Whole-genome CRISPR screen as a tool to identify mechanism of relapse and potential targets for novel drug combinations

Steroid resistance and relapse is one of the major clinical challenges in ALL high-risk cases. Here we performed genome-wide CRISPR screens in t(17;19) patient material, obtained at both diagnosis and relapse stage. PDX samples were generated and transduced with CRISPR(ko) library. To investigate the mechanism of steroid resistance, PDX cells were treated with dexamethasone in both ex vivo and in vivo conditions. We have identified NR3C1 as the main driver of chemo-resistance and relapse. Gene knockout of NR3C1 in diagnostic PDX material, confirmed dex-resistance as a main consequence of NR3C1 loss. Moreover, we have identified few pro-survival members of BCL2 protein family and several negative regulators of mTOR pathway as essential mediators of leukaemic propagation in this relapse PDX sample. Relapse PDX cells were also treated with ABT-199 and several mTORC1 inhibitors. We have observed these cells to be significantly more sensitive to BCL2i than its matched diagnostic pair. Moreover, both diagnostic and relapse samples showed high synergy when treated with BCL2 and mTOR inhibitors, highlighting this novel non-genotoxic drug combinations for further preclinical evaluation.