of Surgery and Anatomy, Faculty of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Claudia C Faria
- Division of Neurosurgery, Centro Hospitalar Lisboa Norte (CHULN), Hospital de Santa Maria, Lisbon, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Martine F Roussel
- Department of Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Frederick Boop
- Department of Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jennifer A Chan
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Ferechte Razavi
- Assistance Publique Hôpitaux de Paris, Hôpital Necker-Enfants Malades, Paris, France
| | - Evelina Silvestri
- Surgical Pathology Unit, San Camillo Forlanini Hospital, Rome, Italy
| | - Roger E McLendon
- Department of Pathology, Duke University, Durham, NC, USA
- Department of Neurosurgery, Duke University, Durham, NC, USA
| | - Eric M Thompson
- Department of Neurosurgery, Duke University, Durham, NC, USA
| | - Marc Ansari
- Cansearch Research Platform for Pediatric Oncology and Hematology, Faculty of Medicine, Department of Pediatrics, Gynecology and Obstetrics, University of Geneva, Geneva, Switzerland
- Division of Pediatric Oncology and Hematology, Department of Women, Child and Adolescent, University Geneva Hospitals, Geneva, Switzerland
| | - Maria L Garre
- U.O. Neurochirurgia, Istituto Giannina Gaslini, Genova, Italy
| | - Fernando Chico
- Department of Neurosurgery, Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico
| | - Pilar Eguía
- Department of Neurosurgery, Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico
| | - Mario Pérezpeña
- Instituto Nacional De Pediatría de México, Mexico City, Mexico
| | - A Sorana Morrissy
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Florence M G Cavalli
- INSERM U900, Institut Curie, Paris, France
- PSL Research University, Institut Curie, Paris, France
- CBIO-Centre for Computational Biology, PSL Research University, MINES ParisTech, Paris, France
| | - Xiaochong Wu
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Craig Daniels
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xi Huang
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jüri Reimand
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - William A Weiss
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Livia Garzia
- Cancer Research Program, McGill University Health Centre Research Institute, Montreal, Quebec, Canada
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Lincoln D Stein
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Adaptive Oncology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Nada Jabado
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Quebec, Canada
- The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - David Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Division of Haematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Olivier Ayrault
- PSL Research University, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Institut Curie, Orsay, France
| | - Jeffrey A Golden
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Brad Doble
- Department of Pediatrics and Child Health and Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Division of Haematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tamra E Werbowetski-Ogilvie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
| | - Hiromichi Suzuki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Kathleen J Millen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada.
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34
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Costa A, Thirant C, Kramdi A, Pierre-Eugène C, Louis-Brennetot C, Blanchard O, Surdez D, Gruel N, Lapouble E, Pierron G, Sitbon D, Brisse H, Gauthier A, Fréneaux P, Bohec M, Raynal V, Baulande S, Leclere R, Champenois G, Nicolas A, Meseure D, Bellini A, Marabelle A, Geoerger B, Mechta-Grigoriou F, Schleiermacher G, Menger L, Delattre O, Janoueix-Lerosey I. Single-cell transcriptomics reveals shared immunosuppressive landscapes of mouse and human neuroblastoma. J Immunother Cancer 2022; 10:jitc-2022-004807. [PMID: 36054452 PMCID: PMC9362821 DOI: 10.1136/jitc-2022-004807] [Citation(s) in RCA: 6] [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] [Accepted: 06/21/2022] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND High-risk neuroblastoma is a pediatric cancer with still a dismal prognosis, despite multimodal and intensive therapies. Tumor microenvironment represents a key component of the tumor ecosystem the complexity of which has to be accurately understood to define selective targeting opportunities, including immune-based therapies. METHODS We combined various approaches including single-cell transcriptomics to dissect the tumor microenvironment of both a transgenic mouse neuroblastoma model and a cohort of 10 biopsies from neuroblastoma patients, either at diagnosis or at relapse. Features of related cells were validated by multicolor flow cytometry and functional assays. RESULTS We show that the immune microenvironment of MYCN-driven mouse neuroblastoma is characterized by a low content of T cells, several phenotypes of macrophages and a population of cells expressing signatures of myeloid-derived suppressor cells (MDSCs) that are molecularly distinct from the various macrophage subsets. We document two cancer-associated fibroblasts (CAFs) subsets, one of which corresponding to CAF-S1, known to have immunosuppressive functions. Our data unravel a complex content in myeloid cells in patient tumors and further document a striking correspondence of the microenvironment populations between both mouse and human tumors. We show that mouse intratumor T cells exhibit increased expression of inhibitory receptors at the protein level. Consistently, T cells from patients are characterized by features of exhaustion, expressing inhibitory receptors and showing low expression of effector cytokines. We further functionally demonstrate that MDSCs isolated from mouse neuroblastoma have immunosuppressive properties, impairing the proliferation of T lymphocytes. CONCLUSIONS Our study demonstrates that neuroblastoma tumors have an immunocompromised microenvironment characterized by dysfunctional T cells and accumulation of immunosuppressive cells. Our work provides a new and precious data resource to better understand the neuroblastoma ecosystem and suggest novel therapeutic strategies, targeting both tumor cells and components of the microenvironment.
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Affiliation(s)
- Ana Costa
- Inserm U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Centre, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Cécile Thirant
- Inserm U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Centre, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Amira Kramdi
- Inserm U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Centre, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Cécile Pierre-Eugène
- Inserm U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Centre, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Caroline Louis-Brennetot
- Inserm U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Centre, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Orphée Blanchard
- Inserm U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Centre, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Didier Surdez
- Inserm U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Centre, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Nadege Gruel
- Inserm U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Centre, Paris, France.,Department of Translational Research, Institut Curie, Paris, France
| | - Eve Lapouble
- Unité de Génétique Somatique, Institut Curie, Paris, France
| | - Gaëlle Pierron
- Unité de Génétique Somatique, Institut Curie, Paris, France
| | - Deborah Sitbon
- Unité de Génétique Somatique, Institut Curie, Paris, France
| | - Hervé Brisse
- Department of Imaging, PSL Research University, Institut Curie, Paris, France
| | | | - Paul Fréneaux
- Department of Biopathology, Institut Curie, Paris, France
| | - Mylène Bohec
- Genomics of Excellence (ICGex) Platform, Institut Curie, Paris, France
| | - Virginie Raynal
- Inserm U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Centre, Paris, France.,Genomics of Excellence (ICGex) Platform, Institut Curie, Paris, France
| | - Sylvain Baulande
- Genomics of Excellence (ICGex) Platform, Institut Curie, Paris, France
| | - Renaud Leclere
- Department of Biopathology, Institut Curie, Paris, France
| | | | - Andre Nicolas
- Department of Biopathology, Institut Curie, Paris, France
| | - Didier Meseure
- Department of Biopathology, Institut Curie, Paris, France
| | - Angela Bellini
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.,Department of Translational Research, Institut Curie, Paris, France.,Laboratory Recherche Translationnelle en Oncologie Pédiatrique (RTOP), Laboratoire "Gilles Thomas", Institut Curie, Paris, France
| | - Aurelien Marabelle
- Inserm U1015 & CIC1428, Université Paris Saclay, Gustave Roussy, Villejuif, France
| | - Birgit Geoerger
- Inserm U1015, Department of Pediatric and Adolescent Oncology, Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Fatima Mechta-Grigoriou
- Inserm U830, Equipe labelisée LNCC, Stress and Cancer Laboratory, PSL Research University, Institut Curie Research Centre, Paris, France
| | - Gudrun Schleiermacher
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.,Department of Translational Research, Institut Curie, Paris, France.,Laboratory Recherche Translationnelle en Oncologie Pédiatrique (RTOP), Laboratoire "Gilles Thomas", Institut Curie, Paris, France
| | - Laurie Menger
- Inserm U932, PSL Research University, Institut Curie, Paris, France
| | - Olivier Delattre
- Inserm U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Centre, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Isabelle Janoueix-Lerosey
- Inserm U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Centre, Paris, France .,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
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35
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Sarikas BR, Ilg M, Markovic M, Sturtzel C, Scheuringer E, Zulini J, Metzelder M, Halbritter F, Distel M, Surdez D, Delattre O, Ovsianikov A, Kovar H. Abstract 6245: 3D-models of pediatric bone sarcomas for personalized therapeutic screening. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-6245] [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
Osteosarcoma (OS) and Ewing sarcoma (ES) are the most common bone cancers in children. They are rare cancers and thus difficult to study due to scarcity of patient material, large genomic instability and a wide histological heterogeneity (in OS) or a lack of satisfactory transgenic animal model and availability of preclinical tests (in ES). There is a dire need for new models and novel therapeutic approaches. Although patient-derived xenografts (PDXs) may recapitulate human tumor biology and predict drug response, propagating PDXs in mice limits its use as a drug-testing platform.
We have established and standardized ES and OS spheroid culture and developed a semi-automated drug-screening platform in tumor spheroids. We established several robust techniques for spheroid formation, with clear pathophysiological gradients, but without central necroses at the onset of drug treatment. We performed RNA-seq comparing spheroid transcription profiles to 2D culture and observed dramatic changes in overall expression patterns. We observed upregulation of genes shown to correlate with poor prognosis in OS patients. We saw upregulation of processes associated with regulation of cell migration, negative regulation of proliferation and modulation of the extracellular matrix (ECM). In addition to ES spheroid models, we created bioprinted 3D-models of ES cell lines and of cells obtained from ES PDXs, using extrusion bioprinting techniques (where cells are encapsulated within the cross-linked polymers, thus allowing homogeneous distribution and high cell density). PDX-derived cells were kept in liquid culture and as 3D-bioprinted constructs, while their transcription profiles were compared with the initial PDX. The mevalonate pathway was the most overrepresented in all ES 3D-models, consistent with predominant upregulation of this metabolic pathway integral to tumor growth and progression. After 15 days in 3D-bioprinted culture, we observed pronounced upregulation of genes involved in ECM signaling, suggesting that the construct promoted in vivo-like tumor-ECM interactions, without further promoting main proliferation and cell survival pathways, which was observed in liquid culture. Furthermore, we showed potential for combinatorial treatment with statins and confirmed feasibility of drug testing in patient-derived 3D models.
Finally, as our spheroid models showed upregulation of many processes involved in metastasis (genes associated with invasion, migration, angiogenesis and hypoxia), we focused on lung as the most common site of metastasis in ES and OS patients. We are thus establishing mixed airway organoid/tumoroid cultures, to investigate further the lung metastatic niche, with a goal to provide proof of concept for patient-specific 3D-models of lung metastatic tumors to guide personalized drug selection for patients with advanced disease.
Citation Format: Branka Radic Sarikas, Mathias Ilg, Marica Markovic, Caterina Sturtzel, Eva Scheuringer, Justine Zulini, Martin Metzelder, Florian Halbritter, Martin Distel, Didier Surdez, Olivier Delattre, Aleksandr Ovsianikov, Heinrich Kovar. 3D-models of pediatric bone sarcomas for personalized therapeutic screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6245.
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Affiliation(s)
| | - Mathias Ilg
- 1St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Marica Markovic
- 2Institute of Materials Science and Technology, TU Wien, Vienna, Austria
| | | | - Eva Scheuringer
- 1St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Justine Zulini
- 3Inserm U830, Équipe Labellisé lncc, Psl Université, Siredo Oncology Centre, Institut Curie, Paris, France
| | - Martin Metzelder
- 4Department of Pediatric Surgery, Medical University Of Vienna, Vienna, Austria
| | | | - Martin Distel
- 1St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Didier Surdez
- 3Inserm U830, Équipe Labellisé lncc, Psl Université, Siredo Oncology Centre, Institut Curie, Paris, France
| | - Olivier Delattre
- 3Inserm U830, Équipe Labellisé lncc, Psl Université, Siredo Oncology Centre, Institut Curie, Paris, France
| | | | - Heinrich Kovar
- 1St. Anna Children's Cancer Research Institute, Vienna, Austria
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Tauziède-Espariat A, Guerrini-Rousseau L, Perrier A, Torrejon J, Bernardi F, Filser M, Varlet P, De Carli E, Pagnier A, Leblond P, Faure-Conter C, Doz F, Bertozzi AI, Mansuy L, Willems M, Palenzuela G, Entz-Werle N, Bourneix C, Hasty L, Delattre O, Blauwblomme T, Beccaria K, Metais A, Ayrault O, Chrétien F, Bourdeaut F, Dufour C, Masliah-Planchon J. MEDB-84. The French experience of ELP1-related medulloblastomas. Neuro Oncol 2022. [PMCID: PMC9165016 DOI: 10.1093/neuonc/noac079.458] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Medulloblastoma (MB), the most frequent embryonic tumor of the cerebellum is classified into four molecular subgroups (WNT group, SHH group, group 3 and group 4). Although the vast majority of MB are sporadic, predisposing genetic diseases have been described in rare WNT MB and more frequently in the SHH group. In a recent pediatric series of SHH-MB, germline alterations of the ELP1 gene have been described in 14% of cases, making this gene the most frequent genetic predisposition in MB. We have investigated the potential interest of ELP1 immunostaining on a large cohort of 132 MB. A complete loss of ELP1 staining was observed in 12 SHH MB (among 57 total SHH MB: 21%). The loss of ELP1 immunostaining was well correlated with the presence of a bi-allelic alteration of the gene except for one case for which the MB had a loss of ELP1 protein expression demonstrated by immunohistochemistry (IHC) and confirmed by whole proteome analysis, although no obvious genetic alteration in the coding sequence of ELP1 could be found. Molecular analysis of a large “molecular” cohort of 266 MB from French centers for which somatic ELP1 was sequenced allows to identify 12 additional MB with bi-allelic ELP1 genetic alterations. Our results demonstrate the benefit of the ELP1 IHC as an accurate and reliable tool to screen ELP1-deficient MB. This new immunohistochemical tool will now be advantageously used to screen SHH MB upfront for genetic alteration in ELP1, and will subsequently help orientating these patients towards genetic counseling.
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Affiliation(s)
| | - Léa Guerrini-Rousseau
- Department of Children and Adolescents Oncology, Gustave Roussy , Villejuif , France
| | - Alexandre Perrier
- Laboratory of Somatic Genetics, Curie Institute Hospital , Paris , France
| | - Jacob Torrejon
- Université Paris Sud, Université Paris-Saclay, CNRS UMR3347, INSERM U1021 , Orsay , France
| | - Flavia Bernardi
- Université Paris Sud, Université Paris-Saclay, CNRS UMR3347, INSERM U1021 , Orsay , France
| | - Mathilde Filser
- Laboratory of Somatic Genetics, Curie Institute Hospital , Paris , France
| | - Pascale Varlet
- Department of Neuropathology, GHU Paris, Sainte-Anne Hospital , Paris , France
| | | | - Anne Pagnier
- Department of Pediatrics, CHU de Grenoble , Grenoble , France
| | - Pierre Leblond
- Institut d'hématologie et d'oncologie pédiatrique, Centre Léon Bérard , Lyon , France
| | - Cécile Faure-Conter
- Institut d'hématologie et d'oncologie pédiatrique, Centre Léon Bérard , Lyon , France
| | - Francois Doz
- SIREDO Center Care, Innovation, Research In Pediatric, Adolescent and Young Adult Oncology, Curie Institute , Paris , France
| | | | - Ludovic Mansuy
- Department of Pediatric onco-hematology, CHU de Nancy , Nancy , France
| | | | | | - Natacha Entz-Werle
- Department of Pediatric onco-hematology, CHU de Strasbourg , Strasbourg , France
| | - Christine Bourneix
- Laboratory of Somatic Genetics, Curie Institute Hospital , Paris , France
| | - Lauren Hasty
- Department of Neuropathology, GHU Paris, Sainte-Anne Hospital , Paris , France
| | - Olivier Delattre
- Laboratory of Somatic Genetics, Curie Institute Hospital , Paris , France
| | | | - Kevin Beccaria
- Department of Pediatric Neurosurgery, Necker Hospital , Paris , France
| | - Alice Metais
- Department of Neuropathology, GHU Paris, Sainte-Anne Hospital , Paris , France
| | - Olivier Ayrault
- Université Paris Sud, Université Paris-Saclay, CNRS UMR3347, INSERM U1021 , Orsay , France
| | - Fabrice Chrétien
- Department of Neuropathology, GHU Paris, Sainte-Anne Hospital , Paris , France
| | - Franck Bourdeaut
- SIREDO Center Care, Innovation, Research In Pediatric, Adolescent and Young Adult Oncology, Curie Institute , Paris , France
| | - Christelle Dufour
- Department of Children and Adolescents Oncology, Gustave Roussy , Villejuif , France
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Filser M, Hamza A, Girard E, Servant N, Renault V, Merchadou K, Bourneix C, Varlet P, Uro-Coste E, Tauziède-Espariat A, Doz F, Bourdeaut F, Delattre O, Masliah-Planchon J. PATH-12. A new powerful tool to simultaneously deliver DNA methylation profile and driver fusions detection based on Nanopore Sequencing. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.596] [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
The fast advances in molecular biology have led to the discovery of new genetic and epigenetic driver events that play a key role in the pathogenesis of central nervous system (CNS) tumors. These data showed the importance of molecular biology, and in particular methylation profiling and fusion detection, to complete the histological examination. Exploring all these complex genomic and epigenomic alterations with the technologies implemented in the routine diagnosis requires massive laboratory equipment. In addition, it could take weeks before getting data that could be important to adapt the diagnosis, prognosis, and to ultimately guide the treatment’s choice. We describe the innovative potential of a nanopore sequencing device to obtain fast and multiple information to characterize CNS tumors. Adaptive-sampling is a software-controlled enrichment unique method that allows simultaneous methylation profiling, copy number landscape assessment, and fusion gene detection. Thereby, this technology brings comprehensive molecular information that could be very important for CNS tumor classification in a very short delay (below one week) and with a relative low cost compared to the combined other molecular analysis needed to get the same information. We report ten cases of diverse CNS tumors with already known oncogenic structural variants such as YAP1-MAMLD1 fused ependymoma, CNS neuroblastoma with FOXR2 activation, CNS high-grade neuroepithelial tumor with BCOR and MEN1 alteration, and atypical teratoid rhabdoid tumors (ATRT). For these tumors, using adaptive sampling with the nanopore sequencing, we were able to detect fusion genes as driver events, while obtaining at the same time the methylation profile to corroborate the tumor classification. Our results with this combined approach, never described before, demonstrate its feasibility as a new extremely powerful tool and show remarkable perspectives for this technology to bring a fast and comprehensive tumor molecular characterization.
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Affiliation(s)
| | | | | | | | - Victor Renault
- Clinical Bioinformatics, Institut Curie , Paris , France
| | | | | | - Pascale Varlet
- Department of Neuropathology, GHU Paris, Sainte-Anne Hospital , Paris , France
| | - Emmanuelle Uro-Coste
- Department of Pathology, Institut Universitaire du Cancer de Toulouse , Toulouse , France
| | | | - Francois Doz
- Pediatric department, Institut Curie , Paris , France
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Lobon-Iglesias M, Andrianteranagna M, Han ZY, Masliah-Planchon J, Tauziede-Espariat A, Frah M, Dufour C, Chauvin C, Bouarich R, Manriquez V, Turczinski S, Delattre O, Baulande S, Ayrault O, Servant N, Beccaria K, Dangouloff-Ros V, Bourdeaut F. ATRT-11. Anatomico-biological correlations define a new layer for ATRT molecular subgroups pointing to potential lineages of origin. Neuro Oncol 2022. [PMCID: PMC9165327 DOI: 10.1093/neuonc/noac079.010] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Atypical teratoid rhabdoid tumors (ATRT) are divided in three molecular subgroups, the so-called MYC, TYR and SHH subgroups. This heterogeneity suggests some diversity in the cells of origin, which remain hypothetical thus far. A careful radiological review of 55 MRI at diagnosis was performed in parallel with a careful analysis of mouse tumor origin in the Rosa26-CreERT2::Smarcbflox/flox model. Methylation, bulk RNAseq and scRNAseq analyses were integrated to these anatomic information to highlight potential origin for each molecularly and anatomically defined subgroups. We demonstrated that mouse Myc-ATRTs derive from extra-parenchymal meningeal areas, a finding consistant with many human MYC ATRT being clearly of intra-cranial extra-axial origin. Although this finding could point to a neural crest origin, transcriptomic features fail to unravel any lineage-specific signature. We also defined a distinct supra-tentorial SHH ATRT subgroup, characterized both in mouse and Humans by neural features pointing to the ganglionic eminence progenitors as the candidate origin. Finally we identified a distinct infra-tentorial SHH ATRT subgroup, not observed in mice, with hindbrain/midbrain boundary progenitor signature. scRNAseq from human SHH infra-tentorial tumors consistently suggest a dedifferentiation process involving the Notch pathway in the oncogenic transformation of hindbrain/midbrain neural progenitors.
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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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Masliah-Planchon J, Maillot L, Rybak N, Simaga F, Hamza A, Villars MG, Delattre O, Bourdeaut F. ATRT-21. Contribution of germline mosaic alterations of SMARCB1 in rhabdoid tumor predisposition syndrome. Neuro Oncol 2022. [PMCID: PMC9164641 DOI: 10.1093/neuonc/noac079.020] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Rhabdoid tumors are rare and aggressive tumors that usually arise in very young children. They are characterized by a bi-allelic inactivation of the SMARCB1 gene. Although the majority of alterations of SMARCB1 are acquired in tumors, a heterozygous germline alteration is seen in one third of patients and defines the rhabdoid tumors predisposition syndrome. Penetrance is almost complete and the vast majority of germline alterations of SMARCB1 are acquired de novo but rare familial cases with a healthy carrier have also been described. Since the advent of more sensitive molecular analysis technologies such as next-generation sequencing (NGS), the number of mosaicisms of genes involved in genetic diseases discovered from blood samples has increased considerably. The aim of our study was to explore the mosaicisms of SMARCB1 in the blood 1/ of children with rhabdoid tumors with at least one alteration of SMARCB1 previously identified in the tumor but not found in the blood with old-fashioned low-sensitivity technologies and 2/ in parents of children with heterozygous germline alteration of SMARCB1. We analyzed a custom NGS panel which covers the SMARCB1 gene with an average depth of 1.500X on blood samples of 111 children with rhabdoid tumors and 32 parents collected at the Institut Curie since 1999. The mosaicism rate found in index cases was 11.7% (13/111) and 3.1% (1/32) in parents. The variant allele frequency vary from 0.8% to 12.9%. Our results also indicate to be cautious about the possible confounding effect of circulating tumor DNA. This hitherto underestimated SMARCB1 mosaicism rate should motivate an optimization of the genetic counseling as well as the oncological monitoring of these children and thus have a significant medical impact given the catastrophic prognosis of rhabdoid tumors.
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Affiliation(s)
| | | | - Noémie Rybak
- Oncogenetic department, Institut Curie , Paris , France
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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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Bouchoucha Y, Tauziède-Espariat A, Gauthier A, Guillemot D, Bochaton D, Vibert J, Carton M, Watson S, Grossetete S, Quignot C, Orbach D, Corradini N, Schleiermacher G, Bourdeaut F, Simbozel M, Dufour C, Minard V, Brahmi M, Tirode F, Pissaloux D, Karanian M, Machet MC, Masliah-Planchon J, Delattre O, Cardoen L, Pierron G, Doz F. ETMR-03. Intra- and extra-cranial BCOR-ITD tumours are separate entities within the BCOR-rearranged family. Neuro Oncol 2022. [PMCID: PMC9165185 DOI: 10.1093/neuonc/noac079.181] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BCOR-ITD tumours form an emerging family of aggressive entities with an internal tandem duplication (ITD) in the last exon of the BCOR gene. The family includes cerebral tumours, termed central nervous system BCOR-ITD (CNS BCOR-ITD), and sarcomatous types described in the kidney as clear cell sarcoma of the kidney (CCSK), in the endometrium as high-grade endometrial stromal sarcoma (HG-ESS), in bone, and in soft tissue as undifferentiated round cell sarcoma (URCS) or primitive myxoid mesenchymal tumour of infancy (PMMTI). Based on a series of 33 retrospective cases, including 10 CNS BCOR-ITD and 23 BCOR-ITD sarcomas, we interrogated the homogeneity of the entity regarding clinical, radiological and histopathological findings, and molecular signatures. Whole transcriptomic sequencing and DNA methylation profiling were used for unsupervised clustering. Histopathological review revealed marked differences between CNS BCOR-ITD and BCOR-ITD sarcomas. These two groups were consistently segregated by unsupervised clustering of expression (n=22) and DNA methylation (n=21) data. Proximity between the two groups may result from common somatic changes within key pathways directly related to the novel activity of the ITD itself. Conversely, comparison of gene signatures with single-cell RNAseq atlases suggests that the distinction between BCOR-ITD sarcomas and CNS BCOR-ITD may result from differences in cells of origin.
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Boller D, Doepfner KT, Laurentiis ADE, Guerreiro AS, Marinov M, Shalaby T, Depledge P, Robson A, Saghir N, Hayakawa M, Kaizawa H, Koizumi T, Ohishi T, Fattet S, Delattre O, Schweri-Olac A, Höland K, Grotzer MA, Frei K, Spertini O, Waterfield MD, Arcaro A. Republication: Targeting PI3KC2β Impairs Proliferation and Survival in Acute Leukemia, Brain Tumours and Neuroendocrine Tumours. Anticancer Res 2022; 42:3217-3230. [PMID: 35641277 DOI: 10.21873/anticanres.15812] [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: 03/21/2012] [Revised: 04/20/2012] [Accepted: 04/23/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND Eight human catalytic phosphoinositide 3-kinase (PI3K) isoforms exist which are subdivided into three classes. While class I isoforms have been well-studied in cancer, little is known about the functions of class II PI3Ks. MATERIALS AND METHODS The expression pattern and functions of the class II PI3KC2β isoform were investigated in a panel of tumour samples and cell lines. RESULTS Overexpression of PI3KC2β was found in subsets of tumours and cell lines from acute myeloid leukemia (AML), glioblastoma multiforme (GBM), medulloblastoma (MB), neuroblastoma (NB), and small cell lung cancer (SCLC). Specific pharmacological inhibitors of PI3KC2β or RNA interference impaired proliferation of a panel of human cancer cell lines and primary cultures. Inhibition of PI3KC2β also induced apoptosis and sensitised the cancer cells to chemotherapeutic agents. CONCLUSION Together, these data show that PI3KC2β contributes to proliferation and survival in AML, brain tumours and neuroendocrine tumours, and may represent a novel target in these malignancies.
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Affiliation(s)
- Danielle Boller
- Division of Clinical Chemistry and Biochemistry, and University Children's Hospital Zurich, Zurich, Switzerland
| | - Kathrin T Doepfner
- Division of Clinical Chemistry and Biochemistry, and University Children's Hospital Zurich, Zurich, Switzerland
| | - Angela DE Laurentiis
- Division of Clinical Chemistry and Biochemistry, and University Children's Hospital Zurich, Zurich, Switzerland
| | - Ana S Guerreiro
- Division of Clinical Chemistry and Biochemistry, and University Children's Hospital Zurich, Zurich, Switzerland
| | - Marin Marinov
- Division of Clinical Chemistry and Biochemistry, and University Children's Hospital Zurich, Zurich, Switzerland
| | - Tarek Shalaby
- Department of Oncology, University Children's Hospital Zurich, Zurich, Switzerland
| | | | | | | | | | | | | | - Takahide Ohishi
- Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Japan
| | | | | | | | - Katrin Höland
- Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Michael A Grotzer
- Department of Oncology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Karl Frei
- Department of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
| | - Olivier Spertini
- Service and Central Laboratory of Hematology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Michael D Waterfield
- PIramed, Slough, Berkshire, U.K.,Ludwig Institute for Cancer Research, Proteomics Unit, London, U.K
| | - Alexandre Arcaro
- Division of Clinical Chemistry and Biochemistry, and University Children's Hospital Zurich, Zurich, Switzerland; .,Department of Clinical Research, University of Bern, Bern, Switzerland
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Buchou C, Laud-Duval K, van der Ent W, Grossetête S, Zaidi S, Gentric G, Corbé M, Müller K, Del Nery E, Surdez D, Delattre O. Upregulation of the Mevalonate Pathway through EWSR1-FLI1/EGR2 Regulatory Axis Confers Ewing Cells Exquisite Sensitivity to Statins. Cancers (Basel) 2022; 14:cancers14092327. [PMID: 35565457 PMCID: PMC9100622 DOI: 10.3390/cancers14092327] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The objective of this project was to search for new dependencies in Ewing sarcoma, a deadly disease for which new therapeutic approaches are urgently needed. A pharmacological screening of off-patent approved drugs (FDA agency) and the investigation of downstream targets of EGR2 were performed. The two approaches showed the MVA pathway as a major dependency in Ewing sarcoma and statin, an inhibitor of this pathway, as a potential new therapeutic agent for the treatment of Ewing sarcoma. Abstract Ewing sarcoma (EwS) is an aggressive primary bone cancer in children and young adults characterized by oncogenic fusions between genes encoding FET-RNA-binding proteins and ETS transcription factors, the most frequent fusion being EWSR1-FLI1. We show that EGR2, an Ewing-susceptibility gene and an essential direct target of EWSR1-FLI1, directly regulates the transcription of genes encoding key enzymes of the mevalonate (MVA) pathway. Consequently, Ewing sarcoma is one of the tumors that expresses the highest levels of mevalonate pathway genes. Moreover, genome-wide screens indicate that MVA pathway genes constitute major dependencies of Ewing cells. Accordingly, the statin inhibitors of HMG-CoA-reductase, a rate-limiting enzyme of the MVA pathway, demonstrate cytotoxicity in EwS. Statins induce increased ROS and lipid peroxidation levels, as well as decreased membrane localization of prenylated proteins, such as small GTP proteins. These metabolic effects lead to an alteration in the dynamics of S-phase progression and to apoptosis. Statin-induced effects can be rescued by downstream products of the MVA pathway. Finally, we further show that statins impair tumor growth in different Ewing PDX models. Altogether, the data show that statins, which are off-patent, well-tolerated, and inexpensive compounds, should be strongly considered in the therapeutic arsenal against this deadly childhood disease.
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Affiliation(s)
- Charlie Buchou
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
| | - Karine Laud-Duval
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
| | - Wietske van der Ent
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
| | - Sandrine Grossetête
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
| | - Sakina Zaidi
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
| | - Géraldine Gentric
- INSERM U830, Équipe Labellisée LNCC, Stress and Cancer Laboratory, PSL Research University, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France;
| | - Maxime Corbé
- Department of Translational Research, The Biophenics High-Content Screening Laboratory, PSL Research University, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (M.C.); (K.M.); (E.D.N.)
| | - Kévin Müller
- Department of Translational Research, The Biophenics High-Content Screening Laboratory, PSL Research University, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (M.C.); (K.M.); (E.D.N.)
| | - Elaine Del Nery
- Department of Translational Research, The Biophenics High-Content Screening Laboratory, PSL Research University, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (M.C.); (K.M.); (E.D.N.)
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
- Balgrist University Hospital, University of Zurich, Zurich, Forchstrasse 340, 8008 Zürich, Switzerland
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
- Correspondence:
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Vibert J, Saulnier O, Collin C, Petit F, Borgman KJE, Vigneau J, Gautier M, Zaidi S, Pierron G, Watson S, Gruel N, Hénon C, Postel-Vinay S, Deloger M, Raynal V, Baulande S, Laud-Duval K, Hill V, Grossetête S, Dingli F, Loew D, Torrejon J, Ayrault O, Orth MF, Grünewald TGP, Surdez D, Coulon A, Waterfall JJ, Delattre O. Oncogenic chimeric transcription factors drive tumor-specific transcription, processing, and translation of silent genomic regions. Mol Cell 2022; 82:2458-2471.e9. [PMID: 35550257 DOI: 10.1016/j.molcel.2022.04.019] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/20/2022] [Accepted: 04/14/2022] [Indexed: 12/11/2022]
Abstract
Many cancers are characterized by gene fusions encoding oncogenic chimeric transcription factors (TFs) such as EWS::FLI1 in Ewing sarcoma (EwS). Here, we find that EWS::FLI1 induces the robust expression of a specific set of novel spliced and polyadenylated transcripts within otherwise transcriptionally silent regions of the genome. These neogenes (NGs) are virtually undetectable in large collections of normal tissues or non-EwS tumors and can be silenced by CRISPR interference at regulatory EWS::FLI1-bound microsatellites. Ribosome profiling and proteomics further show that some NGs are translated into highly EwS-specific peptides. More generally, we show that hundreds of NGs can be detected in diverse cancers characterized by chimeric TFs. Altogether, this study identifies the transcription, processing, and translation of novel, specific, highly expressed multi-exonic transcripts from otherwise silent regions of the genome as a new activity of aberrant TFs in cancer.
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Affiliation(s)
- Julien Vibert
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Olivier Saulnier
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Céline Collin
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Floriane Petit
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Kyra J E Borgman
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR 3664, Laboratoire Dynamique du Noyau, 75005 Paris, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Jérômine Vigneau
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Maud Gautier
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Sakina Zaidi
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Gaëlle Pierron
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Sarah Watson
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; Medical Oncology Department, PSL Research University, Institut Curie Hospital, Paris, France
| | - Nadège Gruel
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Clémence Hénon
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Sophie Postel-Vinay
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France; Drug Development Department, DITEP, Gustave Roussy, Villejuif, France
| | - Marc Deloger
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
| | - Virginie Raynal
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Research University, Institut Curie Research Center, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Research University, Institut Curie Research Center, Paris, France
| | - Karine Laud-Duval
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Véronique Hill
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Sandrine Grossetête
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Florent Dingli
- Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Institut Curie Research Center, Paris, France
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Institut Curie Research Center, Paris, France
| | - Jacob Torrejon
- Institut Curie, CNRS UMR3347, INSERM, PSL Research University, Orsay, France; CNRS UMR 3347, INSERM U1021, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Olivier Ayrault
- Institut Curie, CNRS UMR3347, INSERM, PSL Research University, Orsay, France; CNRS UMR 3347, INSERM U1021, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Thomas G P Grünewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Antoine Coulon
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR 3664, Laboratoire Dynamique du Noyau, 75005 Paris, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Joshua J Waterfall
- INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France.
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR 3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.
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Berlanga P, Pierron G, Lacroix L, Chicard M, Adam de Beaumais T, Marchais A, Harttrampf AC, Iddir Y, Larive A, Soriano Fernandez A, Hezam I, Chevassus C, Bernard V, Cotteret S, Scoazec JY, Gauthier A, Abbou S, Corradini N, André N, Aerts I, Thebaud E, Casanova M, Owens C, Hladun-Alvaro R, Michiels S, Delattre O, Vassal G, Schleiermacher G, Geoerger B. The European MAPPYACTS Trial: Precision Medicine Program in Pediatric and Adolescent Patients with Recurrent Malignancies. Cancer Discov 2022; 12:1266-1281. [PMID: 35292802 PMCID: PMC9394403 DOI: 10.1158/2159-8290.cd-21-1136] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [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: 08/20/2021] [Revised: 11/03/2021] [Accepted: 02/07/2022] [Indexed: 01/07/2023]
Abstract
ABSTRACT MAPPYACTS (NCT02613962) is an international prospective precision medicine trial aiming to define tumor molecular profiles in pediatric patients with recurrent/refractory malignancies in order to suggest the most adapted salvage treatment. From February 2016 to July 2020, 787 patients were included in France, Italy, Ireland, and Spain. At least one genetic alteration leading to a targeted treatment suggestion was identified in 436 patients (69%) with successful sequencing; 10% of these alterations were considered "ready for routine use." Of 356 patients with follow-up beyond 12 months, 107 (30%) received one or more matched targeted therapies-56% of them within early clinical trials-mainly in the AcSé-ESMART platform trial (NCT02813135). Overall, matched treatment resulted in a 17% objective response rate, and of those patients with ready for routine use alterations, it was 38%. In patients with extracerebral tumors, 76% of actionable alterations detected in tumor tissue were also identified in circulating cell-free DNA (cfDNA). SIGNIFICANCE MAPPYACTS underlines the feasibility of molecular profiling at cancer recurrence in children on a multicenter, international level and demonstrates benefit for patients with selected key drivers. The use of cfDNA deserves validation in prospective studies. Our study highlights the need for innovative therapeutic proof-of-concept trials that address the underlying cancer complexity. This article is highlighted in the In This Issue feature, p. 1171.
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Affiliation(s)
- Pablo Berlanga
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service de Génétique, Hospital Group, Institut Curie, Paris, France
| | - Ludovic Lacroix
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Mathieu Chicard
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Research Center, PSL Research University, Institut Curie, Paris, France
| | - Tiphaine Adam de Beaumais
- Clinical Research Direction, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Anne C. Harttrampf
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Yasmine Iddir
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Research Center, PSL Research University, Institut Curie, Paris, France.,Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France
| | - Alicia Larive
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Campus, INSERM U1018, CESP, Université Paris-Saclay, Villejuif, France
| | - Aroa Soriano Fernandez
- Laboratory of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR)-UAB, Barcelona, Spain
| | - Imene Hezam
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Cecile Chevassus
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Campus, INSERM U1018, CESP, Université Paris-Saclay, Villejuif, France
| | - Virginie Bernard
- Institut Curie Genomics of Excellence (ICGex) Platform, Research Center, Institut Curie, Paris, France
| | - Sophie Cotteret
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jean-Yves Scoazec
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Arnaud Gauthier
- Department of Pathology, PSL Research University, Institut Curie, Paris, France
| | - Samuel Abbou
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Nadege Corradini
- Department of Pediatric Oncology, Institut d'Hematologie et d'Oncologie Pédiatrique/Centre Léon Bérard, Lyon, France
| | - Nicolas André
- Department of Pediatric Hematology and Oncology, Hôpital de La Timone, AP-HM, Marseille, France.,UMR Inserm 1068, CNRS UMR 7258, Aix Marseille Université U105, Marseille Cancer Research Center (CRCM), Marseille, France
| | - Isabelle Aerts
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France
| | - Estelle Thebaud
- Department of Pediatric Oncology, Centre Hospitalier Universitaire, Nantes, France
| | - Michela Casanova
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Cormac Owens
- Paediatric Haematology/Oncology, Children's Health Ireland, Crumlin, Dublin, Republic of Ireland
| | - Raquel Hladun-Alvaro
- Division of Paediatric Haematology and Oncology, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Stefan Michiels
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Campus, INSERM U1018, CESP, Université Paris-Saclay, Villejuif, France
| | - Olivier Delattre
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Research Center, PSL Research University, Institut Curie, Paris, France.,Institut Curie Genomics of Excellence (ICGex) Platform, Research Center, Institut Curie, Paris, France.,SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France
| | - Gilles Vassal
- Clinical Research Direction, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gudrun Schleiermacher
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Research Center, PSL Research University, Institut Curie, Paris, France.,SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,Corresponding Author: Birgit Geoerger, Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, 114 Rue Eduard Vaillant, 94805 Villejuif, France. Phone: 33-1-42-11-46-61; Fax: 33-1-42-11-52-75; E-mail:
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Bouchoucha Y, Tauziède-Espariat A, Gauthier A, Guillemot D, Bochaton D, Vibert J, Carton M, Watson S, Grossetête S, Quignot C, Orbach D, Corradini N, Schleiermacher G, Bourdeaut F, Simbozel M, Dufour C, Minard-Colin V, Brahmi M, Tirode F, Pissaloux D, Karanian M, Machet MC, Masliah-Planchon J, Delattre O, Cardoen L, Pierron G, Doz F. Intra- and extra-cranial BCOR-ITD tumours are separate entities within the BCOR-rearranged family. J Pathol Clin Res 2022; 8:217-232. [PMID: 35174661 PMCID: PMC8977275 DOI: 10.1002/cjp2.255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023]
Abstract
BCOR-ITD tumours form an emerging family of aggressive entities with an internal tandem duplication (ITD) in the last exon of the BCOR gene. The family includes cerebral tumours, termed central nervous system BCOR-ITD (CNS BCOR-ITD), and sarcomatous types described in the kidney as clear cell sarcoma of the kidney (CCSK), in the endometrium as high-grade endometrial stromal sarcoma, and in the bone and soft tissue as undifferentiated round cell sarcoma or primitive myxoid mesenchymal tumour of infancy. Based on a series of 33 retrospective cases, including 10 CNS BCOR-ITD and 23 BCOR-ITD sarcomas, we interrogated the homogeneity of the entity regarding clinical, radiological, and histopathological findings, and molecular signatures. Whole-transcriptomic sequencing and DNA methylation profiling were used for unsupervised clustering. BCOR-ITD tumours mostly affected young children with a median age at diagnosis of 2.1 years (range 0-62.4). Median overall survival was 3.9 years and progression-free survival was 1.4 years. This dismal prognosis is shared among tumours in all locations except CCSK. Histopathological review revealed marked differences between CNS BCOR-ITD and BCOR-ITD sarcomas. These two groups were consistently segregated by unsupervised clustering of expression (n = 22) and DNA methylation (n = 21) data. Proximity between the two groups may result from common somatic changes within key pathways directly related to the novel activity of the ITD itself. Conversely, comparison of gene signatures with single-cell RNA-Seq atlases suggests that the distinction between BCOR-ITD sarcomas and CNS BCOR-ITD may result from differences in cells of origin.
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Affiliation(s)
- Yassine Bouchoucha
- SIREDO Oncology Center of Care, Innovation and Research for Children, Adolescent and Young Adults with Cancer, Institut Curie, Paris, France.,Université de Paris, Paris, France
| | - Arnault Tauziède-Espariat
- Université de Paris, Paris, France.,Department of Neuropathology, GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte-Anne, Paris, France.,Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | | | | | - Dorian Bochaton
- Laboratory of Genetics and Biology of Cancer, INSERM U830, Paris, France
| | - Julien Vibert
- Laboratory of Genetics and Biology of Cancer, INSERM U830, Paris, France
| | | | - Sarah Watson
- Laboratory of Genetics and Biology of Cancer, INSERM U830, Paris, France.,Medical Oncology Department, Institut Curie, Paris, France
| | | | - Chloé Quignot
- Laboratory of Genetics and Biology of Cancer, INSERM U830, Paris, France
| | - Daniel Orbach
- SIREDO Oncology Center of Care, Innovation and Research for Children, Adolescent and Young Adults with Cancer, Institut Curie, Paris, France
| | - Nadège Corradini
- Institute of Pediatric Hematology and Oncology IHOPE, Centre Leon Berard, Lyon, France
| | - Gudrun Schleiermacher
- SIREDO Oncology Center of Care, Innovation and Research for Children, Adolescent and Young Adults with Cancer, Institut Curie, Paris, France.,Laboratory of Genetics and Biology of Cancer, INSERM U830, Paris, France
| | - Franck Bourdeaut
- SIREDO Oncology Center of Care, Innovation and Research for Children, Adolescent and Young Adults with Cancer, Institut Curie, Paris, France.,Laboratory of Genetics and Biology of Cancer, INSERM U830, Paris, France
| | - Marie Simbozel
- Department of Pediatric and Adolescent Oncology, INSERM 1015, Gustave Roussy, Paris-Saclay University, Villejuif, France
| | - Christelle Dufour
- Department of Pediatric and Adolescent Oncology, INSERM 1015, Gustave Roussy, Paris-Saclay University, Villejuif, France
| | - Véronique Minard-Colin
- Department of Pediatric and Adolescent Oncology, INSERM 1015, Gustave Roussy, Paris-Saclay University, Villejuif, France
| | - Mehdi Brahmi
- Genetics Epigenetics and Biology of Sarcomas Team, Claude Bernard University Lyon 1, INSERM 1052, CNRS 5286, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France.,Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Franck Tirode
- Genetics Epigenetics and Biology of Sarcomas Team, Claude Bernard University Lyon 1, INSERM 1052, CNRS 5286, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France
| | - Daniel Pissaloux
- Genetics Epigenetics and Biology of Sarcomas Team, Claude Bernard University Lyon 1, INSERM 1052, CNRS 5286, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France.,Department of Biopathology, Centre Léon Bérard, Lyon, France
| | - Marie Karanian
- Genetics Epigenetics and Biology of Sarcomas Team, Claude Bernard University Lyon 1, INSERM 1052, CNRS 5286, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France.,Department of Biopathology, Centre Léon Bérard, Lyon, France
| | | | | | - Olivier Delattre
- SIREDO Oncology Center of Care, Innovation and Research for Children, Adolescent and Young Adults with Cancer, Institut Curie, Paris, France.,Department of Somatic Genetics, Institut Curie, Paris, France.,Laboratory of Genetics and Biology of Cancer, INSERM U830, Paris, France
| | | | - Gaëlle Pierron
- Department of Somatic Genetics, Institut Curie, Paris, France
| | - François Doz
- SIREDO Oncology Center of Care, Innovation and Research for Children, Adolescent and Young Adults with Cancer, Institut Curie, Paris, France.,Université de Paris, Paris, France
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Tauziède-Espariat A, Guerrini-Rousseau L, Perrier A, Torrejon J, Bernardi F, Varlet P, Hasty L, Delattre O, Beccaria K, Métais A, Ayrault O, Chrétien F, Bourdeaut F, Dufour C, Masliah-Planchon J. Immunohistochemistry as a tool to identify ELP1-associated medulloblastoma. Acta Neuropathol 2022; 143:523-525. [PMID: 35199222 PMCID: PMC8960608 DOI: 10.1007/s00401-022-02409-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Arnault Tauziède-Espariat
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, 1, rue Cabanis, 75014, Paris, France.
- Institut de Psychiatrie Et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France.
- Université de Paris, Paris, France.
| | - Léa Guerrini-Rousseau
- Department of Children and Adolescents Oncology, Gustave Roussy, Paris Saclay University, Villejuif, France
- Team "Genomics and Oncogenesis of Pediatric Brain Tumors", INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Alexandre Perrier
- Laboratory of Somatic Genetics, Curie Institute Hospital, Paris, France
| | - Jacob Torrejon
- Institut Curie, PSL Research University, CNRS UMR, INSERM, 91898, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, 91898, Orsay, France
| | - Flavia Bernardi
- Institut Curie, PSL Research University, CNRS UMR, INSERM, 91898, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, 91898, Orsay, France
| | - Pascale Varlet
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, 1, rue Cabanis, 75014, Paris, France
- Institut de Psychiatrie Et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
- Université de Paris, Paris, France
| | - Lauren Hasty
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, 1, rue Cabanis, 75014, Paris, France
| | - Olivier Delattre
- Université de Paris, Paris, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, 91898, Orsay, France
| | - Kévin Beccaria
- Department of Pediatric Neurosurgery, Necker Hospital, APHP, Université Paris Descartes, Sorbonne Paris Cite, 75015, Paris, France
| | - Alice Métais
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, 1, rue Cabanis, 75014, Paris, France
| | - Olivier Ayrault
- Institut Curie, PSL Research University, CNRS UMR, INSERM, 91898, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, 91898, Orsay, France
| | - Fabrice Chrétien
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, 1, rue Cabanis, 75014, Paris, France
- Université de Paris, Paris, France
| | - Franck Bourdeaut
- SIREDO Center Care, Innovation, Research in Pediatric, Adolescent and Young Adult Oncology, Curie Institute and Paris Descartes University, Paris, France
| | - Christelle Dufour
- Department of Children and Adolescents Oncology, Gustave Roussy, Paris Saclay University, Villejuif, France
- Team "Genomics and Oncogenesis of Pediatric Brain Tumors", INSERM U981, Gustave Roussy, Paris Saclay University, Villejuif, France
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49
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Enault M, Minard-Colin V, Corradini N, Leverger G, Thebaud E, Rome A, Proust S, Marie-Cardine A, Defachelles AS, Sarnacki S, Philippe-Chomette P, Delattre O, Masliah-Planchon J, Lacour B, Ferrari A, Brennan B, Orbach D, Bourdeaut F. Extracranial rhabdoid tumours: Results of a SFCE series of patients treated with a dose compression strategy according to European Paediatric Soft tisue sarcoma Study Group recommendations. Eur J Cancer 2022; 161:64-78. [DOI: 10.1016/j.ejca.2021.10.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/30/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022]
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50
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Lepagnol-Bestel AM, Zvara A, Maussion G, Quignon F, Ngimbous B, Ramoz N, Imbeaud S, Loe-Mie Y, Benihoud K, Agier N, Salin PA, Cardona A, Khung-Savatovsky S, Kallunki P, Delabar JM, Puskas LG, Delacroix H, Aggerbeck L, Delezoide AL, Delattre O, Gorwood P, Moalic JM, Simonneau M. Corrigendum to: DYRK1A interacts with the REST/NRSF-SWI/SNF chromatin remodelling complex to deregulate gene clusters involved in the neuronal phenotypic traits of Down syndrome. Hum Mol Genet 2021; 31:2106-2107. [PMID: 34918050 DOI: 10.1093/hmg/ddab346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/12/2020] [Accepted: 01/08/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Agnes Zvara
- Laboratory for Functional Genomics, Biological Research Center, HAS, Szeged, Hungary
| | - Gilles Maussion
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
| | | | - Bedel Ngimbous
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
| | - Nicolas Ramoz
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
| | - Sandrine Imbeaud
- Centre de Génétique Moléculaire, UPR 2167, CNRS, Université Paris-Sud 11, 91405 Orsay, France and Gif/ Orsay DNA Microarray Platform (GODMAP), Gif sur Yvette, France
| | - Yann Loe-Mie
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
| | - Karim Benihoud
- CNRS UMR 8121 Vectorologie et Transfert de Génes, Institut Gustave Roussy, 39, rue Camille Desmoulins, 94805 Villejuif Cedex, France; Université Paris-Sud 11, 91405 Orsay Cedex, France
| | - Nicolas Agier
- Centre de Génétique Moléculaire, UPR 2167, CNRS, Université Paris-Sud 11, 91405 Orsay, France and Gif/ Orsay DNA Microarray Platform (GODMAP), Gif sur Yvette, France
| | | | | | - Suonavy Khung-Savatovsky
- Service de Biologie du Développement/Foetopathologie, Hôpital Robert Debré , AP-HP, Université Paris Diderot-Paris 7, Paris, France
| | | | | | - Laszlo G Puskas
- Laboratory for Functional Genomics, Biological Research Center, HAS, Szeged, Hungary
| | - Hervé Delacroix
- Centre de Génétique Moléculaire, UPR 2167, CNRS, Université Paris-Sud 11, 91405 Orsay, France and Gif/ Orsay DNA Microarray Platform (GODMAP), Gif sur Yvette, France
| | - Lawrence Aggerbeck
- Centre de Génétique Moléculaire, UPR 2167, CNRS, Université Paris-Sud 11, 91405 Orsay, France and Gif/ Orsay DNA Microarray Platform (GODMAP), Gif sur Yvette, France
| | - Anne-Lise Delezoide
- Service de Biologie du Développement/Foetopathologie, Hôpital Robert Debré , AP-HP, Université Paris Diderot-Paris 7, Paris, France
| | | | - Philip Gorwood
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
| | - Jean-Marie Moalic
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
| | - Michel Simonneau
- INSERM U675, IFR02, Faculté de Médecine Xavier Bichat, Université Paris Diderot-Paris 7, Paris, France
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