Introduction
The interaction between the epigenetic proteins Menin and MLL1 is critical for sustaining the expression of self-renewal genes in specific subsets of Acute Myeloid Leukaemia (AML). Disrupting the Menin-MLL1 interaction with menin inhibitors (iMenin) is showing clinical efficacy for the treatment of NPM1c AML, however, de novo and acquired iMenin resistance remains a significant challenge. Aside from the infrequent mutations in Menin that preclude iMenin binding, the molecular mechanisms of iMenin resistance remain largely unknown. The objective of our study is to understand the molecular underpinnings of iMenin resistance in NPM1c AML, in order to identify biomarkers of response and rational combination therapies to overcome resistance.
Methods
A CRISPR base-editor screen across MLL1 and a genome-wide screen were performed in the NPM1c AML cell line, OCIAML3, to identify mutations in MLL1, and gene knockouts that modulate iMenin sensitivity. To identify transcriptional programs that are integral to iMenin response in NPM1c AML, we performed RNA-sequencing across the top gene knockouts that conferred resistance or hypersensitivity to iMenin. These results were overlayed with the iMenin-induced transcriptional profiles and changes in the chromatin landscape across a panel of NPM1c AML models including human and mouse in vitro lines, in vivo PDX and patient samples treated ex vivo.
Results
Surprisingly, the CRISPR screens revealed that loss of MLL1 conferred the strongest iMenin resistance. Indeed, MLL1 knockout cells were able to continuously proliferate under iMenin treatment. RNA-sequencing revealed that (i) the suppression of canonical self-renewal genes (e.g. MEIS1) was not predictive of response and (ii) the induction of interferon signalling was strongly correlated with iMenin sensitivity. In agreement, analysis of ChIPseq data showed that iMenin caused MLL1 redistribution to interferon-stimulated genes (ISGs). Moreover, STING-agonists (which induce ISGs) synergised with iMenin and overcame iMenin resistance in NPM1c AML.
Conclusion
The induction of ISGs is critical for iMenin response in NPM1c AML. Upon iMenin treatment, MLL1 is recruited to ISGs to promote its expression. Interferon response represents an actionable cellular program that can be targeted to overcome iMenin resistance, with STING-agonists showing synergistic cell killing with iMenin.