Abstract C075: Altered RNA splicing causes pancreatic cancer and exposes a therapeutic vulnerability
Authors: Medici Natasha Pinto , Saucedo Diana Martinez , Lee Danny , Ku Li-Ting , Tseng Robert , Shan Xinning , Chu Tianyi , Perez-Piñera Pablo , Cannataro Vincent , Townsend Jeffrey , Iacobuzio-Donahue Christine , Robert Marie , Abdel-Wahab Omar , Leach Steven D. , Escobar-Hoyos Luisa 
Published: January 2024

Recently we reported that pancreatic ductal adenocarcinomas (PDACs) are exquisitely susceptible to a range of anti-RNA splicing therapies. Thus, altered RNA splicing is a non-mutational dependency of PDACs and represents a novel therapeutic target. However, how these alterations drive tumorigenesis and determine therapeutic responses remains unknown. Using unbiased and quantitative methods to evaluate the effects of all somatic mutations on cancer, we found that mutations in RNA splicing factors SF3B1 and RBM10 (~15% of cases) were among the most significant and mutually exclusive to mutations in p53, suggesting that mutations in these splicing factors act as “second-hit” driver mutations in PDAC. To test this hypothesis, we engineered mice to co-express KrasG12D with either Sf3b1 K700E mutation or Rbm10 loss in acinar cells. Importantly, mice harboring KrasG12D and Sf3b1K700E or Rbm10 loss developed autochthonous PDACs in mice. Mechanistically, we found that both mutant splicing factors, in PDACs from mice and patients, induce alterations in exon processing in common mRNAs. Of these target mRNAs, ~67% were found to be degraded by nonsense-mediated mRNA decay (NMD)- a surveillance process that eliminates mRNAs that harbor sudden stops from splicing alterations. Interestingly, NMD-inducing splicing changes by both SF3B1K700E and RBM10 loss mapped to chromosomes 7 and 11 (chromosomes 17 and 19 in patients, respectively), which are home to several tumor-suppressor genes, including p53. This suggests that mutant splicing factors decrease the expression of specific tumor suppressors by promoting altered RNA splicing and downstream RNA degradation for PDAC pathogenesis. Supporting these findings, it was previously reported that loss of p53 in PDAC, the most common “second-hit” mutation in PDAC, leads to deletions in chromosomes 7 and 11 for PDAC pathogenesis (Nature 2022). Given that 70% of PDACs carry mutations in p53, interestingly however, PDACs with mutant splicing factors have wild-type (WT) p53. We determined that SF3B1K700E and RBM10 loss promote increased degradation of p53 compared to WT counterparts but stabilize p53 protein upon DNA damage and RNA splicing perturbations. Forced expression of gain-of-function mutant p53 in PDACs with either SF3B1K700E or RBM10 loss led to synthetic lethality, explaining the mutual exclusivity found in patient samples (described above). Lastly, splicing factor mutant PDACs are more sensitive to Gemcitabine than 5FU, and combination of Gemcitabine with splicing factor modulator, H3B-8800 (in phase 2 clinical trials) synergized to selectively kill mutant splicing cells. Animal testing of this combination therapy is ongoing using patient-derived organoids implanted in the pancreata of immunocompromised mice. These studies uncover novel driver mutations of PDAC that can bypass the effect of WT p53 and highlights a common mechanism of PDAC pathogenesis that depends on decreased expression of tumor suppressors, irrespective of second-hit mutations, exposing a therapeutic vulnerability to splicing modulators.

Citation Format: Natasha Pinto Medici, Diana Martinez Saucedo, Danny Lee, Li-Ting Ku, Robert Tseng, Xinning Shan, Tianyi Chu, Pablo Perez-Piñera, Vincent Cannataro, Jeffrey Townsend, Christine Iacobuzio-Donahue, Marie Robert, Omar Abdel-Wahab, Steven D. Leach, Luisa Escobar-Hoyos. Altered RNA splicing causes pancreatic cancer and exposes a therapeutic vulnerability [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C075.