Diversity and Plasticity of Childhood Tumors (DePiCT)

Team Publications

Year of publication 2017

G-A Franzetti, K Laud-Duval, W van der Ent, A Brisac, M Irondelle, S Aubert, U Dirksen, C Bouvier, G de Pinieux, E Snaar-Jagalska, P Chavrier, O Delattre (2017 Jan 31)

Cell-to-cell heterogeneity of EWSR1-FLI1 activity determines proliferation/migration choices in Ewing sarcoma cells.

Oncogene : DOI : 10.1038/onc.2016.498 Learn more
Summary

Ewing sarcoma is characterized by the expression of the chimeric EWSR1-FLI1 transcription factor. Proteomic analyses indicate that the decrease of EWSR1-FLI1 expression leads to major changes in effectors of the dynamics of the actin cytoskeleton and the adhesion processes with a shift from cell-to-cell to cell-matrix adhesion. These changes are associated with a dramatic increase of in vivo cell migration and invasion potential. Importantly, EWSR1-FLI1 expression, evaluated by single-cell RT-ddPCR/immunofluorescence analyses, and activity, assessed by expression of EWSR1-FLI1 downstream targets, are heterogeneous in cell lines and in tumours and can fluctuate along time in a fully reversible process between EWSR1-FLI1(high) states, characterized by highly active cell proliferation, and EWSR1-FLI1(low) states where cells have a strong propensity to migrate, invade and metastasize. This new model of phenotypic plasticity proposes that the dynamic fluctuation of the expression level of a dominant oncogene is an intrinsic characteristic of its oncogenic potential.Oncogene advance online publication, 30 January 2017; doi:10.1038/onc.2016.498.

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Nathan C Sheffield, Gaelle Pierron, Johanna Klughammer, Paul Datlinger, Andreas Schönegger, Michael Schuster, Johanna Hadler, Didier Surdez, Delphine Guillemot, Eve Lapouble, Paul Freneaux, Jacqueline Champigneulle, Raymonde Bouvier, Diana Walder, Ingeborg M Ambros, Caroline Hutter, Eva Sorz, Ana T Amaral, Enrique de Álava, Katharina Schallmoser, Dirk Strunk, Beate Rinner, Bernadette Liegl-Atzwanger, Berthold Huppertz, Andreas Leithner, Gonzague de Pinieux, Philippe Terrier, Valérie Laurence, Jean Michon, Ruth Ladenstein, Wolfgang Holter, Reinhard Windhager, Uta Dirksen, Peter F Ambros, Olivier Delattre, Heinrich Kovar, Christoph Bock, Eleni M Tomazou (2017 Jan 31)

DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma.

Nature medicine : DOI : 10.1038/nm.4273 Learn more
Summary

Developmental tumors in children and young adults carry few genetic alterations, yet they have diverse clinical presentation. Focusing on Ewing sarcoma, we sought to establish the prevalence and characteristics of epigenetic heterogeneity in genetically homogeneous cancers. We performed genome-scale DNA methylation sequencing for a large cohort of Ewing sarcoma tumors and analyzed epigenetic heterogeneity on three levels: between cancers, between tumors, and within tumors. We observed consistent DNA hypomethylation at enhancers regulated by the disease-defining EWS-FLI1 fusion protein, thus establishing epigenomic enhancer reprogramming as a ubiquitous and characteristic feature of Ewing sarcoma. DNA methylation differences between tumors identified a continuous disease spectrum underlying Ewing sarcoma, which reflected the strength of an EWS-FLI1 regulatory signature and a continuum between mesenchymal and stem cell signatures. There was substantial epigenetic heterogeneity within tumors, particularly in patients with metastatic disease. In summary, our study provides a comprehensive assessment of epigenetic heterogeneity in Ewing sarcoma and thereby highlights the importance of considering nongenetic aspects of tumor heterogeneity in the context of cancer biology and personalized medicine.

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A Bertrand, C Rondenet, J Masliah-Planchon, P Leblond, A de la Fourchardière, D Pissaloux, K Aït-Raïs, D Lequin, A Jouvet, P Freneaux, H Sevestre, D Ranchere-Vince, A Tauziede-Espariat, C-A Maurage, K Silva, G Pierron, O Delattre, P Varlet, D Frappaz, F Bourdeaut (2017 Jan 6)

Rhabdoid component emerging as a subclonal evolution of paediatric glioneuronal tumours.

Neuropathology and applied neurobiology : DOI : 10.1111/nan.12379 Learn more
Summary

Atypical teratoid/rhabdoid tumors (AT/RT) are high-grade tumors partially composed of rhabdoid cells (1). The 1-year overall survival rate is 41% (2). Rhabdoid cells have large eccentric nuclei, a single prominent nucleolus, and abundant cytoplasm with eosinophilic inclusions. The immunohistochemical profile of these cells frequently includes loss of nuclear BAF47 expression due to loss of the SMARCB1 locus combined with a mutation of the other allele (3). This article is protected by copyright. All rights reserved.

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Gudrun Schleiermacher, Olivier Delattre (2017 Jan 2)

Kids Enter the MATCH.

Journal of the National Cancer Institute : DOI : djw305 Learn more
Summary

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Year of publication 2016

Edoardo Missiaglia, Chris J Shepherd, Ewa Aladowicz, David Olmos, Joanna Selfe, Gaëlle Pierron, Olivier Delattre, Zoe Walters, Janet Shipley (2016 Dec 17)

MicroRNA and gene co-expression networks characterize biological and clinical behavior of rhabdomyosarcomas.

Cancer letters : DOI : S0304-3835(16)30623-1 Learn more
Summary

Rhabdomyosarcomas (RMS) in children and adolescents are heterogeneous sarcomas broadly defined by skeletal muscle features and the presence/absence of PAX3/7-FOXO1 fusion genes. MicroRNAs are small non-coding RNAs that regulate gene expression in a cell context specific manner. Sequencing analyses of microRNAs in 64 RMS revealed expression patterns separating skeletal muscle, fusion gene positive and negative RMS. Integration with parallel gene expression data assigned biological functions to 12 co-expression networks/modules that reassuringly included myogenic roles strongly correlated with microRNAs known in myogenesis and RMS development. Modules also correlated with clinical outcome and fusion status. Regulation of microRNAs by the fusion protein was demonstrated after PAX3-FOXO1 reduction, exemplified by miR-9-5p. MiR-9-5p levels correlated with poor outcome, even within fusion gene positive RMS, and were higher in metastatic versus non-metastatic disease. MiR-9-5p reduction inhibited RMS cell migration. Our findings reveal microRNAs in a regulatory framework of biological and clinical significance in RMS.

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Thomas Pincez, Nathalie Clément, Eve Lapouble, Gaëlle Pierron, Maud Kamal, Ivan Bieche, Virginie Bernard, Paul Fréneaux, Jean Michon, Daniel Orbach, Isabelle Aerts, Hélène Pacquement, Franck Bourdeaut, Irene Jiménez, Estelle Thébaud, Caroline Oudot, Cécile Vérité, Sophie Taque, Cormac Owens, François Doz, Christophe Le Tourneau, Olivier Delattre, Gudrun Schleiermacher (2016 Nov 30)

Feasibility and clinical integration of molecular profiling for target identification in pediatric solid tumors.

Pediatric blood & cancer : DOI : 10.1002/pbc.26365 Learn more
Summary

The role of tumor molecular profiling in directing targeted therapy utilization remains to be defined for pediatric tumors. We aimed to evaluate the feasibility of a sequencing and molecular biology tumor board (MBB) program, and its clinical impact on children with solid tumors.

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Tao He, Didier Surdez, Juha K Rantala, Saija Haapa-Paananen, Jozef Ban, Maximilian Kauer, Eleni Tomazou, Vidal Fey, Javier Alonso, Heinrich Kovar, Olivier Delattre, Kristiina Iljin (2016 Oct 30)

High-throughput RNAi screen in Ewing sarcoma cells identifies leucine rich repeats and WD repeat domain containing 1 (LRWD1) as a regulator of EWS-FLI1 driven cell viability.

Gene : 137-146 : DOI : S0378-1119(16)30827-7 Learn more
Summary

A translocation leading to the formation of an oncogenic EWS-ETS fusion protein defines Ewing sarcoma. The most frequent gene fusion, present in 85 percent of Ewing sarcomas, is EWS-FLI1. Here, a high-throughput RNA interference screen was performed to identify genes whose function is critical for EWS-FLI1 driven cell viability. In total, 6781 genes were targeted by siRNA molecules and the screen was performed both in presence and absence of doxycycline-inducible expression of the EWS-FLI1 shRNA in A673/TR/shEF Ewing sarcoma cells. The Leucine rich repeats and WD repeat Domain containing 1 (LRWD1) targeting siRNA pool was the strongest hit reducing cell viability only in EWS-FLI1 expressing Ewing sarcoma cells. LRWD1 had been previously described as a testis specific gene with only limited information on its function. Analysis of LRWD1 mRNA levels in patient samples indicated that high expression associated with poor overall survival in Ewing sarcoma. Gene ontology analysis of LRWD1 co-expressed genes in Ewing tumors revealed association with DNA replication and analysis of differentially expressed genes in LRWD1 depleted Ewing sarcoma cells indicated a role in connective tissue development and cellular morphogenesis. Moreover, EWS-FLI1 repressed genes with repressive H3K27me3 chromatin marks were highly enriched among LRWD1 target genes in A673/TR/shEF Ewing sarcoma cells, suggesting that LRWD1 contributes to EWS-FLI1 driven transcriptional regulation. Taken together, we have identified LRWD1 as a novel regulator of EWS-FLI1 driven cell viability in A673/TR/shEF Ewing sarcoma cells, shown association between high LRWD1 mRNA expression and aggressive disease and identified processes by which LRWD1 may promote oncogenesis in Ewing sarcoma.

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Claire Provost, Aurélie Prignon, Alex Cazes, Valérie Combaret, Olivier Delattre, Isabelle Janoueix-Lerosey, Françoise Montravers, Jean-Noël Talbot (2016 Sep 16)

68Ga-DOTATOC and FDG PET Imaging of Preclinical Neuroblastoma Models.

Anticancer research : 4459-66 Learn more
Summary

Somatostatine receptors subtype 2 (SSTR2) are regarded as a potential target in neuroblastoma (NB) for imaging and promising therapeutic approaches. The purpose of this study was to evaluate and compare the SSTR2 status by (68)Ga-[tetraxetan-D-Phe1, Tyr3]-octreotide ((68)Ga-DOTATOC) positron-emission tomography (PET) and the tumour metabolic activity by (18)F-fluorodeoxyglucose (FDG) PET in different experimental models of NB.

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Mathieu Chicard, Sandrine Boyault, Leo Colmet Daage, Wilfrid Richer, David Gentien, Gaelle Pierron, Eve Lapouble, Angela Bellini, Nathalie Clement, Isabelle Iacono, Stéphanie Bréjon, Marjorie Carrere, Cécile Reyes, Toby Hocking, Virginie Bernard, Michel Peuchmaur, Nadège Corradini, Cécile Faure-Conter, Carole Coze, Dominique Plantaz, Anne Sophie Defachelles, Estelle Thebaud, Marion Gambart, Frédéric Millot, Dominique Valteau-Couanet, Jean Michon, Alain Puisieux, Olivier Delattre, Valérie Combaret, Gudrun Schleiermacher (2016 Jul 22)

Genomic copy number profiling using circulating free tumor DNA highlights heterogeneity in neuroblastoma.

Clinical cancer research : an official journal of the American Association for Cancer Research : DOI : clincanres.0500.2016 Learn more
Summary

The tumor genomic copy number profile is of prognostic significance in neuroblastoma (NB) patients. We have studied the genomic copy number profile of cell free DNA (cfDNA) and compared this to primary tumor aCGH at diagnosis.

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Tsion Zewdu Minas, Didier Surdez, Tahereh Javaheri, Miwa Tanaka, Michelle Howarth, Hong-Jun Kang, Jenny Han, Zhi-Yan Han, Barbara Sax, Barbara E Kream, Sung-Hyeok Hong, Haydar Çelik, Franck Tirode, Jan Tuckermann, Jeffrey A Toretsky, Lukas Kenner, Heinrich Kovar, Sean Lee, E Alejandro Sweet-Cordero, Takuro Nakamura, Richard Moriggl, Olivier Delattre, Aykut Üren (2016 May 19)

Combined experience of six independent laboratories attempting to create an Ewing sarcoma mouse model.

Oncotarget : DOI : 10.18632/oncotarget.9388 Learn more
Summary

Ewing sarcoma (ES) involves a tumor-specific chromosomal translocation that produces the EWS-FLI1 protein, which is required for the growth of ES cells both in vitro and in vivo. However, an EWS-FLI1-driven transgenic mouse model is not currently available. Here, we present data from six independent laboratories seeking an alternative approach to express EWS-FLI1 in different murine tissues. We used the Runx2, Col1a2.3, Col1a3.6, Prx1, CAG, Nse, NEFL, Dermo1, P0, Sox9 and Osterix promoters to target EWS-FLI1 or Cre expression. Additional approaches included the induction of an endogenous chromosomal translocation, in utero knock-in, and the injection of Cre-expressing adenovirus to induce EWS-FLI1 expression locally in multiple lineages. Most models resulted in embryonic lethality or developmental defects. EWS-FLI1-induced apoptosis, promoter leakiness, the lack of potential cofactors, and the difficulty of expressing EWS-FLI1 in specific sites were considered the primary reasons for the failed attempts to create a transgenic mouse model of ES.

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Thomas G P Grünewald, Pascale Gilardi-Hebenstreit, Patrick Charnay, Olivier Delattre (2016 May 4)

[Cooperation between a somatic mutation and a genetic susceptibility variant in Ewing sarcoma].

Médecine sciences : M/S : 323-6 : DOI : 10.1051/medsci/20163204004 Learn more
Summary

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Navin Pinto, Jodi R Mayfield, Gordana Raca, Mark A Applebaum, Alexandre Chlenski, Madina Sukhanova, Rochelle Bagatell, Meredith S Irwin, Anthony Little, Jawhar Rawwas, Yasmin Gosiengfiao, Olivier Delattre, Isabelle Janoueix-Lerosey, Eve Lapouble, Gudrun Schleiermacher, Susan L Cohn (2016 Feb 12)

Segmental Chromosomal Aberrations in Localized Neuroblastoma Can be Detected in Formalin-Fixed Paraffin-Embedded Tissue Samples and Are Associated With Recurrence.

Pediatric blood & cancer : 1019-23 : DOI : 10.1002/pbc.25934 Learn more
Summary

Array comparative genomic hybridization (CGH) analyses of frozen tumors have shown strong associations between the pattern of chromosomal aberrations and outcome in patients with advanced-stage neuroblastoma. New platforms for analyzing chromosomal aberrations using formalin-fixed paraffin-embedded (FFPE) tissue have recently been developed. We sought to determine whether chromosomal microarray analysis (CMA) using FFPE tumors is feasible and if segmental chromosomal aberrations were prognostic of recurrence in localized neuroblastoma.

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Zhi-Yan Han, Wilfrid Richer, Paul Fréneaux, Céline Chauvin, Carlo Lucchesi, Delphine Guillemot, Camille Grison, Delphine Lequin, Gaelle Pierron, Julien Masliah-Planchon, André Nicolas, Dominique Ranchère-Vince, Pascale Varlet, Stéphanie Puget, Isabelle Janoueix-Lerosey, Olivier Ayrault, Didier Surdez, Olivier Delattre, Franck Bourdeaut (2016 Jan 29)

The occurrence of intracranial rhabdoid tumours in mice depends on temporal control of Smarcb1 inactivation.

Nature communications : 10421 : DOI : 10.1038/ncomms10421 Learn more
Summary

Rhabdoid tumours (RTs) are highly aggressive tumours of infancy, frequently localized in the central nervous system (CNS) where they are termed atypical teratoid/rhabdoid tumours (AT/RTs) and characterized by bi-allelic inactivation of the SMARCB1 tumour suppressor gene. In this study, by temporal control of tamoxifen injection in Smarcb1(flox/flox);Rosa26-Cre(ERT2) mice, we explore the phenotypes associated with Smarcb1 inactivation at different developmental stages. Injection before E6, at birth or at 2 months of age recapitulates previously described phenotypes including embryonic lethality, hepatic toxicity or development of T-cell lymphomas, respectively. Injection between E6 and E10 leads to high penetrance tumours, mainly intra-cranial, with short delays (median: 3 months). These tumours demonstrate anatomical, morphological and gene expression profiles consistent with those of human AT/RTs. Moreover, intra- and inter-species comparisons of tumours reveal that human and mouse RTs can be split into different entities that may underline the variety of RT cells of origin.

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Heinrich Kovar, James Amatruda, Erika Brunet, Stefan Burdach, Florencia Cidre-Aranaz, Enrique de Alava, Uta Dirksen, Wietske van der Ent, Patrick Grohar, Thomas G P Grünewald, Lee Helman, Peter Houghton, Kristiina Iljin, Eberhard Korsching, Marc Ladanyi, Elizabeth Lawlor, Stephen Lessnick, Joseph Ludwig, Paul Meltzer, Markus Metzler, Jaume Mora, Richard Moriggl, Takuro Nakamura, Theodore Papamarkou, Branka Radic Sarikas, Francoise Rédini, Guenther H S Richter, Claudia Rossig, Keri Schadler, Beat W Schäfer, Katia Scotlandi, Nathan C Sheffield, Anang Shelat, Ewa Snaar-Jagalska, Poul Sorensen, Kimberly Stegmaier, Elizabeth Stewart, Alejandro Sweet-Cordero, Karoly Szuhai, Oscar M Tirado, Franck Tirode, Jeffrey Toretsky, Kalliopi Tsafou, Aykut Üren, Andrei Zinovyev, Olivier Delattre (2016 Jan 24)

The second European interdisciplinary Ewing sarcoma research summit – A joint effort to deconstructing the multiple layers of a complex disease.

Oncotarget : 8613-24 : DOI : 10.18632/oncotarget.6937 Learn more
Summary

Despite multimodal treatment, long term outcome for patients with Ewing sarcoma is still poor. The second “European interdisciplinary Ewing sarcoma research summit” assembled a large group of scientific experts in the field to discuss their latest unpublished findings on the way to the identification of novel therapeutic targets and strategies. Ewing sarcoma is characterized by a quiet genome with presence of an EWSR1-ETS gene rearrangement as the only and defining genetic aberration. RNA-sequencing of recently described Ewing-like sarcomas with variant translocations identified them as biologically distinct diseases. Various presentations adressed mechanisms of EWS-ETS fusion protein activities with a focus on EWS-FLI1. Data were presented shedding light on the molecular underpinnings of genetic permissiveness to this disease uncovering interaction of EWS-FLI1 with recently discovered susceptibility loci. Epigenetic context as a consequence of the interaction between the oncoprotein, cell type, developmental stage, and tissue microenvironment emerged as dominant theme in the discussion of the molecular pathogenesis and inter- and intra-tumor heterogeneity of Ewing sarcoma, and the difficulty to generate animal models faithfully recapitulating the human disease. The problem of preclinical development of biologically targeted therapeutics was discussed and promising perspectives were offered from the study of novel in vitro models. Finally, it was concluded that in order to facilitate rapid pre-clinical and clinical development of novel therapies in Ewing sarcoma, the community needs a platform to maintain knowledge of unpublished results, systems and models used in drug testing and to continue the open dialogue initiated at the first two Ewing sarcoma summits.

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Year of publication 2015

Melanie Hennchen, Jutta Stubbusch, Ikram Abarchan-El Makhfi, Marco Kramer, Thomas Deller, Cécile Pierre-Eugene, Isabelle Janoueix-Lerosey, Olivier Delattre, Uwe Ernsberger, Johannes B Schulte, Hermann Rohrer (2015 Dec 18)

Lin28B and Let-7 in the Control of Sympathetic Neurogenesis and Neuroblastoma Development.

The Journal of neuroscience : the official journal of the Society for Neuroscience : 16531-44 : DOI : 10.1523/JNEUROSCI.2560-15.2015 Learn more
Summary

The RNA binding protein Lin28B is expressed in developing tissues and sustains stem and progenitor cell identity as a negative regulator of the Let-7 family of microRNAs, which induces differentiation. Lin28B is activated in neuroblastoma (NB), a childhood tumor in sympathetic ganglia and adrenal medulla. Forced expression of Lin28B in embryonic mouse sympathoadrenal neuroblasts elicits postnatal NB formation. However, the normal function of Lin28B in the development of sympathetic neurons and chromaffin cells and the mechanisms involved in Lin28B-induced tumor formation are unclear. Here, we demonstrate a mirror-image expression of Lin28B and Let-7a in developing chick sympathetic ganglia. Lin28B expression is not restricted to undifferentiated progenitor cells but, is observed in proliferating noradrenergic neuroblasts. Lin28 knockdown in cultured sympathetic neuroblasts decreases proliferation, whereas Let-7 inhibition increases the proportion of neuroblasts in the cell cycle. Lin28B overexpression enhances proliferation, but only during a short developmental period, and it does not reduce Let-7a. Effects of in vivo Lin28B overexpression were analyzed in the LSL-Lin28B(DBHiCre) mouse line. Sympathetic ganglion and adrenal medulla volume and the expression level of Let-7a were not altered, although Lin28B expression increased by 12- to 17-fold. In contrast, Let-7a expression was strongly reduced in LSL-Lin28B(DbhiCre) NB tumor tissue. These data demonstrate essential functions for endogenous Lin28 and Let-7 in neuroblast proliferation. However, Lin28B overexpression neither sustains neuroblast proliferation nor affects let-7 expression. Thus, in contrast to other pediatric tumors, Lin28B-induced NB is not due to expansion of proliferating embryonic neuroblasts, and Let-7-independent functions are implicated during initial NB development.

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