Cellular and Molecular Characteristics of Drug Resistance in AML cells Unveiled by Multi-Omics Analysis

Acute myeloid leukemia (AML) exhibits a spectrum of responses to chemotherapy, with drug resistance being a significant clinical challenge. This study employs a multi-omics approach, particularly multiplexed single-cell RNA sequencing (scRNA-seq), to characterize the molecular mechanisms underlying drug resistance in AML cells. We identified significant cellular heterogeneity and a dynamic transcriptomic trajectory in AML cells with specific drug treatment, and discovered a reprogramming towards a more stem-like state. Interestingly, Ara-C-resistant KG-1a cells predominantly originated from G2/M subpopulations, indicating a cell cycle-specific resistance mechanism. Our analysis also revealed that epigenetic changes of DNA methylation and chromatin architechture, and altered transcription factor activities were implicated in rapid Ara-C resistance, whereas exomic mutations did not significantly contribute to it. We suggest both intrinsic and acquired resistance mechanisms act together and build a resultant force that aids AML cells in evading therapeutic interventions. The multidimensional changes observed post-treatment showed a complex interplay in the development of drug resistance. This study provides a cellular and molecular portrait of drug response and resistance in AML, offering potential therapeutic targets and a foundation for future research aimed at overcoming chemoresistance. The Illumina Infinium Human Methylation EPIC (850 K) BeadChip array (Illumina, San Diego, CA, USA) was performed by Novogene Co., Ltd (Beijing, China), following the manufacturer’s instructions. The assay determines DNA methylation levels at >850,000 CpG sites and provides coverage of CpG islands, RefSeq genes, ENCODE open chromatin, ENCODE transcription factor-binding sites, and FANTOM5 enhancers. To increase credibility, two samples (naive and Ara-C resistant KG-1a) were arrayed in each group.