Plastic state transitions and developmental potential predict response to Notch inhibition

The acquisition of immature cell states associated with an emergence of alternative cell fates may result in treatment resistance, yet the transcriptional and epigenetic processes dictating cellular plasticity in cancer remain elusive. To investigate how cell states drive transcriptional heterogeneity and impact developmental hierarchy, we performed single-cell transcriptomics on treated and untreated with NOTCH inhibitor T-cell acute lymphoid leukemia (T-ALL) patient-derived xenograft (PDX) models carrying activating NOTCH1 mutations. We identified cellular plasticity as an underlying mechanism of increased developmental potential which predicts response to Notch inhibition and determines the magnitude of NOTCH1-induced differentiation. Mapping 3D chromatin architecture revealed remodeling of the enhancer landscape by gain of short length enhancer-promoter interactions resulting in extensive transcriptional rewiring and state-specific dependencies in resistant cell states. Our study reveals the epigenetic and transcriptional changes responsible for treatment resistance and identifies drug vulnerabilities that may be exploited as therapeutic strategies for overcoming resistance.