A Role for Rapid Transcription Dynamics in Cytarabine Resistance in Acute Myeloid Leukemia

Chemotherapy resistance remains a critical challenge in the treatment of patients with cancer includingacute myeloid leukemia (AML). While genetic alterations contribute to chemotherapy resistance, rapid adaptive non-genetic mechanisms, particularly transcription dynamics, remain poorly understood. Given the role of cell-intrinsic transcriptional variability in cell fate decisions, understanding and targetingchemotherapy-induced changes in transcription dynamics could offer new strategies to preventchemotherapy resistance. In this study, we demonstrate that short-term treatment with the widely usedchemotherapeutic cytarabine (AraC) leads to the rapid emergence of RNA-induced AML cells withincreased AraC resistance in both cell lines as well as primary patient samples. Mechanistically, throughtranscriptomic analysis as well as high-resolution analysis of transcription dynamics using single molecule RNA FISH, we found rapid induction of transcriptional dynamics and upregulation of keytranscription factors (TFs) - which we term "AraC rapid response TFs" and which include PU.1 andGATA1 - following chemotherapy treatment. At a functional level, short-term pre- and co-treatment withRNA transcription inhibitors effectively suppressed chemotherapy-induced RNA induction and preventedresistance acquisition, in both in vitro and in vivo models. Furthermore, we found that CRISPR-mediatedsuppression of PU.1 and GATA1 induction significantly attenuated AraC resistance. In summary, ourfindings reveal a previously unrecognized role of rapid transcriptional dynamics in AML chemotherapyresistance, highlighting master TFs as key regulators. These insights offer a novel, pharmacologicallyaccessible approach to alleviate chemotherapy resistance, and encourage further testing with the ultimategoal to improve AML treatment outcomes.