Inhibition of MEK and DDR Pathways Induces Synergistic Killing of Novel Mll-Af4 B-ALL Model Harboring Activated Ras Mutations

Childhood B-cell acute lymphoblastic leukemia (B-ALL) that harbor a translocation of the MLL1 and AF4 genes are considered high-risk with poor prognosis (event-free survival (EFS) of 35%-50%), especially when compared to non-MLL-rearranged (MLL-R) childhood ALL (EFS >85%). An important obstacle to developing new therapeutic approaches for this patient population is the lack of models that faithfully recapitulate the short latency and aggressiveness of this disease. Recently, whole genome sequencing of patient childhood MLL-R leukemias revealed that activating mutations of the proto-oncogenes involved in signaling, most prominently, N or K-RAS were found in nearly 50% of patients. Patients with these co-occurring mutations have an even poorer overall survival rate, indicating that a model harboring both mutations is of extreme interest.

Here, we report the generation of a highly aggressive, serially transplantable B-ALL by the retroviral overexpression of activating N-Ras^G12D mutant in bone marrow of an inducible knock-in Mll-Af4 murine model that we have previously published. Recipient mice injected with Mll-Af4/N-Ras^G12Dpre-leukemic bone marrow cells developed an acute B-ALL (B220⁺CD43⁺IgM^-) with short latency to development of disease (median 35 days). Furthermore, the resultant primary B-ALL was serially transplantable into sub-lethally irradiated recipients with accelerated latency to secondary and tertiary disease developing at a median of 20 and 12 days, respectively.

As our model includes an activating mutation in N-Ras, we wanted to see if the cells would be sensitive to small molecule inhibitors of downstream effectors of Ras. Pre-leukemic Mll-Af4/N-Ras^G12D cells were sensitive to two different MEK inhibitors, Trametinib or PD901, in vitro. Furthermore, in vivo treatment of tertiary B-ALL mice with Trametinib showed significant reduction in leukemia burden after 7 days of treatment, as well as increase in survival, compared to vehicle controls. However, prolonged in vivo treatment with Trametinib eventually led to loss of sensitivity and development of B-ALL in our mouse model, suggesting that Trametinib alone is insufficient to prevent leukemia progression.

As single agent MEK inhibition was insufficient to generate long-term durable responses, we conducted RNA-Sequencing of primary Mll-Af4/N-Ras^G12D leukemias to discover pathways amenable for therapeutic intervention. Gene set enrichment analysis suggested that targeting the DNA damage response (DDR) pathway as an attractive therapeutic opportunity. We were able to demonstrate an increased basal level of replicative stress in our Mll-Af4/Nras^G12D pre-leukemic cells and sensitivity to small molecule inhibition of ATR, a master regulator of the G2 to M transition of cell cycle progression, with AZ20, a selective ATR inhibitor. In vitro and in vivo treatment with AZ20 led to increased leukemia cytotoxicity. However, similar to Trametinib treatment, tertiary B-ALL mice eventually succumbed to disease with prolonged AZ20 treatment in vivo.

Since neither single agent MEK nor ATR inhibition could prevent leukemic progression in vivo, we tested the combination and found increased cytotoxicity and cell cycle arrest in vitro at concentrations well below the IC50, as compared to single agent treatment. In vivocombination treatment also demonstrated decreased leukemia burden and significant prolonged survival compared to either AZ20 or Trametinib alone. Lastly, we tested out the efficacy of combination therapy in human B-ALL patient derived xenograft harboring both MLL-AF4 and activating N-RASmutations. 250,000 human primary leukemic blasts were transplanted into non-irradiated immune-compromised mice and treated with vehicle, single agent, or the combination for 14 days. Similar to the results seen in our mouse model, combination treatment with Trametinib and AZ20 led to significant reductions in leukemic burden.

In summary, our model of B-ALL faithfully recapitulates the short latency and aggressiveness of this disease and was predictive of response in human patient samples harboring MLL-AF4 and activating N-RAS mutations to small molecule inhibitor therapy to MEK and DDR pathways. In the future, this model can be used as a platform to not only better understand the molecular events governing and sustaining leukemogenesis, but also as a discovery platform for novel therapeutic combinations.