Dynamic evolution of venetoclax resistance in acute myeloid leukemia unveiled by longitudinal single-cell RNA-seq

Despite extensive investigation into venetoclax resistance mechanisms in acute myeloid leukemia (AML), the dynamics of bone marrow (BM) microenvironment remodeling during venetoclax-based therapies remain poorly characterized at single-cell resolution. Using paired single-cell RNA sequencing of BM specimens from AML patients undergoing DAV therapy (venetoclax/decitabine/cytarabine; pre- vs post-treatment), we systematically mapped therapy-induced transcriptional reprogramming, regulatory network alterations, and niche crosstalk across clinical response subgroups. Our analysis revealed two pivotal mechanisms governing therapeutic outcomes: First, pre-existing immune-activating niches marked by elevated HLA class I presentation synergized with therapy-enhanced CD8⁺ T cell cytotoxicity and reduced tumor-promoting stroma-leukemia interactions to facilitate favorable responses. Second, responder leukemic cells exhibited transposable element (TE)-associated type I interferon signaling upregulation. Primitive leukemic clones displayed IMPDH2-high states linked to BCL2 inhibitor sensitivity, while resistant monocytic populations upregulated glycolysis and MCL1 to bypass BCL2 dependence. Leveraging these insights, we established a prognostic signature predicting patient responses to venetoclax-based therapies, validated in independent cohorts (Tumor Profiler, BeatAML2). High-risk patients identified by this signature demonstrated heightened sensitivity to IGF-1R inhibition. Functional validation in an established resistant cell line model confirmed that IGF-1R inhibition synergized with DAV by suppressing glucose uptake and differentiation. This study provides a comprehensive single-cell atlas of BM microenvironment evolution during venetoclax-based therapy, proposes a prognostic biomarker, and identifies a clinically actionable strategy to overcome therapeutic resistance in AML.