Diversité et plasticité des tumeurs de l’enfant

Publications de l’équipe

Année de publication : 2018

Genevieve C Kendall, Sarah Watson, Lin Xu, Collette A LaVigne, Whitney Murchison, Dinesh Rakheja, Stephen X Skapek, Franck Tirode, Olivier Delattre, James F Amatruda (2018 Jun 6)

transgenic zebrafish models identify as a mediator of rhabdomyosarcoma tumorigenesis.

eLife : DOI : 10.7554/eLife.33800 En savoir plus
Résumé

Alveolar rhabdomyosarcoma is a pediatric soft-tissue sarcoma caused by fusion oncogenes and is characterized by impaired skeletal muscle development. We developed human -driven zebrafish models of tumorigenesis and found that exhibits discrete cell lineage susceptibility and transformation. Tumors developed by 1.6-19 months and were primitive neuroectodermal tumors or rhabdomyosarcoma. We applied this transgenic zebrafish model to study how leverages early developmental pathways for oncogenesis and found that is a unique target. Ectopic expression of the human ortholog, , inhibits myogenesis in zebrafish and mammalian cells, recapitulating the arrested muscle development characteristic of rhabdomyosarcoma. In patients, is overexpressed in fusion-positive versus fusion-negative tumors. Finally, overexpression is associated with reduced survival in patients in the context of the fusion. Our novel zebrafish rhabdomyosarcoma model identifies a new target, /, that contributes to impaired myogenic differentiation and has prognostic significance in human disease.

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Deveau, P., Colmet Daage, L., Oldridge, D., Bernard, V., Bellini, A., Chicard, M., Clement, N., Lapouble, E., Combaret, V., Boland, A., Meyer, V., Deleuze, J.-F., Janoueix-Lerosey, I., Barillot, E., Delattre, O., Maris, J.M., Schleiermacher, G., and Boeva, V (2018 Jun 1)

QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction

Bioinformatics : 34 : 1808,1816 : DOI : 10.1093/bioinformatics/bty016. En savoir plus
Résumé

Motivation:

In cancer, clonalevolution is assessed basedon information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonalpopulations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering [reducing dispersion in variant allele frequency estimates (VAFs)] and using all biologically relevant variants.

Results:

We present a framework for defining cancerclones using most reliable variants of high depth of coverage and assigning functionalmutationsto the detected clones. The key element of our framework is QuantumClone, a methodfor variant clustering into clones basedon VAFs, genotypes of corresponding regions and information about tumor purity. We validated QuantumCloneand our framework on simulated data. We then applied our framework to whole genome sequencing data for 19 neuroblastoma trios each including constitutional, diagnosis and relapse samples. We confirmed an enrichment of damaging variants within such pathways as MAPK (mitogen-activated protein kinases), neuritogenesis, epithelial-mesenchymal transition, cell survival and DNA repair. Most pathways had more damaging variants in the expanding clones compared to shrinking ones, which can be explained by the increased total number of variants between these two populations. Functionalmutational rate varied for ancestral clones and clones shrinking or expanding upon treatment, suggesting changes in clone selection mechanisms at different time points of tumor evolution.

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Franck Bourdeaut, Olivier Delattre (2018 May 14)

Genetic predisposition to medulloblastomas: just follow the tumour genome.

The Lancet. Oncology : 722-723 : DOI : S1470-2045(18)30289-4 En savoir plus
Résumé

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Janoueix-Lerosey, I., Lopez-Delisle, L., Delattre, O., and Rohrer, H (2018 May 2)

The ALK receptor in sympathetic neuron development and neuroblastoma

Cell and Tissue Research : 325, 337 : DOI : https://doi.org/10.1007/s00441-017-2784-8 En savoir plus
Résumé

The ALKgene encodes a tyrosine kinase receptorcharacterized by an expression pattern mainly restricted to the developing central and peripheral nervous systems. In 2008, the discovery of ALKactivating mutations in neuroblastoma, a tumor of the sympatheticnervous system, represented a breakthrough in the understanding of the pathogenesis of this pediatric cancer and established mutated ALKas a tractable therapeutic target for precision medicine. Subsequent studies addressed the identity of ALKligands, as well as its physiological function in the sympathoadrenal lineage, its role in neuroblastomadevelopmentand the signaling pathways triggered by mutated ALK. This review focuses on these different aspects of the ALKbiology and summarizes the various therapeutic strategies relying on ALKinhibition in neuroblastoma, either as monotherapies or combinatory treatments.

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Julien Masliah-Planchon, Dominique Lévy, Delphine Héron, Fabienne Giuliano, Catherine Badens, Paul Fréneaux, Louise Galmiche, Jean-Marc Guinebretierre, Cécile Cellier, Joshua J Waterfall, Khadija Aït-Raïs, Gaëlle Pierron, Christophe Glorion, Isabelle Desguerre, Christine Soler, Anne Deville, Olivier Delattre, Jean Michon, Franck Bourdeaut (2018 May 1)

Does ATRX germline variation predispose to osteosarcoma? Three additional cases of osteosarcoma in two ATR-X syndrome patients.

European journal of human genetics : EJHG : 1217-1221 : DOI : 10.1038/s41431-018-0147-x En savoir plus
Résumé

Osteosarcoma is the most common malignant bone tumor in adolescents and young adults. Most osteosarcomas are sporadic but the risk of osteosarcoma is also increased by germline variants in TP53, RB1 and RECQL4 genes. ATRX germline variations are responsible for the rare genetic disorder X-linked alpha-thalassemia mental retardation (ATR-X) syndrome characterized by severe developmental delay and alpha-thalassemia but no obvious increased risk of cancer. Here we report two children with ATR-X syndrome who developed osteosarcoma. Notably, one of the children developed two osteosarcomas separated by 10 years. Those two cases raise the possibility that ATRX germline variant could be associated with an increased risk of osteosarcoma.

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Watson, S., Perrin, V., Guillemot, D., Reynaud, S., Coindre, J.-M., Karanian, M., Guinebretière, J.-M., Freneaux, P., Le Loarer, F., Bouvet, M., Galmiche-Rolland, L., Larousserie, F., Longchampt, E., Ranchere-Vince, D., Pierron, G., Delattre, O., and Tirode, F (2018 Mar 30)

Transcriptomic definition of molecular subgroups of small round cell sarcomas

The Journal of Pathology : 245 : 29, 40 : DOI : doi.org/10.1002/path.5053 En savoir plus
Résumé

Sarcoma represents a highly heterogeneous group of tumours. We report here the first unbiased and systematic search for gene fusions combined with unsupervised expression analysis of a series of 184 small round cell sarcomas. Fusion genes were detected in 59% of samples, with half of them being observed recurrently. We identified biologically homogeneous groups of tumours such as the CIC‐fused (to DUX4, FOXO4or NUTM1) and BCOR‐rearranged (BCORCCNB3, BCORMAML3, ZC3H7B–BCOR, and BCORinternal duplication) tumour groups. VGLL2‐fused tumours represented a more biologically and pathologically heterogeneous group. This study also refined the characteristics of some entities such as EWSR1–PATZ1spindle cell sarcoma or FUS–NFATC2bone tumours that are different from EWSR1–NFATC2tumours and transcriptionally resemble CIC‐fused tumour entities. We also describe a completely novel group of epithelioid and spindle‐cell rhabdomyosarcomas characterized by EWSR1–or FUS–TFCP2fusions. Finally, expression data identified some potentially new therapeutic targets or pathways. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

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Gregorio J Petrirena, Julien Masliah-Planchon, Quentin Sala, Bertrand Pourroy, Didier Frappaz, Emeline Tabouret, Thomas Graillon, Jean-Claude Gentet, Olivier Delattre, Olivier Chinot, Laetitia Padovani (2018 Mar 9)

Recurrent extraneural sonic hedgehog medulloblastoma exhibiting sustained response to vismodegib and temozolomide monotherapies and inter-metastatic molecular heterogeneity at progression.

Oncotarget : 10175-10183 : DOI : 10.18632/oncotarget.23699 En savoir plus
Résumé

Response to targeting and non-targeting agents is variable and molecular information remains poorly described in patients with recurrent sonic-hedgehog-driven medulloblastoma (SHH-MB).

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Veronica Ferrucci, Pasqualino de Antonellis, Francesco Paolo Pennino, Fatemeh Asadzadeh, Antonella Virgilio, Donatella Montanaro, Aldo Galeone, Iolanda Boffa, Ida Pisano, Iolanda Scognamiglio, Luigi Navas, Donatella Diana, Emilia Pedone, Sara Gargiulo, Matteo Gramanzini, Arturo Brunetti, Laura Danielson, Marianeve Carotenuto, Lucia Liguori, Antonio Verrico, Lucia Quaglietta, Maria Elena Errico, Valentina Del Monaco, Valeria D'Argenio, Felice Tirone, Angela Mastronuzzi, Vittoria Donofrio, Felice Giangaspero, Daniel Picard, Marc Remke, Livia Garzia, Craig Daniels, Olivier Delattre, Fredrik J Swartling, William A Weiss, Francesco Salvatore, Roberto Fattorusso, Louis Chesler, Michael D Taylor, Giuseppe Cinalli, Massimo Zollo (2018 Mar 1)

Metastatic group 3 medulloblastoma is driven by PRUNE1 targeting NME1-TGF-β-OTX2-SNAIL via PTEN inhibition.

Brain : a journal of neurology : 1300-1319 : DOI : 10.1093/brain/awy039 En savoir plus
Résumé

Genetic modifications during development of paediatric groups 3 and 4 medulloblastoma are responsible for their highly metastatic properties and poor patient survival rates. PRUNE1 is highly expressed in metastatic medulloblastoma group 3, which is characterized by TGF-β signalling activation, c-MYC amplification, and OTX2 expression. We describe the process of activation of the PRUNE1 signalling pathway that includes its binding to NME1, TGF-β activation, OTX2 upregulation, SNAIL (SNAI1) upregulation, and PTEN inhibition. The newly identified small molecule pyrimido-pyrimidine derivative AA7.1 enhances PRUNE1 degradation, inhibits this activation network, and augments PTEN expression. Both AA7.1 and a competitive permeable peptide that impairs PRUNE1/NME1 complex formation, impair tumour growth and metastatic dissemination in orthotopic xenograft models with a metastatic medulloblastoma group 3 cell line (D425-Med cells). Using whole exome sequencing technology in metastatic medulloblastoma primary tumour cells, we also define 23 common ‘non-synonymous homozygous’ deleterious gene variants as part of the protein molecular network of relevance for metastatic processes. This PRUNE1/TGF-β/OTX2/PTEN axis, together with the medulloblastoma-driver mutations, is of relevance for future rational and targeted therapies for metastatic medulloblastoma group 3.10.1093/brain/awy039_video1awy039media15742053534001.

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Lopez-Delisle, L., Pierre-Eugène, C., Louis-Brennetot, C., Surdez, D., Raynal, V., Baulande, S., Boeva, V., Grossetête-Lalami, S., Combaret, V., Peuchmaur, M., Delattre, O., and Janoueix-Lerosey, I (2018 Jan 11)

Activated ALK signals through the ERK-ETV5-RET pathway to drive neuroblastoma oncogenesis

Oncogene : 37 : 1417, 1429 : DOI : doi.org/10.1038/s41388-017-0039-5 En savoir plus
Résumé

Activating mutations of the ALKreceptor occur in a subset of neuroblastomatumors. We previously demonstrated that Alkmutations cooperate with MYCN overexpression to induce neuroblastomain mice and identified Ret as being strongly upregulated in MYCN/Alkmuttumors. By a genetic approach in vivo, we now document an oncogenic cooperation between activatedRet and MYCN overexpression in neuroblastomaformation. We show that MYCN/RetM919Ttumors exhibit histological features and expression profiles close to MYCN/Alkmuttumors. We show that RET transcript levels decrease precedes RET protein levels decrease upon ALKinhibition in neuroblastomacell lines. Etv5 was identified as a candidate transcription factor regulating Ret expression from murine MYCN/Alkmuttumor transcriptomic data. We demonstrate that ETV5 is regulated both at the protein and mRNA levels upon ALKactivation or inhibition in neuroblastomacell lines and that this regulation precedes RET modulation. We document that ALKactivation induces ETV5 protein upregulation through stabilization in a MEK/ERK-dependent manner. We show that RNAi-mediated inhibition of ETV5 decreases RET expression. Reporter assays indicate that ETV5 is able todriveRET gene transcription. ChIP-seq analysis confirmed ETV5 binding on the RET promoter and identified an enhancer upstream of the promoter. Finally, we demonstrate that combining RET and ALKinhibitors reduces tumor growth more efficiently than each single agent in MYCN and AlkF1178L-driven murine neuroblastoma. Altogether, these results define the ERK-ETV5-RETpathwayas a critical axis driving neuroblastomaoncogenesisdownstream of activatedALK.

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Année de publication : 2017

Mathieu Chicard, Leo Colmet-Daage, Nathalie Clement, Adrien Danzon, Mylène Bohec, Virginie Bernard, Sylvain Baulande, Angela Bellini, Paul Deveau, Gaëlle Pierron, Eve Lapouble, Isabelle Janoueix-Lerosey, Michel Peuchmaur, Nadège Corradini, Anne Sophie Defachelles, Dominique Valteau-Couanet, Jean Michon, Valérie Combaret, Olivier Delattre, Gudrun Schleiermacher (2017 Dec 2)

Whole-Exome Sequencing of Cell-Free DNA Reveals Temporo-spatial Heterogeneity and Identifies Treatment-Resistant Clones in Neuroblastoma.

Clinical cancer research : an official journal of the American Association for Cancer Research : 939-949 : DOI : 10.1158/1078-0432.CCR-17-1586 En savoir plus
Résumé

Neuroblastoma displays important clinical and genetic heterogeneity, with emergence of new mutations at tumor progression. To study clonal evolution during treatment and follow-up, an innovative method based on circulating cell-free DNA (cfDNA) analysis by whole-exome sequencing (WES) paired with target sequencing was realized in sequential liquid biopsy samples of 19 neuroblastoma patients. WES of the primary tumor and cfDNA at diagnosis showed overlap of single-nucleotide variants (SNV) and copy number alterations, with 41% and 93% of all detected alterations common to the primary neuroblastoma and cfDNA. CfDNA WES at a second time point indicated a mean of 22 new SNVs for patients with progressive disease. Relapse-specific alterations included genes of the MAPK pathway and targeted the protein kinase A signaling pathway. Deep coverage target sequencing of intermediate time points during treatment and follow-up identified distinct subclones. For 17 seemingly relapse-specific SNVs detected by cfDNA WES at relapse but not tumor or cfDNA WES at diagnosis, deep coverage target sequencing detected these alterations in minor subclones, with relapse-emerging SNVs targeting genes of neuritogenesis and cell cycle. Furthermore a persisting, resistant clone with concomitant disappearance of other clones was identified by a mutation in the ubiquitin protein ligase Modelization of mutated allele fractions in cfDNA indicated distinct patterns of clonal evolution, with either a minor, treatment-resistant clone expanding to a major clone at relapse, or minor clones collaborating toward tumor progression. Identification of treatment-resistant clones will enable development of more efficient treatment strategies. .

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Léa Guerrini-Rousseau, Christelle Dufour, Pascale Varlet, Julien Masliah-Planchon, Franck Bourdeaut, Marine Guillaud-Bataille, Rachid Abbas, Anne-Isabelle Bertozzi, Fanny Fouyssac, Sophie Huybrechts, Stéphanie Puget, Brigitte Bressac-De Paillerets, Olivier Caron, Nicolas Sevenet, Marina Dimaria, Sophie Villebasse, Olivier Delattre, Dominique Valteau-Couanet, Jacques Grill, Laurence Brugières (2017 Nov 30)

Germline SUFU mutation carriers and medulloblastoma: clinical characteristics, cancer risk, and prognosis.

Neuro-oncology : 1122-1132 : DOI : 10.1093/neuonc/nox228 En savoir plus
Résumé

Germline mutations of suppressor of fused homolog (SUFU) predispose to sonic hedgehog (SHH) medulloblastoma. Germline SUFU mutations have been reported in nevoid basal cell carcinoma syndrome (NBCCS), but little is known about the cancer risk and clinical spectrum.

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Céline Chauvin, Amaury Leruste, Arnault Tauziede-Espariat, Mamy Andrianteranagna, Didier Surdez, Aurianne Lescure, Zhi-Yan Han, Elodie Anthony, Wilfrid Richer, Sylvain Baulande, Mylène Bohec, Sakina Zaidi, Marie-Ming Aynaud, Laetitia Maillot, Julien Masliah-Planchon, Stefano Cairo, Sergio Roman-Roman, Olivier Delattre, Elaine Del Nery, Franck Bourdeaut (2017 Nov 16)

High-Throughput Drug Screening Identifies Pazopanib and Clofilium Tosylate as Promising Treatments for Malignant Rhabdoid Tumors.

Cell reports : 1737-1745 : DOI : S2211-1247(17)31539-5 En savoir plus
Résumé

Rhabdoid tumors (RTs) are aggressive tumors of early childhood characterized by SMARCB1 inactivation. Their poor prognosis highlights an urgent need to develop new therapies. Here, we performed a high-throughput screening of approved drugs and identified broad inhibitors of tyrosine kinase receptors (RTKs), including pazopanib, and the potassium channel inhibitor clofilium tosylate (CfT), as SMARCB1-dependent candidates. Pazopanib targets were identified as PDGFRα/β and FGFR2, which were the most highly expressed RTKs in a set of primary tumors. Combined genetic inhibition of both these RTKs only partially recapitulated the effect of pazopanib, emphasizing the requirement for broad inhibition. CfT perturbed protein metabolism and endoplasmic reticulum stress and, in combination with pazopanib, induced apoptosis of RT cells in vitro. In vivo, reduction of tumor growth by pazopanib was enhanced in combination with CfT, matching the efficiency of conventional chemotherapy. These results strongly support testing pazopanib/CfT combination therapy in future clinical trials for RTs.

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Barbara Hero, Nathalie Clement, Ingrid Øra, Gaelle Pierron, Eve Lapouble, Jessica Theissen, Claudia Pasqualini, Dominique Valteau-Couanet, Dominique Plantaz, Jean Michon, Olivier Delattre, Marc Tardieu, Gudrun Schleiermacher (2017 Nov 15)

Genomic Profiles of Neuroblastoma Associated With Opsoclonus Myoclonus Syndrome.

Journal of pediatric hematology/oncology : 93-98 : DOI : 10.1097/MPH.0000000000000976 En savoir plus
Résumé

Opsoclonus myoclonus syndrome (OMS), often called « dancing eyed syndrome, » is a rare neurological condition associated with neuroblastoma in the majority of all childhood cases. Genomic copy number profiles have shown to be of prognostic significance for neuroblastoma patients. The aim of this retrospective multicenter study was to analyze the genomic copy number profiles of tumors from children with neuroblastoma presenting with OMS at diagnosis. In 44 cases of neuroblastoma associated with OMS, overall genomic profiling by either array-comparative genomic hybridization or single nucleotide polymorphism array proved successful in 91% of the cases, distinguishing tumors harboring segmental chromosome alterations from those with numerical chromosome alterations only. A total of 23/44 (52%) tumors showed an segmental chromosome alterations genomic profile, 16/44 (36%) an numerical chromosome alterations genomic profile, and 1 case displayed an atypical profile (12q amplicon). No recurrently small interstitial copy number alterations were identified. With no tumor relapse nor disease-related deaths, the overall genomic profile was not of prognostic impact with regard to the oncological outcome in this series of patients. Thus, the observation of an excellent oncological outcome, even for those with an unfavorable genomic profile of neuroblastoma, supports the hypothesis that an immune response might be involved in tumor control in these patients with OMS.

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Boeva, V., Louis-Brennetot, C., Peltier, A., Durand, S., Pierre-Eugène, C., Raynal, V., Etchevers, H.C., Thomas, S., Lermine, A., Daudigeos-Dubus, E., Geoerger, B., Orth, M.F., Grünewald, T.G.P., Diaz, E., Ducos, B., Surdez, D., Carcaboso, A.M., Medvedeva, I., Deller, T., Combaret, V., Lapouble, E., Pierron, G., Grossetête-Lalami, S., Baulande, S., Schleiermacher, G., Barillot, E., Rohrer, H., Delattre, O., and Janoueix-Lerosey, I. (2017 Sep 1)

Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries.

Nature Genetics : DOI : 10.1038/ng.3921 En savoir plus
Résumé

Neuroblastoma is a tumor of the peripheral sympathetic nervous system, derived from multipotent neural crest cells (NCCs). To define core regulatory circuitries (CRCs) controlling the gene expression program of neuroblastoma, we established and analyzed the neuroblastoma super-enhancer landscape. We discovered three types of identity in neuroblastoma cell lines: a sympathetic noradrenergic identity, defined by a CRC module including the PHOX2B, HAND2 and GATA3 transcription factors (TFs); an NCC-like identity, driven by a CRC module containing AP-1 TFs; and a mixed type, further deconvoluted at the single-cell level. Treatment of the mixed type with chemotherapeutic agents resulted in enrichment of NCC-like cells. The noradrenergic module was validated by ChIP-seq. Functional studies demonstrated dependency of neuroblastoma with noradrenergic identity on PHOX2B, evocative of lineage addiction. Most neuroblastoma primary tumors express TFs from the noradrenergic and NCC-like modules. Our data demonstrate a previously unknown aspect of tumor heterogeneity relevant for neuroblastoma treatment strategies.

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Franzetti GA, Laud-Duval K, van der Ent W, Brisac A, Irondelle M, Aubert S, Dirksen U, Bouvier C, de Pinieux G, Snaar-Jagalska E, Chavrier P, Delattre O, (2017 Jun 22)

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

Oncogene- : DOI : 10.1038/onc.2016.498 En savoir plus
Résumé

Ewingsarcomais characterized by the expression of the chimeric EWSR1-FLI1transcription factor. Proteomic analyses indicate that the decrease of EWSR1-FLI1expression leads to major changes in effectors of the dynamics of the actin cytoskeleton and the adhesion processes with a shift from cell-to-cellto cell-matrix adhesion. These changes are associated with a dramatic increase of in vivo cell migrationand invasion potential. Importantly, EWSR1-FLI1expression, evaluated by single-cell RT-ddPCR/immunofluorescence analyses, and activity, assessed by expression of EWSR1-FLI1downstream targets, are heterogeneous in cell lines and in tumours and can fluctuate along time in a fully reversible process between EWSR1-FLI1highstates, characterized by highly active cell proliferation, and EWSR1-FLI1lowstates where cellshave 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.

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