Targeting Venetoclax Resistance in TP53-Mutated Acute Myeloid Leukemia

Introduction: The combination therapy of Venetoclax (Ven) and Azacitidine (Aza) has shown remarkable improvements in the treatment of acute myeloid leukemia (AML) patients not eligible for chemotherapy. Nevertheless, patients with TP53-mutated AML are more prone to have a refractory disease or develop rapid resistance. A recent study indicated that a combined expression ratio of BCL-2, BCL-XL and MCL-1 proteins in leukemic stem cells predicts clinical response to Ven+Aza (Waclawiczek et al. 2023). Furthermore, our previous work has demonstrated that erythroid and megakaryoblastic leukemia blasts are more dependent on BCL-XL than BCL-2 (Kuusanmäki et al. 2023). Emerging evidence suggests that the erythroid-biased differentiation and gene signature is enhanced in many TP53-mutated patients (Rodriquez-Meira et al. 2022). Here we hypothesized that in TP53-mutated AML, leukemic blasts correspond more closely to megakaryocyte-erythroid progenitors (MEPs) leading to an unfavorable BCL-2 family expression ratio, which can be associated with poor responses to Ven. Consequently, we aimed to identify novel compounds targeting this specific patient subgroup.

Methods: We utilized flow cytometry to analyze the mean fluorescent intensity (MFI) of BCL-2 family proteins (BCL-2, BCL-XL, MCL-1) in the CD34+ blast cells of 16 bone marrow-derived AML samples taken before Ven+Aza therapy (TP53^mut n=8, TP53^wt n=8). Ex vivo drug testing was performed with eight compounds and blast-specific drug responses were analyzed after 48 hours with flow cytometry. RNA sequencing was performed on CD34+ or CD117+ cells enriched from 35 pre-Ven+Aza treatment samples. To assess erythroid signature scores, we calculated the mean expression of six different erythroid genes (GATA1, KLF1, ZFPM1, GATA2, GYPA, TFRC) for each patient, following the approach by Rodriquez-Meira et al. 2022. The expression levels of 19 intracellular proteins, including BCL-2, BCL-XL, MCL-1, were quantified from the corresponding cell population of the samples by mass cytometry (CyTOF).

Results: In the comparison of BCL-2 family protein expression and treatment responses, BCL-XL levels were significantly higher (p=0.03) in the treatment-resistant group, while no differences were found in BCL-2 or MCL-1 (Figure 1A). In the TP53-mutated blasts, a trend of decreased BCL-2 was identified compared to the TP53 wild-type blasts (p=0.08), but no difference in BCL-XL or MCL-1 levels was noted. However, all three Ven+Aza-refractory TP53-mutants exhibited high BCL-XL expression compared to the treatment-responsive TP53-mutated patients.

Next, we assessed whether an erythroid-like phenotype was associated with TP53 mutation status by computing the erythroid gene signature scores from the RNAseq data of enriched blasts. Erythroid scores were increased among TP53-mutated samples (p=0.04), and interestingly, a higher erythroid score was linked to lower BCL-2 protein expression, regardless of TP53 mutation status (Figure 1B). Finally, we assessed the drug efficacy of eight pre-selected compounds, including BCL-2 family inhibitors. As expected, Ven was ineffective in the TP53-mutated samples. In contrast, the TP53-mutated blasts showed higher ex vivo sensitivity to Navitoclax (BCL-2/BCL-XL inhibitor) (Nav IC50=90nM, Ven IC50>1000nM). Additionally, LCL-161 (IAPs inhibitor) demonstrated notable efficacy in the TP53-mutants and was significantly more effective compared to the wild-type controls (LCL-161 IC50=300nM, Ven IC50>1000nM).

Discussion: Here, we show that increased BCL-XL protein expression is associated with clinical resistance to Ven+Aza. Furthermore, the link between erythroid gene signature and BCL-2 expression suggests that especially those AML blasts harboring TP53 mutations might have impaired BCL-2 expression due to a closer resemblance to MEPs. The increased sensitivity of TP53-mutated AML cells to LCL-161 demonstrated in the study, highlights the potential of targeting extrinsic apoptosis pathway via inhibiting the inhibitors of apoptosis proteins (IAPs). Furthermore, co-targeting of BCL-2/BCL-XL might provide alternative therapeutic approach in Ven resistant TP53-mutated patients. These findings are currently being validated with a larger patient cohort.