Abstract A003: A Splicing Switch in ERK1 Controlled by SMNDC1 Drives MAPK Pathway Reactivation and Resistance to KRAS inhibitors in PDAC

Abstract 30% of PDACs frequently overexpress RNA-binding proteins (RBPs), including splicing factors; however, the functional impact of aberrant splicing in PDAC progression and therapy resistance remains poorly understood. Here, we identify Survival Motor Neuron Domain Containing 1 (SMNDC1) as a key regulator of alternative splicing that sustains oncogenic MAPK signaling through exon retention in KRAS-driven pancreatic ductal adenocarcinoma (PDAC). Transcriptomic analyses revealed that SMNDC1 amplification promotes retention of cassette exons, notably exon 4 (E4) of MAPK3 (ERK1), which encodes the full activation loop, including the ERK1 activating phosphosites (Thr202/Tyr204). E4 inclusion is lower in benign, non-malignant cells in contrast to PDAC cells and tumors with elevated SMNDC1. Forced exclusion of E4 using antisense oligonucleotides (ASOs) reduced ERK1 phosphorylation, downregulated ERK target genes, and inhibited tumor initiation. Notably, SMNDC1 expression and MAPK3 E4 inclusion were elevated in PDAC cells with acquired resistance to KRAS inhibitors (KRASi: RMC-6236, adagrasib, MRTX1133, and sotorasib) and MEK inhibitors (selumetinib, trametinib). We found that PDAC cells resistant to KRAS inhibitors were resensitize to these compounds upon forcing the exclusion of E4 with ASOs or by knocking down SMNDC1. To further interrogate E4’s function in therapy resistance and oncogenic signaling, we generated isogenic PDAC lines stably expressing only either ERK1+E4 or ERK1∆E4 isoforms. ERK1+E4 cells demonstrated enhanced proliferation, MAPK signaling and resistance to KRASi. Contrary, ERK1∆E4 cells exhibited reduced oncogenic signaling, compensatory ERK2 activation, impaired proliferation, and did not re-sensitized cells to KRASi. Mechanistically, we found that ERK1∆E4 protein is rapidly degraded in cells thus acting as a dominant negative. Lastly, we hypothesized that targeting SMNDC1 in PDACs in mice could be a therapeutic approach to target KRASi-resistant tumors. Using a new SMNDC1 inhibitor (SMNDCi) we found that MRTX1133-resistant tumors decreased tumor growth in xenografts supporting the translational relevance of this approach. Together, our findings identify a previously unrecognized splicing-based mechanism of MAPK activation and therapy resistance. SMNDC1-mediated MAPK3 E4 inclusion constitutes a tunable switch for ERK1 stabilization and oncogenic output, offering a novel therapeutic vulnerability in KRAS-driven PDACs. Citation Format: Md Afjalus Siraj, Deanne Yugawa, Yushan Zhang, Gilbert Giri, Prabir Chakraborty, Grant Goda, Muaz faruque, Geet Rao, Daniel Dominguez, Stefan Kubicek, Resham Bhattacharya, Luisa Escobar-Hoyos, Priyabrata Mukherjee. A Splicing Switch in ERK1 Controlled by SMNDC1 Drives MAPK Pathway Reactivation and Resistance to KRAS inhibitors in PDAC [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research—Emerging Science Driving Transformative Solutions; Boston, MA; 2025 Sep 28-Oct 1; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_3):Abstract nr A003.