Group comparison based on genetic information reveals lineage-specific therapeutic vulnerabilities in acute myeloid leukemia

ABSTRACT Cancer is a genetic disease with specific mutations or fusions. Therapies targeting cancer cell-specific essential genes are expected to have efficient anticancer effects with fewer side effects. To explore such cancer cell-specific vulnerabilities, we established a two-group comparison system to predict essential genes in each cancer subtype using the data from the Cancer Dependency Map (DepMap). We applied this analytical method to acute myeloid leukemia (AML) and identified PCYT1A and BCL2L1 as a specific vulnerability in MLL-rearranged AML and TP53 -mutated AML, respectively. Interestingly, further investigation revealed that PCYT1A is in fact a critical regulator in monocytic AML including those with MLL-rearrangements, and BCL2L1 is essential in acute erythroid leukemia in which TP53 is frequently mutated. These results highlighted the importance of cell of origin, rather than the genetic aberrations alone, to identify subtype-specific vulnerabilities in AML. The DepMap-based two-group comparison approach could accelerate the discovery of subtype-specific therapeutic targets in diverse cancers.