Background: Despite the overall success achieved in treating childhood cancers, a major challenge is to find alternative treatment options for those children who suffer relapse. This requires more detailed understanding of the molecular pathways responsible for maintaining and promoting an aggressive drug resistant phenotype, as well as the successful targeting of these pathways.
Materials and methods: We are implementing a molecular profiling approach to individual tumours, which includes Fluidigm Biomark qRT-PCR analysis (a panel of 96 marker genes), next-generation sequencing (Ion Proton custom AmpliSeq panel of 480 genes) and automated immunohistochemistry (IHC, 30 antibodies to 25 proteins/ phosphoproteins).
Results: Preliminary testing of a subset of these genes has been conducted on 12 cell lines representing the major childhood cancer subtypes, as well as 8 patient-derived primary cultures including 4 inflammatory myofibroblastic tumours, 2 diffuse intrinsic pontine gliomas and 2 acute lymphoblastic leukaemias (ALL). The potential for molecular profiling to assist in drug selection was subsequently tested in high throughput in vitro drug sensitivity assays using a drug library based on the profiling data. Gene expression has also been analysed in forty five cell lines from mice bearing patient-derived ALL xenografts. The individualised mouse xenografts will allow in vivo testing of the efficacy of molecularly targeted drugs. We are now undertaking a retrospective study of diagnostic frozen and formalin fixed paraffin embedded samples from 55 paediatric cancer patients who subsequently experienced relapse.
Conclusion: We have implemented a screening approach to identify molecular targets in paediatric cancer patients who have failed the best current treatments available, and for whom treatment options following relapse are extremely limited. The ultimate goal is to undertake a multicentre prospective clinical trial in paediatric patients with recurrent or refractory solid tumours or leukaemias for whom targeted drug therapy will be identified using molecular profiling.