Predictors of Response and Rational Combinations for the Novel MCL-1 Inhibitor MIK665 in Acute Myeloid Leukemia
Authors: Saad Joseph , Newman Rhiannon , Khabusheva Elmira , Aakko Sofia , Durand Eric , Tambe Mahesh B. , Kuusanmäki Heikki , Parsons Alun , Miettinen Juho J. , Javarappa Komal Kumar , Ikonen Nemo , Kontro Mika , Porkka Kimmo , Maacke Heiko , Woo Janghee , Halilovic Ensar , Heckman Caroline A. 
Published: December 2024

Background
Elevated MCL-1 expression has been shown to play a central role in apoptosis escape and to mediate primary resistance to the approved BCL-2 inhibitor venetoclax in acute myeloid leukemia (AML) (Li, 2019). Preclinical investigations of MCL-1 inhibitors have yielded promising results, with several of them progressing to clinical investigation. However, results have shown diverse responses in patients, attributable to disease heterogeneity (Tantawy, 2023), and highlighting the need for further characterization of MCL-1 inhibitor activity in AML.
Aims
The objective of this study was to evaluate the activity of the MCL-1 inhibitor MIK665 in AML, with the aim of identifying molecular predictors of response. Furthermore, this work sought to identify suitable drug combination partners to restore sensitivity in cases of MIK665 resistance.
Methods
The study cohort was composed of bone marrow samples from 42 patients with AML, collected following written informed consent and in accordance with the declaration of Helsinki. After mononuclear cell isolation, samples were subjected to ex vivo drug testing using a multiparametric flow cytometry-based assay, allowing the assessment of drug response at the single cell level. Samples were also subjected to genomic and transcriptomic profiling using whole exome and RNA sequencing. Gene expression and dependency analysis was performed on a panel of AML cell lines using data available on DepMap. HEL cells with ABCB1 knockout were generated using CRISPR-Cas9 technology, and drug sensitivity was evaluated in the cell lines using the CellTiter-Glo viability assay.
Results
By contrasting MIK665-sensitive and resistant samples, we observed that sensitive samples had a more differentiated phenotype, characterized by the expression of hematopoietic maturation-associated genes such as LILRA2 and IL17RA. This aligned with previous studies having showed that mature AML phenotypes are more dependent on MCL-1 for survival (Pei, 2020).
Importantly, we also observed that MIK665-resistant samples had significantly higher ABCB1 (also known as multi-drug resistance protein MDR1 or P-glycoprotein P-gp) expression compared to sensitive samples. Logistic regression and ROC curve analysis revealed a strong performance of ABCB1 expression in separating MIK665-resistant samples from responsive ones, with a positive predictive value of 72.7%. Interestingly, samples with high ABCB1 expression also had a significantly higher expression of BCL2L1, a finding replicated in our DepMap analysis in AML cell lines. Knockout of ABCB1 in HEL cells, which have a high basal level of ABCB1 expression and resistance to MIK665, did not lead to an increased sensitivity to MIK665, indicating that ABCB1 does not cause resistance to MIK665, but is strongly predictive of it. In an attempt to induce sensitivity, we treated MIK665-resistant AML samples having high ABCB1 expression with a combination of MIK665 and venetoclax. The combination was more effective at eliminating malignant cells than either of the agents alone. Interestingly, the combination also restored sensitivity in AML samples with primary venetoclax resistance.
Conclusion
Overall, this study shows that hematopoietic differentiation markers are associated with sensitivity of AML samples to MCL-1 inhibition by MIK665, whereas elevated expression of ABCB1 is a predictor of resistance. Moreover, this work demonstrates that a combination of MIK665 with venetoclax can restore sensitivity in patient populations resistant to either of the single agents, a finding warranting further clinical evaluation. The value of this work lies in the discovery of biomarkers of response to MIK665, which can aid in the stratification of AML patients for MIK665-based treatments.