Finding therapeutic targets in FLT3-ITD AML using a systems biology approach

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Leukaemia is a blood cell cancer that arises when stem cells or immature blood cells are hit by a series of mutations in their DNA. The consequence is that the cell starts to activate genes that are not normally active, or genes are altered to make abnormal proteins, or no protein at all. If such a protein is required to switch other genes on or off, the consequences can be devastating. The reason for this is that the finely balanced order in which genes are switched on or off during blood cell development is now disturbed. In the early stages, a single mutation may have little effect, and many apparently normal people already carry some mutations in their blood cells. However, additional mutations create a domino effect. First, some target genes are de-regulated by the mutations. This can lead to stem cells that grow more than they should, but are otherwise quite normal and still can form normal blood cells. Over time additional changes occur that tip the balance from a cell that grows a bit too much, to cells where blood cell development grinds to a halt and the cells become malignant. Such cells do not develop into normal blood cells, but form leukemic cells that keep growing and growing until they finally take over the body. Acute myeloid leukaemia (AML) is the most common acute leukaemia in adults. Despite improvements in supportive care, outcome typically remains poor for older AML patients. It has long been known that AML cannot be classified as just one disease but is highly heterogeneous, involving different genetic mutations and highly variable clinical outcomes. The FLT3-ITD mutation is a growth-promoting mutation, and one of the mutations that has the most devastating effects. It occurs in about 25% of all cases, and generates a continuously active protein that cannot be switched off, which tells cells to grow indefinitely. The clinical prognosis of having such a mutation is dire, and treatment with drugs targeting the FLT3-ITD protein soon results in the development of drug resistance and relapse. The Bonifer/Cockerill group has recently embarked on a series of experiments which highlighted how gene regulation is altered in AML with FLT3-ITD and deviates from normal cells. This was made possible by modern technology that looks at many genes simultaneously. We have uncovered a network of genes which are likely to be essential for the development and maintenance of FLT3-ITD AML. These include the transcriptional regulators RUNX1 and AP-1 which control the abnormal expression of FLT3-ITD AML-specific proteins. We have now teamed up with the Heidenreich lab who developed an in vivo model of human FLT3-ITD AML and the lab of John Bushweller from the University of Virginia who has developed novel drugs that target RUNX1 directly. Our proposed work will build on our results and is designed to (i) identify new targets for therapy, (ii) understand which genes are affected by different drug and (iii) use optimized drugs in mouse models of AMLs to prepare the stage to test these novel molecules in a clinical trial. In this work we will use inhibitory RNA molecules to block the production of proteins that are aberrantly expressed in FLT3-ITD AML. We will use this screen to identify which of the abnormally expressed genes are vital to the growth of these AML cells. Once we have identified genes and pathways that control the gene regulatory network we will use specific reagents and chemical inhibitors to block these points in the AML network, and block leukaemia development. These will include (a) a drug that than specifically block the binding of the DNA-binding transcriptional regulator RUNX1, (b) A shortened version of the FOS protein which acts as a dominantly acting repressor of all members of the AP-1 family of transcriptional regulators, and (3) combinations of clinically approved inhibitors of FLT3-ITD and MAPK signalling, which we predict will be more effective than therapies using single agents.