Cohesin haploinsufficiency and inv(16) cooperate to reinforce Fli1 gene transcriptional programs during acute myeloid leukemia initiation and maintenance

Core binding factor (CBF) acute myeloid leukemias most commonly harbor the translocations t(8;21) or inv(16). Cohesin mutations are less commonly observed in inv(16) than in t(8;21), suggesting that they may negatively impact leukemic initiation or maintenance in this setting. We used a mouse model of inv(16) with haploinsufficiency of the cohesin subunit Smc3 and paradoxically found that inv(16);Smc3D/+ mice have a reduced leukemic latency compared to inv(16);Smc3+/+ mice, suggesting a role for cohesin loss in leukemic initiation or maintenance. Given the known role of cohesin haploinsufficiency in altering chromatin accessibility, we demonstrated an increase in chromatin accessibility in inv(16);Smc3 D/+ HSPCs prior to leukemia development, with an enrichment for Fli1 DNA binding motifs. We also observe an increase in Fli1 expression and enhanced Fli1 target expression in the most primitive hematopoietic stem cells using scRNA-seq, linking enhanced Fli1 activity in the inv(16);Smc3D/+ setting to leukemic initiation consistent with elevated RAS activity, which is common in inv(16) AML. We further show that Fli1 is essential for the maintenance stage of inv(16);Smc3D/+ AML. Our data demonstrate that cohesin loss drives both leukemic initiation and maintenance in inv(16) AML, identifying Fli1 as a previously unrecognized therapeutic vulnerability.