Dynamic heterogeneity towards drug resistance in AML cells is primarily driven by epigenomic mechanism unveiled by multi-omics analysis
Yulong Zhang, Yanfang Lu, Liyao Mai, Zebin Wen, Min Dai, Siwen Xu, Xianwei Lin, Yongjian Luo, Yinbin Qiu, Yuting Chen, Zhanying Dong, Caiming Chen, Wei Meng, Xingguang Luo, Guanchuan Lin, Paul Kwong Hang Tam, Xinghua Pan
Abstract
INTRODUCTION: Acute myeloid leukemia (AML) is a hematologic malignancy characterized by aggressive proliferation and chemoresistance, leading to poor patient outcomes. Despite advances in chemotherapy, resistance mechanisms remain inadequately understood, particularly at the cellular and molecular level. OBJECTIVES: This study aims to elucidate the cellular and molecular mechanisms underlying drug resistance in AML cells. METHODS: A multi-omics approach was employed, integrating single-cell RNA sequencing (scRNA-seq), chromatin accessibility profiling (scATAC-seq), DNA methylation analysis, and whole-exome sequencing (WES). AML cell lines (KG-1a, Kasumi-1, and HL-60) were treated with standard chemotherapeutic agents, including cytarabine (Ara-C), daunorubicin (DNR), azacitidine (AZA), and decitabine (DEC). Additionally, we developed a novel multiplexed scRNA-seq strategy, NAMUL-seq, to enhance the efficiency and scalability of single-cell transcriptomic research. RESULTS: We observed substantial cellular heterogeneity and dynamic transcriptomic trajectories in AML cells subjected to various treatments, uncovering a tendency for reprogramming towards a more stem-like state. Notably, Ara-C-resistant KG-1a cells predominantly originated from G2/M phase subpopulations, suggesting a resistance mechanism linked to specific cell cycle stages. Our findings further indicate that rapid Ara-C resistance is primarily driven by epigenomic changes, including alterations in DNA methylation, chromatin architecture, and transcription factor activity, whereas exonic mutations played a minimal role. CONCLUSION: This study demonstrates that AML drug resistance is predominantly driven by epigenomic mechanisms rather than genetic mutations. This study provides a detailed cellular and molecular characterization of AML drug response and resistance, identifying potential therapeutic targets and laying the groundwork for future efforts to overcome chemoresistance.