Darwinian Evolution of Acute Lymphoblastic Leukaemia

Overall survival for paediatric ALL is favourable, but after relapse this rate drops dramatically. Many patients who relapse will have an aggressive drug resistant disease, clonally evolved from a presentation or ancestral clone, acquiring mutations in a Darwinian manner. We previously characterised a presentation/relapse pair derived from a t(17;19) pre B ALL patient sample in which the relapse has a 5q deletion spanning 5 genes, including NR3C1, the glucocorticoid receptor. Competitive transplantation showed the presentation outcompetes the relapse, except under dexamethasone treatment. This lead to the hypothesis that one of the 5 deleted genes was responsible for the reduction in fitness. To test this we used the pre B ALL cell line 697 (t(1:19)), transduced with lentiviral vectors carrying shRNA targeting the deleted genes. We conducted a small scale screen in which shRNA adversely affecting fitness were expected to be lost. NR3C1 function was also tested using mifepristone, a potent antagonist, however we found that in the first 24 hours there is a degree of agonist activity preceding reductions in gene expression. Furthermore, in vivo experiments with mifepristone have shown no effect on survival. It has been decided mifepristone is not a viable option to reduce NR3C1 signalling. We concluded NR3C1 deletion, although rare in primary samples may not cause reduced fitness in the original patient sample. Gene expression analysis of patient derived xenograft material was used to determine other possible candidate genes. From this, a list of 95 genes differentially expressed between presentation and relapse has been produced. This list implicates epigenetic mechanisms as a possible cause for reduced fitness as well as identifying several other interesting candidate genes.