Abstract B127: Synthetic Lethality Through Combined BET and CDK9 Inhibition in MYC-Amplified Pancreatic Ductal Adenocarcinoma
Paulina N. Esguerra, Michela Cadarso, Sasha Livingwell, Md Shahadat Hossan, Olivia Wong, Jeremy D. KratzAbstract
Background:
Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer-related mortality and comprises molecular subtypes characterized by MYC amplification (14%) or MYC overexpression (40%), both of which drive tumor proliferation, metabolic reprogramming, and cellular plasticity. MYC dysregulation is associated with poor clinical outcomes and resistance, but its direct targeting remains a challenge. Here, we investigate the response of a patient-derived cancer organoid (PCO) model of PDAC as a function of MYC amplification to evaluate the synthetic lethality of dual transcriptional inhibition through BET inhibition (ZEN3694) and CDK9 inhibition (SLS009).
Methods:
A MYC-amplified PCO (Copy number 35) was treated with ZEN3694 (500nM), SLS009 (200nM) or the combination. Apoptosis and necrosis were assessed at 72h with caspase-3/7 and TO-PRO staining, respectively with cycloheximide (200 μM) as a positive control. One-way ANOVA followed by Tukey's post hoc test was used to compare mean percentage of area stained between treatment groups. Dose-response combination matrices were generated and viability was measured at 144h using 3D CellTiter-Glo (CTG, 50% v/v). Drug Synergy was quantified via SynergyFinder 3.0 (Zero Interaction Potency (ZIP), Bliss Independence (Bliss), Highest Single Agent (HSA)). Protein was isolated at 24h for Western blot analysis of total and Ser2/Ser5-phosphorylated RNA polymerase II, MYC and MCL-1. Blots were imaged using the LI-COR Odyssey imaging system and quantified with Image Studio software.
Results:
Following 72h treatment with SLS009 or ZEN3694 there was an observed mean Caspase-3/7 stained area of 14.78% and 5.178%, and mean TO-PRO staining of 15.68% and 5.131%, respectively. The combination of ZEN3694 and SLS009 further increased Caspase-3/7 staining to 25.65% (p< 0.001) and TO-PRO staining to 22.84% (p< 0.001). Dual treatment achieved synergy scores ranging between 17-21 indicating increased therapeutic activity. Western blot analysis showed on-target activity for the combination including reduced phosphorylation of RNA Pol II (Ser2/Ser5) (p< 0.0002 and p< of 0.0015) and decrease in T-Rpb1 (NTD) (p< 0.0162) consistent with transcriptional pausing. Furthermore, expression of short-lived transcription factors MYC and MCL-1 were both downregulated (both p< 0.0001).
Conclusions:
This study demonstrates that dual BET and CDK9 inhibition promotes transcriptional pausing and suppresses key regulators in transcriptionally driven cancers. Additionally, combining ZEN3694 and SLS009 exhibited in vitro synergy in and induced both apoptosis and necrosis, as well as demonstrating on-target transcriptional inhibition. Notably, these effects were achieved using ZEN3694 at a concentration substantially below physiological values, suggesting that SLS009 can potentiate the activity of BET inhibition. Ongoing studies are exploring this combination in other PDO models with diverse mutational backgrounds, with future work aimed at validating these findings in vivo to assess therapeutic efficacy and toxicity.
Citation Format:
Paulina N. Esguerra, Michela Cadarso, Sasha Livingwell, Md Shahadat Hossan, Olivia Wong, Jeremy D. Kratz. Synthetic Lethality Through Combined BET and CDK9 Inhibition in MYC-Amplified Pancreatic Ductal Adenocarcinoma [abstract]. In: Proceedings of the AACR Conference on Pancreatic Cancer: New Frontiers in Biology and Therapeutic Development; 2026 Sep 25-28; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(18_Suppl_2):Abstract nr B127.