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.
