Redeployed drug inducing MLL fusion degradation

Introduction:

Acute leukemias in infants are quite rare but generate a great interest due to the aggressive clinical features. The survival rate for these infants is less than 50%. The fast majority of infant acute leukemias are characterized cytogenetically by balanced chromosomal translocations involving the mixed lineage leukemia (MLL) gene. Leukemic therapies that degrade the driver oncogene are associated with loss of cancer cell self-renewal and excellent cure rates. Therefore, therapy that degrades the MLL fusion gene would offer new hope to these patients. Developing a brand new drug takes a big amount of effort, money and time. To translate a new molecule in a potential drug it takes approximately 13 – 15 years. It is crucial to reduce this time frame, decrease costs and improve success rates. One approach that could provide the quickest possible transition from bench to bedside is called “drug repositioning”. This refers to the identification of new therapeutic indications for known drugs. This strategy reduces discovery risks because all tested drugs have already passed through several stages of preclinical testing. The aim of this study is to identify clinically approved drugs capable of degrading leukemic fusion proteins.

Method:

Firstly, we generated a leukemic fusion gene cell line expressing the MLL-AF9 gene fused to a firefly luciferase. Then we tested all compounds presents in the Prestwick chemical library on the leukemic cell line generated in order to identify compounds showing anti-leukemic activity. The degradation of leukemic fusion protein was monitored by analysing changes in luciferase activity. We initially identified 25 putative positive hits and subsequently using a different readout methodology we validated 7 drugs on different MLL rearranged cell lines.

Results:

We showed that we are able to degrade MLL-fusion proteins in a panel of human MLL rearranged cell lines and in primary human cells expressing MLL-AF9. We down-regulated also the expression of MLL target genes, including HOXA9, MEIS1 and c-MYB. While target genes downregulation was measured already after short drug treatments, the MLL proteins degradation was detectable after longer treatments. We showed that this dysregulation was due to a loss in MLL transcriptional regulation impairing the DNA binding of MLL fusion proteins. Functionally, this resulted in a loss of self-renewal of the leukemic stem cells, as shown by methylcellulose colony forming assays. RNA-seq experiments showed that the our signature is negatively enriched in MLL-AF9 and MLL-AF4 gene sets already published.

Conclusions:

In conclusion, we showed how the inactivation of the MLL-fusion proteins and down-regulation of MLL target genes resulted in a block of leukemic stem cell self-renewal. We are validating these findings in a pre-clinical in vivo model.