<i>SF3B1</i> mutations provide genetic vulnerability to copper ionophores in human acute myeloid leukemia

Abstract

In a phenotypical screen of 56 acute myeloid leukemia (AML) patient samples and using a library of 10,000 compounds, we identified a hit with increased sensitivity toward <i>SF3B1</i>-mutated and adverse risk AMLs. Through structure-activity relationship studies, this hit was optimized into a potent, specific, and nongenotoxic molecule called UM4118. We demonstrated that UM4118 acts as a copper ionophore that initiates a mitochondrial-based noncanonical form of cell death known as cuproptosis. CRISPR-Cas9 loss-of-function screen further revealed that iron-sulfur cluster (ISC) deficiency enhances copper-mediated cell death. Specifically, we found that loss of the mitochondrial ISC transporter <i>ABCB7</i> is synthetic lethal to UM4118. <i>ABCB7</i> is misspliced and down-regulated in <i>SF3B1</i>-mutated leukemia, creating a vulnerability to copper ionophores. Accordingly, ABCB7 overexpression partially rescued <i>SF3B1</i>-mutated cells to copper overload. Together, our work provides mechanistic insights that link ISC deficiency to cuproptosis, as exemplified by the high sensitivity of <i>SF3B1</i>-mutated AMLs. We thus propose <i>SF3B1</i> mutations as a biomarker for future copper ionophore-based therapies.