A complex mutational signature generated by cytarabine resistance

T-cell acute lymphoblastic leukemia (T-ALL) patients generally respond well to chemotherapy, but T-ALL cells at relapse are typically resistant to chemotherapy. The specific mechanisms leading to chemoresistance are incompletely understood. We used Mcm2 hypomorph T-ALL cell lines, which are prone to copy number variant mutations, to identify acquired mutations that underlie chemoresistance. We found acquired copy number variants leading to resistance to a wide spectrum of chemotherapeutic agents and focused on cell lines that inactivated both Dck and Trp53, leading to cytarabine resistance and a unique mutational signature. This signature is characterized by C > T mutations in a GCG trinucleotide context, T > C in a GTC context, T > G in GTC and GTT contexts, and C > G in a GCC context. Ongoing cytarabine exposure is not required for this mutational signature. Further analyses revealed that the T > C in GTC context is associated with proliferation rate, while the C > G in GCC context is associated with Trp53 mutations. These findings provide new insight into the genetic evolution of chemoresistance, add to emerging evidence that chemotherapeutic agents can produce characteristic mutational signatures, and demonstrate that mutagenic effects of chemotherapy can be indirect, acting through selection of clones with distinct mutation profiles and a resultant mutator phenotype.