Potent Ikaros Degradation By the Cereblon E3 Ligase Modulator CC-92480 Is Effective in Combination with Menin-MLL1 Inhibition in MLL1-Rearranged and NPM1-Mutant AML
Authors: Bourgeois Wallace , Aubrey Brandon J. , Cutler Jevon A. , Donovan Katherine A. , Hatton Charles , Theall Alexandra C. P. , Nowak Radoslaw P. , McGeehan Gerard M. , Fischer Eric S. , Armstrong Scott A. 
Published: November 2021

Abstract
Acute myeloid leukemia (AML) has a poor prognosis despite intensive therapy. Novel therapies directed at molecular drivers of AML are needed. Ongoing clinical trials with inhibitors of the Menin and Mixed Lineage Leukemia 1 (KMT2A/MLL1) protein-protein interaction for patients with MLL1-rearranged (MLL1-r) and Nucleophosmin mutant (NPM1c) AML have promising early results. We have identified Ikaros degradation as a synergistic therapeutic target with Menin-MLL1 inhibition in MLL1-r AML and identified the novel cereblon E3 ligase modulator (CELMoD) CC-92480 as an efficacious compound in vitro and in vivo in MLL1-r and NPM1c AML models.
To find genetic targets that synergize with Menin-MLL1 inhibition, we performed a genome-scale CRISPR-Cas9 functional genetic screen in the Molm-13 (MLL1-AF9) AML cell line. Using the MAGeCKFLUTE pipeline, comparison of 14 days of treatment with VTP-50469 (Menin-MLL1 inhibitor) versus DMSO identified IKZF1 deletion as one of the most negatively selected genes when treated with VTP-50469 (IKZF1 codes for the hematopoietic transcription factor Ikaros). To validate this finding, CRISPR-Cas9-based competition assays were performed in Cas9-expressing MLL1-r and NPM1c AML cell lines by monitoring of sgRNA-RFP expression over time via flow cytometry. IKZF1 was a dependency in all four MLL1-r cell lines and both NPM1c cell lines evaluated. The sgRNAs targeting IKZF1 depleted faster when cells were treated with VTP-50469.
To evaluate the effect of Ikaros protein degradation in these AML cell lines, we assessed proliferation upon treatment with three Ikaros-degrading compounds: the Immunomodulatory Imide Drug (IMiD) lenalidomide and the CELMoDs CC-220 and CC-92480. CELMoDs are a derivative class of IMiDs with much more potent Ikaros degradation (lenalidomide &lt; CC-220 &lt; CC-92480) and Phase I activity in multiple myeloma patients refractory to prior IMiD therapy. Cells were plated with 5 different doses per drug. Every 3 days cells were split, drug was replenished, and live cell counts were obtained using viability staining and flow cytometry. Evaluation of the absolute IC 50 in 7 MLL1-r or NPM1c AML cell lines at day 9 showed that 6 cell lines were sensitive to CC-92480 (absolute IC 50 range: &lt;0.1-to-3.6 nM), 5 were sensitive to CC-220 (absolute IC 50 range: 15.7-to-215.3 nM), and only two were sensitive to lenalidomide (absolute IC 50 of 267.0 nM and 555.3 nM). These data suggest that greater Ikaros degradation leads to greater efficacy in vitro. Lenalidomide, CC-220, and CC-92480 all synergized with VTP-50469 to inhibit proliferation.
Apoptosis assays were performed in the MLL1-r AML cell lines Molm-13 and MV4;11 using annexin V staining following 6 days of treatment with DMSO, lenalidomide, CC-220, and CC-92480 with and without VTP-50469. For both cell lines, 5 µM lenalidomide, 1 µM CC-220, and 3 nM CC-92480 increased apoptosis less than two-fold as single agents while VTP-50469 did so only 2.5-fold and 3.7-fold compared to DMSO control. Strikingly, the combination of each of these IMiD or CELMoD doses with VTP-50469 induced apoptotic markers at least 7.5-fold compared to DMSO control. This cooperativity between Ikaros protein degradation and Menin-MLL1 inhibition could be explained by their combined targeting of a HOXA/MEIS1 transcriptional program as Ikaros degradation in MLL1-r AML cell lines perturbs expression of HOXA9 target genes without altering the expression of HOXA9 itself.
We next tested CC-92480 in four patient derived xenograft (PDX) models of AML: one NPM1c and three MLL1-r models. In these experiments, NSG-S mice were engrafted with PDX samples (&gt;7 mice per treatment cohort). Following detection of leukemia in peripheral blood, mice were randomized to receive vehicle control, lenalidomide 50 mg/kg (in two of the four PDXs), or CC-92480 10 mg/kg for 28-55 days and survival benefit was assessed. In these models, CC-92480 increased median survival compared to DMSO by 28.3% (p &lt; 0.05), 66% (p &lt;0.0005), 128% (p &lt; 0.0005), and 133% (p &lt; 0.0001). In two of these experiments CC-92480 was also compared to lenalidomide and increased survival by 23.4% (p &lt; 0.0005) and 28.1% (p &lt; 0.05).
In summary, the preclinical activity of CC-92480 in MLL1-r and NPM1c AML models, particularly in combination with Menin-MLL1 inhibition, supports translation of this compound or a similarly potent, Ikaros-degrading CELMoD into clinical trials for these molecular subtypes of AML.

Disclosures
Aubrey: Walter and Eliza Hall Institute of Medical Research: Patents & Royalties: Receives proceeds from Royalties and Milestone payments related to the BCL2-inhibitor, ABT-199/venetoclax. McGeehan: Syndax Pharmaceuticals: Current Employment, Current equity holder in publicly-traded company. Fischer: Neomorph Inc.: Current holder of individual stocks in a privately-held company, Current holder of stock options in a privately-held company; C4 Therapeutics: Current equity holder in publicly-traded company; EcoR1 Capital: Consultancy; Sanofi: Consultancy; Astellas: Consultancy; Deerfield: Consultancy; RA Capital: Consultancy; Novartis: Research Funding; Astellas: Research Funding; Deerfield: Research Funding; Ajax: Research Funding; Jengu Therapeutics: Current holder of individual stocks in a privately-held company; Civetta Therapeutics: Current holder of individual stocks in a privately-held company. Armstrong: AstraZeneca: Research Funding; Syndax: Research Funding; Novartis: Research Funding; Janssen: Research Funding; Mana Therapeutics: Consultancy; Accent Therapeutics: Consultancy; OxStem Oncology: Consultancy; C4 Therapeutics: Consultancy; Cyteir Therapeutics: Consultancy; Vitae/Allergan Pharma: Consultancy; Imago Biosciences: Consultancy; Neomorph Inc: Consultancy, Current holder of individual stocks in a privately-held company.