Clinical and co-clinical genomics of paediatric solid tumours with a special focus in DIPG

Abstract

Cure rates for paediatric solid cancers have not improved in the last decade. Delivering precision medicine to stratify patients based on their molecular profiling is a key goal to support existing and upcoming adaptive clinical trials. To this end, I have developed and validated a clinically targeted sequencing panel comprising of 78 genes for a first version of 92 genes for an expanded version of the assay. Using the paediatric panel, a total of 255 patients were sequenced and potentially targetable mutations were found in 50% of patients. This methodology is currently being used for clinical decision making in every child with a solid tumour in the UK, as part of the National Health Service diagnostic service. Furthermore, I have developed a specific panel for the detection of structural variants in paediatric brain tumours which includes 24 genes. Using the fusion-panel, relevant structural variants were identified in the HERBY clinical trial, including novel internal tandem duplications in NTRK2. In addition, plasma and CSF samples from the HERBY clinical trial and other studies were used to identify molecular alterations in circulating tumour DNA in patients with paediatric HGG patients and DIPG. Moreover, in a prospective biopsy-stratified clinical trial (BIOMEDE), I combined detailed molecular profiling linked to drug screening in newly-established patient-derived models of DIPG in vitro and in vivo. A high degree of in vitro sensitivity to the MEK inhibitor trametinib was identified in samples harbouring genetic alterations targeting the MAPK pathway. However, treatment of PDX models and the patient with trametinib at relapse failed to elicit a significant response. Resistant clones in a BRAF-G469V model were generated identifying the emergence of acquired mutations in MEK1/2. These cells showed the hallmarks of mesenchymal transition revealing up-regulation of invasion and migration biomarkers. Resistant clones were sensitive to tyrosine kinase inhibitor dasatinib and combinations of trametinib with dasatinib and the ERK inhibitor ulixertinib showed synergistic effects in vitro. This work demonstrates the value of targeted sequencing for a precise classification of novel, molecularly based therapies in children with cancer. Furthermore, I show the feasibility in generating patient-specific, testable hypotheses that may be clinically translated in a subset of patients. In addition, I describe the detection of MAPK pathway alterations as a therapeutic target in DIPG and demonstrate the importance of resistance modelling to find rational combinatorial treatments.