Targeting the mevalonate or Wnt pathways to overcome CAR T-cell resistance in TP53-mutant AML cells

TP53-mutant acute myeloid leukemia (AML) and myelodysplastic neoplasms (MDS) are characterized by chemotherapy resistance and represent an unmet clinical need. Chimeric antigen receptor (CAR) T-cell therapy might be a promising therapeutic option for TP53-mutant AML/MDS. However, the impact of TP53 deficiency in AML cells on the efficacy of CAR T-cells is unknown. We here show that CAR T-cells engaging TP53-deficient leukemia cells exhibit a prolonged interaction time, upregulate exhaustion markers, and are unable to control AML cell outgrowth in vitro and in vivo compared to TP53 wildtype cells. Transcriptional profiling revealed that the mevalonate pathway is upregulated in TP53-deficient AML cells under CAR T-cell attack, while CAR T-cells engaging TP53-deficient AML cells downregulate the Wnt pathway. In vitro rational targeting of either of these pathways rescues AML cell sensitivity to CAR T-cell-mediated killing. We thus demonstrate that TP53 deficiency confers resistance to CAR T-cell therapy and identify the mevalonate pathway as a therapeutic vulnerability of TP53-deficient AML cells engaged by CAR T-cells, and the Wnt pathway as a promising CAR T-cell therapy-enhancing approach for TP53-deficient AML/MDS. To investigate whether, and if so, how TP53 deficiency in AML cells might confer resistance to CAR T-cell therapy, we took advantage of a recently developed, CRISPR/Cas9-engineered TP53 isogenic AML cell line (MOLM13-TP53) with either TP53+/+ or TP53-/- mutational status. Anti-CD33 CAR T-cells and MOLM13-TP53+/+ or MOLM13-TP53-/- cells were co-incubated for six days, sorted from each other by flow cytometry, and subjected to high-throughput sequencing using a NovaSeq 6000 Sequencing System (Illumina®), the SUSHI bioinformatics pipeline, and gene set enrichment software of UCSD and Broad.