Abstract PR-11: Altered mRNA splicing mimics chromosome loss and drives pancreatic cancer
Authors: Medici Natasha Pinto , Martinez-Saucedo Diana , Lee Danny , Chu Tianyi , Tseng Robert , Cannataro Vincent , Townsend Jeffrey , Iacobuzio-Donahue Christine , Robert Marie , Abdel-Wahab Omar , Leach Steven D. , Escobar-Hoyos Luisa 
Published: September 2024

Abstract
Aiming to identify novel driver mutations that cause pancreatic ductal adenocarcinoma (PDAC), besides p53 mutations, we performed a genetic interaction analysis based on the concept of mutually exclusive mutations, which suggests that mutations exclusive to one another function within the same pathway. Using our unbiased quantitative methods to evaluate the effects of somatic mutations on cancer, we analyzed 3900 human PDAC cases to prioritize mutations among hundreds that appear at low frequencies (5-10%) and are mutually exclusive with p53 mutations. Mutations in RNA splicing factors SF3B1 and RBM10 (∼15% of cases) were among the most significant and mutually exclusive to mutant p53. Thus, we hypothesized that aberrant RNA splicing promoted by mutant SF3B1K700E and truncated RBM10 (RBM10 loss) lead to tumorigenesis and therapy resistance. Through the generation of engineered mouse models to co-express KrasG12D with either Sf3b1K700E or Rbm10 loss in pancreatic cells, we observed that mice harboring KrasG12D and Sf3b1 K700E or Rbm10 loss—like mutant p53—caused PDAC in mice. To identify the RNA splicing mechanism that leads to PDAC formation, we performed deep RNA sequencing and unbiased transcriptome-wide splicing analyses in isolated PDAC cells bearing wild-type SF3B1K700E and RBM10 loss derived from murine and patient PDACs. We established that SF3B1 and RBM10 mutations induce wide splicing changes, primarily affecting exon selection. Since two-thirds of these changes may lead to nonsense-mediated decay (NMD), a mechanism that eliminates aberrant mRNA, we tested whether these changes could trigger this response. Using cycloheximide-dependent NMD inhibition, we confirmed that these mutations cause NMD, resulting in post-transcriptional gene expression loss in mouse chromosomes 2, 7, 11, and 17, also conserved in human models. Intriguingly, recent studies in Nature (2022) have shown that in murine PDACs with loss-of-function p53 mutations, genetic loss of chromosomes 11 and 7 is necessary for PDAC development. These results suggest that mutations in SF3B1 and RBM10, and p53 loss, affect the same chromosomal loci, albeit through different mechanisms, to promote PDAC, supporting the mutual exclusivity findings from patient samples. To determine a personalized therapy for patients with mutant splicing-factor tumors, we found that PDACs with these mutations are more sensitive to Gemcitabine, a component of a PDAC standard-of-care therapy. Moreover, these mutations sensitize cells to small-molecule splicing inhibitor H3B-8800— currently in phase 2 trial for hematologic malignancies. Lastly, we found that combining Gemcitabine and H3B-8800 synergizes to kill mutant splicing cells selectively in vitro and in vivo. We are starting a phase 2 trial for Gemcitabine/Abraxane with escalating doses of H3B-8800 for tumors that have either SF3B1K700E, RBM10 loss, or neomorphic p53, all of which have aberrant RNA splicing. This work has determined novel drivers and mechanisms of PDAC development and a precision therapeutic strategy for treating PDAC patients.
Citation Format: Natasha Pinto Medici, Diana Martinez-Saucedo, Danny Lee, Tianyi Chu, Robert Tseng, Vincent Cannataro, Jeffrey Townsend, Christine Iacobuzio-Donahue, Marie Robert, Omar Abdel-Wahab, Steven D. Leach, Luisa Escobar-Hoyos. Altered mRNA splicing mimics chromosome loss and drives pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr PR-11.