3D enhancer dynamics dictate treatment response in T-cell acute lymphoblastic leukemia

Methods

Here, we assessed alterations in 3D chromatin structures differentiating responder and non-responder models by evaluating enhancer rewiring and mapping of the associated loops using H3K27ac HiChIP. After performing full-length single-cell RNA sequencing of 3,129 leukemic cells from both models, before and after treatment with a NOTCH inhibitor, we characterized transcriptional states by assessing developmental potential using CytoTRACE and identified state-specific gene-regulatory networks (GRN) driving state transitions using SCENIC.

Apoptotic priming and functional validation of anti-apoptotic dependencies were determined by BH3 profiling. Results Analyzing 3D chromatin architecture and single-cell transcriptomics from responder and non-responder models, we show that gain of short enhancer-promoter interactions underlies increased developmental potential in non-responders. Moreover, this extensive enhancer rewiring is associated with the loss of active transcriptional regulators and a state transition towards more immature states co-expressing multi-lineage markers allowing for the emergence of novel dependencies such as the transcription factor ATF4 and its downstream anti-apoptotic target MCL1 Conclusions: Resistance to NOTCH inhibition remains a therapeutic challenge in T-ALL.

We revealed that 3D enhancer mapping and detailed characterization of developmental states present a novel approach to develop biomarkers that predict treatment response and may allow to identify subsets of T-ALL patients resistant to therapy upfront.