Combined Targeting of the Menin-MLL1 Chromatin Complex and FLT3 As a Novel Therapeutic Concept Against NPM1 Mutant or MLL-Rearranged AML with Mutated FLT3

NPM1mutant (NPM1^mut) and MLL1-rearranged (MLL-r) acute myeloid leukemias (AMLs) exhibit aberrant expression of HOX and MEIS1 transcription factors and commonly harbor an activating mutation in the receptor tyrosine kinase FLT3. Pharmacologic inhibition of the menin-MLL1 complex reverses leukemogenic gene expression including MEIS1 and FLT3 and represents a therapeutic opportunity for the treatment of these leukemias. Here, we investigate the contribution of the menin-MLL1 complex to leukemic FLT3 signaling and assess the therapeutic potential of dual menin-MLL1 and FLT3 targeting.

First, we performed RNA sequencing to delineate transcriptional changes associated with menin-MLL1 inhibition (-i) using the small molecule inhibitor MI503 in NPM1^mut and MLL-r AMLs (OCI-AML3 and MV411 cells). In both leukemias, we confirmed MEIS1 and its target gene FLT3 to be among the most significantly downregulated genes. These results were validated in several human cell lines of NPM1^mut or MLL-r AMLs and in a genetically engineered murine AML model harboring an NPM1^mut and an internal tandem duplication mutation in the FLT3 gene (Npm1^mut/+Flt3^ITD/+,now referred to as Npm1^mutFlt3^ITD). Allele-specific qPCR upon MI503 treatment confirmed profound suppression of the FLT3^ITD allele present in the MLL-r MV411 and MOLM13 cells. Total FLT3 protein expression was also reduced upon MI503 treatment in all tested NPM1^mut and MLL-r AMLs.

Next, we assessed the therapeutic potential of combined menin-MLL1-i and FLT3-i in the FLT3-ITD positive MLL-r and NPM1^mut leukemias. We found dramatic synergistic growth inhibition and substantially enhanced apoptosis when combining MI503 with the specific small molecule FLT3 inhibitor AC220 (Quizartinib) compared to monotreatment or vehicle control in the FLT3^ITD positive MLL-r MV4-11 and MOLM-13 cells. Similar results were obtained when MI503 was combined with other specific FLT3 inhibitors - Crenolanib and Gilteritinib. As the murine Npm1^mutFlt3^ITD AML cells harbor the Flt3^ITD F692L gatekeeper mutation that conveys drug resistance to most FLT3 inhibitors, we used Ponatinib as a combination partner for MI503 in these cells and found similar synergistic suppression of proliferation and colony formation. No drug sensitivity to single or combo treatment was observed in the human HL60 and NB4 cells, or the murine Hoxa9-Meis1 transformed cells (all wildtype for NPM1, MLL, FLT3).

To investigate the mechanism of drug synergy we then performed immunoblotting of phosphorylated (activated) FLT3 (pFLT3). As expected, we observed reduced pFLT3 upon direct FLT3 inhibition with AC220 and found decreased total FLT3 and pFLT3 with MI503 monotreatment. Of note, we observed the most pronounced pFLT3 reduction with combo treatment, most likely reflecting the cooperative effect of direct pFLT3 inhibition with AC220 and transcriptional suppression of total FLT3 via MI503. Transcriptional profiling revealed most dramatic reduction of FLT3 downstream signature gene expression including MYC and MYC-dependent genes upon combinatorial treatment compared to single drug or vehicle controls. Ectopic expression of Meis1 or Hoxa9-Meis1 in the Npm1^mutFlt3^ITD cells led to increased Flt3 gene and protein expression and partially rescued the anti-proliferative effect of MI503 and combined menin-MLL1-i and FLT3-i.

Next, we assessed the combo drug regimen in a cell line derived leukemic xenograft murine model in vivo. We found significantly reduced leukemia burden defined by bone marrow engraftment after 14 days of treatment within the combo versus the single drug or vehicle control animals. In a separate experiment, animals that had been treated with the drug combo in vivo had a dramatically enhanced survival compared to the control groups. We then evaluated single and combo drug effects on five primary human NPM1^mutFLT3^ITD AML patient samples in a human stroma cell co-culture model. The most profound anti-leukemic effect was again detected with the combo treatment compared to all other controls.

In summary, we demonstrate synergistic on-target activity against mutant FLT3 signaling with combined menin-MLL1 and FLT3 inhibition in leukemias with NPM1^mut or MLL-r in vitro and in vivo. This concept may represent a novel therapeutic opportunity against these AMLs harboring a prognostically adverse FLT3-ITD.