Ras Isoforms Research Articles

Inhibition of farnesylation of Ras-GTPases ameliorates inflammation-induced loss of endothelial barrier integrity and leukocyte transmigration

Abstract Background and Aims The family of small GTPases (Rho- and Ras-GTPases) is known to regulate endothelial cytoskeleton dynamics and hence barrier integrity. The role of Rho GTPases (RhoA and Rac1) in endothelial barrier integrity is well characterized; however, little is known about the role of Ras-GTPases. The activity of small GTPases is regulated by several mechanisms, including post-translational prenylation (farnesylation or geranylgeranylation). The Ras-GTPases are preferentially post-translationally farnesylated by farnesyl transferases (FTs). The aim of the present study was to investigate whether inhibition of farnesylation of Ras-GTPases protects loss of endothelial barrier integrity induced by inflammatory mediators. Methods and Results Treatment of human primary endothelial cells (ECs; HUVEC and lung microvascular ECs) with pharmacological inhibitor of farnesyl transferases (FTIs), LB42708 (LB) and tipifarnib, stabilized basal endothelial barrier function (albumin-flux) and abrogated thrombin-induced hyperpermeability in a concentration- and time-dependent manner reaching maximum at a concentration of 2 mmol/L after 12 h of incubation. These concentrations of the FTIs reduced farnesylation of all the Ras isoforms but not the geranylgeranylation of Rho GTPases. Likewise, LB abrogated the TNFa-induced leucocyte transendothelial migration (Trans-well assay). Interestingly, FTIs treatment caused an enhanced translocation of VE-cadherin to cell-cell junctions (confocal microscopy) without exerting any effect on the actin cytoskeleton or endothelial contractile machinery; mainly regulated by Rho GTPases. The Ca2+-switch experiments demonstrated an inhibition of VE-cadherin internalization. These data were reproduced by lentiviral-mediated stable over-expression of the prenylation-dead mutants of Ras isoforms but not RhoA or Rac1. Conclusion The novel data of the present study demonstrate that FTIs protect endothelial barrier function against inflammatory mediator-induced endothelial hyperpermeability. We propose that FTIs are novel drug candidates for the treatment of edematous conditions (such as lung edema) where endothelial barrier integrity is compromised.

Structural insights into the complex of oncogenic KRas4BG12V and Rgl2, a RalA/B activator.

About a quarter of total human cancers carry mutations in Ras isoforms. Accumulating evidence suggests that small GTPases, RalA, and RalB, and their activators, Ral guanine nucleotide exchange factors (RalGEFs), play an essential role in oncogenic Ras-induced signalling. We studied the interaction between human KRas4B and the Ras association (RA) domain of Rgl2 (Rgl2RA), one of the RA-containing RalGEFs. We show that the G12V oncogenic KRas4B mutation changes the interaction kinetics with Rgl2RA The crystal structure of the KRas4BG12V: Rgl2RA complex shows a 2:2 heterotetramer where the switch I and switch II regions of each KRasG12V interact with both Rgl2RA molecules. This structural arrangement is highly similar to the HRasE31K:RALGDSRA crystal structure and is distinct from the well-characterised Ras:Raf complex. Interestingly, the G12V mutation was found at the dimer interface of KRas4BG12V with its partner. Our study reveals a potentially distinct mode of Ras:effector complex formation by RalGEFs and offers a possible mechanistic explanation for how the oncogenic KRas4BG12V hyperactivates the RalA/B pathway.

A new ferrocene derivative blocks K-Ras localization and function by oxidative modification at His95.

Ras proteins are membrane-bound GTPases that regulate essential cellular processes at the plasma membrane (PM). Constitutively active mutations of K-Ras, one of the three Ras isoforms in mammalian cells, are frequently found in human cancers. Ferrocene derivatives, which elevate cellular reactive oxygen species (ROS), have shown to block the growth of non-small cell lung cancers harboring oncogenic mutant K-Ras. Here, we tested a novel ferrocene derivative on the growth of pancreatic ductal adenocarcinoma and non-small cell lung cancer. Our compound, which elevated cellular ROS levels, inhibited the growth of K-Ras-driven cancers, and abrogated the PM binding and signaling of K-Ras in an isoform-specific manner. These effects were reversed upon antioxidant supplementation, suggesting a ROS-mediated mechanism. We further identified that K-Ras His95 residue plays an important role in this process, and it is putatively oxidized by cellular ROS. Together, our study demonstrates that the redox system directly regulates K-Ras/PM binding and signaling via oxidative modification at the His95, and proposes a role of oncogenic mutant K-Ras in the recently described antioxidant-induced growth and metastasis of K-Ras-driven cancers.

Toll-like receptor 2 selectively modulates Ras isoforms expression in Leishmania major infection

Leishmania infection of macrophages results in altered Ras isoforms expression and Toll-like receptor-2 (TLR2) expression and functions. Therefore, we examined whether TLR2 would selectively alter Ras isoforms’ expression in macrophages. We observed that TLR2 ligands- Pam3CSK4, peptidoglycan (PGN), and FSL- selectively modulated the expression of Ras isoforms in BALB/c-derived elicited macrophages. Lentivirally-expressed TLR1-shRNA significantly reversed this Ras isoforms expression profile. TLR2-deficient L. major-infected macrophages and the lymph node cells from the L. major-infected mice showed similarly reversed Ras isoforms expression. Transfection of the macrophages with the siRNAs for the adaptors- Myeloid Differentiation factor 88 (MyD88) and Toll-Interleukin-1 Receptor (TIR) domain-containing adaptor protein (TIRAP)- or Interleukin-1 Receptor-Associated Kinases (IRAKs)- IRAK1 and IRAK4- significantly inhibited the L. major-induced down-regulation of K-Ras, and up-regulation of N-Ras and H-Ras, expression. The TLR1/TLR2-ligand Pam3CSK4 increased IL-10 and TGF-β expression in macrophages. Pam3CSK4 upregulated N-Ras and H-Ras, but down-regulated K-Ras, expression in C57BL/6 wild-type, but not in IL-10-deficient, macrophages. IL-10 or TGF-β signaling inhibition selectively regulated Ras isoforms expression. These observations indicate the specificity of the TLR2 regulation of Ras isoforms and their selective modulation by MyD88, TIRAP, and IRAKs, but not IL-10 or TGF-β, signaling.

Exploring switch II pocket conformation of KRAS(G12D) with mutant-selective monobody inhibitors

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 selective to KRAS(G12D) over KRAS(wild type) and other oncogenic KRAS mutations, as well as over the G12D mutation in HRAS and NRAS. 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 α3 helix, and captured this pocket in the most widely open form reported to date. Unlike other G12D-selective polypeptides reported to date, the monobody used its backbone NH group to directly recognize the side chain of KRAS Asp12, a feature that closely resembles that of a small-molecule inhibitor, MTRX1133. The monobody also directly interacted with H95, a residue not conserved in RAS isoforms. 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 monobody generated hundreds of functional and nonfunctional single-point mutants, which 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 further illustrate the plasticity of the S-II pocket, which may be exploited for the design of next-generation KRAS(G12D)-selective inhibitors.

A Call for Discovery and Therapeutic Development for Cutaneous Neurofibromas

A Call for Discovery and Therapeutic Development for Cutaneous Neurofibromas

A Pan-KRAS Inhibitor Impedes Common KRAS Oncoproteins and Tumor Growth.

A pan-KRAS inhibitor is selective for the inactive state of multiple KRAS mutants, sparing other RAS isoforms.

Comprehensive ctDNA analysis to identify genome-instability and actionable mutation landscape in gynecologic cancers.

e17503 Background: Gynaecology malignancies are the second most prevalent cancers in women worldwide with rapid progression, high relapse, and mortality. Although HRR pathway inhibitors can greatly benefit clinical outcomes, patients without HRR pathway mutations may remain unbenefited while being profiled for tissue DNA or with a small target gene panel. Compelling data suggest that plasma genotyping shows a wide diversity of cancer mutations along genome instability indicators compared to tumor tissue. Here, we analyzed the mutational landscape of ctDNA and tissue DNA (tDNA) obtained from gynecologic cancer patients. We demonstrate the clinical utility of a comprehensive gene panel to identify multiple actionable mutations and genome instability indicators from ctDNA samples. Methods: We retrospectively analyzed the mutational landscape of 22 ovarian and endometrial cancer patients using target-hybridization enrichment of ctDNA and tDNA. Libraries prepared using a custom-designed comprehensive gene panel OncoIndx, targeting 600 cancer-relevant exons including MSI and HRR pathway genes, were sequenced on the Illumina NGS platform in pair-end mode. Variant calling was performed with an in-house developed bioinformatics pipeline. Results: NGS analysis revealed a total of 127 mutations consisting SNVs (45.6 %), truncations (40.94 %), amplifications (4.72 %), splice variants (4.72 %), and frameshift (3.94 %). Genome-wide mutational analysis showed a slightly higher mean TMB (15.7) for endometrial tumors compared to ovarian samples (11.85). The mean HRD score (45 %) was high for 90 % of patients and corroborated well with the HRR pathway gene mutation. 30 % of patients without HRR gene mutations including BRCA 1/2 had a high average HRD score (43 %) (LOH/TAI/LST) and may qualify for PARP inhibitors (PARPi). Alterations in Ras isoforms (H, K, and N) were the most frequent (36 %) followed by TP53 and PI3K (32 %). At the pathway level, DDR gene-variants were most frequently followed by alterations in proliferative signaling genes. ctDNA showed a wider mutational landscape, including clinically significant mutations, compared to tDNA. Additionally, ctDNA analysis revealed the presence of novel variants of SUFU and KIT, which remain unexplored in the context of cancer stem cells and relapse. Conclusions: Comprehensive mutational landscape showed the presence of genome-wide instability and the presence of mutations in the HRR pathway. Our results suggest that patients with high HRD scores and Ras pathway instability may benefit from Ras pathway inhibitors-PARPi combination. Mutational landscapes obtained from ctDNA were significantly wider and revealed multiple actionable targets compared to tDNA suggesting ctDNA as a viable and informative alternative for genotyping of gynecological cancers.

Pan-KRAS inhibitor disables oncogenic signalling and tumour growth

KRAS is one of the most commonly mutated proteins in cancer, and efforts to directly inhibit its function have been continuing for decades. The most successful of these has been the development of covalent allele-specific inhibitors that trap KRAS G12C in its inactive conformation and suppress tumour growth in patients1–7. Whether inactive-state selective inhibition can be used to therapeutically target non-G12C KRAS mutants remains under investigation. Here we report the discovery and characterization of a non-covalent inhibitor that binds preferentially and with high affinity to the inactive state of KRAS while sparing NRAS and HRAS. Although limited to only a few amino acids, the evolutionary divergence in the GTPase domain of RAS isoforms was sufficient to impart orthosteric and allosteric constraints for KRAS selectivity. The inhibitor blocked nucleotide exchange to prevent the activation of wild-type KRAS and a broad range of KRAS mutants, including G12A/C/D/F/V/S, G13C/D, V14I, L19F, Q22K, D33E, Q61H, K117N and A146V/T. Inhibition of downstream signalling and proliferation was restricted to cancer cells harbouring mutant KRAS, and drug treatment suppressed KRAS mutant tumour growth in mice, without having a detrimental effect on animal weight. Our study suggests that most KRAS oncoproteins cycle between an active state and an inactive state in cancer cells and are dependent on nucleotide exchange for activation. Pan-KRAS inhibitors, such as the one described here, have broad therapeutic implications and merit clinical investigation in patients with KRAS-driven cancers.

CD40 induces selective routing of Ras isoforms to subcellular compartments.

Ras GTPases are central to cellular signaling and oncogenesis. The three loci of the Ras gene encode for four protein isoforms namely Harvey-Ras (H-Ras), Kirsten-Ras (K-Ras 4A and 4B), and Neuroblastoma-Ras (N-Ras) which share ~ 80% sequence similarity and used to be considered functionally redundant. The small molecule inhibitors of Ras lack specificity for the isoforms leading to widespread toxicity in Ras-targeted therapeutics. Ras isoforms' tissue-specific expression and selective association with carcinogenesis, embryonic development, and infection suggested their non-redundancy. We show that CD40, an antigen-presenting cell (APC)-expressed immune receptor, induces selective relocation of H-Ras, K-Ras, and N-Ras to the Plasma membrane (PM) lipid rafts, mitochondria, endoplasmic reticulum (ER), but not to the Golgi complex (GC). The two palmitoylated Ras isoforms-H-Ras and N-Ras-have a similar pattern of colocalization into the lipid-rich raft microdomain of the PM at early time points when compared to non-palmitoylated K-Ras (4B) with polylysine residues. CD40-induced trafficking of H-Ras and K-Ras to mitochondria and ER was found to be similar but different from that of N-Ras. Trafficking of all the Ras isoforms to the GC was independent of CD40 stimulation. The receptor-driven trafficking and spatial segregation of H-Ras, K-Ras, and N-Ras imply isoform-specific subcellular signaling platforms for the functional non-redundancy of Ras isoforms. PDB structures have been modified to illustrate various signaling proteins.

Abstract A016: Expanded RAS proteoform landscape in malignant cell lines revealed by top-down mass spectrometry

Abstract The RAS family of GTPases (HRAS, KRAS4A, KRAS4B, NRAS) provide a formidable challenge to standard proteomic workflows. Linking key N-terminal mutations (e.g., G12C, G13D) with C-terminal post-translational modifications (PTMs) on a given RAS isoform by proteolytic digestion and peptide-based analysis is further complicated by their high sequence identity, low endogenous abundance, and labile PTMs. Conversely, top-down mass spectrometry (TDMS), which measures intact and modified protein forms (proteoforms), can precisely identify and confidently localize mutations and PTMs within each RAS isoform sequence. Moreover, by combining immunoprecipitation with TDMS (IP-TDMS), endogenous RAS proteoforms can be isolated to near-homogeneity from malignant cell lines, detected at high signal-to-noise ratios via selected ion monitoring, and targeted for optimized MS2-based characterization to provide molecular detail simply unachievable by other proteomic methods. The NCI RAS Initiative has developed an optimized RAS proteoform assay incorporating IP-TDMS analysis on an Orbitrap Fusion Lumos mass spectrometer. We initially employed recombinant versions of each RAS isoform to determine the optimal targeted MS2 fragmentation (tMS2) parameters for sequence characterization and localization of endogenous PTMs. We next isolated FLAG-tagged KRAS4B -WT, -G12D, and -G12C expression constructs from HeLa cells to refine our liquid chromatography and tMS2 parameters while targeting stoichiometrically abundant KRAS4B proteoforms within each population. We then isolated FLAG-tagged HRAS-, KRAS4A-, KRAS4B-, and NRAS-G12V proteins from HeLa or Panc1 cells for further refinement of isoform-specific tMS2 parameters with emphasis on capturing unusual or labile PTMs (e.g. palmitoylation). This allowed us to visualize and directly compare the most abundant RAS isoform-specific proteoform populations within these cellular contexts. Complementary peptide-based analyses were performed on all samples to validate RAS isoform-specific PTM landscapes and facilitate detection of their respective endogenous versions. Finally, we applied our optimized IP-TDMS workflow to a panel of well-characterized malignant and RAS mutant cell lines with the goal of expanding our knowledge of the endogenous RAS proteoform landscape. In doing so, we identified a wealth of novel HRAS, KRAS4A, KRAS4B, and NRAS proteoforms bearing stoichiometrically abundant PTMs differing markedly from the established literature. We also performed direct comparisons between isoform- and mutation-specific RAS proteoforms, revealing clear indications of context dependence. These initial results further underscore the potential for top-down proteomics to broaden our understanding of RAS-dependent signaling within a range of cancer contexts. They also reveal that extensive investigations remain to be performed to elucidate the roles of RAS PTMs and proteoforms in normal and oncogenic signaling. Citation Format: Caroline J. DeHart, Robert A. D'Ippolito, Kanika Sharma, Nicole Fer, Brian Smith, Mackenzie Meyer, Scott Eury, Abigail Neish, Katie Powell, Vanessa Wall, William Burgan, Dominic Esposito, Anna E. Maciag, Frank McCormick, Dwight V. Nissley. Expanded RAS proteoform landscape in malignant cell lines revealed by top-down mass spectrometry [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 A016.

Abstract A018: A top-down proteomic assay to evaluate KRAS4B-compound engagement

Abstract The RAS family of GTPases (HRAS, KRAS, NRAS) continue to present formidable challenges to the design of compounds that successfully and specifically target oncogenic RAS mutant populations in cancer. Although recent advances have led to the successful development of inhibitors specific to KRAS G12C (such as Sotorasib [Amgen] and Adagrasib [Mirati Therapeutics]), ongoing efforts seek to develop additional targeted inhibitors for oncogenic mutants of KRAS. Development of new KRAS targeted inhibitors requires the understanding of how a mutation impacts the accessibility of key residues within the protein, along with how each candidate compound interacts with populations of mutant and wild-type proteins. Proteomic analyses, typically comprising peptide-based methods to confirm compound localization or quantify binding kinetics, represent a key validation step for each phase of the inhibitor development process. However, these methods may not always provide a clear picture of how effectively the compound binds to the protein, how specific the compound is to the target residue, and how concentration or incubation time may impact these factors. To address this, we have developed a novel assay to evaluate target engagement in vitro employing top-down proteomics, which entails the analysis of intact protein molecules and their modified forms (proteoforms). By analyzing intact labeled or compound-treated recombinant KRAS4B proteins, we can directly visualize and precisely characterize each species within a sample. This method allows us to easily detect nonspecific binding, identify targeting of incorrect residues, and characterize unanticipated compound reaction products within a short LC-MS run, all facilitated by targeted MS2 fragmentation. Moreover, we have developed complementary methods for RAS proteoform quantitation, allowing for the evaluation of compound engagement to all proteoforms with greater accuracy than traditional peptide-based methods. We first performed a proof-of-concept experiment using a panel of KRAS4B G12D_C118S proteins with selected residues modified to cysteine to evaluate reactivity to maleimide-biotin over time. We then applied our optimized top-down assay to determine the engagement of targeted covalent inhibitors Sotorasib and Adagrasib with KRAS WT, G12C, or G13C in both the active (GppNHp) and inactive (GDPβS) states. Finally, we selected three compounds from a large-scale screen against a UCSF Small Molecule Discovery Center compound library and evaluated each for specificity to KRAS4B G13C over KRAS4B WT and KRAS4B G12C. Our results show the concentration dependence of target engagement and directly map compound binding location(s) without disrupting the protein’s primary structure. Moreover, our ability to target discrete compound additions for top-down MS2 fragmentation provides context and order of preferential labeling of KRAS4B. Our hope is that this methodology may help accelerate the identification of new successful targeted inhibitors for KRAS and other RAS isoforms by the greater RAS community. Citation Format: Robert A. D'Ippolito, Caroline J. DeHart, Dana Rabara, Maria Abreu Blanco, Emily Alberico, Nitya Ramakrishnan, Stephanie Widmeyer, Simon Messing, David Turner, Michelle Arkin, Anna Maciag, Andrew Stephen, Dominic Esposito, Frank McCormick, Dwight V. Nissley. A top-down proteomic assay to evaluate KRAS4B-compound engagement [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 A018.

Abstract A037: Oncogenic RAS signals from lysosomes to activate mTORC1 in multiple myeloma

Abstract Oncogenic mutations of both NRAS and KRAS are common in multiple myeloma (MM), an incurable malignancy of plasma cells. However, the mechanisms of pathogenic RAS signaling in MM have remained enigmatic, and there is little evidence to support a dominant role for classical MAPK signaling downstream of RAS in this disease. We recently used an unbiased proteogenomic approach to dissect RAS signaling in MM and discover that mutant isoforms of RAS organized a signaling complex with the amino acid transporter, SLC3A2, and MTOR on lysosomes, which directly activated mTORC1 by co-opting amino acid sensing pathways (PMID: 36115844). To gain further insights into this novel mode of RAS signaling located away from the plasma membrane, we have employed mass spectrometry to characterize proteins associated with lysosomes isolated from MM cell lines. We observed that RAS isoforms, SLC3A2 and several components of the mTORC1 signalosome were purified with lysosomes, consistent with RAS activation of mTORC1 on lysosomes. To identify novel regulators of oncogenic RAS signaling at the lysosome, we used phospho-proteomics to identify proteins with significantly reduced levels of phosphorylation following acute inhibition of KRAS activity with the KRAS G12D inhibitor, MRTX1133, in a MM cell line bearing a KRAS G12D mutation. Many of these phospho-proteins were also associated with lysosomes, including MTOR, which had substantially reduced phosphorylation at the amino-acid dependent phosphorylation site S1261 following KRAS inhibition. Pathway analysis of proteins present in lysosomes and phosphorylated downstream of oncogenic KRAS showed enrichment for proteins that regulate intracellular trafficking. Among these proteins, we found that disruption of a RAB GAP essential for survival in RAS-dependent MM cells substantially reduced associations between RAS and MTOR and nearly abolished RAS-dependent mTORC1 activity. These data suggest that mutant RAS utilizes lysosomal resident proteins to coordinate the colocalization of itself with mTORC1 on lysosomes to drive pathogenic signaling in MM. More generally, these studies suggest that targeting the intracellular localization of RAS may be an alternative route to inhibit oncogenic RAS signaling in MM. Citation Format: Arnold Bolomsky, Ryan M. Young. Oncogenic RAS signals from lysosomes to activate mTORC1 in multiple myeloma [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 A037.

Abstract A032: Targeting RAS beyond KRAS, a review

Abstract RAS proteins belong to the family of GTPases and plays instrumental role in cellular growth and proliferation and dysregulation of RAS signalling is one of the key drivers of tumorigenesis. The RAS protein has four isoforms namely KRAS4A, KRAS4B, NRAS and HRAS with amino acid codons 12, 13 and 61 as common hotspots for RAS mutations. Each of these hotspot mutations appears across several cancer types, however each of them have been noted to have specific distribution across different tissues. For example, mutations in codon 12 of KRAS are most common in pancreatic, lung and colorectal cancer, NRAS mutations affecting Q61 and G12 are most prevalent in melanoma and haematological malignancies, respectively, and HRAS mutations are more frequently altered in thyroid, bladder and head and neck cancers. Substantial efforts have been made to develop small molecule inhibitors targeting KRASG12C, with demonstrated success in clinic. Early success with KRASG12C has prompted researchers targeting other RAS isoforms, such as H-RAS and N-RAS to address RAS mutated cancer burden. Discovery of pan-RAS monobody that binds to all RAS isoforms have opened new opportunities. Development of small molecule inhibitors of RAS membrane association is gaining potential as a therapeutic strategy to curb RAS signalling; Lonafarnib and Tipifarnib, inhibitors of farnesyltransferase that lipidate Ras to facilitate membrane localization, have shown effectiveness in HRAS mutated cancers and are in active clinical evaluation. Although the lack of a hydrophobic binding pocket in NRAS poses challenges to drug targeting, specific strategies such as amphiphile-mediated depalmitoylation to target the post-translational modification of NRAS and reduce its activity are being investigated. The wide variety of approaches to target the RAS signalling pathway, beyond KRAS, have resulted in a broadening patent landscape. While finding ways to specifically target RAS mutants remains a daunting challenge, herculean efforts to make clinically useful RAS-targeted drugs are beginning to provide a bounty of weapons to fight against RAS-driven tumors. Citation Format: Neetu Singh, Darren R. Tyson, Partha Pratim Sarma, Sathish Katike, Prashant K. Bhavar, Uday Kumar Surampudi. Targeting RAS beyond KRAS, a review [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 A032.

Abstract B023: Inhibition of RAS signaling and tumorigenesis through targeting novel vulnerabilities

Abstract RAS GTPases are important mediators of oncogenesis with nearly 30% of human tumors harboring mutant RAS proteins. However, pharmacological inhibition of RAS has proven challenging. We have employed Monobody technology to discover novel vulnerabilities in RAS that can be exploited to inhibit RAS signaling and tumorigenesis. Monobodies are single-domain synthetic binding proteins that achieve levels of affinity and selectivity similar to antibodies. In contrast to antibodies, Monobodies are fully functional in the reducing environment of the cytoplasm and thus are particularly suitable as genetically encoded “tool biologics”. We previously developed the NS1 Monobody that inhibited RAS by targeting the α4-α5 allosteric lobe to prevent RAS self-association and nanoclustering, and NS1 has become a widely used tool in the RAS research community. Following on this success, we sought to identify additional vulnerabilities in RAS. Based on our discovery that nucleotide-free RAS (apoRAS) inhibits PIK3C2B function, we assessed the feasibility of selectively targeting this state of RAS as an approach to inhibit oncogenic RAS function. Here, we have developed several Monobodies and extensively characterized one of them, R15. Although NS1 was agnostic to the nucleotide state of RAS, R15 bound exclusively to the apo state of all three RAS isoforms but did not interact with nucleotide-loaded RAS. When expressed in cells, R15 selectively inhibited the signaling and transforming activity of RAS mutants with elevated intrinsic nucleotide exchange rates (i.e., “fast exchange mutants”), such as G13D and Q61L. Surprisingly, R15 bound and inhibited RAS(G12D) mutants which are not reported to be fast exchange. Biochemical studies demonstrated that RAS captured with R15 from cell lysates was indeed nucleotide free, suggesting that R15 traps apoRAS and prevents nucleotide reloading. Finally, intracellularly expressed R15 selectively inhibited the tumor forming capacity of human cell lines driven by fast exchange RAS mutants but not RAS(G12V) in mouse xenografts. Thus, in contrast to conventional wisdom, our approach has established a new opportunity to selectively inhibit certain RAS mutants by targeting the apo state of RAS with drug-like molecules. Citation Format: Imran Kahn, Akiko Koide, Mariyam Zuberi, Gayatri Ketavarapu, Eric Denbaum, Kai Wen Teng, J. Matthew Rhett, Russell Spencer-Smith, G. Aaron Hobbs, Earnest Ramsay Camp, Shohei Koide, John P. O'Bryan. Inhibition of RAS signaling and tumorigenesis through targeting novel vulnerabilities [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 B023.

Abstract IA05: Uncovering new structural insights into RAS interactions with effectors and regulators

Abstract RAS proteins, which act as binary molecular switches, are implicated in approximately 20% of all cancer cases and are known to play a critical role in the initiation and progression of some of the deadliest cancers, such as lung, colon, and pancreatic cancers. When RAS proteins are in the GTP-bound state, they interact with various effector proteins, such as RAF Kinase, PI 3-Kinase, and RalGDS, leading to the activation of multiple signaling pathways in the cell. Our recent structural studies, including investigations into the KRAS-SIN1 (RBD-PH domain), KRAS-RAF1 (RBD-CRD), and SHOC2-MRAS-PP1C complex, have provided new insights into the vital role played by the switch-II and interswitch regions in the interaction between RAS and downstream effectors and regulators. These findings extend beyond the earlier observations that the switch-I region of RAS proteins alone plays a more significant role in RAS-effector interactions. Furthermore, research into the KRAS4a-SIN1 complex and the reported interaction between KRAS4a and hexokinase have given us a glimpse into the isoform-specific RAS-effector interaction. Finally, the investigation of the SHOC2-MRAS-PP1C complex has also revealed the crucial role played by other members of the RAS subfamily, such as MRAS, in RAF activation by canonical RAS isoforms. Collectively, these studies have shed new light on the mechanisms by which RAS interacts with downstream effectors and regulators. Citation Format: Dhirendra K. Simanshu. Uncovering new structural insights into RAS interactions with effectors and regulators [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 IA05.

Abstract B015: Wildtype RAS activity and PI3K signaling as new vulnerabilities in cells with acquired resistance to sotorasib

Abstract 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.

Abstract IA17: Use of RAS isoforms in nerve tumors

Abstract Neurofibromatosis Type I (NF1) is a common genetic disorder caused by mutations in the NF1 gene, which encodes a RAS-GAP. NF1 loss of function renders patients susceptible to tumors including NF1-/- benign neurofibromas, which can transform into atypical neurofibromas with NF1 and CDKN2A loss, and then lethal malignant peripheral nerve sheath tumors with NF1. CDKN2A, and PRC2 component loss. NF1 mutations are also common in many sporadic cancers. NF1 loss is known to increase or prolong wild type RAS activation, but the relative contribution of RAS paralogs (classical H-, N-, K-RAS and non-classical R-RAS, TC21, MRAS) to NF1 nerve tumorigenesis remains unknown. Our goal was to define the critical RAS paralog mediating the effect of NF1 protein deficiency due to NF1 mutations in neurofibromas and atypical neurofibromas, and to test whether targeting specific RAS paralogs might provide therapeutic strategies. Our data shows that KRAS is activated in RAS protein in NF1-deficient human and mouse Schwann cells (SCs), and in atypical Schwann cells. We find that a PKC agonist, prostratin, known to kill KRAS mutant cells, also selectively kills NF1 mutant Schwann cells in vitro and in mouse neurofibromas, and reduces tumor growth in a xenograft model of atypical neurofibroma. Prostratin acts through use of a subset of PKC isoforms. We anticipate that these findings can ultimately be used to develop an effective RAS targeting therapy for NF1 tumor prevention and treatment. Supported by: NIH R37 NS083580 and R01 NS12082 (N.R.), CancerFree KIDS (N.R.) and a Strauss Fellow Award (L.H.). Citation Format: Nancy Ratner, Liang Hu, Jay Pundavela, Jonathan A. Epstein. Use of RAS isoforms in nerve tumors [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 IA17.

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 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.