Abstract LB079: Pancreatic clonal replica tumors display functional heterogeneity in response to KRAS pharmacological inhibition and reveal unique epigenetic vulnerabilities to overcome resistance
Authors: Lyu Hengyu , Minelli Rosalba , Deckard Charles E. , Seth Sahil , Huang Justin , Jiang Hong , Peoples Michael D. , Lam Meggie , Bristow Christopher A. , Gerlach Daniel , Tontsch-Grunt Ulrike , Li Chieh-Yuan , Ho I-Lin , Vellano Christopher P. , Hofmann Marco H. , Heffernan Timothy P. , Marszalek Joseph R. , Viale Andrea , Carugo Alessandro 
Published: June 2022

Introduction: Pre-existing tumor heterogeneity may allow tumors to escape treatment via selection and expansion of drug-resistant clones. Recent discovery of KRAS targeted therapies (e.g. SOS1i, KRASG12Ci, etc.) has dramatically changed the clinical outlook for patients with KRAS mutant tumors. Here, we generated and utilized pancreatic clonal replica tumors (CRTs) to identify drug-resistant clones of KRAS inhibitors (e.g. SOS1i and MEKi, KRASG12Di). Deep clonal characterization of KRAS inhibition revealed a novel epigenetic vulnerability which may inform on unbiased combination strategies to prolong responses for pancreatic cancer patients.

Experimental procedures: Our CRT platform combines high-complexity in vivo lineage tracing with quantitative assessments of adaptive responses to therapeutics. In this study we generated a KRASG12D-driven CRT xenograft model of pancreatic ductal adenocarcinoma and treated the CRTs with MEKi, SOSi, and MEKi + SOSi. Upon comprehensive analysis of the clonal composition associated with each drug treatment, we identified, isolated, and validated a collection of clones with differential response to MEKi + SOS1i or KRASG12Di. Deep molecular characterization of sensitive and resistance clones identified novel combination strategies to overcome resistance to KRAS inhibitors.

Results: We found that KRAS inhibition greatly impacted CRT clonal composition and tumor heterogeneity. Well-controlled reconstitution experiments with CRT-informed treatment-naïve clones confirmed the pre-existing nature of the differential clonal response to KRAS inhibitors in pancreatic cancer. Transcriptomic profiling of clonal diversity further revealed a BRD3-driven molecular plasticity in resistant clones that may drive resistance to MEKi + SOS1i or KRASG12Di. Pharmacological combination of MEKi (trametinib) + SOS1i (BI-3406) or KRASG12Di (MRTX1133) with BETi (BI 894999 and dBET6) exhibited combination benefits in preclinical pancreatic cancer models.

Conclusions: Our study suggests that pre-existing heterogeneous subclones with epigenetic plasticity contribute to escaping direct KRAS inhibition in pancreatic cancer and provides a new avenue to overcome such resistance by combining KRAS inhibitors with BET inhibitors.

Citation Format: Hengyu Lyu, Rosalba Minelli, Charles E. Deckard, Sahil Seth, Justin Huang, Hong Jiang, Michael D. Peoples, Meggie Lam, Christopher A. Bristow, Daniel Gerlach, Ulrike Tontsch-Grunt, Chieh-Yuan Li, I-Lin Ho, Christopher P. Vellano, Marco H. Hofmann, Timothy P. Heffernan, Joseph R. Marszalek, Andrea Viale, Alessandro Carugo. Pancreatic clonal replica tumors display functional heterogeneity in response to KRAS pharmacological inhibition and reveal unique epigenetic vulnerabilities to overcome resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB079.