Oral Presentation Advances in Neuroblastoma Research Congress 2016

Fusion-transcripts are associated with an unfavorable phenotype in neuroblastoma (#113)

Fakhera Ikram 1 2 3 4 , Lynnette Fernández-Cuesta 5 6 , Frederik Roels 1 2 , Sven Lindner 7 , Ruth Volland 1 2 , Matthieu Foll 5 , Falk Hertwig 1 2 , Martin Peifer 2 6 , Yvonne Kahlert 1 2 , Yupeng Cun 2 6 , Anne Engesser 1 2 , James D McKay 5 , Muhammad Idrees 4 , Janina Fischer 1 2 , Barbara Hero 1 2 , Frank Berthold 1 2 , Wenqian Zhang 8 , Zhiyu Peng 8 9 , Leming Shi 10 , Johannes H Schulte 11 , Roman K Thomas 6 , Matthias Fischer 1 2 12
  1. Department of Pediatric Oncology and Hematology, University Children’s Hospital of Cologne, Cologne, Germany
  2. Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
  3. Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
  4. Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
  5. Genetic Cancer Susceptibility group, Section of Genetics, International Agency for Research on Cancer, IARC-WHO, Lyons, France
  6. Department of Translational Genomics, University of Cologne, Cologne, Germany
  7. Department of Pediatric Oncology and Hematology, University Children’s Hospital, Essen, Germany
  8. BGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, BGI, Guangdong, China
  9. BGI-Guangzhou, No. 280, Waihuan East Road, Guangzhou Higher Education Mega Center, Guangzhou, China
  10. Center for Pharmacogenomics,, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai , China
  11. Department of Pediatric Oncology and Hematology, Charité University Medicine, Berlin, Germany
  12. Max Planck Institute for Metabolism Research, University of Cologne, Cologne, Germany

Background: We aimed to systematically determine the spectrum of fusion-transcripts and their potential relevance for neuroblastoma pathogenesis.

Methods: We analyzed 498 primary tumors by RNA-sequencing. Fusion-transcripts were validated by dideoxynucleotide sequencing. Genomic rearrangements were determined in eleven samples by whole-genome-sequencing. Ectopic FGFR2 expression and FGFR2 knockdown was performed in JoMa1 neural crest progenitor cells and NBL-S neuroblastoma cells, respectively.

Results: We detected a total of 97 fusion-transcripts in 78 tumors, involving 169 genes. In 16/20 cases, genomic rearrangements corresponding to the fusion-transcripts were identified, indicating that they mostly represent fusion-genes. We found that chromosomes 2, 12 and 17 were significantly enriched for genes involved in fusion-transcripts (p<0.05). Fifty-two and 45 fusion-transcripts were predicted to be potentially protein-coding and truncating, respectively. We observed that the 3’-partners of the fusion-genes had significantly higher expression levels in the index cases than their wild-type counterparts in the remaining cohort, suggesting that transcriptional dysregulation is a major effect of the underlying genomic event. Similar to SNV patterns in neuroblastoma, the spectrum of fusion-transcripts was heterogeneous, with most fusion-genes being private events. We noted, however, that fusion-transcripts were significantly enriched for genes annotated in the COSMIC database (p<0.001), and comprised genes previously associated with neuroblastoma (e.g., FOXR1, HACE1 and TERT), pointing towards their potential mechanistic relevance. As an example, we evaluated the functional effect of FGFR2, the full-length coding sequence of which was involved in a KLHL13-FGFR2 fusion. Ectopic expression of FGFR2 resulted in augmented clonogenic growth, while FGFR2 knock-down significantly impaired proliferation. Finally, we observed that the outcome of patients whose tumors harbored fusion-transcripts was significantly worse than that of patients without fusion-transcripts, both in the entire cohort and in patient subgroups, such as MYCN-amplified or high-risk patients.

Conclusions: Our data suggest that fusion-transcripts resulting from genomic rearrangements contribute to an unfavorable neuroblastoma phenotype.