Integrated single-cell transcriptomics reveal E2F1-driven multidrug resistance in medulloblastoma and identify Palbociclib as a therapeutic candidate

Abstract Purpose Medulloblastoma (MB) is a malignant pediatric brain tumor where tumor recurrence driven by acquired multidrug resistance remains a paramount clinical challenge. Resolving the intratumoral heterogeneity underlying this resistance is urgently required to identify novel therapeutic targets. Methods Single-cell RNA sequencing data and large-scale bulk transcriptomes were integrated and comprehensively analyzed. Multidrug-resistant subpopulations were identified by mapping ridge regression-based drug sensitivity predictions to single-cell profiles. Developmental trajectories and core regulatory networks were reconstructed, and essential transcription factors were functionally evaluated by computational vector field perturbations. The prognostic value of specific cellular states was assessed, and potential therapeutic antagonists were screened using computational databases and spatial molecular docking. Results Two distinct multidrug-resistant reservoirs were identified, an E2F1 -driven DNA repair state exhibiting cross-resistance to genotoxic agents, and a ZIC5 -regulated neuronal differentiation state associated with Hedgehog signaling. Trajectory inference and in silico perturbations demonstrated that the continuous accumulation of E2F1 is critical for maintaining the chemoresistant DNA repair phenotype. Clinical deconvolution revealed that elevated E2F1 expression acts as a robust indicator of poor overall survival. Subsequently, computational pharmacogenomic screening and molecular docking identified palbociclib as a highly potent inhibitor capable of precisely binding and targeting the CDK4/6-E2F1 axis. Conclusion An E2F1 -driven DNA repair program and a ZIC5 -associated differentiation state directly govern distinct multidrug resistance mechanisms in MB. Targeting the CDK4/6-E2F1 axis with palbociclib represents a promising precision therapeutic strategy to overcome chemoresistance in high-risk patients.