MRTX1133 sensitivty across the PRISM cohort of cell lines.

Genetic and copy number variants at resistance to adagrasib or sotorasib across the novel cohort of PDAC and GI cancer patients.

Supplemental Table 5A: Drug sensitivity metrics from MRTX1133-treated KRASG12D patient-derived organoids. Supplemental Table 5B: MRTX1133 dose response across KRASG12D mutated patient-derived organoids.

Supplemental Table 4A: Differential gene expression analysis between MRTX1133 sensitive and resistant KRASG12D cell lines. Supplemental Table 4B: Analysis of Copy number and RPPA datasets between MRTX1133 sensitive and resistant KRASG12D cell lines.

Supplemental Figure 1: Acquired resistance to KRASG12C inhibition in PDAC and other GI cancers. Supplemental Figure 2: MRTX1133 sensitivity across KRASG12D mutant in vitro models of PDAC. Supplemental Figure 3: Isogenic models of acquired resistance to MRTX1133. Supplemental Figure 4: In vivo treatment and tumor monitoring for the KPC PDAC mouse model. Supplemental Figure 5: Genomic characterization of KPC tumors. Supplemental Figure 6: snRNA-seq quality metrics and description of the tumor microenvironment. Supplemental Figure 7: Identification and characterization of malignant cell populations. Supplemental Figure 8: Characterization of malignant metaprograms in KPC tumors. Supplemental Figure 9: Treatment with MRTX1133 induces modest changes in the immune microenvironment following tumor regression. Supplemental Figure 10: Treatment of 6694C2-LM tumors with MRTX1133 reduces granulocytes but has little effect on T cells. Supplemental Figure 11: Neoadjuvant and adjuvant therapy in a metastatic model of PDAC.

List of genes in each NMF metaprograms

Characterization of acquired resistance to KRASG12C inhibition across studies and cancer types.

Mutation and sequence alterations from whole exome sequencing of in vitro models of acquired resistance to MRTX1133.

List of reagents and antibodies used in the study

Supplemental Table 7A: Clinical evaluation and characterisitcs of KPC mice treated until clinical endpoint. Supplemental Table 7B: Clinical evaluation and characterisitcs of KPC mice treated for 3 days.

KRAS inhibitors demonstrate clinical efficacy in pancreatic ductal adenocarcinoma (PDAC); however, resistance is common. Among patients with KRASG12C-mutant PDAC treated with adagrasib or sotorasib, mutations in PIK3CA and KRAS, and amplifications of KRASG12C, MYC, MET, EGFR, and CDK6 emerged at acquired resistance. In PDAC cell lines and organoid models treated with the KRASG12D inhibitor MRTX1133, epithelial-to-mesenchymal transition and PI3K-AKT-mTOR signaling associate with resistance to therapy. MRTX1133 treatment of the KrasLSL-G12D/+; Trp53LSL-R172H/+; p48-Cre (KPC) mouse model yielded deep tumor regressions, but drug resistance ultimately emerged, accompanied by amplifications of Kras, Yap1, Myc, Cdk6, and Abcb1a/b, and co-evolution of drug-resistant transcriptional programs. Moreover, in KPC and PDX models, mesenchymal and basal-like cell states displayed increased response to KRAS inhibition compared to the classical state. Combination treatment with KRASG12D inhibition and chemotherapy significantly improved tumor control in PDAC mouse models. Collectively, these data elucidate co-evolving resistance mechanisms to KRAS inhibition and support multiple combination therapy strategies.Significance: Acquired resistance may limit the impact of KRAS inhibition in patients with PDAC. Using clinical samples and multiple preclinical models, we define heterogeneous genetic and non-genetic mechanisms of resistance to KRAS inhibition that may guide combination therapy approaches to improve the efficacy and durability of these promising therapies for patients.See related commentary by Marasco and Misale, p. 2018

Abstract KRAS is a major oncogenic driver in pancreatic ductal adenocarcinoma (PDAC) and is mutationally activated in approximately 90% of cases, with the glycine-to-aspartic acid substitution at position 12 (p.G12D) being the most prevalent alteration. Mutations in this oncogene have been associated with more aggressive disease and poorer outcomes and have remained “undruggable” for more than three decades. However, the recent development of mutant-specific small molecule inhibitors of KRAS has given hope for the treatment of this highly lethal and treatment-refractory malignancy. Here we evaluated the genomic and transcriptional mechanisms of resistance to MRTX1133, a first-in-class inhibitor of KRASG12D, in an autochthonous mouse model of PDAC. We leveraged single-nucleus RNA sequencing and whole-exome sequencing on 17 tumors from KPC mouse specimens (LSL-KrasG12D/+; LSL-Trp53R172H/+; p48-Cre) that were treated with either MRTX1133 or the vehicle, including 6 samples from mice that developed acquired resistance to KRASG12D inhibition. Our analysis has uncovered that resistance is multifaceted and characterized by both emergent genomic and transcriptional features. Genetically, resistant tumors harbored clonal and subclonal amplifications in the HIPPO pathway, cell cycle regulators, and ABC transporters. Transcriptionally, we employed non-negative matrix factorization and identified recurrent gene expression programs in resistant and vehicle samples. Using this approach, we uncovered the existence of an intermediate phenotype between classical and mesenchymal cell states that is enriched in tumors with evolved resistance to MRTX1133. In summary, our study provides a high-resolution genomic and transcriptional landscape of resistance to KRAS targeting in a preclinical in vivo model of PDAC, highlighting the complexity of treatment resistance and identifying various pathways and effectors that may serve as potential new targets for combination therapy. Citation Format: Julien Dilly, Laleh Abbassi, Connor J. Hennessey, Giselle A. Uribe, Brendan Parent, Annan Yang, Kevin S. Kapner, Ziyue Li, Kyle E. Evans, Shatavisha Dasgupta, Megan T. Hoffman, Li Qiang, Felix P. Hambitzer, Seema Chugh, Alex K. Shalek, Stephanie K. Dougan, Brian M. Wolpin, Jonathan A. Nowak, Srivatsan Raghavan, Peter S. Winter, Andrew J. Aguirre. Dissecting acquired resistance to KRASG12D inhibition in a mouse model of pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1933.