Targeted therapies to the KRAS oncogene have shown significant success in treatment of lung adenocarcinoma (LuAD). Challenges emerge when tumors acquire resistance to these targeted KRAS inhibitors (KRASi). Recent studies have reported several mechanistic pathways associated with the development of resistance which includes nuclear localization of YAP. TP53 mutations are the predominant genetic changes responsible for inducing resistance to targeted therapies and chemotherapy drugs. Mutations in TP53 lead to the inhibition of the tumor and metastasis suppressor TAp63 and the activation of the oncogenic isoform ΔNp63. We have previously shown that loss of ΔNp63 in KRAS driven LuAD results in fewer tumors indicating an oncogenic role for ∆Np63 in LuAD. Here, we demonstrate that cells and tumors resistant to KRAS G12C inhibitors (KRASiR) exhibit increased expression of ∆Np63 while the sensitive cells express lower levels of ∆Np63. The KRASiR cells showed increased total and nuclear localization of YAP/TAZ along with increased expression of ∆Np63 in the nucleus. KRASiR resistant cells also had increased proliferation, mitochondrial membrane potential and mitochondrial fusion, promoting oxidative phosphorylation in KRASiR LUAD cells. We further found that ΔNp63 is crucial for driving resistance to KRAS G12C inhibitor in vivo using genetically engineered mouse models and patient derived xenografts. Therefore, ΔNp63 is an ideal target to overcome acquired resistance to KRAS inhibitors. Additionally, using atomic force microscopy (AFM), we found that KRASiR cells are stiffer, and that tissue stiffness regulated by YAP/∆Np63 can also result in KRASi resistance. ChIP-seq analysis for ∆Np63 and YAP bound targets are revealing the molecular basis of the mechanisms driving resistance to KRAS G12C inhibitors. Santanu Adhikary, Marco Napoli, Suehelay Acevedo, Christina L. Carr, Jaden R. Baldwin, Nicole Hackel, Hitendra S. Solanki, Yaakov E. Stern, Laxmi Swetha Karanam, Duy T. Nguyen, Eric B. Haura, Elsa R. Flores. Mechanisms regulating resistance to KRAS inhibitor driven by DNp63/YAP regulation of tissue stiffness and metabolic alterations in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5509.

Fibroblast Growth Factors and their receptors (FGFRs) comprise a cell signaling module that can stimulate signaling by Ras and the kinases Raf, MEK, and ERK to regulate animal development and homeostatic functions. In Caenorhabditis elegans, the sole FGFR ortholog EGL-15 acts with the GRB2 ortholog SEM-5 to promote chemoattraction and migration by the sex myoblasts (SMs) and fluid homeostasis by the hypodermis (Hyp7). Cell-specific differences in EGL-15 signaling were suggested by the phenotypes caused by egl-15(n1457), an allele that removes a region of its C-terminal domain (CTD) known to bind SEM-5. To determine how mutations altered EGL-15 activity in the SMs and Hyp7, we used the kinase reporter ERK-KTR to measure activation of the ERK ortholog MPK-1. Consequences of egl-15(n1457) were cell-specific, resulting in loss of MPK-1 activity in the SMs and elevated activity in Hyp7. Previous studies of Hyp7 showed that loss of the CLR-1 phosphatase causes a fluid homeostasis defect termed “Clear” that is suppressed by reduction of EGL-15 signaling, a phenotype termed “Suppressor of Clear” (Soc). To identify mechanisms that permit EGL-15 signaling in Hyp7, we conducted a genetic screen for Soc mutants in the clr-1; egl-15(n1457) genotype. We report the identification of SOC-3, a protein with putative SEM-5-binding motifs and PH and PTB domains similar to DOK and IRS proteins. In combination with the egl-15(n1457) mutation, loss of either soc-3, the GAB1 ortholog soc-1, or the SHP2 ortholog ptp-2, reduced MPK-1 activation. We generated alleles of soc-3 to test the requirement for the SEM-5-binding motifs, finding that residue Tyr356 is required for function. We propose that EGL-15-mediated SM chemoattraction relies solely on the direct interaction between SEM-5 and the EGL-15 CTD. In Hyp7, EGL-15 signaling uses two mechanisms: the direct SEM-5 binding mechanism; and an alternative, CTD-independent mechanism involving SOC-3, SOC-1, and PTP-2. This work demonstrates that FGF signaling uses distinct, tissue-specific mechanisms in development, and identifies SOC-3 as a potential adaptor that facilitates Ras pathway activation by FGFR.

Abstract Background: KRASG12C-GDP Inhibitors such as sotorasib and adagrasib have demonstrated clinical benefit in lung cancer patients harboring an oncogenic KRASG12C mutation. However, the durability of monotherapy benefit is limited by the development of resistance. Hence, identification of novel treatment approaches to overcome resistance and extend duration of benefit becomes necessary to address this unmet clinical need. Experimental Design: We generated two NSCLC models of KRASG12C−GDP inhibitor acquired resistance, named sotorasib-R LU65 (cell-line derived, in vitro) and adagrasib-R LUN156 (PDX-derived, in vivo) following extended treatment with sotorasib and adagrasib, respectively. We then performed transcriptomic and mass spectrometry-based phosphoproteomics analyses on baseline and KRASG12C-GDP inhibitor-resistant samples to determine resistance and escape mechanisms. Results: In the sotorasib-R LU65 cells, we discovered upregulation of various RTKs including HER2, HER3, and AXL using a mass spectrometry-based proteomics approach and Immunoblot analysis. Simultaneously, from a transcriptome analysis, we observed activation of RAS and PI3K/AKT signaling in these cells. In the adagrasib-R LUN156 model, increased phosphorylation of MET was observed via phospho-RTK array and by immunoblotting. Transcriptomic analysis revealed an enrichment for RAS pathway dependency in the adagrasib-R tumor models. RAS GTP-binding assessed by RAF-RBD pulldown and multiple reactions monitoring mass-spectrometry suggest increased GTP-bound RAS isoforms in sotorasib-R LU65 cells and active RAS signaling in adagrasib-R LUN156. Given the convergence of our findings on re-activation/maintenance of wild-type RAS signaling as a means of resistance to KRASG12C-GDP-state inhibitors, we hypothesized that RMC-7977, a tri-complex RASMULTI-GTP inhibitor, which inhibits signaling via mutant and wild-type RAS, had the potential to counteract these mechanisms. We tested RMC-7977 monotherapy, which drove complete tumor regressions in the adagrasib-R LUN156 model. Additionally, RMC-7977 attenuated tumor growth in sotorasib-R cell derived LU65 xenograft model wherein we observed co-activation of PI3K/AKT signaling. Thus, we tested a combination with the pan-PI3K inhibitor pictilisib and observed combinatorial activity consistent with our findings. Conclusions: These data suggest that in KRASG12C-GDP inhibitor-resistant models RTK activation maintains MAPK dependency and in the case of one model, PI3K signaling. Consistent with these mechanisms, RMC-7977 as a single agent or in combination with pictilisib drove significant tumor regressions in these models. These preclinical results indicate RASMULTI-GTP inhibition alone or combination with PI3K inhibition has the potential to address KRASG12C-GDP inhibitor resistance. Citation Format: Hitendra S. Solanki, Harshit Shah, Denis Imbody, Bina Desai, Paul A. Stewart, Bin Fang, Yaakov Stern, Lancia N. Darville, John M. Koomen, Andriy Marusyk, Ethan Ahler, Ida Aronchik, Mallika Singh, Eric B. Haura. RTK signaling and WT RAS activity as vulnerabilities in tumors with acquired resistance to GDP-state selective KRASG12C inhibitors in preclinical models [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 1924.

Abstract Sotorasib demonstrated efficacy in patients with non-small cell lung cancer (NSCLC). However, a substantial proportion of patients do not respond. There is therefore a clear need for a predictive biomarker to guide treatment decisions. Proximity ligation assay (PLA) is an immunofluorescent-based approach for analysis of endogenous protein-protein interactions, in which the signal can be detected only when two target proteins are within 40 nm. This method measures drug-targetable signaling-associated protein complexes in cells and tissues. KRAS activity has recently been shown to be related to the sensitivity to sotorasib. We therefore conducted a preclinical study to evaluate whether RAS activation inferred by PLA might predict response to KRASG12C inhibitors. We first examined panRAS:CRAF PLA reaction for a KRASG12C-mutant H358 NSCLC cell line, by comparing a complete PLA reaction with both panRAS and CRAF antibodies and an incomplete PLA reaction in the absence of either panRAS or CRAF antibodies. We observed high panRAS:CRAF PLA intensity in H358 with both antibodies, which was abrogated in the absence of either panRAS or CRAF antibodies. We next evaluated the specificity of the PLA reaction by RNA interference. Transfection with sipanRAS or siCRAF resulted in a reduction in panRAS:CRAF PLA signal. We then performed panRAS:CRAF PLA with a panel of KRAS G12C-mutant NSCLC cell lines. The intensity of panRAS:CRAF PLA signal varied between these cell lines, with H358 and LU65 having higher and H1792 and LU99 having lower intensity of panRAS:CRAF PLA signal. To further understand the RAS-RAF interaction, we evaluated a CRAF-RAS binding domain pulldown assay for the cell lines. Different levels of CRAF-bound panRAS were observed in the cell lines, with H358 and LU65 having higher and H1792 and LU99 having lower level of CRAF-bound panRAS. The intensity of panRAS:CRAF PLA strongly correlated with CRAF-bound panRAS (r = 0.70, P = 0.037), suggesting that panRAS:CRAF PLA works sufficiently well to detect the RAS-RAF complex. We investigated the antitumor efficacy of AMG510 in vitro and found that a heterogeneous response to AMG510 was observed in the cell lines, with the 50% inhibitory concentration values of AMG510 for H358 and LU65 below 30 nmol/L and those for H1792, and LU99 above 10 μmol/L. The intensity of panRAS:CRAF PLA was strongly associated with the sensitivity of the G12C-mutated cells to AMG510 (r = 0.74, P = 0.01). We next examined sections of FFPE tumors from NSCLC cell line-derived xenograft models. The panRAS:CRAF PLA signal was higher in mice with sotorasib-sensitive H358 than with resistant H1792 (P = 0.02). Our results suggest that RAS:RAF PLA may have values as a predictive marker to identify which patients can obtain the greatest benefit from sotorasib. Citation Format: Ryoji Kato, Hitendra S. Solanki, Denis Imbody, Anurima Majumder, Yaakov Stern, Liznair Bridenstine, Joseph Johnson, Eric B. Haura. RAS:RAF proximity ligation assay may predict response to KRASG12C inhibitors in NSCLC [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr A001.

Sotorasib demonstrated efficacy in patients with non-small cell lung cancer (NSCLC). However, a substantial proportion of patients do not respond. There is therefore a clear need for a predictive biomarker to guide treatment decisions. Proximity ligation assay (PLA) is an immunofluorescent-based approach for analysis of endogenous protein-protein interactions, in which the signal can be detected only when two target proteins are within 40 nm. This method measures drug-targetable signaling-associated protein complexes in cells and tissues. KRAS activity has recently been shown to be related to the sensitivity to sotorasib. We therefore conducted a preclinical study to evaluate whether RAS activation inferred by PLA might predict response to KRASG12C inhibitors. We first examined panRAS:CRAF PLA reaction for a KRASG12C-mutant H358 NSCLC cell line, by comparing a complete PLA reaction with both panRAS and CRAF antibodies and an incomplete PLA reaction in the absence of either panRAS or CRAF antibodies. We observed high panRAS:CRAF PLA intensity in H358 with both antibodies, which was abrogated in the absence of either panRAS or CRAF antibodies. We next evaluated the specificity of the PLA reaction by RNA interference. Transfection with sipanRAS or siCRAF resulted in a reduction in panRAS:CRAF PLA signal. We then performed panRAS:CRAF PLA with a panel of KRAS G12C-mutant NSCLC cell lines. The intensity of panRAS:CRAF PLA signal varied between these cell lines, with H358 and LU65 having higher and H1792 and LU99 having lower intensity of panRAS:CRAF PLA signal. To further understand the RAS-RAF interaction, we evaluated a CRAF-RAS binding domain pulldown assay for the cell lines. Different levels of CRAF-bound panRAS were observed in the cell lines, with H358 and LU65 having higher and H1792 and LU99 having lower level of CRAF-bound panRAS. The intensity of panRAS:CRAF PLA strongly correlated with CRAF-bound panRAS (r = 0.70, P = 0.037), suggesting that panRAS:CRAF PLA works sufficiently well to detect the RAS-RAF complex. We investigated the antitumor efficacy of AMG510 in vitro and found that a heterogeneous response to AMG510 was observed in the cell lines, with the 50% inhibitory concentration values of AMG510 for H358 and LU65 below 30 nmol/L and those for H1792, and LU99 above 10 μmol/L. The intensity of panRAS:CRAF PLA was strongly associated with the sensitivity of the G12C-mutated cells to AMG510 (r = 0.74, P = 0.01). We next examined sections of FFPE tumors from NSCLC cell line-derived xenograft models. The panRAS:CRAF PLA signal was higher in mice with sotorasib-sensitive H358 than with resistant H1792 (P = 0.02). Our results suggest that RAS:RAF PLA may have values as a predictive marker to identify which patients can obtain the greatest benefit from sotorasib. Citation Format: Ryoji Kato, Hitendra S. Solanki, Denis Imbody, Anurima Majumder, Yaakov Stern, Liznair Bridenstine, Joseph Johnson, Eric B. Haura. RAS:RAF proximity ligation assay may predict response to KRASG12C inhibitors in NSCLC [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr A001.

Purpose: Sotorasib (AMG510) has demonstrated remarkable response in lung cancer patients with tumors driven by oncogenic KRASG12C mutation. However, recently published clinical data identified acquired mutations in RAS and other genomic alterations as potential mechanisms of resistance. The cause of resistance in more than half of the patient cohort was undetermined with genomic sequencing. We hypothesize that rewiring of signaling networks could be the newly acquired vulnerabilities in cells progressing after sotorasib treatment. Experimental Design: We performed whole exome sequencing, transcriptomic profiling, and mass spectrometry-based proteomics/phosphoproteomics of the parental and sotorasib resistant isogenic line of LU65 (LU65-AMGR). The omics analyses were integrated with functional screens to prioritize a set of druggable targets/pathways. Results: We did not observe obvious acquired mutations that drive resistance to sotorasib in LU65-AMGR cells. To investigate compensatory signaling critically important for the survival/growth of LU65-AMGR cells, we studied signaling perturbations using mass spectrometry-based phosphoproteomics approach. We identified 430 and 1,574 phosphosites differentially expressed in resistant cells (± 1.5-fold & p < 0.05) with phosphotyrosine (pY) and global phosphoproteome (pS/T/Y) enrichment, respectively. Analysis of phosphoproteomics data identified increased phosphorylation of multiple RTKs including EGFR, HER2, HER3, IGF1R, AXL and PDGFRA, including others. RAS-GTP pull-down show increased levels of RAS-GTP and NRAS-GTP in the resistant cells. RAS isoform quantification using parallel reaction monitoring (MRM) mass spectrometry further confirmed increased activity of NRAS in pull-down samples. Transcriptomic analysis revealed elevated genes responsible for anti-apoptosis pathways mediated by PI3K/AKT signaling. Enrichment of transcription factors such as AP1 and AP-2A could drive enhanced EGF expression and EGFR phosphorylation in sotorasib resistant cells. Consistent with enhanced RTK and RAS activity, Western blots confirmed higher phosphorylation of ERK and AKT in LU65-AMGR cells. We show higher EGFR phosphorylation in resistant cells when compared to the parental counterpart. While LU65 cells viability is reduced markedly by sotorasib combination with afatinib, an irreversible HER family inhibitor, resistant cells showed lesser effect on cell viability with afatinib combination. Consistent with our in vitro observations, the sotorasib and afatinib combination treatment significantly regressed tumor growth only in LU65 xenografts, but not in LU65-AMGR xenografts. Conclusions: Our data suggest that activation of multiple RTKs maintains RAS activity and PI3K signaling in LU65-AMGR cells. Thus, dual pan-RAS and PI3K inhibition could serve as promising strategy of treatment in relapsed tumors identified with WT RAS and PI3K signaling activation. Citation Format: Denis Imbody, Hitendra S. Solanki, Bina Desai, Paul A. Stewart, Yaakov Stern, Ryoji Kato, Anurima Majumder, Liznair Bridenstine, Aobuli Xieraili, Bin Fang, Lancia Darville, Fumi Kinose, John M. Koomen, Uwe Rix, Andriy Marusyk, Eric B. Haura. Wildtype RAS activity and PI3K signaling as new vulnerabilities in cells with acquired resistance to sotorasib [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr B015.

Sotorasib demonstrated efficacy in patients with non-small cell lung cancer (NSCLC). However, a substantial proportion of patients do not respond. There is therefore a clear need for a predictive biomarker to guide treatment decisions. Proximity ligation assay (PLA) is an immunofluorescent-based approach for analysis of endogenous protein-protein interactions, in which the signal can be detected only when two target proteins are within 40 nm. This method measures drug-targetable signaling-associated protein complexes in cells and tissues. KRAS activity has recently been shown to be related to the sensitivity to sotorasib. We therefore conducted a preclinical study to evaluate whether RAS activation inferred by PLA might predict response to KRASG12C inhibitors. We first examined panRAS:CRAF PLA reaction for a KRASG12C-mutant H358 NSCLC cell line, by comparing a complete PLA reaction with both panRAS and CRAF antibodies and an incomplete PLA reaction in the absence of either panRAS or CRAF antibodies. We observed high panRAS:CRAF PLA intensity in H358 with both antibodies, which was abrogated in the absence of either panRAS or CRAF antibodies. We next evaluated the specificity of the PLA reaction by RNA interference. Transfection with sipanRAS or siCRAF resulted in a reduction in panRAS:CRAF PLA signal. We then performed panRAS:CRAF PLA with a panel of KRAS G12C-mutant NSCLC cell lines. The intensity of panRAS:CRAF PLA signal varied between these cell lines, with H358 and LU65 having higher and H1792 and LU99 having lower intensity of panRAS:CRAF PLA signal. To further understand the RAS-RAF interaction, we evaluated a CRAF-RAS binding domain pulldown assay for the cell lines. Different levels of CRAF-bound panRAS were observed in the cell lines, with H358 and LU65 having higher and H1792 and LU99 having lower level of CRAF-bound panRAS. The intensity of panRAS:CRAF PLA strongly correlated with CRAF-bound panRAS (r = 0.70, P = 0.037), suggesting that panRAS:CRAF PLA works sufficiently well to detect the RAS-RAF complex. We investigated the antitumor efficacy of AMG510 in vitro and found that a heterogeneous response to AMG510 was observed in the cell lines, with the 50% inhibitory concentration values of AMG510 for H358 and LU65 below 30 nmol/L and those for H1792, and LU99 above 10 μmol/L. The intensity of panRAS:CRAF PLA was strongly associated with the sensitivity of the G12C-mutated cells to AMG510 (r = 0.74, P = 0.01). We next examined sections of FFPE tumors from NSCLC cell line-derived xenograft models. The panRAS:CRAF PLA signal was higher in mice with sotorasib-sensitive H358 than with resistant H1792 (P = 0.02). Our results suggest that RAS:RAF PLA may have values as a predictive marker to identify which patients can obtain the greatest benefit from sotorasib. Citation Format: Ryoji Kato, Hitendra S. Solanki, Denis Imbody, Anurima Majumder, Yaakov Stern, Liznair Bridenstine, Joseph Johnson, Eric B. Haura. RAS:RAF proximity ligation assay may predict response to KRASG12C inhibitors in NSCLC [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr A001.

Abstract TThe discovery of small molecule inhibitors that target mutant KRASG12C has revolutionized the treatment paradigm for KRASG12C-mutant non-small cell lung cancer (NSCLC). While the initial response rates to KRASG12C inhibitors (KRASG12Ci) are approximately 40%, the development of heterogenous resistance mechanisms remains a challenge. Understanding the heterogeneity of resistance mechanisms is critical in overcoming this obstacle. Autopsy samples provide valuable insights into therapy resistance and genomic evolution. Moffitt’s Rapid Tissue Donation (RTD) program offers patients with lung malignancies the opportunity to donate primary and metastatic tumor samples, as well as non-tumoral tissue samples and body fluids, for research purposes after their death. 16 patients with KRASG12C-mutant NSCLC enrolled into the RTD, and 15 were treated with KRASG12Ci. Postmortem samples from seven patients were collected to date, including 38 tumor samples from lung, liver, lymph nodes, soft tissue, adrenal, spleen, pancreas, brain and epicardium samples. Radiological measurements were used to evaluate therapy response in each lesion. 26/38 tumor samples were non-responding to treatment whereas the remaining 12 were stable/responding lesions. Among the seven patients, five had both non-responding and stable/responding lesions and the remaining two had only non-responding lesions. Whole exome sequencing (WES) and transcriptomic analyses (RNA-Seq) were performed in 7 tumoral samples and 1 non-tumoral liver sample from one single patient. KRASG12C mutation and PTENR55M mutations were found in all tumor lesions, irrespective of therapy response. A PIK3CAE542K mutation was present in all tumor lesions, except for one subcutaneous tumor that did not respond to treatment. In the non-responding lung tumor, as well as the stable metastatic lymph node, a MAP2K3A203S mutation was identified. Notably, the non-responding liver lesions exhibited an ERBB3A17G mutation, whereas the responding liver lesion did not. Gene expression analyses comparing non-responding and responding liver lesions revealed an upregulation of genes associated with hypoxia, epithelial mesenchymal transition, and inflammation in the non-responding lesions, while a subgroup of genes regulated by MYC was upregulated in the responding liver lesion. Additional genomic analyses of other autopsy samples are underway. Our findings reveal that therapy resistance may be driven by pathway alterations instead of genomic alterations. The collection of rapid autopsy specimens from primary and metastatic tissue sites from patients with KRASG12C-mutant NSCLC is essential to understand the heterogeneous KRASG12Ci mechanisms of resistance and explore biomarkers that may guide clinical decision-making in these patients. Citation Format: Hilal Ozakinci, Gina Nazario, Yaakov Stern, Hitendra S Solanki, Dung-Tsa Chen, Rose Trevor, Matthew Schabath, Paul Stewart, Jamie K Teer, Amer Beg, Theresa A Boyle, Eric Haura, Bruna Pellini. Rapid autopsy provides unique research opportunity to evaluate KRASG12C inhibitor resistance mechanisms in non-small cell lung cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C046.

KRASG12C inhibitors such as sotorasib and adagrasib have shown efficacy in patients with non-small cell lung cancer (NSCLC). However, a substantial proportion of patients do not respond. Therefore, there is a clear need for predictive biomarkers to guide treatment. The proximity ligation assay (PLA) is an immunofluorescent-based approach utilized to analyze endogenous protein-protein interactions. The method allows for the assessment of signaling-associated protein complexes, which can serve as potential targets for specific inhibitors. In particular, KRASG12C inhibitors can disrupt these complexes by interfering with the interaction between RAS and its effector RAF. By providing insights into the presence of these protein complexes, PLA offers a predictive readout for inhibitor sensitivity. We thus conducted a preclinical study to evaluate if a RAS-CRAF PLA could inform on the presence of RAS-RAF protein complexes and predict the response to KRASG12C inhibitors. To assess the specificity of the panRAS-CRAF PLA, we employed RNA interference in a KRASG12C-mutant H358 NSCLC cell line, wherein knockdown of either panRAS or CRAF resulted in a reduction in the panRAS-CRAF PLA signal. Pharmacological inhibition of RAS-RAF interaction with sotorasib also reduced the panRAS-CRAF PLA signal. We next performed panRAS-CRAF PLA in a panel of 11 KRASG12C-mutant NSCLC cell lines, revealing a higher number of panRAS-CRAF PLA spots in H358, LU65, and HCC1171. To further investigate the RAS-RAF interaction, we assessed the abundance of CRAF-bound RAS-GTP by quantifying the binding of RAS-GTP to the RAS-binding domain of CRAF. H358, LU65, and HCC1171 exhibited the highest levels of RAS-GTP among the 11 cell lines. We observed a strong correlation between the number of panRAS-CRAF PLA foci and the levels of CRAF-bound RAS-GTP (r = 0.87, P = 0.0002). These results indicated that the enhanced level of RAS-GTP for CRAF proteins facilitates the formation of RAS-CRAF complexes, thereby augmenting the panRAS-CRAF PLA signals. We then evaluated the in vitro antitumor activity of sotorasib across the G12C-mutated cell lines and found that the 50% inhibitory concentration values of sotorasib for H358, LU65, and HCC1171 were below 30 nmol/L. The panRAS-CRAF PLA was strongly associated with the sensitivity to sotorasib (r = 0.81, P = 0.002). We subsequently assessed the association of panRAS-CRAF PLA with efficacy of adagrasib in a patient-derived xenograft (PDX) cohort. PanRAS-CRAF PLA was assessed on sections of formalin-fixed paraffin-embedded tumors derived from vehicle-treated control groups at the end of efficacy studies in 18 NSCLC PDX models. Our findings revealed a significant association between high panRAS-CRAF PLA signal and increased sensitivity to adagrasib (r = 0.61, P = 0.008). Our results suggest that panRAS-CRAF PLA may serve as a predictive marker to identify patients who could derive optimal benefit from KRASG12C inhibitors, and may direct combination therapy approaches to those patients less likely to benefit from single-agent therapy. Citation Format: Ryoji Kato, Hitendra S. Solanki, Denis Imbody, Anurima Majumder, Yaakov Stern, Liznair Bridenstine, Harika Gundlapalli, Ida Aronchik, Joseph Johnson, Eric B. Haura. High RAS-RAF binding as assessed via proximity ligation assay is associated with sensitivity to KRASG12C inhibitors in NSCLC [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B006.

The development of covalent inhibitors targeting KRASG12C mutations offers a precision medicine approach to a large cohort of lung cancer patients previously lacking opportunities for targeted therapy. Despite promising initial responses ranging from disease control to partial response in most patients undergoing treatment, the efficacy of these inhibitors has been limited by a short duration of response. Several strategies have been advanced to delay or prevent acquired drug resistance in lung cancer patients treated with KRASG12C inhibitors. Many of these involve co-administration of other targeted therapies to prevent activation of Ras-dependent mitogen activated protein kinase (MAPK) signaling, which is a hallmark response to KRASG12C inhibitors. While this approach has proven effective in some patients, combination clinical trials and postmortem analysis of tumors that progressed on KRASG12C inhibitors demonstrate that non-MAPK-dependent mechanisms of resistance remain a major challenge. We have developed a panel of lung cancer cell lines with acquired resistance to the KRASG12C inhibitor sotorasib. While Erk phosphorylation is observed in all resistant models, treatment with a panel of Ras and MAPK pathway inhibitors demonstrates differential dependence on MAPK pathway activity, including complete MAPK independence in a resistant model derived from the H358 cell line. Mutation, transcription and phosphoproteomic analysis revealed that these resistant models exhibit metabolic reprogramming and activation of a variety of DNA damage response pathways. Based on differential phosphorylation of the transcriptional elongation kinases CDK12 and CDK13 in KRASG12C-treated cells, we hypothesized that inhibiting these kinases might prevent or revert acquired drug resistance. Our prior studies demonstrate that CDK12/13 inhibition reduces expression of a broad spectrum of DNA damage response and metabolic genes, and RNA sequencing confirms that these pathways are sensitive to the CDK12/13 inhibitor SR-4835 in both sotorasib-sensitive and -resistant cells. Resistant cells show differential responses to specific DNA damage-directed therapies and cell-line specific metabolic reprogramming, but up-front combinatorial treatment with SR-4835 prevents the development of acquired resistance to sotorasib across these models. Combined treatment with sotorasib and SR-4835 does not prevent Erk phosphorylation rebound; thus, the mechanism of SR-4835 in suppressing acquired resistance is independent of MAPK pathway reactivation. In vivo combination of sotorasib and SR-4835 potentiates drug response and prevents drug resistance in the H358 cell line, which can develop both MAPK-dependent and -independent drug resistance. These results demonstrate that targeting transcriptional elongation kinases in combination with sotorasib may benefit a broader spectrum of patients than MAPK-directed combination therapies and provide rationale for suppressing the DNA damage response and metabolic reprogramming as an approach to extend the efficacy of KRASG12C inhibitors. Citation Format: Yaakov E. Stern, Pompom Ghosh, Hitendra S. Solanki, Denis Imbody, Liznair Bridenstine, Hannah L. Walker-Mimms, John W. Mosior, Andrii Monastyrskyi, Derek R. Duckett, Eric B. Haura. Targeting transcriptional elongation kinases prevents adaptation to KRASG12C inhibitors in both MAPK-dependent and -independent models of acquired resistance [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr B035.

Despite the presence of the KRASG12C oncogene, not all patients respond to KRASG12C inhibitors (e.g., sotorasib, adagrasib) and duration of response has been variable. We hypothesized that subtypes of KRASG12C lung cancers could be responsible for such differential effects. To define subtypes, we performed targeted exon sequencing, transcriptomics, proteomics, and phosphoproteomics on 46 frozen surgically resected KRASG12C lung adenocarcinomas. We employed unbiased consensus clustering methods, pathway analysis, and PTM-SEA to identify kinase signatures from phosphoproteomics data. Transcriptomics data revealed 4 clusters. Pathway enrichment showed that gene cluster (GC) 1 was enriched for immune pathways including interferon gamma response. Epithelial-mesenchymal transition (EMT), assessed by a TGF-β gene signature, was also enriched in GC1. 100% of GC1 overlapped the Proximal-Inflammatory subtype (Wilkerson et al.) and 53% with the mesenchymal subtype (Daemen et al.). GC2 was enriched for inflammatory response and TNF-alpha signaling. GC3 represented a metabolic phenotype with enriched xenobiotic metabolism and other metabolism pathways. 83% of GC3 overlapped with the Terminal Respiratory Unit subtype (Wilkerson et al.) and 56% with the proliferative subtype (Daemen et al.). GC4 only had 5 samples and did not have any significant enrichment. We next identified four proteomic clusters with distinct biology. Protein Cluster 1 (PC1) was enriched for immune pathways, PC2 was enriched for EMT, and PC3 was enriched for TNF/NF-κβ signaling. PC4 was enriched for xenobiotic and fatty acid metabolism and had significantly more KEAP1 mutations. We observed concordance of protein based clusters with mRNA based clusters, as PC1 largely overlapped with GC1 (70%) and PC4 largely overlapped with GC3 (86%). Cell type inference using xCell largely recapitulated the immune subtypes identified by transcriptomics and proteomics. GC1/PC1 had significantly more CD8+ effector memory T-cells, CD4+ Th2 T-cells, and M1 macrophages, while GC3/PC4 had significantly less of these same cell types. Collectively, GC1/PC1 represents 43% of the cohort and was defined by enrichment of immune pathways, elevated immune populations, and significantly higher PD-L1. Finally, we leveraged the phosphoproteomics data to determine whether signaling activity differs across subtypes. Using PTM-SEA, we identified phosphoproteomic signatures of activity for 50 kinases and pathways. We identified 26% of samples (N=12) with high EGFR activity, which is known to affect sensitivity of cells to KRASG12C inhibitors. The EGFR-high samples were observed across all genomic, transcriptomic, and proteomic subtypes. Our results suggest concordance of some transcriptomic and proteomic subtypes, including an immune subtype, while a metabolic protein subtype and EGFR high signaling subtype may provide additional subclasses with potential relevance for treatment responses. Additional phosphoproteomics signatures such as PLK1 and AKT1 may identify subtypes amenable to combination therapy approaches. Citation Format: Paul A. Stewart, Hitendra Solanki, Eric Welsh, Yaakov Stern, Denis Imbody, Yonghong Zhang, Bruna Pellini, Bin Fang, Sean Yoder, Steven Eschrich, Jamie Teer, John Koomen, Eric B. Haura. Proteogenomic landscape of KRASG12C lung adenocarcinomas reveals new subtypes and potential combination therapies [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr A007.

Abstract Background: Amplification of KRASG12C mutant allele has been reported as one of the resistance mechanisms in tumors progressed to Sotorasib, the FDA approved KRASG12C(OFF) inhibitor. An identical mechanism was observed in one of our H358 xenograft tumors relapsed to Sotorasib. The cell line generated from relapsed tumor represents an appropriate in vitro model to study therapeutic opportunities in KRASG12C tumors developing secondary resistance to Sotorasib via KRASG12C amplification. Methods: We generated five Sotorasib resistant cell lines using relapsed tumors of Sotorasib-treated H358 xenografts (MR1-MR5) and two vehicle-treated tumors (MV1 and MV2). Whole exome sequencing (WES), Taqman copy number analysis and digital PCR to study mutant allelic fractions were performed to investigate acquired mechanisms of resistance. We have also generated a Dox-inducible system for H358 cells to overexpress KRASG12C protein and mimic KRAS amplification. Results: We observed loss of sensitivity to Sotorasib in models MR1-MR5, when compared to MV1 and MV2. Western blot analysis show EMT-associated signatures in all resistant lines except MR2. The WES of resistant lines shows higher allelic frequency of KRASG12C mutation in MR2, which is homozygous (through loss of heterozygosity). The dPCR analysis further confirmed higher mutant allelic frequency in MR2. Copy-number analysis revealed the presence of more than 10 copies of KRAS in MR2. MR2 model represents the best model to investigate therapeutic options in KRASG12C tumors developing secondary resistance to Sotorasib via KRASG12C amplification. Both RAS-RAF Proximity Ligation and Raf-RBD pull down assays confirm enhanced RAS signaling in MR2 cells. The combination of KRASG12C(OFF) and SHP2 inhibitors, or single agent KRASG12C(ON) or RASMULTI(ON) inhibitors suppressed enhanced MAPK signaling in MR2 cells and drove tumor suppressions in MR2 mice xenografts. Conclusions: The stronger inhibition of KRAS pathway is necessary to suppress enhanced MAPK signaling in KRASG12C mutated lung cancer that developed secondary resistance to Sotorasib treatment through KRASG12C amplification. These preclinical data suggest that KRASG12C(OFF)/SHP2 inhibitors combo, or single agent KRASG12C(ON)I or RASMULTI(ON)I represent potential therapeutic strategies for these relapsed tumors. Citation Format: Hitendra S Solanki, Denis Imbody, Bina Desai, Ryoji Kato, Paul A Stewart, Yaakov Stern, Anurima Majumder, Liznair Bridenstine, Bhaswati Sarca, Daria Miroshnychenko, Ida Aronchik, Andriy Marusyk, Eric B Haura. Sotorasib/SHP2 inhibitors combo, KRASG12C(ON)I and RASMULTI(ON)I effectively target KRASG12C tumors developing secondary resistance to Sotorasib via KRASG12C amplification [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B084.

Receptor tyrosine kinases (RTKs) are recognized as targets of precision medicine in human cancer upon their gene amplification or constitutive activation, resulting in increased downstream signal complexity including heterotypic crosstalk with other RTKs. The Met RTK exhibits such reciprocal crosstalk with several members of the human EGFR (HER) family of RTKs when amplified in cancer cells. We show that Met signaling converges on HER3-tyrosine phosphorylation across a panel of seven MET-amplified cancer cell lines and that HER3 is required for cancer cell expansion and oncogenic capacity in vitro and in vivo. Gene expression analysis of HER3-depleted cells identified MPZL3, encoding a single-pass transmembrane protein, as HER3-dependent effector in multiple MET-amplified cancer cell lines. MPZL3 interacts with HER3 and MPZL3 loss phenocopies HER3 loss in MET-amplified cells, while MPZL3 overexpression can partially rescue proliferation upon HER3 depletion. Together, these data support an oncogenic role for a HER3-MPZL3 axis in MET-amplified cancers.