Overcoming mutational complexity in acute myeloid leukemia by inhibition of critical pathways

Targeting leukemogenic mutations identified by functional single-cell genomics eliminated human AML in vivo. The right treatments for the right mutations A variety of mutations have been observed in cancer cells from patients with acute myeloid leukemia, but it can be difficult to know which of these mutations contribute to tumorigenesis and should therefore be targeted. To address this issue, Saito et al. isolated subpopulations of leukemic cells with specific mutations and monitored their leukemogenic capacity in immunosuppressed mice. By combining this approach with genomic analysis, the authors were able to identify mutations that drive the evolution of leukemia and figure out effective approaches to target them. Numerous variant alleles are associated with human acute myeloid leukemia (AML). However, the same variants are also found in individuals with no hematological disease, making their functional relevance obscure. Through NOD.Cg-PrkdcscidIl2rgtmlWjl/Sz (NSG) xenotransplantation, we functionally identified preleukemic and leukemic stem cell populations present in FMS-like tyrosine kinase 3 internal tandem duplication–positive (FLT3-ITD)+ AML patient samples. By single-cell DNA sequencing, we identified clonal structures and linked mutations with in vivo fates, distinguishing mutations permissive of nonmalignant multilineage hematopoiesis from leukemogenic mutations. Although multiple somatic mutations coexisted at the single-cell level, inhibition of the mutation strongly associated with preleukemic to leukemic stem cell transition eliminated AML in vivo. Moreover, concurrent inhibition of BCL-2 (B cell lymphoma 2) uncovered a critical dependence of resistant AML cells on antiapoptotic pathways. Co-inhibition of pathways critical for oncogenesis and survival may be an effective strategy that overcomes genetic diversity in human malignancies. This approach incorporating single-cell genomics with the NSG patient-derived xenograft model may serve as a broadly applicable resource for precision target identification and drug discovery.