Dissecting PCD-driven molecular landscapes in AML: a multi-omic framework for prognostication and therapeutic...

Acute myeloid leukemia (AML) remains a molecularly heterogeneous malignancy with poor prognosis, necessitating robust biomarkers for risk stratification. By integrating single-cell RNA-seq and multiomics data from 2,680 AML samples across 10 cohorts, we demonstrate that dysregulated programmed cell death (PCD) pathways are significantly elevated in AML cells and correlate with adverse outcomes. Unsupervised clustering identified two PCD-driven subtypes: Subtype A exhibits high PCD activity, an immunosuppressive microenvironment (M2 macrophages, upregulated PD-L1/HAVCR2), increased somatic mutations (NPM1/DNMT3A/FLT3), and poor survival, while Subtype B shows lower PCD activity, immune-active features, and better prognosis. As an exploratory analysis, subtype-specific therapeutic vulnerabilities were revealed: Subtype A displays predicted sensitivity to immune checkpoint inhibitors (anti-PD-1) and tipifarnib, whereas Subtype B responds better to cytarabine/doxorubicin. We developed PCDRScore-a prognostic model incorporating 13 PCD-related genes via machine learning-which outperformed existing models (higher C-index) in 10 validation cohorts and remained independent of clinicopathological factors. A nomogram combining PCDRScore, age, and cytogenetic risk enhanced clinical applicability. Crucially, experimental validation confirmed significant upregulation of key model genes (HIP1, SQLE, VNN1) in AML patient samples and cell lines (P < 0.05), reinforcing the model's biological relevance. These findings establish PCD dysregulation as a central axis of AML heterogeneity, providing a framework for precision risk stratification and hypothesis-generating immunophenotype-guided therapy.