Oral Presentation Advances in Neuroblastoma Research Congress 2016

The transcriptomic landscape of bone marrow-derived disseminated tumor cells of high-risk neuroblastoma patients (#13)

Fikret Rifatbegovic 1 , M. Reza Abbasi 1 , Christian Frech 1 , Sabine Taschner-Mandl 1 , Maximilian Kauer 1 , Andreas Weinhäusel 2 , Ruth Ladenstein 1 3 , Inge M. Ambros 1 , Peter F. Ambros 1 3
  1. CCRI, Children's Cancer Research Institute, Vienna, Austria
  2. Health & Environment, AIT Austrian Institute of Technology GmbH, Vienna, Austria
  3. Department of Pediatrics, Medical University of Vienna, Vienna, Austria

Background

Dissemination of tumor cells into the bone marrow (BM) is a frequent event in stage M neuroblastoma (NB) patients. So far, several studies have investigated gene expression signatures of primary NB tumors. Although BM aspirates are routinely obtained at different time points in current high risk neuroblastoma studies, e.g. HR-NBL1, the gene expression profiles of BM derived disseminated tumor cells (DTC) are poorly explored.

Methods

We established and validated a magnetic bead-based method for enrichment of DTCs from the BM suitable for subsequent RNA-Seq analysis of GD2 positive cells. RNAs of the enriched DTCs (n=43), the corresponding DTC-depleted BMs (n=43), the matched tumor samples (n=5) and the non-matched tumor samples (n=22) were sequenced (single-end, 50 bases reads). The data analysis was performed using a custom RNA-Seq pipeline built with Anduril.

Results

Our preliminary data clearly revealed distinct expression signatures separating DTCs and DTC-depleted BM cells with 2039 genes significantly differentially expressed (q ≤ 1x10-10; |logFC| ≥ 3).

Despite highly concordant expression profiles of DTCs and primary tumors, clear differences with 278 significantly differentially expressed genes (q ≤ 1x10-10; |logFC| ≥ 3) became apparent. While in primary tumors genes necessary for angiogenesis are up-regulated, the DTCs seem to adapt to the environment by down-regulation of angiogenesis specific genes and up-regulation of genes encoded by mitochondrial DNA.

Even though the gene expression signature of DTCs at diagnosis compares to a large extent to the signature of DTCs at relapse, we identified 89 differentially expressed genes (q ≤ 0.1; |logFC| ≥ 2). Interestingly, members of the MAGE gene family are found to be mainly expressed in non-MYCN amplified relapse samples.    

Conclusion

BM-derived disseminated NB cells are characterized by an expression signature that most likely reflects their adaptation to the BM niche. Furthermore, we expect that the differential expression signature of DTCs at diagnosis versus relapse will help in deciphering the processes leading to relapse.