Oral Presentation Advances in Neuroblastoma Research Congress 2016

Dissecting neuroblastoma specific regulatory networks through epigenome mapping and transcriptional profiling of neuroblastoma and neural crest cell lines (#40)

Caroline Louis 1 , Virginie Raynal 1 2 , Heather Etchevers 3 , Sophie Thomas 4 , Alban Lermine 5 , Valérie Combaret 6 , Sylvain Baulande 2 , Gudrun Schleiermacher 7 , Olivier Delattre 1 , Valentina Boeva 8 , Isabelle Janoueix-Lerosey 1
  1. Institut Curie, PSL Research University, Inserm U830, Paris, France
  2. Institut Curie Genomics of Excellence (ICGex) Platform, Paris, France
  3. INSERM U910, Faculté de Médecine, , Marseille,, France
  4. INSERM U1163, Laboratory of Embryology and Genetics of Congenital Malformations, Paris Descartes - Sorbonne Paris Cité University , Imagine Institute , Paris, France
  5. INSERM Unité 900 - Mines ParisTech - Institut Curie " Bioinformatics and Computational Systems Biology of Cancer", Paris, France
  6. Centre Léon-Bérard, Laboratoire de Recherche Translationnelle, Lyon, France
  7. Laboratoire RTOP "Recherche Translationelle en Oncologie Pédiatrique"; INSERM U830 and Department of Pediatric Oncology, Institut Curie, Paris, France
  8. Institut Curie, Centre de Recherche; Inserm, U900; Mines ParisTech, PSL Research University; Institut Cochin; Inserm, U1016; CNRS UMR 8104; Université Paris Descartes UMR-S1016., Paris, France

Neuroblastoma is a cancer of the peripheral nervous system, a structure that derives from the neural crest. The MYCN and ALK genes have been shown to be major drivers of neuroblastoma oncogenesis and more recently abnormalities of ARID1A/ARID1B, ATRX and TERT genes have been associated with a high-risk phenotype.

Here, we performed comprehensive epigenome mapping of 19 neuroblastoma and 2 human neural crest cell lines. Epigenome profiles for the chromatin marks H3K4me3 (active or poised promoters), H3K27me3 (PRC2-based repression) and H3K27ac (active promoters, enhancers and super-enhancers) were generated using ChIP-seq whereas transcriptional profiles were defined by RNA-seq analysis. The genomic alterations of the analyzed neuroblastoma cell lines have been previously characterized. The HMCan (Histone Modifications in Cancer) and Rose algorithms were used to identify distinct chromatin states and particularly super-enhancers.

Integrative bioinformatics analysis of the obtained profiles for neuroblastoma and neural crest samples and the use of epigenome profiles for other cancer types form the ENCODE project allowed us to identify neuroblastoma specific promoters, enhancers and super-enhancers. Unsupervised hierarchical clustering using neuroblastoma specific super-enhancers separated neuroblastoma cell lines from other cancer types and from neural crest cell lines. However, among neuroblastoma cell lines, no clear separation emerged according to the MYCN or ALK status. Our data revealed super-enhancers in key neuroblastoma oncogenes including two distinct super-enhancers within the ALK gene. The strength of super-enhancers correlated linearly with gene expression. Bivalent promoters marked by H3K4me3 and H3K27me3 were also defined in both neuroblastoma and neural crest samples. Interestingly, whereas only the H3K4me3 mark was detected on the ALK promoter in neuroblastoma cell lines expressing this gene, the ALK promoter appeared to be bivalent in neural crest samples with no ALK expression detected by RNA-seq. Additional analysis is ongoing to further define the specific regulatory networks that drive neuroblastoma identity and oncogenesis.