Systems analysis of nucleic acids to model outcome and biological characteristics of neuroblastoma

Neuroblastoma (NB) cells in the bone marrow (BM) at diagnosis are powerful indicators of poor outcome, the BM being a frequent reservoir for drug refractory disease. Improved outcome for some children will only be realised when treatments to eradicate BM disease have been developed. I have therefore isolated NB cells from BM aspirates of children with high-risk disease and investigated the self-renewal, migratory capacity and clinical significance of this disease. I have optimised methods for analysis and reporting of miRNA expression profiles using TaqMan® miRNA arrays to identify miRNAs or miRNA regulated pathways that are drivers of BM disease and investigated the potential of miRNAs as biomarkers of risk in liquid biopsies including BM aspirates and blood. The median infiltration of BM with NB cells was 17% (range 0-94%); a high infiltration of BM with NB cells was predictive of a worse EFS (p=0.0012). Heterogeneous self-renewing capacity was observed in both colony and spheroid formation assays. Colony formation predicted EFS (p=0.012). Migratory cells were identified in all NB cultures; the migration index was highly heterogeneous (median 127±23, n=93, range 7.5-427.5) and did not predict EFS. Hierarchical clustering of NB miRNA profiles revealed that NB cells from BM are heterogeneous. Pathway analysis revealed enrichment of the PI3K pathway in propagated NB cells. Treatment of cells with PI3K inhibitors reduced the viable NB cell number, validating the approach taken. Furthermore miR-618, reported to modulate growth via the PI3K pathway, was significantly associated with both self-renewal and survival. Circulating miRNAs in BM and PB predicted EFS. In conclusion, NB cells from the BM of children with high-risk disease are highly heterogeneous. miRNAs are suitable candidates as circulating biomarkers of risk for more personalised treatment, although further investigations are needed to functionally validate their specific roles and design miRNA-mediated therapies.