Targeting RAS Research Articles

Abstract B019: ASO-mediated NRAS knockdown overcomes gilteritinib late resistance in FLT3-AML

Abstract The internal tandem duplication of the FLT3 receptor (FLT3-ITD) leads to constitutive receptor activation and is one of the most common mutations (~30%) in acute myeloid leukemia (AML), resulting in poor prognosis. Multiple FLT3 inhibitors (FLT3i) have been developed, including the potent FDA-approved FLT3i, gilteritinib. However, AML patients only respond to gilteritinib for approximately 6 months due to the emergence of drug resistance. Through an approach that integrated genomic, metabolomic, proteomic, and phosphoproteomic analyses with complementary genetic and pharmacologic screens, we demonstrated that gilteritinib resistance occurs in a stepwise manner with two distinct phases of early and late resistance (Joshi et al., Cancer Cell, 2021). While gilteritinib efficiently eliminates leukemia cells in the blood, residual cells survive within the bone marrow, where they are protected by extrinsic microenvironmental factors fostering early resistance. These lingering cells eventually develop intrinsic mutations in NRAS that allow them to resist gilteritinib treatment, leading to late resistance. Acquisition of mutations in the RAS pathway, particularly NRAS, are a common mode of late resistance (~11%) for many patients that relapse on FLT3i. Developing therapeutics to block NRAS activity remains a challenge with the lack of direct small-molecule inhibitors. Indirect approaches to inhibit mutant NRAS/MAPK pathway signaling have also not met much clinical success. Hence, therapeutic nucleic acid-based approaches, including antisense oligonucleotides (ASOs), may offer an alternative approach to target NRAS-driven cancers. We evaluated the effectiveness of a novel ASO targeting NRAS mRNA to restore gilteritinib sensitivity in resistant cultures in vitro and in primary AML patient samples ex vivo. We first assessed the potency of the NRAS ASO in both gilteritinib-sensitive and late resistant MOLM-14 AML cell lines (N=9) that expressed wild-type or mutant NRAS (G12S or G12D) via free uptake of ASO. NRAS expression was evaluated by qPCR after 48 hours. ASO treatment down-regulated mutant NRAS mRNA expression in a dose-dependent manner with an IC50 of < 1 µM and decreased NRAS protein levels. No changes in NRAS mRNA or protein levels were observed with non-targeting ASO control. Decreased NRAS mRNA expression restored sensitivity to gilteritinib in late-resistant cultures, leading to decreased cell viability and increased apoptosis. A similar trend was observed in primary AML cells from patients (N=2) that relapsed on gilteritinib, where reduction of approximately 50% of mutant NRAS mRNA robustly sensitized patient cells to gilteritinib. In contrast, the combination of gilteritinib and the MEK inhibitor trametinib was not as effective in either cell cultures or patient samples. Our results suggest that ASO-mediated knockdown of NRAS may circumvent the development of resistance and improve the durability of FLT3i. Citation Format: Sunil K. Joshi, Janét Pittsenbarger, Xiaolin Luo, Hadi Maazi, Alexey Revenko, Brian J. Druker, Elie Traer. ASO-mediated NRAS knockdown overcomes gilteritinib late resistance in FLT3-AML [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 B019.

Abstract B005: RAS inhibitors to treat luminal B breast cancer

Abstract Since RAS mutations are rare in Breast Cancer, RAS has not traditionally been considered as an important driver of this disease. However, RAS signaling pathways are frequently hyper-activated in breast cancers and genetic/epigenetic inactivation of RAS negative regulators (GAPs) is common. This is particularly true for Luminal B breast cancer. Luminal breast cancer makes up the majority of Breast Cancers, ~ 65% of cases. The Luminal B form makes up around 1/3 of these. Although current therapeutic options for luminal A (surgery, endocrine therapy) can be reasonably effective, Luminal B tumors are much more dangerous. These tumors are less sensitive to therapy in the first place and have a high frequency of relapse. Moreover, Luminal B tumors tend to occur more frequently in younger women and have a higher incidence of metastasis. One recent analysis has shown that Luminal B cancers have little better overall survival rates than the notorious triple negative breast cancers. Therefore, better therapies for Luminal B breast cancer are urgently required. One approach may be to target the hyper-active wild-type RAS oncoprotein that drives many of these tumors. We have in used in silico library screening followed by Medicinal Chemistry optimization to develop a series of novel small molecules that bind to all three main RAS proteins and block RAS function. We have validated the agents by using Microscale Thermophoresis binding procedures to quantify recombinant protein interaction. We used 3D growth inhibition and protein-based RAS signaling assays to quantify the biological action of the agents. Finally, we validated one of the more effective agents in vivo against a Luminal B cell line xenograft. This may be the first example of an effective anti-RAS therapy in breast cancer. It serves as proof of principal for the use of ant-RAS drugs in Luminal B disease. As basal breast cancers often exhibit loss of function of the RAS GAP called NF1, this strategy may have applications beyond Luminal B disease. Citation Format: Geoff Clarke, Howard Donninger, Raphael Jigo, Tariq Arshad, Becca von Baby, Rachel Ferrill, Mike Sabo, Joe Burlison, John Trent. RAS inhibitors to treat luminal B breast cancer [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 B005.

Abstract A014: Inhibition of KrasG12D with a novel small molecule inhibitor alters the pancreatic cancer microenvironment

Abstract Approximately 90% of pancreatic ductal adenocarcinoma (PDAC) patients harbor an oncogenic KRAS mutation, with Gly-to-Asp mutations (KrasG12D) being most common. PDAC is characterized by a robust, immunosuppressive tumor microenvironment that is rich in myeloid-derived suppressor cells (MDSCs) and has a paucity of T cells. The majority of therapeutic interventions in PDAC are ineffective, in part, due to this immunosuppressive TME. We aimed to examine the efficacy of a small molecule KrasG12D inhibitor, MRTX1133, in implantable and autochthonous PDAC models with an intact immune system. In vitro studies validated the specificity and potency of MRTX1133. In vivo, MRTX1133 prompted deep tumor regressions in all models tested, including complete or near-complete remissions after 14d. MRTX1133 treatment additionally reduced metastatic burden after 7d of treatment. An increase in tumor cell death was identified after only 36h of treatment, with concomitant loss of tumor cell proliferation. Inhibition of KrasG12D led to marked shifts in the TME composition. MRTX1133-treated tumors had an increase in fibroblasts, collagen deposition, and blood vessel density. There was a robust increase in M1-like macrophages after MRTX1133 treatment. Further, there was a loss of MDSCs, along with an increase in cytotoxic T cells. Proteome profiling on tumor cells treated with MRTX1133 identified a loss of tumor cell-derived GM-CSF (a MDSC recruiter), as well as an increase in CCL2 (a macrophage recruiter), providing evidence that MRTX1133 alters the TME through tumor secreted factors. T cells were necessary for MRTX1133’s full anti-tumor effect, and T cell depletion accelerated tumor regrowth after therapy. These results validate the specificity, potency, and efficacy of MRTX1133 in immunocompetent KrasG12D-mutant PDAC models, providing a rationale for clinical testing and a platform for further investigation of combination therapies. Citation Format: Samantha B. Kemp, Noah Cheng, Nune Markosyan, Rina Sor, Il-Kyu Kim, Jill Hallin, Jason Shoush, Liz Quinones, Natalie Brown, Jared B. Bassett, Nikhil Joshi, Salina Yuan, Molly Smith, William P. Vostrejs, Kia Z. Perez-Vale, Benjamin Kahn, Feiyan Mo, Timothy R. Donahue, Caius G. Radu, Cynthia Clendenin, James G. Christensen, Robert H. Vonderheide, Ben Z. Stanger. Inhibition of KrasG12D with a novel small molecule inhibitor alters the pancreatic cancer microenvironment [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 A014.

Abstract B025: The RAF/MEK clamp avutometinib (VS-6766) enhances antitumor efficacy of KRAS G12C and G12D inhibitors through vertical inhibition of RAS, RAF and MEK. </title>

Abstract KRAS is the most frequently mutated RAS family member. Within non-small cell lung cancer (NSCLC), G12C is the most prevalent KRAS mutation (~13%) and the KRAS G12C inhibitors (G12Ci) sotorasib and adagrasib are now FDA approved. However, it has been shown that simultaneous targeting of multiple nodes in the MAPK pathway may be optimal for deeper and more durable responses. Furthermore, acquired mutations in the MAPK pathway occur clinically upon progression on sotorasib or adagrasib, altogether supporting the need for clinical combinations with G12Ci. Based on the clinical success of G12Ci, several KRAS G12D inhibitors (G12Di) are now being developed as G12D is the most prevalent KRAS mutation across human cancers including pancreatic (~28%) and colorectal (~11%) cancers. Avutometinib (VS-6766; avuto) is a RAF/MEK clamp that potently inhibits MEK kinase activity and induces a dominant negative RAF-MEK complex preventing phosphorylation of MEK by ARAF, BRAF and CRAF. This unique mechanism allows avuto to block MEK signaling without the compensatory re-activation of MEK that appears to limit the efficacy of MEK-only inhibitors. Here, we tested whether addition of avuto to G12Ci or G12Di could improve MAPK pathway blockade and anti-tumor efficacy. Avuto was synergistic with sotorasib and adagrasib in reducing viability of a panel of KRAS G12C cancer cell lines in 3D culture, and the combination of avuto + G12Ci showed improved depth and duration of MAPK pathway inhibition, stronger inhibition of cell cycle/proliferation markers and stronger activation of pro-apoptotic markers relative to G12Ci alone. In mouse models, avuto enhanced efficacy of G12Ci in KRAS G12C NSCLC xenograft models. Furthermore, avuto potentiated G12Ci efficacy in a KRAS(+/G12C);p53null NSCLC GEMM model with avuto + G12Ci combination inducing complete response in 25% of the mice. To evaluate efficacy of avuto against KRAS mutations that have been observed clinically upon acquired resistance to G12Ci, proliferation of Ba/F3 cells expressing these mutations was assessed. While avuto potently inhibited (IC50 < 15 nM) proliferation of cells bearing KRAS G12C/R68S, G12C/H95D or G12C/Y96C mutations, adagrasib showed diminished potency (IC50 ≥ 85 nM) against all 3 of these mutations and sotorasib showed diminished potency (IC50 ≥ 150 nM) against G12C/R68S and G12C/Y96C. Accordingly, avuto strongly inhibited tumor growth of an in vivo model expressing KRAS G12C/Y96D, while sotorasib was ineffective. Similarly, avuto was found to be synergistic with the G12Di MRTX1133 in reducing viability of a panel of KRAS G12D cancer cell lines, and avuto enhanced anti-tumor efficacy of MRTX1133 in KRAS G12D colorectal (CR3300) and pancreatic (PA1252) cancer PDX models. These results support ongoing clinical studies of avutometinib in combination with sotorasib (NCT05074810) and adagrasib (NCT05375994) for patients with KRAS G12C NSCLC. Additionally, these preclinical data support combination of avutometinib with a G12D inhibitor for patients with KRAS G12D colorectal or pancreatic cancers. Citation Format: Silvia Coma, Monica Musteanu, Cristina Caffarra, Alessia Mira, Enrico Patrucco, Julien Dilly, Andrew J. Aguirre, Mariano Barbacid, Chiara Ambrogio, Jonathan A. Pachter. The RAF/MEK clamp avutometinib (VS-6766) enhances antitumor efficacy of KRAS G12C and G12D inhibitors through vertical inhibition of RAS, RAF and MEK. </title> [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 B025.

Abstract B016: High throughput application of the NanoBiT Biochemical Assay for the discovery of selective p110α isoform binders that block its interaction with KRAS

Abstract RAS proteins contribute to the activation of p110α by directly interacting with its RAS binding domain (RBD), resulting in the promotion of cellular functions such as cell growth, proliferation and survival. Previously, we have shown that blocking the interaction of p110α with oncogenic RAS, by introducing specific mutations in the RBD, had a significant impact on tumor initiation and growth in mouse models, whilst having little effect on the health of normal adult mice. These studies highlight the significance of the p110α/KRAS protein-protein interaction (PPI) in tumor progression and maintenance and strongly suggest its importance as a drug target. Thus, we initiated a drug discovery project aiming to identify molecules that bind to p110α and perturb its interaction with KRAS. However, the rather weak binding affinity of the p110α/KRAS interaction (Kd = 3 μM) and the poor solubility of p110α raised significant issues when considering the use of currently available biochemical assays. The NanoLuc® Binary Technology (NanoBiT®) assay was originally developed to detect PPIs in live mammalian cells. However, the assay in its current state was not ideal for high throughput screening (HTS) due to the requirement for large-scale cell based assays. Therefore, we developed the NanoBiT Biochemical Assay (NBBA) as a more suitable and cost-effective approach. The NBBA centres on expressing modified target proteins of interest in mammalian cells and then screening cell lysates rather than live cells. We have previously shown that the NBBA is suitable for detection of both strong and weak PPIs, as exemplified by KRAS/RAF and KRAS/PI3K. Here we present the first application of NBBA for HTS of the KRAS/p110α PPI, using tagged Sm-KRAS-G12D and Lg-p110α. The NBBA proved to be stable and produced good Z’ factor metrics. Our primary screen of more than 720,000 compounds on KRAS/p110α cell lysates produced around 8,000 initial hits. A concentration response screen comparing KRAS/p110α with two other p110 isoforms, p110δ and p110γ, identified selective p110α-specific compounds and enabled derivation of IC50s for these hits. We identified around 30 compounds showing greater than 20-fold selectivity towards p110α versus p110δ and p110γ with IC50 <2μM. These compounds will be further characterized by Surface Plasmon Resonance for selectivity, affinity toward p110α and efficacy in blocking its interaction with KRAS. The most suitable hits will be followed up by co-crystallization with p110α to aid further elucidation of the nature of the interaction and extended optimisation of these compounds. Citation Format: Mohamed (Soly) Soliman Ismail, Jonathan Tart, Gareth Davies, Graham Sproat, Tiziana Monterverde, David Hancock, Santosh Adhikari, Christopher Stubbs, Carolyn Blackett, Geoff Holdgate, Jason Kettle, Julian Downward. High throughput application of the NanoBiT Biochemical Assay for the discovery of selective p110α isoform binders that block its interaction with KRAS [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 B016.

Abstract B036: Treatment modalities in KRAS-driven cancer

Abstract KRAS is the most common RAS isoform, found to be altered in 22% of RAS-mutated cancers. The mutant protein is found most prevalently in pancreatic cancer followed by colorectal, non-small cell lung cancer and other solid tumors. Due to its structural complexity, KRAS remained “undruggable” for several decades. Recently, the discovery of a specific protein binding pocket has led to the development of small molecule inhibitors that potently bind and inhibit KRAS downstream signalling. The accelerated FDA approval of sotorasib and adagrasib for treatment of NSCLC patients harbouring KRASG12C-mutation and further clinical evaluation of several other inhibitors of KRASG12C are under investigation, however emergence of resistance and limited efficacy beyond non-small cell lung cancer is a major concern. Targeting KRAS mutations other than KRASG12C (i.e., without a mutant-specific cysteine residue) with small molecules, has been considered much more challenging, especially for developing covalent inhibitors. Small molecule targeting of KRASG12D (e.g. MRTX1133), is under active preclinical investigation and small molecule drugs that target other KRAS-activating mutations (G12S, G12R and G12V) are being intensely explored. A variety of novel alternative approaches are also being investigated to target tumors driven by mutant KRAS, such as (i) targeting complementary signalling pathways (ii) enhancing mutant KRAS protein degradation using PROTACS, (iii) developing pan-KRAS small molecules inhibitors, (iv) anti-KRAS immune cell-based therapies, (v) small interfering RNAs to block mutant KRAS expression and (vi) anti-KRAS vaccines. Here, we aim to provide a comprehensive overview of current status and future prospect of these modalities, in the context of RAS-mutated cancers. Citation Format: Darren R. Tyson, Neetu Singh, Prashant K. Bhavar, Partha Pratim Sarma, Uday Kumar Surampudi, Sathish Katike. Treatment modalities in KRAS-driven cancer [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 B036.

Abstract B021: Pan-RAS IMM-1-104 activity in humanized 3D tumor models is independent of specific amino acid substitution

Abstract Introduction: Novel dual-MEK inhibitor IMM-1-104 is under clinical investigation for use in RAS-addicted solid tumors. Approved KRAS G12C inhibitors are available but cover a limited subset of patients. For example, the KRAS G12C substitution occurs in only 1-3% of pancreatic cancers. We assessed response to IMM-1-104 across RAS mutant preclinical models to determine whether a preference was observed for mutation position, or for specific amino acid substitutions. Experimental Procedures: Response to IMM-1-104 was measured in a humanized 3D tumor growth assay across 133 tumor models. Sixty-nine of these models have a reported RAS mutation, and all models are being mutationally profiled by whole exome sequencing, with the majority (~75%) completed to date. The RAS-mutant panel spans 11 tissue types and includes a subset of 30 confirmed KRAS G12 mutated cell lines drawn from three major indications: 12 pancreatic, 11 lung, and 7 colorectal cancer models. Based on the 3D assay, cell lines were classified into sensitive, intermediate, and resistant to IMM-1-104. The distribution of responses was then assessed across mutation position and amino acid substitutions. Summary of New Data: In the full dataset across 69 RAS-mutant models, at least one model displayed response to IMM-1-104 (sensitive or intermediate) for each observed mutation in K/N/HRAS. That is, no particular mutation position or amino acid substitution was exclusively found to be resistant. Association of response with amino acid identity was further evaluated in a subset of lines for the most frequently altered residue in KRAS, G12. A distribution of responses was observed for each amino acid substitution. The G12 substitutions having at least four cell lines each total across the three indications included G12C (8 lines), D (5 lines), R (4 lines), and V (11 lines). Across cell lines for each of these substitutions, multiple response categories were observed. In each case, half or more lines fell into the intermediate category with the rest falling into one or both of the other response categories. For example, out of the 8 KRAS G12C lines, 6 showed intermediate response, 1 showed resistance, and 1 showed sensitivity. Examining these distributions together, no significant statistical relationship was seen between the amino acid substitution and response categories by Fisher’s exact test. Conclusions: Across 69 RAS-mutated cell lines, each mutation position or amino acid substitution was associated with sensitive or intermediate response in at least one line. Looking at the most commonly mutated position in KRAS, across 30 KRAS G12 mutated cell lines from three cancer indications, no significant preference was observed with respect to response to IMM-1-104 for a particular amino acid at G12. These observations suggest potential relevance of IMM-1-104 to a broad RAS-driven patient population. Citation Format: Sarah Kolitz, Praveen Nair, Mai Johnson, Jason Funt, Peter J. King, Kevin D. Fowler, Anna Travesa, Frank Wang, John Brothers II, Amy Axel, Scott Barrett, Benjamin J. Zeskind, Brett Hall. Pan-RAS IMM-1-104 activity in humanized 3D tumor models is independent of specific amino acid substitution [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 B021.

Abstract IA11: Three-dimensional genomic mapping of human pancreatic tissue reveals striking multifocality and genetic heterogeneity in precancerous lesions

Abstract Pancreatic intraepithelial neoplasia (PanIN) is a precursor to pancreatic cancer and represents a critical opportunity for cancer interception. However, the number, size, shape, and connectivity of PanINs in human pancreatic tissue samples are largely unknown. In this study, we quantitatively assessed human PanINs using CODA, a novel machine-learning pipeline for 3D image analysis that generates quantifiable models of large pieces of human pancreas with single-cell resolution. Using a cohort of 38 large slabs of grossly normal human pancreas from surgical resection specimens, we identified striking multifocality of PanINs, with a mean burden of 13 spatially separate PanINs per cm3 of sampled tissue. Extrapolating this burden to the entire pancreas suggested a median of approximately 1000 PanINs in an entire pancreas. In order to better understand the clonal relationships within and between PanINs, we developed a pipeline for CODA-guided multi-region genomic analysis of PanINs, including targeted and whole exome sequencing. Multi-region assessment of 37 PanINs from eight additional human pancreatic tissue slabs revealed that almost all PanINs contained hotspot mutations in the oncogene KRAS, but no gene other than KRAS was altered in more than 20% of the analyzed PanINs. PanINs contained a mean of 13 somatic mutations per region when analyzed by whole exome sequencing. The majority of analyzed PanINs originated from independent clonal events, with distinct somatic mutation profiles between PanINs in the same tissue slab. A subset of the analyzed PanINs contained multiple KRAS mutations, suggesting a polyclonal origin even in PanINs that are contiguous by rigorous 3D assessment. This study leverages a novel 3D genomic mapping approach to describe, for the first time, the spatial and genetic multifocality of human PanINs, providing important insights into the initiation and progression of pancreatic neoplasia. Citation Format: Laura D. Wood. Three-dimensional genomic mapping of human pancreatic tissue reveals striking multifocality and genetic heterogeneity in precancerous lesions [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 IA11.

Abstract A027: Defining the role of PER1 and circadian rhythm dysregulation in KRAS/LKB1-mutant lung adenocarcinoma

Abstract KRAS and LKB1 are frequently co-mutated in lung adenocarcinoma and characterize a particularly aggressive, metastatic, and treatment-resistant subtype of this disease. We recently published that the outputs of biological rhythm pathways downstream of the AMPK kinase are altered in KRAS/LKB1-mutant tumors. In a live-cell phenotyping screen we used RNAseq to identify the circadian clock genes PER1 and PER2 as uniquely upregulated in partially transformed and invasive KRAS/LKB1-mutant human bronchial epithelial cells. We have analyzed expression of individual circadian clock genes in KRAS-mutant and KRAS/LKB1-mutant patient tumors and found that expression of the PER genes, particularly PER1, is increased in the KRAS/LKB1 subtype of lung adenocarcinoma. At the protein level, PER1 expression is increased in KRAS/LKB1-mutant HBECs as compared to KRAS-mutant cells. Addback of wild-type LKB1 in A549 cells, which are KRAS/LKB1-mutant, results in a decrease in PER1 protein levels, confirming that LKB1 has a role in controlling PER1 levels. Multiple phosphorylation events lead to PER1 nuclear translocation to control its role as a transcriptional repressor in the core clock. In circadian-synced HBECs, PER1 enters the nucleus in KRAS-mutant cells, but remains cytosolic in KRAS/LKB1-mutant cells. In circadian-synced A549 cells, we also observed a lack of nuclear PER1 localization. Addback of wild-type LKB1 restored nuclear localization of PER1, as did expression of kinase-dead LKB1, suggesting that LKB1’s regulation of PER1 localization is kinase-independent. Our current and future experiments aim to determine how clock-controlled gene expression may be altered in KRAS/LKB1-mutant cells, what the functional impact of altered PER1 expression and localization is on growth of KRAS/LKB1-mutant tumors, and whether pharmacological manipulation of LKB1-related signaling pathways can restore nuclear localization of PER1. Citation Format: Rebecca E. Parker, Junghui Koo, Bhakti Dwivedi, Adam I. Marcus, Melissa Gilbert-Ross. Defining the role of PER1 and circadian rhythm dysregulation in KRAS/LKB1-mutant lung adenocarcinoma [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 A027.

Abstract A039: RAS signaling strength determines phenotypic response in the colon

Abstract The RAS (KRAS, NRAS and HRAS) genes are the most frequently mutated in cancer and are highly specific to tissue type by isoform and codon, yet the underlying cause for this selection is unknown. Mutations in KRAS, but not NRAS, frequently occur and act as oncogenic events in colorectal cancer. Biochemically, activating mutations in RAS increase the abundance of the GTP-bound active state, however, the position and substitution of the mutated amino acid affect the ‘on’ and ‘off’ rates of the RAS-GTP/GDP cycle. Alterations in codon 61 result in the largest accumulation of RAS-GTP. While this leads to robust pathway activation, codon 61 mutations are rarely observed in KRAS-mutant colorectal cancers. To study the effect of the isoform and codon mutations in colorectal tumor formation, we engineered mouse models to express codon 12 or 61 mutations in Kras and Nras. Our mouse models recapitulate the clinical RAS isoform and allelic selection. We found Kras G12D provided the greatest proliferative effect. To further understand this allelic selection, we investigated the interplay between RAS signaling strength and intestinal epithelial cell composition. We observed a correlation between RAS signaling strength and induction of stem cell differentiation. Together, our data provide insights to the preference for KRAS mutations in human colorectal cancers and provides a rationale for allelic selection. Citation Format: Amanda R. Moore, Sandra Melo Carlos, Elaine E. Storm, Lisa M. McGinnis, Shiva Malek, Frederic J. de Sauvage. RAS signaling strength determines phenotypic response in the colon [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 A039.

Abstract A005: Canine hemangiosarcoma as a model for RAS-mutated human cancers: Preliminary data

Abstract Canine cancer patients represent an important translational model for human cancer research with their spontaneous tumor pathogenesis and the many histological, genetic, molecular and clinical similarities between canine and human tumors. Canine tumors provide an opportunity to investigate shared biomarkers and their response to therapeutic interventions over an accelerated timeline compared to human cancers due to differences in expected lifespan and other factors. Dogs, like humans, have three related RAS genes, HRAS, KRAS, and NRAS, with extremely similar genetic sequence and resultantly high protein homology. These proteins have many key molecular functions including roles in cell proliferation and survival. Across multiple human cancer types, recurrent gain-of-function missense mutations in the RAS-family genes occur primarily at codons 12, 13, and 61. These mutations result in constitutively active RAS proteins. The frequencies of mutations across the three RAS genes and codons have been hypothesized to lead to distinct biological behaviors. Mutations are most common in KRAS, then NRAS followed by HRAS. We investigated RAS-family genetic mutations in a dataset of 213 canine patients with hemangiosarcoma (HSA), a common, aggressive malignancy derived from endothelial cells for which treatment with both surgery and traditional chemotherapies often fail to prolong survival beyond six months. Recent publications show that genomic profiling of canine HSA tumors can help group tumors into subtypes with potential for guiding therapy selection and improving outcomes. All 213 dogs had tumor tissue sequenced via the FidoCure® Precision Medicine Platform targeted sequencing panel and were followed until time of death or were censored to the date patients were last known to be living. All SNVs and Indels detected were missense mutations. Unlike human pan-cancer data, somatic mutations in NRAS (n=32) were most common with only 1 dog with a somatic KRAS mutation and no dogs with somatic HRAS mutations. Similar to human RAS mutations, affected codons were primarily codon 61 (n=28), codon 13 (n=5), and codon 12 (n=1). Pairwise survival comparisons between dogs with missense mutations in NRAS codon 61 showed that this mutation was associated with better prognosis (n=28, MST 251 [CI 213;327]) compared to dogs with missense mutations at other codons in the NRAS and KRAS genes (n=5, MST 66 [CI 64;NA], p=1.58E-05) and compared to dogs without missense mutations in the RAS family of genes (n=180, MST 123 [CI 100;149], p=0.036). These preliminary findings of similarities between canine and human tumors and associations between mutated codons and prognosis in our growing dataset create an important opportunity to accelerate cancer research, including clinical and biopharmaceutical studies, with great potential benefit to both dogs and humans. Citation Format: Michelle E. White, Garrett Harvey, Lucas Rodrigues, Chase Schwalbach, Dorothy Girimonte, Aubrey Miller, Abigail Hull, Lindsay Lambert, Christina Lopes, Gerald Post. Canine hemangiosarcoma as a model for RAS-mutated human cancers: Preliminary data [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 A005.

Abstract B013: Exploring the switch II pocket of KRAS(G12D) with mutant-selective monobody inhibitors

Abstract The G12D mutation is among the most common KRAS mutations associated with cancer, in particular pancreatic cancer. Here, we have developed monobodies, small synthetic binding proteins, that are highly selective to KRAS(G12D) over KRAS(wild type) and other oncogenic KRAS mutations, as well as over HRAS(G12D). Crystallographic studies revealed that, similar to other KRAS mutant-selective inhibitors, the initial monobody bound to the S-II pocket, the groove between switch II and alpha 3 helix. Strikingly, the monobody captured a shape of the S-II pocket distinct from previously reported structures. Unlike other G12D-selective polypeptides reported to date, the monobody used its backbone NH group to directly recognize the side chain of RAS Asp12. This feature closely resembles that of a small-molecule KRAS(G12D) inhibitor, MRTX1133. The monobody also directly interacted with H95, a residue not conserved in HRAS. These features rationalize the high selectivity toward the G12D mutant and the KRAS isoform. Structure-guided affinity maturation resulted in monobodies with low nM KD values. Deep mutational scanning of a G12D-specific monobody generated hundreds of functional and nonfunctional single-point mutants, from which we identified crucial residues for binding and those that contributed to the selectivity toward the GTP- and GDP-bound states. When expressed in cells as genetically encoded reagents, these monobodies engaged selectively with KRAS(G12D) and inhibited KRAS(G12D)-mediated signaling and tumorigenesis. These results demonstrate the feasibility of targeting KRAS(G12D) functions using a mutant selective inhibitor and will guide the development of next-generation KRAS(G12D)-selective inhibitors. Citation Format: Takamitsu Hattori, Padma Akkapeddi, Imran Khan, Akiko Koide, Eliezra Glasser, Gayatri Ketavarapu, Michael Whaby, Mariyam Zuberi, Kai Wen Teng, Julia Lefler, Lorenzo Maso, Injin Bang, Michael C. Ostrowski, John P. O’Bryan, Shohei Koide. Exploring the switch II pocket of KRAS(G12D) with mutant-selective monobody inhibitors [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 B013.

Abstract A003: COVALENT-102: A phase 1/1b dose finding study of BMF-219, an oral covalent menin inhibitor, in patients with metastatic non-small cell lung cancer (NSCLC), pancreatic cancer (PDAC), and colorectal cancer (CRC) with activating KRAS mutations

Abstract Background: BMF-219 is a selective covalent inhibitor of menin, a transcriptional regulator of oncogenic signaling pathways in multiple cancers, that inhibits the menin/MYC interaction and downregulates the expression of MYC and MYC target genes, including KRAS. Mechanism of Action (hypothesis): In addition to MYC disruption, inhibition of the Menin-MLL complex by BMF-219 alters JunD genomic function, a crucial factor for KRAS-driven tumorigenesis. Inhibition of the Menin-MLL complex suppresses expression of Rasgrf1, which is essential for generation of the active RAS-GTP conformation of KRAS, activation of downstream pathways, and tumorigenesis. Preclinically, BMF-219 shows sustained potent abrogation of menin-dependent oncogenic signaling. BMF-219 exerts pan-mutant KRAS anticancer activity that is independent of the specific KRAS-activating mutation. Methods: COVALENT-102 (NCT05631574) is a prospective, open-label, multicenter, dose finding study evaluating the safety, tolerability, and clinical activity of escalating doses of BMF-219 administered daily in patients with unresectable, locally advanced, or metastatic NSCLC (Cohort 1), PDAC (Cohort 2) & CRC (Cohort 3) with activating KRAS mutations who have received standard therapy. All indications as a group will follow a 3+3 dose escalation design. BMF-219 will be administered orally daily as continuous therapy as 28-days treatment cycle until progression or intolerability/unacceptable toxicity. Following conclusion of the dose-escalation, each indication will enroll patients in expansion cohorts independently to obtain further safety and efficacy data. Eligible patients include those with any KRAS mutation & (Cohort 1) stage IIIB/IV NSCLC with 2-4 prior lines of therapy including immune checkpoint inhibitors (ICI) &/or platinum-based chemo ± bevacizumab with ECOG PS 0-2; (Cohort 2) stage III/IV PDAC with ≥ 1 prior line of therapy including either FOLFIRINOX or gemcitabine/nab-paclitaxel, ECOG PS 0-1; or (Cohort 3) stage III/IV CRC with ≥ 1 prior line of therapy including FOLFOX or FOLFIRI ± bevacizumab (prior ICI if MSI-H/dMMR), ECOG PS 0-2. Patients must have documented progression & measurable disease as defined by RECIST 1.1. Patients with prior KRAS inhibitor exposure are eligible. Key exclusion criteria include symptomatic &/untreated CNS metastasis, prior menin inhibitor therapy, and clinically significant cardiovascular disease. The primary objective is to determine the optimal biological dose (OBD)/recommended Phase 2 dose (RP2D) of BMF-219 monotherapy. Secondary objectives include further evaluation of safety & tolerability, characterization of the pharmacodynamics and pharmacokinetics of BMF-219, and efficacy based on duration of response (DOR) & disease control rate (DCR). Assessment of progression-free survival (PFS), overall survival (OS) & time to response (TTR) are part of the exploratory endpoints. The first patient in the study is anticipated to be dosed in Q4 of 2022. Citation Format: Stacey A. Cohen, Christos Fountzilas, David Sommerhalder, Sandip Patel, Ai Benson, Kai He, Apar Ganti, Alex Spira, Bhagyashree (Kelshikar) Yadav, Alex Cacovean, Steve Morris, Tom Butler, David Hong. COVALENT-102: A phase 1/1b dose finding study of BMF-219, an oral covalent menin inhibitor, in patients with metastatic non-small cell lung cancer (NSCLC), pancreatic cancer (PDAC), and colorectal cancer (CRC) with activating KRAS mutations [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 A003.

Abstract PR10: IK-595, a MEK-RAF complex inhibitor, obviates CRAF mediated resistance resulting in superior RAS/MAPK pathway inhibition and anti-tumor activity in RAS/RAF altered cancers

Abstract Alterations in the RAS/RAF/MEK/ERK pathway are the most common drivers of oncogenesis. Although MEK is a clinically validated cancer target and several MEK inhibitors have been approved by the FDA, their clinical utility is limited to BRAFV600 mutant cancers and NF1 mutant neurofibromas. The limitations of these approved MEK inhibitors are inherently related to a narrow therapeutic window and their inability to completely inhibit MAPK signaling. Specifically, RAS mutant cancer cells have a stronger dependency on CRAF for MAPK signal transduction. The MEK inhibition and the subsequent reduction of phosphorylated ERK (pERK) by the approved MEK inhibitors triggers the relief of the ERK-dependent negative feedback control on CRAF, leading to CRAF mediated MEK reactivation and pERK rebound. In addition, CRAF has kinase independent functions that contribute to its anti-tumor apoptotic activities. We developed IK-595, a potent inhibitor of the MEK-RAF complex, to overcome the limitations of available MEK inhibitors. IK-595 stabilizes the MEK-BRAF and MEK-CRAF protein complexes both biochemically and in cells. By trapping MEK in an inactive complex with RAF, it blocks RAF-dependent MEK phosphorylation, limiting CRAF mediated MEK reactivation that hinders the efficacy of approved MEK inhibitors in RAS mutant tumors. Importantly, IK-595 demonstrates persistent and further inhibition of ERK phosphorylation than trametinib and VS-6766. This translates to potent inhibition of cell proliferation across a variety of MAPK pathway altered cancer cell lines, including cells with KRAS and NRAS mutations and RAF alterations. Moreover, IK-595 synergizes with KRASG12C, pan-RAF, and mTOR inhibitors in vitro, leading to enhanced anti-proliferation in cancer cells. In addition, IK-595 inhibits MEK and ERK phosphorylation and ERK target gene DUSP6 expression in vivo, driving robust anti-tumor efficacy in multiple KRAS and NRAS mutant, and CRAF amplified, mouse tumor models. Lastly, the pharmacokinetic properties of IK-595 provide a broader therapeutic window compared to available MEK inhibitors. Together, IK-595 is a novel MEK-RAF complex inhibitor that prolongs pathway inhibition, minimizing the potential for resistance, while providing an optimal therapeutic window for patients. Citation Format: Eric Haines, Michael Burke, Rachel Catterall, Victor De Jesus, Bin Li, Joseph D. Manna, George Punkosdy, Oksana Zavidij, Sarah R. Wessel, Grace Werosta, Jill Cavanaugh, Sheila Newhouse, Aravind Basavapathruni, Lan Xu, Sergio Santillana, X. Michelle Zhang, Sabine K. Ruppel. IK-595, a MEK-RAF complex inhibitor, obviates CRAF mediated resistance resulting in superior RAS/MAPK pathway inhibition and anti-tumor activity in RAS/RAF altered cancers [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 PR10.

Abstract B006: Novel direct RAS inhibitors for pancreatic cancer

Abstract RAS oncogenes are frequently activated by mutations in pancreatic and lung cancer, where they appear to act as driving mutations. This study examines the activity of a series of novel direct RAS inhibitors with a predicted unique interaction region. We have used in silico library screening followed by Medicinal Chemistry optimization to develop the compounds. We have validated the agents using Microscale Thermophoresis to quantify binding to recombinant RAS protein as well as NMR analysis of the drug/RAS complex. We used 3D growth inhibition assays in mutant RAS cell lines and protein-based RAS signaling assays to quantify and characterize the action of the family of inhibitors. We have identified compounds that bind wild type K-RAS and H-RAS but exhibit preferential binding to the K-RAS-G12D and KRAS-G12C mutants. We can suppress the association of mutant RAS protein with its effector RAF-1 in treated cells. We also observe suppression of mutant RAS signaling and inhibition of 3D cell growth of mutant RAS cell lines with the agents. As the compound family are predicted to bind to a different site than either AMG-510 (K-RAS G12C specific) or MRTX-1133 (K-RAS G12D specific), agents we have also tested co-operative activity with these drugs. Our compounds enhanced the effects of MRTX-1133 against K-RAS G12D cells and had a similar effect on AMG-510 in K-RAS G12C cell lines. These agents may serve as novel anti-RAS therapeutics and may have potential to enhance the activity or suppress resistance to AMG-510 and MRTX-1133. Citation Format: Geoff Clarke, Tariq Arshad, Howard Donninger, Becca von Baby, Rachel Ferrill, Mike Sabo, Joe Burlison, John Trent. Novel direct RAS inhibitors for pancreatic cancer [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 B006.

Abstract A019: The role of KRAS ubiquitination in lung cancer heterogeneity

Abstract Lung cancer is the most frequent cancer with an aggressive clinical course and high mortality rates. About 30% of non-small lung cancer is driven by activating mutations in KRAS (Kirsten rat sarcoma virus). KRAS signaling is tightly controlled through a series of post-transcriptional mechanisms, whereas dysregulation of KRAS activity is translated into heterogeneous clinical behavior. We, and others, have recently implicated leucine zipper-like transcriptional regulator 1 (LZTR1), an adaptor of the CUL3-containing E3 ligase complex, in the control of RAS ubiquitination. Heterozygous loss of LZTR1 is found in one-third of lung adenocarcinomas and co-occurs with oncogenic KRAS mutations, suggesting that LZTR1 loss could contribute to lung cancer by modulating KRAS signaling and affecting the drug response. Both WT and oncogenic KRAS mutant protein levels were modulated by LZTR1 according to a Global protein screen (GPS) scoring regulators of KRAS stability. LZTR1 also directly ubiquitinated mutant KRAS in lung cancer cells. To assess the impact of LZTR1 on KRAS-driven lung cancer, we then used the Kras-G12D mouse model. We found that either homozygous, or heterozygous knockout of Lztr1 cooperates with oncogenic KRAS and promotes tumor initiation and progression at early stages of lung cancer development. The observed phenotype arises from the changes of the immune tumor microenvironment mediated by the differential activation of RAL-B (Ras-related protein Ral-b) signaling in the absence of LZTR1. These results shed a novel light on the crosstalk between dysregulation of KRAS ubiquitination, paracrine communication exerted by the cancer cells through secreted cytokines, and the immune response in lung cancer, which has thwarted the effectiveness of therapy to date. Citation Format: Tonci Ivanisevic. The role of KRAS ubiquitination in lung cancer heterogeneity [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 A019.

Abstract IA20: The impact of RAS inhibition on tumor immune evasion

Abstract The approval of two KRAS G12C mutant-specific inhibitory drugs, sotorasib and adagrasib, has markedly improved the treatment of lung cancer patients harbouring KRAS G12C oncogenic mutations. However, development of acquired drug resistance is very common after initial responses, and impact on overall survival is small. Additional therapies will therefore need to be combined with KRASG12C inhibitors if long-term cures are to be achieved. Due to the immunosuppressive nature of the signaling network controlled by oncogenic KRAS, targeted KRAS G12C inhibition can indirectly affect anti-tumour immunity. This has served as a rationale for combination with immune checkpoint blockade (ICB), which we have shown leads to additional therapeutic benefit in immunogenic/hot, but not immune evasive/cold, pre-clinical lung tumour models. However, in clinical trials in KRAS G12C mutant lung cancer, combination of KRAS G12C inhibitors with PD-(L)1 blockade has yet to show improved outcome, either due to toxicities or lack of efficacy, possibly linked to prior progression on immunotherapy. Study of the response of KRAS G12C mutant lung tumours to KRAS G12C inhibitory drugs using spatial and multi-omic technologies has highlighted the role of particular populations of immune cells in the tumor microenvironment in impeding immune attack on the tumor. In immune evasive lung cancer, following KRAS G12C inhibitor treatment a community of cells is identified within the tumor containing dendritic cells, CD8+ T cells and dying tumor cells, which appears to function as an antigen presentation hub. This community is restrained by T reg cells, whose coordinate targeting markedly improves the impact of KRAS G12C inhibitors. In an immunogenic/hot mouse model of KRAS G12C mutant lung cancer, tertiary lymphoid structures are seen along with tumor-binding antibodies, which target endogenous retrovirus (ERV) envelope glycoproteins on the tumor cells. ERV-targeting B cell responses are amplified by ICB in both humans and mice, and by targeted KRAS G12C inhibition in the murine model. ERV-reactive antibodies exert anti-tumour activity that extend survival in the murine model and ERV expression predicts the outcome of ICB in human lung adenocarcinoma. Rational, mechanism-based exploitation of the impact of KRAS inhibition on tumor immune evasion provides opportunities for successful combination therapy of RAS mutant cancers. Citation Format: Julian Downward. The impact of RAS inhibition on tumor immune evasion [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 IA20.

Abstract B034: Determination of KRAS- and ERK-regulated phosphoproteomes in KRAS-mutant cancers

Abstract Direct inhibitors of mutationally activated KRAS are currently under intense preclinical and clinical development, with one KRASG12C mutant-selective inhibitor approved. However, treatment-associated resistance to KRASG12C inhibitors has been reported, with ~60% of relapsed patients acquiring mutations in signaling components both upstream and downstream, and at the level of RAS itself, that led to reactivation of RAF-MEK-ERK and PI3K-AKT effector pathways. Unexpectedly, we found that ectopic expression of constitutively activated MEK1, ERK1 or ERK2, but not AKT1, drove near-complete resistance to direct inhibitors of KRASG12C or KRASG12D in KRAS-mutant pancreatic ductal adenocarcinoma (PDAC). Despite comprehensive studies, how ERK supports KRAS-dependent cancer growth remains poorly understood. Therefore, we focused on delineating the ERK-dependent phosphoproteome. We treated a panel of six KRAS-mutant PDAC cell lines acutely (1 h) and long-term (24 h) with the highly selective ERK1/2 inhibitor SCH772984. Our proteomics analyses identified 5,117 phosphosites on 2,252 proteins significantly dysregulated by ERK inhibition. We first compared our PDAC ERK phosphoproteome with a recent compendium of published direct/indirect ERK substrates identified in non-PDAC cells and found, surprisingly, only 12% overlap. Thus, our dataset substaintially extends the complexity of ERK-regulated phosphoproteins, in part, reflecting a pancreatic cancer selective profile. To elucidate the kinase network that drives our PDAC ERK-dependent phosphoproteome, we utilized our newly described global atlas of kinase-substrate specificities and reported kinase-substrate interaction datasets. This revealed a highly dynamic kinome dominated by ERK at 1 h, then dominated by ERK-regulation of CDK1-6 cell cycle components and RHO GTPase signaling. Next, we established the subcellular distribution of the PDAC ERK phosphoproteome, then evaluated data from DepMap, and found enrichment of nuclear ERK substrates that displayed strong dependencies in PDAC. We also determined the KRASG12C-regulated phosphoproteome in pancreatic, lung, and colorectal cancer cells using the KRASG12C selective inhibitor MRTX1257. We used our global atlas of kinase-motif specificities and ERK-regulated phosphoproteome to determine KRAS-regulated signaling pathways in KRASG12C mutant cancers. We found a high correlation between KRAS- and ERK-regulated phosphorylations, primarily driven by CDK substrates. However, we also noted key differences, principally in DNA damage response pathways not identified in our ERK-regulated phosphoproteome. Finally, we performed a high-throughput drug sensitivity and resistance screen of (DSRT) comprised of >500 clinically actionable drugs in combination with a KRASG12C inhibitor, and found ERK inhibitors as top hits. In summary, our studies establish a comprehensive profile of KRAS-ERK signaling output that may define new therapeutic targets for targeting KRAS- and ERK-dependent cancer growth. Citation Format: Jennifer E. Klomp, Jeff A. Klomp, Nathaniel J. Diehl, Cole A. Edwards, Kristina Drizyte-Miller, Priya S. Hibshman, Runying Yang, Alexis J. Morales, Khalilah E. Taylor, Mariaelena Pierobon, Emanuel F. Petricoin III, Johnson L. Jared, Emily M. Huntsman, Tomer M. Yaron, Markus Vähä-Koskela, Laura E. Herring, Alex W. Prevatte, Natalie K. Barker, Lee M. Graves, Wennerberg Krister, Lewis C. Cantley, James G. Christensen, Adrienne D. Cox, Channing J. Der, Clint A. Stalnecker. Determination of KRAS- and ERK-regulated phosphoproteomes in KRAS-mutant cancers [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 B034.

Abstract A002: Early changes in circulating cell free KRAS G12C as a possible blood-based response biomarker for adagrasib in non-small cell lung cancer (NSCLC). </title>

Abstract Introduction: While tumor imaging has a fundamental role in drug development as a determinant of clinical response it may not always be a rapid measure of treatment effect. Changes in plasma ctDNA levels, on the other hand, has the potential to be a more readily available measure of response. Here we report on early plasma response measurements of KRAS G12C ctDNA by digital droplet PCR (ddPCR) in a Phase 2 trial of Adagrasib, a potent, orally available, small molecule covalent inhibitor of KRAS G12C, in patients with advanced non-small cell lung cancer with KRAS G12C mutation. Methods/Results: To study the timing of plasma response, we performed serial ddPCR on 60 KRAS G12C-mutant NSCLC patients that participated in cohort A of the KRYSTAL-1 phase 2 clinical trial. Cohort A evaluated adagrasib at 600 mg orally BID in patients with NSCLC previously treated with platinum-based chemotherapy. We analyzed the change in ctDNA levels at 2 specific intervals: between cycles 1 and 2 (i.e. initial change) and at start of cycles 4. Of 60 pts, 7 pts were excluded because of missing C1D1 draws, 13 pts were excluded for non-detectable KRAS G12C level at C1D1 and 1 patient was excluded because of a missing C2D1 draw leaving us with 39 evaluable patients for plasma response assessment. We found that most of the response in ctDNA could be seen during the initial 3-4 week treatment period, well before the first scan at 6-8 weeks. 38 pts (97.4%) showed any decrease in plasma levels from baseline levels. 35 patients (89.7%) show a decrease >90% and 33 pts (84.6%) achieved complete clearance at C2D1. Patients with complete ctDNA clearance at C2D1 showed improved ORR (60.6% vs 33.3%), while ctDNA clearance at C4 was associated with an improved survival (12.6 months vs 5.4 months) and PFS (HR 0.3). Conclusion: Our results support using early plasma response of KRAS G12C assessed at 2-3 weeks to inform the interpretation of initial imaging performed at 6-8 weeks Citation Format: Cloud Paweletz, Grace A. Heavey, Yanan Kuang, Thian Kheoh, Kenna Anderes, James Christensen, Pasi A. Jänne. Early changes in circulating cell free KRAS G12C as a possible blood-based response biomarker for adagrasib in non-small cell lung cancer (NSCLC). </title> [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 A002.

Abstract A001: RAS:RAF proximity ligation assay may predict response to KRASG12C inhibitors in NSCLC

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.