Abstract 4398: Dysregulating transcription and epigenetic remodeling using dual BRD4 and CDK9 inhibition in pancreatic ductal adenocarcinoma

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is the most common cause of mortality for pancreatic cancers with a five-year survival rate of only 13%. These malignancies acquire resistance to therapeutics through dysregulation of epigenomic and transcriptional signals, however few investigations have considered combination therapies to disrupt these pathways. BRD4 and CDK9 are both promising targets playing key roles in epigenomic and transcription regulation and are both upregulated in PDAC. Here, we evaluate the potential of dual BRD4 and CDK9 inhibition as a strategy to disrupt global transcriptional and epigenomic regulation in PDAC. Methods: PDAC patient-derived cancer organoids (PCOs) were established from live tissue samples. PCOs were treated with single agents, VIP152 and ZEN3694, or the combination. ZEN3694 was treated continuously while VIP152 was removed after 24 hours to mimic in vivo pharmacokinetics. Western blotting was used to analyze phosphorylation of RNA polymerase II at serine 2 (pRPB1-s2) and anti-apoptotic proteins after 24 hours of treatment. Differential expression and peak calls were made on bulk mRNA and CUT&Tag sequencing (RNA-seq and CUT&Tag) performed on treated PCOs. PCOs were collected after 144 hours of treatment for RNA-seq and 48 hours for CUT&Tag. gProfiler was used for pathway analysis for both sequencing sets. Results: Western blot analysis revealed combination therapy achieved downregulation of pRPB1-s2 and anti-apoptotic proteins compared to single agents. RNA-seq yielded no pathway dysregulation for VIP152 treated PCOs across 2 unique PDAC lines. The number of dysregulated pathways increased in the combination treated group compared to ZEN3694 in PDAC2 (ZEN3694 n=156, combination n=235), however this was not seen in PDAC1 (ZEN3694 n=69, combination n=37). Pathway analysis from CUT&Tag of PDAC1 for pRPB1-s2 revealed significant pathway dysregulation in the combination (n=186) with no single agent disruption. These pathways included biologically relevant gene sets such as ‘Pancreatic Cancer Subtypes’ (adj p<0.001), ‘response to stimulus’ (adj p<0.001), and ‘signal transduction’ (adj p<0.001) across both sequencing sets. CUT&Tag also revealed a significant decrease in pRPB1-s2 binding across all matched significant differential peak calls (VIP152=-0.21, ZEN3694=-0.23, combination=-0.74 p<0.001), and a decrease in open chromatin markers (H3K4me3=-0.64 p<0.001 and H3K27ac=-0.56 p<0.001) compared to both single agents (VIP152=-0.15 and -0.20; ZEN3694=-0.15 and -0.14). Conclusion: Here, we show preclinical evidence that combination treatment of VIP152 and ZEN3694 synergistically dysregulates PDAC transcription and remodels the epigenomic landscape. Future directions will include exploring Myc amplified subtype specific selectivity and in vivo validation of toxicity and efficacy. Citation Format: Lucas J. Koeppel, Austin Stram, Robert J. Millikin, Md Shahadat Hossan, Ron Stewart, Jeremy D. Kratz. Dysregulating transcription and epigenetic remodeling using dual BRD4 and CDK9 inhibition in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4398.