Differentiation-focused CRISPR Screen identifies LSD1 and Menin as combination therapy targets that induce terminal differentiation in AML

Project Summary Acute myeloid leukemia (AML) is a lethal blood cancer characterized by a differentiation “block” that prevents myeloid progenitor maturation resulting in uncontrolled proliferation. Chemotherapy, the current standard of care, is often ineffective and can result in cytotoxicity and relapse. New treatment options are desperately needed to

treat AML’s poor prognosis. Differentiation therapy is a novel method that aims to reactivate latent maturation programs and induce cell cycle exit. This therapeutic strategy is curative in the promyelocytic (APL) AML subtype but underexplored in other AMLs. Epigenetic factors help sustain the characteristic AML differentiation block.

The demethylase LSD1 has emerged as a promising target for differentiation therapy. Pharmacologic inhibition of LSD1 (LSD1i) induces cellular differentiation in many AML subtypes. However, the extent of differentiation varies between AML models, with a modest effect in aggressive AML models. Therefore, LSD1i will not induce

terminal differentiation as a monoagent treatment. We hypothesized that targeting additional epigenetic regulators simultaneously with LSD1i may induce complete, terminal differentiation and lead to disease remission. To identify potentiators of LSD1i, we conducted CRISPR gain-of-differentiation screens with a

chromatin-focused sgRNA library in multiple AML cell models with or without LSD1i co-treatment. These screens unveiled a synergistic induction of differentiation when KO of MEN1 is combined with LSD1i. I confirmed that combinatorial small molecule inhibition of LSD1 and MEN1 induces differentiation and reduces proliferation most

commonly in MLL-rearranged AMLs, and to a lesser extent in selected MLL-wild type AMLs. This proposal has two aims: First, I will test the therapeutic potential of targeting MEN1 in combination with LSD1 inhibitors in primary patient samples ex vivo and in patient-derived AML transplant models. Patient samples will be treated

with a MEN1 inhibitor in combination with LSD1 inhibitors, and effects on differentiation and proliferation will be quantified. Secondly, I will determine the epigenomic mechanisms by which MEN1 and LSD1 inhibition synergize to induce terminal differentiation, and then test whether these mechanisms are conserved in primary patient

samples.