Characterization of Mechanisms of Acquired Venetoclax-Insensitivity in B-Cell Precursor Acute Lymphoblastic Leukemia

Deregulation of cell death pathways is a hallmark of many cancers and contributes to leukemogenesis and treatment failure in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Different pro- and anti-apoptotic molecules control apoptosis signaling. While pro-apoptotic BCL-2 homology domain 3 (BH3) proteins induce cellular death, apoptosis induction is counter-regulated by anti-apoptotic molecules like B-cell lymphoma 2 (BCL-2). Therefore, inhibition of anti-apoptotic molecules has been developed as therapeutic strategy. Venetoclax (VEN) selectively binds to BCL-2, which leads to the release of pro-apoptotic molecules such as BIM resulting in apoptosis induction. In BCP-ALL, we and others showed preclinical activity of VEN and first clinical trials have started to evaluate VEN in ALL. Despite high activity, resistance can be acquired over time and acquisition of BCL2 mutations has been reported in CLL patients. In this study, we modeled VEN resistance in BCP-ALL and investigated underlying mechanisms in order to identify potential strategies to overcome VEN insensitivity.

Starting from the BCP-ALL cell line RS4;11, five parallel VEN insensitive lines were generated by exposure to increasing concentrations of VEN over time (49 passages, over 8 months of continuous treatment). Simultaneously, five control lines were exposed to corresponding concentrations of solvent (DMSO). Measuring half maximal effective concentrations (EC₅₀) over time showed increasing EC₅₀ values from 4 nM to 26.2 µM in all VEN treated lines, reflecting acquired resistance in our model.

Importantly, no mutations of the BCL2 gene were identified by sequencing at high coverage (Illumina AmpliSeq, 650- to 5951-fold), excluding acquisition of BCL2 mutations as mechanism of resistance. Next, we assessed expression levels of the mitochondrial apoptosis regulators BCL-2, MCL-1 and BCL-XL by western blot analysis. Comparing VEN insensitive to control cell lines, no differences in expression of the target molecule BCL-2 and similar levels of BCL-XL were observed. Most interestingly, all five VEN insensitive lines showed significant up-regulation of MCL-1 compared to all control lines.

We next investigated the dependence of apoptosis signaling on different BCL-2 family members by exposing ALL cells to synthetic BH3-only peptides, which specifically bind to different regulators of mitochondrial apoptosis signaling (BH3-profiling), followed by analysis of apoptosis induction. Interestingly, dependence on BCL-2 was clearly reduced in all VEN insensitive lines indicated by almost lost mitochondrial priming. On the other hand, VEN insensitive ALL cells showed increased dependence on MCL-1.

In order to analyze whether our modeled VEN resistance can be overcome by targeting MCL-1, we investigated sensitivity of these cells to the MCL-1 inhibitor S63845. High EC₅₀ values for S63845 were found in all VEN insensitive and corresponding control lines, indicating low anti-MCL-1 activity. Importantly, the combination of S63845 with VEN synergistically induced cell death, showing that acquired VEN insensitivity in BCP-ALL can be overcome by co-targeting BCL-2 and MCL-1.

To get insight into the molecular mechanisms underlying the synergism, we treated VEN insensitive ALL cells with VEN, S63845 or both and investigated binding of BIM to either BCL-2 or MCL-1 by immunoprecipitation. In the presence of VEN, clearly lower co-precipitation of BIM with BCL-2 but increased co-precipitation with MCL-1 was observed, indicating that pro-apoptotic BIM displaced from BCL-2 by VEN is sequestered by MCL-1, thereby counter-regulating VEN activity. Inversely, the MCL-1 inhibitor S63845 reduced binding of BIM to MCL-1 but increased BIM binding to BCL-2. Most interestingly, upon combination of both inhibitors, lower BIM binding to both BCL-2 and MCL-1 was found. This indicates that co-targeting MCL-1 can block the sequestration of pro-apoptotic BIM from BCL-2 to MCL-1, overcoming VEN resistance.

Taken together, we show that acquired VEN resistance in BCP-ALL is characterized by up-regulated expression of counter-regulatory MCL-1 and can be overcome by simultaneous BCL-2 and MCL-1 inhibition, which prevents sequestration of BIM by MCL-1 after release from BCL-2.