Evasion of apoptosis is a defining hallmark of cancer and a major driver of therapeutic failure in many malignancies including acute myeloid leukaemia (AML). Although selective inhibition with the BCL-2 inhibitor Venetoclax has demonstrated substantial clinical efficacy, resistance frequently arises through dysregulation of apoptotic and pro-survival signalling networks. AML cells emerge and persist within the highly stressful bone marrow microenvironment, characterized by limited nutrient availability, cytokine deprivation, and intense cellular competition, necessitating robust adaptive mechanisms to sustain leukaemia cells survival and evade apoptosis.
Given the epigenetically driven nature of AML, we hypothesised that leukemic cells exploit and co-opt epigenetic mechanisms to coordinate cellular stress resilience and resistance to BCL-2 inhibition by modulating pro- and anti-apoptotic gene expression. To examine this, we conducted pooled loss-of-function CRISPR screens targeting ~1,145 epigenetic regulators across multiple AML cell lines (MV4:11 and OCI-AML3) under Venetoclax treatment.
These screens revealed context-specific epigenetic dependencies that govern AML cell survival under pharmacologic stress. JMJD6 emerged as a key mediator of Venetoclax resistance, as its loss effectively sensitized AML cells to BCL-2 inhibition. In contrast, depletion of ZNF787 or BAP1 conferred Venetoclax resistance, consistent with roles in maintaining apoptotic pathways. Transcriptomic profiling following JMJD6 depletion revealed induction of the pro -apoptotic gene BMF and repression of survival associated genes MRC2 and BCL2L2, supporting a role for JMJD6 in transcriptional programs that enforce apoptotic evasion. Consistent with this, pharmacological inhibition of JMJD6 synergized with Venetoclax to enhance apoptotic cell death in AML models.
Collectively, our findings define an epigenetic regulatory network that coordinates stress adaptation and apoptotic control in AML. These context-dependent epigenetic vulnerabilities provide a mechanistic basis for therapeutic resistance and identify actionable targets to restore apoptotic sensitivity and improve outcomes in AML.