Oral Presentation Advances in Neuroblastoma Research Congress 2016

High frequency of mutations in chromatin remodeling genes in neuroblastoma (#45)

Angela Bellini 1 , Nadia Bessoltane 1 , Nathalie Clement 1 , Virginie Bernard 2 , Leo Colmet Daage 3 , Virginie Raynal 4 , Eve Lapouble 5 , Gaelle Pierron 3 , Mathieu Chicard 3 , Isabelle Janoueix-Lerosey 6 , Caroline Louis-Brennetot 3 , Valentina Boeva 7 , Franck Bourdeaut 3 , Jean Michon 3 , Olivier Delattre 6 , Gudrun Schleiermacher 8
  1. Laboratoire RTOP "Recherche Translationelle en Oncologie Pédiatrique" and INSERM U830, Institut Curie, Paris, France
  2. Plateforme ICGEX and U900 INSERM, Institut Curie, Paris, France
  3. Institut Curie, Paris, France
  4. Plateforme de Séquençage ICGEX, Institut Curie, Paris, France
  5. Unité de Génétique Somatique, Institut Curie, Paris, France
  6. U830 INSERM, Institut Curie, Paris, France
  7. U900 INSERM, Institut Curie, Paris, France
  8. Laboratoire RTOP "Recherche Translationelle en Oncologie Pédiatrique", INSERM U830 and Department of Pediatric Oncology, Institut Curie, Paris, France

Background: Chromatin remodeling complexes including SWI/SNF are implicated in a wide variety of cellular processes including nuclear organization, chromosomal stability and gene expression, and mutations in SWI/SNF components play an important role in many cancer types. In neuroblastoma (NB), recent whole-genome/whole-exome sequencing efforts results have detected genetic alterations in chromatin remodeling genes such as ARID1A and ARID1B.

 

Methods: To explore the potential recurrence of genetic alterations in chromatin remodeling genes in a clinically representative cohort of NB patients (255 diagnostic samples), we designed a TruSeq Custom Amplicon panel (TSCA, Illumina) targeting 33 SWI/SNF genes (261.686bp). Libraries prepared from 50ng of genomic DNA were subjected to 150bp paired-end sequencing, with a high coverage (mean 2000X). After sequence alignment, two analyses were initiated. Clonal/sub-clonal mutations were detected by ACGT-base calling approach and statistical comparison between samples and controls. Structural variations will be searched for by gene dosage normalization within and between samples/controls.

Furthermore, a series of 31 NB cell lines and 6 germline controls were included in this study.

 

Results: A total of 96 clonal mutations (mutated allele fraction >20%) were detected. Overall, 35% of NB patients showed a mutation in at least one chromatin-remodeling gene; the most frequently mutated genes were ARID1A (10/255), ARID1B (3/255), BRD7 (3/255), MLL3 (10/255) and SMARCC2 (6/255) genes. Furthermore, 11 NB cell lines showed a clonal mutation in at least one of the studied genes. Mutations detected in NB cells lines were validated by RNA sequencing. Analyses to detect sub-clonal mutations and structural variations are ongoing.

No statistically significant differences in survival of patients with chromatin-remodeling genes wild-type versus chromatin-remodeling genes mutated at clonal level were observed.

 

Conclusions: The high frequency of clonal mutations highlights the dysregulation of chromatin remodeling in pediatric tumorigenesis and suggests potential new approaches for the management of patients with neuroblastoma.