Oral Presentation Advances in Neuroblastoma Research Congress 2016

Clonal reconstruction in neuroblastoma shows enrichment of mutations in cell survival and DNA-repair pathways at relapse (#114)

Paul Deveau 1 2 3 4 5 6 , Derek Oldridge 7 8 9 , Leo Colmet Daage 1 4 , Virginie Bernard 1 , Nathalie Clement 1 , Eve Lapouble 10 , Angela Bellini 1 4 , Mathieu Chicard 1 4 , Isabelle Isabelle Janoueix-Lerosey 1 , Emmanuel Barillot 1 2 5 6 , Olivier Delattre 1 4 , John Maris 7 8 9 , Gudrun Schleiermacher 1 4 , Valentina Boeva 1 2 5 6 11 12 13 14 , Valérie Combaret
  1. Institut Curie, Paris, France
  2. PSL Research University, Paris, France
  3. Univ. Paris-Sud, Orsay, France
  4. Inserm U830, Paris, France
  5. Inserm U900, Paris, France
  6. Mines-ParisTech, Paris, France
  7. Division of Oncology, Children′s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
  8. Center for Childhood Cancer Research, Children′s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
  9. Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania,, Philadelphia, Pennsylvania, USA
  10. Unité de Génétique Somatique, Institut Curie, Paris, France
  11. Institut Cochin, Paris, France
  12. Inserm, U1016, Paris, France
  13. CNRS UMR 8104, Paris, France
  14. CNRS UMR 8104, Paris, France

Neuroblastoma genomes show few recurrent somatic alterations except MYCN amplification and ALK mutations, this suggests that signaling pathways rather than specific genes are altered in neuroblastoma and participate in oncogenic clone expansion.

               To investigate this hypothesis, for 22 neuroblastoma patients we applied whole genome sequencing to triplet libraries (germline DNA, diagnosis and relapse tumors; 15 data sets published previously). We characterized putative driver mutations as mutations present in genes from the cancer census list or from the pathways of the Atlas of Cancer Signaling Networks (ACSN); we restricted ASCN pathways to those enriched in mutations. Then we applied our method QuantumClone (https://cran.r-project.org/web/packages/QuantumClone/) to predict subclonal structure for the 22 triplet samples and assign somatic driver mutations to distinct subclones. In contrast to other existing approaches, QuantumClone uses copy number information when evaluating mutation cellular prevalence and assigning mutations to corresponding subclones. Therefore, on datasets with complex clonal architecture or medium read coverage, QuantumClone shows superior performance compared to other published algorithms.

Application of QuantumClone to our data identified up to ten different clones in the diagnosis-relapse tumor pairs. Assignment of putative driver mutations to the reconstructed clones showed an enrichment of driver mutations in the relapse specific clones (p-value=0.0479, Fisher test). In particular, mutations in the apoptosis, cell survival and DNA repair pathways have been shown to be enriched at the relapse (Figure 1). Mutations in the MAPK pathway were enriched in the founding clone both at diagnosis and at relapse.

Our analysis suggests evolution of alteration in distinct signaling pathways during neuroblastoma progression.

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