Tyrosine Kinase Inhibitor Independent Gene Expression Signature in CML Offers New Targets for LSPC Eradication Therapy

SIMPLE SUMMARY: Chronic myeloid leukaemia (CML) is initiated by a group of cancer cells called leukaemia stem cells (LSC). These LSC can survive current tyrosine kinase inhibitor (TKI) treatments and, upon treatment withdrawal, are able to re-initiate the disease. Thus, eradicating the LSC would likely cure CML. In this study, we have identified a number of genes whose expression is different between LSC and their healthy counterparts (haematopoietic stem cells) but are not affected by TKI treatment. We hypothesised that these genes may be potential therapeutic targets against LSC and used two different drugs, gemtuzumab–ozogamicin and cyclosporine A, to treat CML in vitro. We found that both drugs have a stronger effect on CML cells than on healthy cells. Therefore, we propose that the list of genes we identified could represent a novel source of therapeutic targets against CML. ABSTRACT: Tyrosine kinase inhibitors (TKI) have revolutionised the treatment of CML. However, TKI do not eliminate the leukaemia stem cells (LSC), which can re-initiate the disease. Thus, finding new therapeutic targets in CML LSC is key to finding a curative treatment. Using microarray datasets, we defined a list of 227 genes that were differentially expressed in CML LSC compared to the healthy controls but were not affected by TKI in vitro. Two of them, CD33 and PPIF, are targeted by gemtuzumab–ozogamicin and cyclosporin A, respectively. We treated CML and the control CD34(+) cells with either drug with or without imatinib to investigate the therapeutic potential of the TKI-independent gene expression programme. Cyclosporine A, in combination with imatinib, reduced the number of CML CFC compared with non-CML controls, but only at supra-therapeutic concentrations. Gemtuzumab–ozogamicin showed an EC(50) of 146 ng/mL, below the plasma peak concentration of 630 ng/mL observed in the AML patients and below the EC(50) of 3247 ng/mL observed in the non-CML cells. Interestingly, gemtuzumab–ozogamicin seems to promote cell cycle progression in CML CD34(+) cells and demonstrated activation of the RUNX1 pathway in an RNAseq experiment. This suggests that targeting the TKI-independent genes in CML LSC could be exploited for the development of new therapies in CML.