Clonal evolution mediates Menin-inhibitor resistance inKMT2A-rearranged leukemias

Abstract

Inhibitors of the Menin-KMT2A interaction are emerging as promising agents for the treatment of KMT2A-rearranged (KMT2A-r) acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). Menin is required for the recruitment of the KMT2A-fusion to a subset of its target genes. We evaluated the efficacy of Menin-inhibition in KMT2A-r leukemias with high-risk features: high-risk KMT2A fusion partners in AML (MLLT10, MLLT4), infant ALL, and serial samples from patients with multiply relapsed ALL. We find that AML with high-risk fusion partners is sensitive to Menin-inhibition in xenografts. In contrast, highly pretreated samples from patients with KMT2A-AFF1 ALL are largely resistant. Menin inhibitor resistance in these patients is acquired, as Menin inhibition shows in vivo efficacy against leukemia samples obtained earlier in the disease course of the same patient. Transcriptomic analysis documents sustained on-target efficacy of the Menin inhibitor on a transcriptional level in resistant cells. However, genomic analysis documented the emergence of multiple co-mutations that may be sufficient to drive AML, and may mediate independence from the KMT2A-fusion induced transcription program. Our data suggest that it will be critical to use Menin-inhibitors upfront or in early lines of therapy before substantial clonal evolution has occurred.