Mutation Patterns Predict Drug Sensitivity in Acute Myeloid Leukemia

Abstract Acute myeloid leukemia (AML) is an aggressive malignancy of myeloid progenitor cells characterized by successive acquisition of genetic alterations. This inherent heterogeneity poses challenges in the development of precise and effective therapies. To gain insights into the genetic influence on drug response and optimize treatment selection, we performed targeted sequencing, ex vivo drug screening, and single-cell genomic profiling on leukemia cell samples derived from AML patients. We detected genetic signatures associated with sensitivity or resistance to specific agents. By integrating large public datasets, we discovered statistical patterns of co-occurring and mutually exclusive mutations in AML. The application of single-cell genomic sequencing unveiled the co-occurrence of variants at the individual cell level, highlighting the presence of distinct sub- clones within AML patients. Machine learning models were built to predict ex vivo drug sensitivity using the genetic variants. Notably, these models demonstrated high accuracy in predicting sensitivity to some drugs, such as MEK inhibitors. Our study provides valuable resources for characterizing AML patients and predicting drug sensitivity, emphasizing the significance of considering subclonal distribution in drug response prediction. These findings provide a foundation for advancing precision medicine in AML. By tailoring treatment based on individual genetic profiles and functional testing, as well as accounting for the presence of subclones, we envision a future of improved therapeutic strategies for AML patients. One Sentence Summary: Integrative computational and experimental analysis of mutation patterns and drug responses provide biologic insight and therapeutic guidance for patients with adult AML.