Oral Presentation Advances in Neuroblastoma Research Congress 2016

Chromosomal rearrangements juxtapose active enhancer elements to oncogenes in high‐risk neuroblastoma (#115)

Daniel Dreidax 1 , Moritz Gartlgruber 1 , Elena Afanasyeva 1 , Larissa Savelyeva 1 , Ron Schwessinger 2 , Martin Peifer 3 4 , Matthias Fischer 4 5 6 , Stefan Groeschel 7 , Kai-Oliver Henrich 8 , Young-Gyu Park 1 , Carl Herrmann 2 , Frank Westermann 1
  1. Division Neuroblastoma Genomics (B087), German Cancer Research Center (DKFZ), Heidelberg, Germany
  2. Division Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
  3. Department of Translational Genomics, Center of Integrated On cology Cologne–Bonn, University of Cologne, Cologne, Germany
  4. Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
  5. Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
  6. Max Planck Institute for Metabolism Research, Cologne, Germany
  7. Department of Translational Oncology (G100) , German Cancer Research Center (DKFZ), Heidelberg, Germany
  8. Division Neuroblastoma Genomics (B087), German Cancer Research Center (DKFZ), Heidelberg, Germany

Background: Exome sequencing studies revealed that neuroblastomas (NBs) harbor a low overall mutation rate with only few recurrently mutated genes leaving the molecular etiology of a large proportion of NBs elusive. In the present study, we applied a whole genome sequencing (WGS) approach to uncover structural rearrangements in noncoding regions that could potentially drive NB.

 Methods: WGS was applied to search for structural rearrangements in NB tumors and cell lines. A protocol for chromatin immunoprecipitation sequencing (ChIP-seq) of tumors was established and used to identify active enhancer elements in NB. Circular chromatin conformation capture sequencing (4C-seq) was used to assay for physical promoter-enhancer interactions. Genomic excision of enhancer elements was performed by means of CRISPR/Cas9-techniques.

 Results: WGS analyses revealed that chromosomal rearrangements are common in NB with the most frequent event encompassing the telomerase gene (TERT) which is rearranged in 25% of high-risk cases. ChIP-seq analyses confirmed that rearrangements commonly juxtapose active enhancer elements to TERT and other oncogenes involved in translocation events in NB tumors and cell lines. 4C-seq analyses provided evidence for physical interactions of translocated enhancer elements with the promoters of the respective oncogenes. This is in line with elevated expression of the affected genes in rearranged cases. Currently, we test the functional relevance of enhancer translocations by CRISPR/Cas9-mediated excision of the enhancer elements in translocated NB cells. Furthermore, we test therapeutic concepts targeting enhancer-mediated gene deregulation with CDK7- or BET- inhibitors.  

 Conclusions: The study reveals that structural rearrangements in high-risk NB frequently juxtapose strong enhancers to oncogenes, leading to de novo physical promoter-enhancer interactions and overexpression of the oncogenes in rearranged cases. This mechanism of oncogene activation by enhancer hijacking may open a therapeutic window for epigenetic drugs, including BET inhibitors or CDK7 inhibition, in high-risk NBs.