image: Regulatory aberrations caused by transcription factors and CRE mutations are related to the development of AML disease, and mtDNA lineage tracing is used to identify AML relapse-related clones and relapse markers.
Credit: ©Science China Press
Disruptions in transcriptional regulation during hematopoiesis can lead to abnormal hematopoietic differentiation and the development of leukemia. Understanding the underlying mechanisms of disease progression is therefore essential for improving treatment strategies. In this study, the authors employed a mitochondrial single-cell assay for transposase-accessible chromatin with sequencing mitochondria single-cell ATAC-seq (mtscATAC-seq) along with single-cell RNA sequencing (scRNA-seq) to comprehensively characterize acute myeloid leukemia (AML) cells. By constructing a single-cell hematopoietic reference atlas and mapping AML tumor cells to it, the study identified significant alterations in the chromatin accessibility of cis-regulatory elements (CREs) associated with AML differentiation. Notably, these CRE accessibility changes were found to be linked to mutations in the WT1 transcription factor gene. Specifically, mutations in the zinc finger domain of WT1 were associated with reduced chromatin accessibility and hypermethylation at the regulatory regions of target genes, leading to their downregulation. The pathogenic potential of five WT1 zinc finger domain mutations was validated experimentally.
Additionally, the study revealed that some changes in CRE accessibility were attributable to mutations within the CREs themselves. One such mutation introduced a novel CEBPB binding motif, enhancing CEBPB binding to enhancers, thereby activating enhancer activity and gene expression, and ultimately promoting AML proliferation. These findings were further validated using luciferase reporter assays and prime editing experiments.
Given the high risk of relapse in AML, elucidating the mechanisms of disease progression and identifying reliable prognostic biomarkers are critical for improving therapeutic outcomes. To this end, the study integrated mitochondrial DNA lineage tracing with machine learning–based modeling to identify relapse-associated clones that share features with leukemia stem cells (LSCs). Marker genes identified in these clones demonstrated improved predictive power for drug resistance and relapse risk, offering new avenues for AML prognosis research.
Collectively, the findings underscore the utility of integrating mtscATAC-seq, lineage tracing, and gene regulatory network analysis to uncover regulatory aberrations and trace relapse-prone AML clones, thereby advancing our understanding of AML pathogenesis and relapse.
See the article:
Integrative scATAC-seq and mtDNA mutation analysis reveals disease-driven regulatory aberrations in AML.
https://doi.org/10.1016/j.scib.2025.07.009
Journal
Science Bulletin