Utility of the Base Editing System for Introducing Drug-Resistant Gene Mutations Into Human Leukemia Cellular Models

Background Recent genomic analyses of poor prognostic and relapsed leukemia have revealed the involvement of diverse gene mutations in treatment resistance. These gene mutations are classified into two groups: mutations involving resistance to specific agents such as the BCR::ABL1 fusion gene mutations (typically T315I mutation) in tyrosine kinase inhibitor (TKI) resistance and those involving the resistance to diverse therapeutic modalities such as the TP53 gene mutations. In the latter type, although their associations with drug resistance have been clinically demonstrated, the direct association with resistance to each therapeutic modality remains to be fully elucidated. To overcome treatment resistance induced by these gene mutations, appropriate leukemic cellular models are urgently required. Using the cytidine base editing (CBE) system, we introduced two types of mutations through C-to-T transition into human leukemia cell lines and evaluated their significance in the drug sensitivities. Methods We applied the CBE system to introduce the T315I (ACT to ATT) mutation of the BCR::ABL1 fusion gene in a human Philadelphia chromosome-positive leukemia cell line and to introduce the T125M (ACG to ATG) mutation of the TP53 gene in a human B-cell precursor acute lymphoblastic leukemia (BCP-ALL) cell line. Results We first confirmed an introduction of the T315I mutation in one of four BCR::ABL1 alleles as a result of base editing in the obtained TKI-resistant subline. We also identified the additional C-to-T transition at adjacent codon 314 (ATC), which resulted in a silent mutation, in the same allele. We next confirmed that the obtained subline acquired the T125M mutation of the TP53 gene without additional C-to-T transition. In the T125M subline, transcriptional activities of the p53 protein were disrupted and the sensitivities to diverse chemotherapeutic drugs and irradiation were reduced. Conclusion Our observations demonstrated the utility of the CBE system for introducing specific nucleotide transitions into human leukemia cell lines.