ACSL4-Associated Lipid Metabolism is a Distinct Therapeutic Vulnerability in KMT2A-Rearranged Acute Myeloid Leukemia

Deregulation of lipid metabolism has been shown to be involved in leukemogenesis and disease progression of acute myeloid leukemia (AML), yet vulnerabilities within the lipidome remain largely unexplored. Through comprehensive analysis of CRISPR-Cas9 screening data, we identified a specific dependency of a subset of AML cell lines on the gene acyl-CoA synthetase long chain family member 4 ( ACSL4 ). Particularly those AML cell lines with chromosomal rearrangements involving the gene lysine methyltransferase 2A ( KMT2A ) showed an increased dependency on ACSL4 . Using CRISPR interference (CRISPRi)- and shRNA-mediated knockdown of ACSL4 in both KMT2A -rearranged ( KMT2A r) and non- KMT2A r AML cells, we confirmed the dependency of KMT2A r AML on ACSL4 . The knockdown of Acsl4 in a KMT2A r mouse model resulted in reduced colony-forming capacity ex vivo and significantly delayed leukemia onset in vivo . To understand molecular differences between ACSL4 -dependent and non-dependent AML cells upon ACSL4 knockdown, we performed a multi-omics approach, including transcriptomics, proteomics, and lipidomics. Integration of these data revealed an upregulation of lipid metabolism pathways exclusively in ACSL4 -dependent cell lines. We generated a 12 gene-containing KMT2A r- ACSL4 dependency signature (KRADS12) and confirmed its association with KMT2A r and survival in AML patients. Collectively, our findings highlight an unknown vulnerability in the aggressive KMT2A r AML subtype.