Abstract A036: Elucidating MYC allelic imbalance and therapeutic response in pancreatic ductal adenocarcinoma via patient-derived organoids
Audrey G. Sawyer, Lauryn E. Flannagan, Paulina N. Esguerra, Md Shahadat Hossan, Jeremy D. KratzAbstract
Background:
Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer with an unmet need for novel precision based therapies. While KRAS canonically drives tumor progression, MYC amplification has emerged as a critical downstream resistance mechanism. Efforts have been made to elucidate the role of MYC amplification in PDAC, but the extent to which MYC copy number heterogeneity impacts targeted therapeutic response in PDAC tumors remains unclear. We investigated the impact of subclonal heterogeneity of patient-derived organoids (PDOs) to model MYC allelic imbalance.
Methods:
PDOs were seeded at low density to establish single cell derived subclones, which were expanded into distinct organoid lines. DNA from each subclone was analyzed using the QIAGEN QIAcuity dPCR kit to assess MYC copy numbers present within each clone. Subclones were then seeded on a 96 well plate (ibidi, Inc) and treated with a CDK9 inhibitor Tambiciclib (SLS009, 200 nM), pan-RAS inhibitor Daraxonrasib (RMC-6236, 20 nM), or in combination with a 72 hour end point to evaluate the influence of MYC copy number on therapeutic response. SLS009 was removed after 24 hours to mimic human pharmacokinetics. Cell viability was assessed using the markers HOESCHT, Caspase-3/7 for apoptosis and ToPro3 for necrosis via Cytation5.
Results:
Eleven single cell derived subclones were established from a MYC amplified PDO line. dPCR was performed on the parent PDAC culture and subclones. Parent culture had an average copy number of 35 copies, while the subclones showed average copy numbers between 14-17. Subsequent studies with the parent culture (MYC-H) and a selected subclone (MYC-L) were analyzed for treatment response to SLS009, RMC-6236, and in combination. MYC-L had significantly increased apoptosis (28.68% v. 17.88% in parent culture, p<0.0001) and necrosis (22.50% v. 14.51% in parent culture p<0.0001) when treated with SLS009. Additionally, MYC-L had increased apoptosis (47.97% v. 26.59% in parent culture, p<0.0001) and necrosis (30.22% v. 24.82% in parent culture, p<0.0001) when treated with the combination. Finally, percent change in size was significantly decreased for MYC-L compared to MYC-H when treated with SLS and in combination (p<0.0001). There was no significant difference in apoptosis and necrosis between MYC-H and MYC-L when treated with RMC-6236. However, percent change in size was significantly decreased for MYC-L relative to MYC-H when treated with RMC-6236 (p<0.0001).
Conclusion:
Expansion of parent PDAC organoids can have increased MYC copy numbers compared to derived subclones, suggesting MYC copy number can have intratumoral heterogeneity through extended passage. Furthermore, the results suggest that a greater MYC copy number may impact sensitivity to RMC-6236. MYC-H conferred significantly reduced apoptosis and necrosis when compared to MYC-L, across shared molecular profiles. Ongoing work is comparing across varied degrees of MYC copy number, validating background molecular heterogeneity, and investigating novel combination therapies to disrupt transcription.
Citation Format:
Audrey G. Sawyer, Lauryn E. Flannagan, Paulina N. Esguerra, Md Shahadat Hossan, Jeremy D. Kratz. Elucidating MYC allelic imbalance and therapeutic response in pancreatic ductal adenocarcinoma via patient-derived organoids [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 A036.