RAS-mutant Cells Research Articles

Abstract 3280: Combination of MYC and class IIa HDAC inhibition potentiates anti-tumor efficacy in non-small cell lung cancer

Abstract Lung cancer is the leading cause of cancer-related mortality among both men and women in the United States. Immune checkpoint blockade has emerged as a promising therapy for advanced non-small cell lung cancer (NSCLC); however, only a subset of patients responds to this treatment regimen. Therefore, combinatorial therapeutic strategies to enhance anti-tumor immunity and efficacy of immunotherapy are in urgent need. Our group and others have demonstrated the potential of MYC inhibition in NSCLC to render the tumor microenvironment (TME) more immune permissive by upregulating antigen presentation machinery and chemokines that recruit effector lymphocytes. We performed a dedicated reanalysis of published transcriptome data from two distinct cancer types, prostate and lung, which were treated with novel MYC inhibiting agents, MYCi975 and Omomyc, respectively. These data revealed augmentation of two class IIa histone deacetylases (HDACs), HDAC5 and HDAC9, upon MYC inhibition. In addition to the suggested interaction between MYC and Class IIa HDACs derived from our transcriptional analyses, class IIa HDACs have an established role in tumorigenesis, angiogenesis, and poor prognosis of cancer patients, thus implying that therapeutic benefits could be derived from dual inhibition of MYC and class IIa HDAC. Elucidation of the basal relationship between Class IIa HDACs and the immune microenvironment of NSCLC was derived through correlative analyses of TCGA Lung adenocarcinoma and squamous carcinoma RNA-seq data. These data revealed a conserved positive correlation across non-small cell lung cancer between class IIa HDAC RNA levels, Treg score, and Treg/CD8 ratio by immune deconvolution analysis. Evaluation of combinatorial treatment efficacy of MYCi plus Class IIa HDACi was undertaken using 19 NSCLC cell lines, which recapitulate the mutational and histological landscape of NSCLC. These data identified a genotype-driven drug synergy, wherein EGFR mutant cell lines presented as resistant, and Ras mutant cell lines presented as sensitive to our combination drug paradigm. In summary, we defined a positive association between Class IIa HDAC expression and Treg score in TCGA NSCLC samples, suggesting a possibility of immune-modulation via class IIa HDAC inhibition. Furthermore, we identified transcriptional augmentation of class IIa HDAC induced by MYC repression, which indicates a potential novel therapeutic opportunity. Finally, we determined that inhibition of class IIa HDACs potentiates MYC inhibitor-driven anti-tumor efficacy across a diverse set of NSCLC cell lines. Citation Format: Jina Park, Michelle Vaz, Ray-Whay C. Yen, Stephen B. Baylin, Michael J. Topper. Combination of MYC and class IIa HDAC inhibition potentiates anti-tumor efficacy in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3280.

Antitumor activity of KIN-2787, a next-generation pan-RAF inhibitor, in combination with MEK inhibition in preclinical models of human NRAS mutant melanoma.

e15099 Background: NRAS mutations which activate MAPK signaling represent oncogenic driver alterations in approximately 20% melanoma cases in the US. NRAS mutant melanomas are uniquely dependent upon CRAF rather than BRAF for activation of downstream MEK/ERK signaling. In BRAF mutant melanoma, approved RAF-targeted therapies are commonly used in combination with a MEK inhibitor which provides clinical benefit by inhibition of two targets within the oncogenic MAPK signaling pathway. Emerging data with pan-RAF inhibitors in early clinical development suggests benefit with and without combined MEK inhibition, yet no approved targeted therapy exists for NRAS mutant melanoma patients. KIN-2787 is a novel, orally available pan-RAF inhibitor designed to be effective in RAF-dependent cancers, regardless of isoform. Methods: Kinome profiling was evaluated by radiometric enzyme assay at Reaction Biology across 688 kinases (including wild type, atypical, and mutant). Cellular activity was assessed by suppression of downstream MAPK pathway signaling and cell growth inhibition in human tumor cell lines. Combination cell growth inhibition studies were performed in 9x5 dose matrices with KIN-2787 and binimetinib, respectively. Extended cell growth inhibition effects were assessed by Incucyte imaging. In vivo KIN-2787 and combination efficacy was evaluated in NRAS mutant xenograft models. Results: Kinome profiling of KIN-2787 revealed exquisite selectivity with only 2 of 669 non-RAF family kinases inhibited > 75% at 1 M KIN-2787 and retained ̃10x and 70x selectivity window against those two kinases, DDR1 and p38b, respectively, relative to RAF kinases. We previously reported KIN-2787 activity across BRAF, NRAS, and KRAS mutant tumor cell lines with greatest sensitivity in Class II and III dimer-driven BRAF models. Here, we evaluated NRAS mutant, BRAF WT melanoma for combination potential with binimetinib. Melanoma tumor cell lines bearing NRAS hotspot mutations demonstrated synergistic benefit with KIN-2787 combined with binimetinib. Daily KIN-2787 plus binimetinib treatment in NRAS mutant melanoma xenograft models resulted in significant tumor growth inhibition benefit relative to either agent alone and was associated with added MAPK pathway biomarker suppression. Conclusions: KIN-2787 is a highly selective, potent, next-generation, pan-RAF inhibitor with activity across BRAF and RAS mutant human tumor cell models. Preclinical in vitro and in vivo studies using KIN-2787 in combination with binimetinib demonstrated significant combination benefit in NRAS mutant melanoma models. Taken together with its unique selectively, these data support use of KIN-2787 in combination therapy in this patient segment. A Phase 1/1b dose escalation and expansion clinical trial evaluating the safety and efficacy of KIN-2787 is ongoing (NCT04913285).

Synthetic lethal kinases in Ras/p53 mutant squamous cell carcinoma.

The oncogene Ras and the tumor suppressor gene p53 are frequently co-mutated in human cancer and mutations in Ras and p53 can cooperate to generate a more malignant cell state. To discover novel druggable targets for cancers carrying co-mutations in Ras and p53, we performed arrayed, kinome focused siRNA and oncology drug phenotypic screening utilizing a set of syngeneic Ras mutant squamous cell carcinoma (SCC) cell lines that also carried co-mutations in selected p53 pathway genes. These cell lines were derived from SCCs from carcinogen-treated inbred mice which harbored germline deletions or mutations in Trp53, p19Arf, Atm, or Prkdc. Both siRNA and drug phenotypic screening converge to implicate the phosphoinositol kinases, receptor tyrosine kinases, MAP kinases, as well as cell cycle and DNA damage response genes as targetable dependencies in SCC. Differences in functional kinome profiles between Ras mutant cell lines reflect incomplete penetrance of Ras synthetic lethal kinases and indicate that co-mutations cause a rewiring of survival pathways in Ras mutant tumors. This study describes the functional kinomic landscape of Ras/p53 mutant chemically-induced squamous cell carcinoma in both the baseline unperturbed state and following DNA damage and nominates candidate therapeutic targets, including the Nek4 kinase, for further development.

Validation of a small molecule inhibitor of PDE6D-RAS interaction with favorable anti-leukemic effects

RAS mutations prevalent in high-risk leukemia have been linked to relapse and chemotherapy resistance. Efforts to directly target RAS proteins have been largely unsuccessful. However, since RAS-mediated transformation is dependent on signaling through the RAS-related C3 botulinum toxin substrate (RAC) small GTPase, we hypothesized that targeting RAC may be an effective therapeutic approach in RAS mutated tumors. Here we describe multiple small molecules capable of inhibiting RAC activation in acute lymphoblastic leukemia cell lines. One of these, DW0254, also demonstrates promising anti-leukemic activity in RAS-mutated cells. Using chemical proteomics and biophysical methods, we identified the hydrophobic pocket of phosphodiester 6 subunit delta (PDE6D), a known RAS chaperone, as a target for this compound. Inhibition of RAS localization to the plasma membrane upon DW0254 treatment is associated with RAC inhibition through a phosphatidylinositol-3-kinase/AKT-dependent mechanism. Our findings provide new insights into the importance of PDE6D-mediated transport for RAS-dependent RAC activation and leukemic cell survival.

Insights Into Ferroptosis, a Novel Target for the Therapy of Cancer.

Ferroptosis is a new form of programmed cell death (PCD) characterized by an excess iron accumulation and subsequent unbalanced redox states. Ferroptosis is different from the already reported PCD and has unique morphological features and biochemical processes. Ferroptosis was first elaborated by Brent R. Stockwell’s lab in 2012, in which small molecules erastin and RSL-3 induce PCD in Ras mutant cell lines. Ferroptosis involves various physiological processes and occurrence of disease and especially shows strong potential in cancer treatment. Development of small molecule compounds based on Stockwell’s research was found to kill cancer cells, and some FDA-approved drugs were discovered to result in ferroptosis of cancer cells. Radiotherapy and checkpoint therapy have been widely used as a treatment for many types of cancer. Recently, some papers have reported that chemotherapy, radiotherapy, and checkpoint therapy induce ferroptosis of cancer cells, which provides new strategies for cancer treatment. Nevertheless, the limitless proliferation of tumor cells and the lack of cell death mechanisms are important reasons for drug resistance for tumor therapy. Therefore, we reviewed the molecular mechanism of ferroptosis and sensitivity to ferroptosis of different cancer cells and tumor treatment strategy.

Abstract P252: IMM-1-104: a novel, oral, selective dual-MEK inhibitor that displays broad antitumor activity and high tolerability across RAS and RAF mutant tumors in vivo

Abstract Background: Inappropriate activation of the MAPK pathway, often stemming from mutations in RAS or RAF, represents one of the most common oncogenic events in human cancer. Therefore, MEK1 and MEK2 (MEK), which lie downstream of RAS and RAF but upstream of ERK, have represented an attractive drug target for over two decades. Unfortunately, first generation MEK inhibitors have been limited by pathway reactivation events and serious on-target drug toxicities that restrain clinical utility, especially in patients with RAS mutant tumors. We sought to develop a new approach to MEK inhibition that would be more effective in RAS mutant tumors and with improved tolerability. IMM-1-104 is a novel dual-MEK inhibitor that is designed to disrupt phosphorylation of MEK and subsequently prevent activation of ERK1 and ERK2 (ERK). IMM-1-104’s dual-MEK mechanism resists RAF activation of MEK, and its short drug half-life allows for chronic dosing while maintaining a near-zero drug trough for improved tolerability. Materials & Methods: IMM-1-104 was profiled across a series of preclinical experiments to assess its physicochemical and drug-like properties. Cell-free and cell-based in vitro as well as in vivo characteristics were evaluated, including four independent in vivo pharmacology rodent studies in lung, colon and skin tumor models. Results: IMM-1-104 is a highly selective, orally bioavailable, non-ATP competitive, allosteric dual-MEK inhibitor. At drug exposures up to 1 micromolar (uM) in cell-free and in situ kinome screens, thermodynamic interactions and altered activity levels were observed for MEK1 and MEK2. At higher drug exposures up to 10 uM, IMM-1-104 also thermodynamically interacted with RAF1 (CRAF) and prompted reduction of KSR1 and KSR2 activation markers. IMM-1-104 displayed dual-MEK activity (i.e., RAS mutant tumor cell reductions in both ERK and MEK phosphorylation) across multiple human tumor cell-based models including A549 (KRAS-G12S) lung, A375 (BRAF-V600E) and SK-MEL-2 (NRAS-Q61R) melanoma. Pharmacokinetic studies in rodent models revealed a drug plasma half-life for IMM-1-104 of approximately 1.3 hours. In vivo tumor pharmacology studies in A549 and A375 achieved tumor stasis (i.e., 85% to 95% Tumor Growth Inhibition) with regressions observed in Colon-26 and SK-MEL-2. Conclusions: The dual-MEK mechanism and short half-life of IMM-1-104 has proven to be broadly active and well-tolerated in multiple RAS and RAF mutant preclinical tumor models in rodents. IMM-1-104 drives deep, cyclic inhibition of the MAPK pathway (improving tolerability) while resisting pathway bypass mechanisms (improving activity). Our collective data suggest that RAS and RAF mutant tumor cells are not able to tolerate periods of deep but cyclic MAPK pathway inhibition. Overall, these results are consistent with on and off signaling events that can significantly impact cell fate decisions (i.e. signaling dynamics). Citation Format: Peter J. King, Kevin D. Fowler, Sarah E. Kolitz, Scott Barrett, Benjamin J. Zeskind, Brett M. Hall. IMM-1-104: a novel, oral, selective dual-MEK inhibitor that displays broad antitumor activity and high tolerability across RAS and RAF mutant tumors in vivo [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P252.

Abstract LBA007: Discovery and characterization of oncogenic KRAS:RAF1 conformational modulators with in vitro and in vivo MAPK inhibition

Abstract Oncogenic mutations in the RAS family are the most frequently occurring among human cancers. The recent development of KRAS-targeted covalent inhibitors display efficacy in KRAS-mutant tumors; however, this approach is limited to KRASG12C mutant cancers. Here, we describe a novel drug discovery program to target the full-scope of mutant RAS-driven cancers through allosteric inhibition of the oncogenic KRAS-RAF1 signaling complex. To identify novel allosteric inhibitors, we developed a second harmonic generation (SHG) assay to detect conformational changes in the KRAS-RAF1 membrane-bound complex. Fully processed farnesylated and methylated KRAS4b-G12D protein (KRASG12D-FMe) was complexed with the RAF1 N-terminal RAS-binding domain (RBD) and cysteine rich domain (CRD) and immobilized on a phosphatidylserine-enriched bilayer. The RAF1RBD-CRD protein was rendered SHG-active by chemical conjugation and tethered to the bilayer by KRASG12D-FMe, thus replicating the physiological complex orientation. Ligands that disrupted or altered the orientation of the complex relative to the surface were identified from a curated diversity library of 60,000 chemical compounds based on % SHG signal change relative to baseline. Validated hit compounds were selected for SAR characterization and development wherein newly synthesized molecules were assayed by SHG and inhibition of cellular ERK phosphorylation by HTRF. Quanta (QTX) molecules were confirmed to rapidly inhibit ERK phosphorylation across multiple RAS-mutant cell lines by Western blot. Biochemical cellular target engagement studies reveal inhibition of RAF1:BRAF dimerization downstream of allosteric modulation of the KRAS:RAF1 signaling complex. Mass spectrometry with a photoactive derivative identified modified residues clustered along the KRAS:RAF1 interface, thus providing structural evidence for this unique mechanism of action. In addition to MAPK inhibition, we observe inhibition of cellular proliferation across mutant RAS cell lines. Cellular growth assays in the presence of QTX molecules combined with the SHP-2 inhibitor, RMC4550, displayed synergistic growth inhibition, providing a rationale combination therapy. Moreover, RAS-mutant cell-line derived xenograft tumors treated with QTX inhibitors elicited significant tumor growth inhibition and dose-dependent reductions in the pharmacodynamic MAPK targets, P-ERK and DUSP6, which is consistent with anti-tumor activity. This research illustrates a promising approach towards the development of mutant RAS-targeted inhibitors with a unique mechanism of action and target engagement. Citation Format: Elizabeth Donohue Vo, Juan Luengo, Hong Lin, Jerry Chen, Ben Reid, Brooke McDonough, Norman Fultang, Jillian Silva, Cameron Pitt. Discovery and characterization of oncogenic KRAS:RAF1 conformational modulators with in vitro and in vivo MAPK inhibition [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr LBA007.

Exploring Better Strategies for RAS Mutation-Associated EGFR-Targeted Resistance in Colorectal Cancer: From the Perspective of Cancer Community Ecology

RAS is the most common mutated gene in colorectal cancer (CRC), and its occurrence is associated with primary and acquired resistance to anti-epidermal growth factor receptor (EGFR) blockade. Cancer community ecology, such as the competitive exclusion principle, is a valuable focus and would contribute to the understanding of drug resistance. We have presented several articles on RAS mutant clonal evolution monitoring during anti-EGFR treatment in CRC. In these articles, the availability of serially collected samples provided a unique opportunity to model the tumor evolutionary process from the perspective of cancer community ecology in those patients upon treatment. In this perspective article, we presented a theoretical basis and evidence from several experimental or phase II clinical trials for the contemporary application of ecological mechanisms in CRC treatment. In general, a reduction in targetable RAS wild-type cells to a maximum tolerated extent, such as continuous treatment, might lead to the competitive release of inextirpable RAS mutant cells and cancer progression. A full understanding of subclonal competition might be beneficial in managing CRC. Several ecological strategies, including anti-EGFR treatment reintroduced at an appropriate point of time for RAS mutant patients, intermittent treatment instead of continuous treatment, the appropriate sequence of nonselective targeted therapy, and combination therapy, were proposed.

Dual Inhibition of Histone Deacetylases and the Mechanistic Target of Rapamycin Promotes Apoptosis in Cell Line Models of Uveal Melanoma

PurposeOver 90% of uveal melanomas harbor pathogenic variants of the GNAQ or GNA11 genes that activate survival pathways. As previous studies found that Ras-mutated cell lines were vulnerable to a combination of survival pathway inhibitors and the histone-deacetylase inhibitor romidepsin, we investigated whether this combination would be effective in models of uveal melanoma.MethodsA small-scale screen of inhibitors of bromodomain-containing protein 4 (BRD4; OTX-015), extracellular signal-related kinase (ERK; ulixertinib), mechanistic target of rapamycin (mTOR; AZD-8055), or phosphoinositide 3-kinase (PI3K; GDC-0941) combined with a clinically relevant administration of romidepsin was performed on a panel of uveal melanoma cell lines (92.1, Mel202, MP38, and MP41) and apoptosis was quantified by flow cytometry after 48 hours. RNA sequencing analysis was performed on Mel202 cells treated with romidepsin alone, AZD-8055 alone, or the combination, and protein changes were validated by immunoblot.ResultsAZD-8055 with romidepsin was the most effective combination in inducing apoptosis in the cell lines. Increased caspase-3 and PARP cleavage were noted in the cell lines when they were treated with romidepsin and mTOR inhibitors. RNA sequencing analysis of Mel202 cells revealed that apoptosis was the most affected pathway in the romidepsin/AZD-8055-treated cells. Increases in pro-apoptotic BCL2L11 and decreases in anti-apoptotic BIRC5 and BCL2L1 transcripts noted in the sequencing analysis were confirmed at the protein level in Mel202 cells.ConclusionsOur data suggest that romidepsin in combination with mTOR inhibition could be an effective treatment strategy against uveal melanoma due in part to changes in apoptotic proteins.

Overview of Ferroptosis and Synthetic Lethality Strategies.

Ferroptosis, a term first proposed in 2012, is iron-dependent, non-apoptotic regulatory cell death induced by erastin. Ferroptosis was originally discovered during synthetic lethal screening for drugs sensitive to RAS mutant cells, and is closely related to synthetic lethality. Ferroptosis sensitizes cancer stem cells and tumors that undergo epithelial−mesenchymal transition and are resistant to anticancer drugs or targeted therapy. Therefore, ferroptosis-inducing molecules are attractive new research targets. In contrast, synthetic lethal strategies approach mechanisms and genetic abnormalities that cannot be directly targeted by conventional therapeutic strategies, such as RAS mutations, hypoxia, and abnormalities in the metabolic environment. They also target the environment and conditions specific to malignant cells, have a low toxicity to normal cells, and can be used in combination with known drugs to produce new ones. However, the concept of synthetic lethality has not been widely adopted with ferroptosis. In this review, we surveyed the literature on ferroptosis-related factors and synthetic lethality to examine the potential therapeutic targets in ferroptosis-related molecules, focusing on factors related to synthetic lethality, discovery methods, clinical application stages, and issues in drug discovery.

Abstract 2269: The spindle assembly checkpoint as a therapeutic vulnerability in RIT1-mutant lung adenocarcinoma

Abstract Standard care of lung cancer is moving away from chemotherapy in favor of personalized approaches based on specific mutations in each tumor. Genome-sequencing studies have identified somatic mutations in the small GTPase RIT1 (Ras-like in all tissues) in lung adenocarcinoma patients. Of the identified mutations, M90I is the most recurrent. Thousands of patients per year are diagnosed with RIT1-driven cancer, but treatment options are limited. A targeted therapy for RIT1-driven disease could greatly improve patient outcomes. Little is known about how RIT1 drives cellular transformation. To genetically dissect signaling pathways downstream of RIT1, we performed a genome-wide CRISPR/Cas9 screen in isogenic PC9 lung adenocarcinoma cells in which cell survival is dependent on expression of RIT1M90I. We found that RIT1-mutant cells were highly dependent on components of the Spindle Assembly Checkpoint (SAC), including the Aurora kinases (A and B). The SAC is a surveillance mechanism that ensures proper chromosome segregation during mitosis. We hypothesized that RIT1M90I weakened the SAC and rendered cells vulnerable to loss of mitotic regulators. To explore this, we performed time-lapse imaging in HeLa H2B-GFP cells stably expressing RIT1M90I. In parental cells, the median duration of mitosis was 70.5 min (95% CI = 63 – 82 min), while in RIT1M90I-mutant cells, this was reduced to 48 min (95% CI = 45 – 51 min). Mitotic index was unaffected, suggesting that RIT1M90I does not regulate mitotic entry. This difference in mitotic timing was eliminated by treatment with reversine, an inhibitor that abolishes the SAC, demonstrating that RIT1M90I perturbs mitotic timing at the level of the SAC. If RIT1M90I weakens the SAC, we would expect higher prevalence of chromosomal abnormalities (such as chromosome bridges) in RIT1M90I-mutant cells. Indeed, analysis of fixed-cell populations indicated that RIT1M90I-mutant cells showed higher prevalence of mitotic abnormalities (79% of RIT1M90I-mutant cells compared to 46% of parental cells, 95% CI= 15 – 53). These data support the hypothesis that RIT1M90I weakens the SAC and imply that further SAC perturbation could be lethal. To explore this, we performed a small molecule screen of 160 clinically-relevant inhibitors in PC9-RIT1M90I and PC9-KRASG12V cells. Intriguingly, RIT1M90I-mutant cells were more sensitive than RAS-mutant cells to alisertib and barasertib, inhibitors of Aurora kinase A and B, respectively. Furthermore, alisertib or barasertib treatment abrogated soft agar colony formation in RIT1M90I-mutant cells but not in RAS-mutant cells. Together with our functional genomic analysis, we propose a model whereby expression of RIT1M90I weakens the SAC, thereby accelerating mitosis, increasing the abundance of mitotic abnormalities, and rendering cells vulnerable to genetic knockdown of SAC genes or small molecule inhibition of Aurora kinases A/B. Citation Format: Amanda Riley, Athea Vichas, Naomi T. Nkinsi, Phoebe C. Parrish, Shriya Kamlapurkar, Alice H. Berger. The spindle assembly checkpoint as a therapeutic vulnerability in RIT1-mutant lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2269.

Abstract 2373: Expression of exosomal let-7g in biofluids and outcome in colon cancer patient treated with anti-EGFR therapy

Abstract Introduction: Monoclonal antibodies against the Epidermal Growth Factor Receptor (EGFR) such as cetuximab or panitumumab are used for the treatment of metastatic colorectal cancer (mCRC) patients. Unfortunately, most patients develop resistance against these therapies within months. Several studies have shown that aberrations in the RAS pathway are responsible for resistance. However, even in metastases that are refractory to anti-EGFR treatment a significant fraction of RAS wild-type (wt) cells remain. These findings suggest a cross-talk between RAS mutant and wt cells in mediating resistance in the wt compartment. Methods: Mouse and patient-derived organoids from mCRC as well as CRC cell lines were used to test the contribution of extracellular vesicles in mediating resistance in RAS wt cells. Using conditioned media, transfection experiments and liquid biopsies (plasma and urine) from patients differential expression of the let-7g microRNA was demonstrated in microvesicles from cetuximab sensitive and resistant cells. Changes in expression of let-7g were further analyzed by in-situ hybridization in tissues. Results: Conditioned media from RAS mutant organoids rendered RAS wt organoids resistant against cetuximab treatment. Basal let-7g expression from pre-treatment plasma and urine samples of RAS wt patients correlated with clinical outcome and changes in let-7g circulating levels mirrored clinical behavior. In-situ hybridization in tissues confirmed changes in expression of the let-7g microRNA observed in plasma and urine samples. Conclusions: Our data suggest that let-7g microRNA might function as a paracrine mediator of anti-EGFR resistance and might be exploited as a non-invasive biomarker of resistance to cetuximab treatment. Further work is ongoing to characterize the molecular mechanisms underpinning let-7g mediated effect on anti-EGFR sensitivity in RAS wt CRC cells. Citation Format: Jens C. Hahne, Andrea Lampis, Michele Ghidini, Margherita Ratti, Chiara Senti, Rodolfo Passalacqua, Luciano Cascione, Chiara Braconi, Owen Sansom, Matteo Fassan, Nicola Valeri. Expression of exosomal let-7g in biofluids and outcome in colon cancer patient treated with anti-EGFR therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2373.

Occurence of RAS reversion in metastatic colorectal cancer patients treated with bevacizumab.

Background: A disappearance of RAS mutations in the plasma of about 50% of mCRCs (metastatic colorectal cancers) treated with bevacizumab-based chemotherapy has been reported. Our aim was to evaluate the same issue at tissue level.Materials and Methods: Using next-generation sequencing and real-time PCR approaches, we characterized the primary tumor (PT) and paired liver metastases in 28 RAS mutant mCRCs. Patients were subdivided into 3 treatment groups: 1) bevacizumab plus chemotherapy; 2) chemotherapy alone; 3) any systemic therapy (control group). In groups 1 and 2, liver metastases were resected after removal of PT and subsequent neoadjuvant systemic therapy.Results: RAS mutant alleles are at the same percentage in PT and liver metastases in the control group, while a significant reduction of the level of RAS mutations was detected in 57.1% of cases in group 1 and in 8.3% of cases in group 2. Differences among groups are statistically significant (p = 0.038).Conclusions: Most of mCRC patients treated with bevacizumab-containing regimens experience a strong reduction of RAS mutant cells, suggesting bevacizumab as particularly active against RAS mutant cells. This finding might have potential therapeutic implications, as anti-EGFR could be reconsidered in primarily RAS mutant patients reverted to a wild-type status after bevacizumab exposure.

Inhibition of RAF dimers: it takes two to tango.

The RAS-regulated RAF–MEK1/2–ERK1/2 pathway promotes cell proliferation and survival and RAS and BRAF proteins are commonly mutated in cancer. This has fuelled the development of small molecule kinase inhibitors including ATP-competitive RAF inhibitors. Type I and type I½ ATP-competitive RAF inhibitors are effective in BRAFV600E/K-mutant cancer cells. However, in RAS-mutant cells these compounds instead promote RAS-dependent dimerisation and paradoxical activation of wild-type RAF proteins. RAF dimerisation is mediated by two key regions within each RAF protein; the RKTR motif of the αC-helix and the NtA-region of the dimer partner. Dimer formation requires the adoption of a closed, active kinase conformation which can be induced by RAS-dependent activation of RAF or by the binding of type I and I½ RAF inhibitors. Binding of type I or I½ RAF inhibitors to one dimer partner reduces the binding affinity of the other, thereby leaving a single dimer partner uninhibited and able to activate MEK. To overcome this paradox two classes of drug are currently under development; type II pan-RAF inhibitors that induce RAF dimer formation but bind both dimer partners thus allowing effective inhibition of both wild-type RAF dimer partners and monomeric active class I mutant RAF, and the recently developed “paradox breakers” which interrupt BRAF dimerisation through disruption of the αC-helix. Here we review the regulation of RAF proteins, including RAF dimers, and the progress towards effective targeting of the wild-type RAF proteins

LXH254, a Potent and Selective ARAF-Sparing Inhibitor of BRAF and CRAF for the Treatment of MAPK-Driven Tumors.

Targeting RAF for antitumor therapy in RAS-mutant tumors holds promise. Herein, we describe in detail novel properties of the type II RAF inhibitor, LXH254. LXH254 was profiled in biochemical, in vitro, and in vivo assays, including examining the activities of the drug in a large panel of cancer-derived cell lines and a comprehensive set of in vivo models. In addition, activity of LXH254 was assessed in cells where different sets of RAF paralogs were ablated, or that expressed kinase-impaired and dimer-deficient variants of ARAF. We describe an unexpected paralog selectivity of LXH254, which is able to potently inhibit BRAF and CRAF, but has less activity against ARAF. LXH254 was active in models harboring BRAF alterations, including atypical BRAF alterations coexpressed with mutant K/NRAS, and NRAS mutants, but had only modest activity in KRAS mutants. In RAS-mutant lines, loss of ARAF, but not BRAF or CRAF, sensitized cells to LXH254. ARAF-mediated resistance to LXH254 required both kinase function and dimerization. Higher concentrations of LXH254 were required to inhibit signaling in RAS-mutant cells expressing only ARAF relative to BRAF or CRAF. Moreover, specifically in cells expressing only ARAF, LXH254 caused paradoxical activation of MAPK signaling in a manner similar to dabrafenib. Finally, in vivo, LXH254 drove complete regressions of isogenic variants of RAS-mutant cells lacking ARAF expression, while parental lines were only modestly sensitive. LXH254 is a novel RAF inhibitor, which is able to inhibit dimerized BRAF and CRAF, as well as monomeric BRAF, while largely sparing ARAF.

Scaffold association factor B (SAFB) is required for expression of prenyltransferases and RAS membrane association

Inhibiting membrane association of RAS has long been considered a rational approach to anticancer therapy, which led to the development of farnesyltransferase inhibitors (FTIs). However, FTIs proved ineffective against KRAS-driven tumors. To reveal alternative therapeutic strategies, we carried out a genome-wide CRISPR-Cas9 screen designed to identify genes required for KRAS4B membrane association. We identified five enzymes in the prenylation pathway and SAFB, a nuclear protein with both DNA and RNA binding domains. Silencing SAFB led to marked mislocalization of all RAS isoforms as well as RAP1A but not RAB7A, a pattern that phenocopied silencing FNTA, the prenyltransferase α subunit shared by farnesyltransferase and geranylgeranyltransferase type I. We found that SAFB promoted RAS membrane association by controlling FNTA expression. SAFB knockdown decreased GTP loading of RAS, abrogated alternative prenylation, and sensitized RAS-mutant cells to growth inhibition by FTI. Our work establishes the prenylation pathway as paramount in KRAS membrane association, reveals a regulator of prenyltransferase expression, and suggests that reduction in FNTA expression may enhance the efficacy of FTIs.

Pan-RAF Inhibition Shows Anti-Leukemic Activity in RAS-Mutant Acute Myeloid Leukemia Cells and Potentiates the Effect of Sorafenib in Cells with FLT3 Mutation.

Simple SummaryWe demonstrate that the pan-RAF inhibitor LY3009120 induces apoptosis and inhibits proliferation in AML cells harboring RAS or FLT3 mutations through action on the RAS/RAF/MEK/ERK and the AKT/mTOR pathways. Notably, pan-RAF inhibition combined with Ara-C overcomes drug resistance mediated by bone marrow-derived mesenchymal stem cells. Furthermore, the combination of LY3009120 and tyrosine kinase inhibition with sorafenib appears to synergistically increase apoptosis in AML cells carrying FLT3-ITD mutation.RAF molecules play a critical role in cell signaling through their integral impact on the RAS/RAF/MEK/ERK signaling pathway, which is constitutively activated in a sizeable subset of acute myeloid leukemia (AML) patients. We evaluated the impact of pan-RAF inhibition using LY3009120 in AML cells harboring mutations upstream and downstream of RAF. LY3009120 had anti-proliferative and pro-apoptotic effects and suppressed pERK1/2 levels in leukemic cells with RAS and FLT3 mutations. Using reverse protein phase array analysis, we identified reductions in the expression/activation of cell signaling components downstream of RAF (activated p38) and cell cycle regulators (Wee1/cyclin B1, Cdc2/Cdk1, activated Rb, etc.). Notably, LY3009120 potentiated the effect of Ara-C on AML cells and overcame bone marrow mesenchymal stromal cell-mediated chemoresistance, with RAS-mutated cells showing a notable reduction in pAKT (Ser473). Furthermore, the combination of LY3009120 and sorafenib resulted in significantly higher levels of apoptosis in AML cells with heterozygous and hemizygous FLT3 mutations. In conclusion, pan-RAF inhibition in AML using LY3009120 results in anti-leukemic activity, and combination with Ara-C or sorafenib potentiates its effect.

Healthy Donors Harbor Memory T Cell Responses to RAS Neo-Antigens.

Simple SummaryMemory T cells from healthy individuals respond to stimulation with peptides derived from cancer-specific RAS mutations, thus suggesting that healthy individuals have been challenged with RAS mutations earlier in life.The RAS mutations are the most frequently occurring somatic mutations in humans, and several studies have established that T cells from patients with RAS-mutant cancer recognize and kill RAS-mutant cells. Enhancing the T cell response via therapeutic cancer vaccination against mutant RAS results in a clinical benefit to patients; thus, T cells specific to RAS mutations are effective at battling cancer. As the theory of cancer immuno-editing indicates that healthy donors may clear malignantly transformed cells via immune-mediated killing, and since T cells have been shown to recognize RAS-mutant cancer cells, we investigated whether healthy donors harbor T-cell responses specific to mutant RAS. We identified strong and frequent responses against several epitopes derived from the RAS codon 12 and codon 13 mutations. Some healthy donors demonstrated a response to several mutant epitopes, and some, but not all, exhibited cross-reactivity to the wild-type RAS epitope. In addition, several T cell responses were identified against mutant RAS epitopes in healthy donors directly ex vivo. Clones against mutant RAS epitopes were established from healthy donors, and several of these clones did not cross-react with the wild-type epitope. Finally, CD45RO+ memory T cells from healthy donors demonstrated a strong response to several mutant RAS epitopes. Taken together, these data suggest that the immune system in healthy donors spontaneously clears malignantly transformed RAS-mutant cells, and the immune system consequently generates T-cell memory against the mutations.

Abstract IA25: Targeting MEK1/2 inhibitor resistance in RAS-mutated cancers

Abstract Although the RAF>MEK>ERK MAP kinase pathway is key to the development of many RAS-mutated cancers, efforts to target this pathway with pharmacologic inhibitors have failed to deliver clinical benefit to patients. Here we show that inhibition of RAS>RAF>MEK>ERK signaling in RAS-mutated cancer cell lines elicits autophagy, a process of cellular recycling that protects cancer cells from the potentially cytotoxic effects of RAF>MEK>ERK pathway inhibition. Furthermore, combined inhibition of MEK1/2 plus autophagy displays synergistic antiproliferative effects against cell lines in vitro and promotes regression of xenografted patient-derived tumors in mice. Finally, treatment of a cancer patient with the combination of trametinib plus hydroxychloroquine resulted in a partial, but nonetheless striking, disease response. These data suggest that this combination therapy may represent a novel strategy to target RAS-driven malignancies such as melanoma, lung, and pancreatic cancer. Citation Format: Conan Kinsey, Soledad Camolotto, Amelie Boespflug, Katrin Gullien, Amanda Truong, Mona Foth, Jill Shea, Michael Seipp, Jeffrey Yap, Lance Burrell, David Lum, Jonathan Whisenant, Courtney Cavalier, Kaitren Rehbein, Stephanie Cutler, Kajsa Afotler, Alana Welm, Bryan Welm, Courtney Scaife, Eric Snyder, Martin McMahon. Targeting MEK1/2 inhibitor resistance in RAS-mutated cancers [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr IA25.

Abstract IA18: The PI3K isoforms in myeloid leukemia and hematopoietic stem cells

Abstract The Class IA PI3 kinase isoforms (p110α, β, and δ) transduce many growth factor signals that are important for the proliferation, differentiation, and self-renewal of hematopoietic stem cells (HSCs). Mutations in growth factor receptors or RAS proteins are commonly observed in patients with acute myeloid leukemia (AML), leading to activation of the PI3K/AKT pathway. Therefore, PI3K inhibition is an attractive therapeutic strategy for a large subset of AML patients. We previously reported that p110α is dispensable for HSC function, suggesting that redundancy exists between the Class IA isoforms in HSCs (Gritsman et al., J Clin Invest 2014). However, we have identified a specific role for p110α in RAS-mutated myeloid leukemia. Furthermore, we found that the p110α-selective inhibitor BYL-719 can sensitize RAS-mutated leukemic cells to the MEK inhibitor MEK-162. While PI3K inhibitors have multiple clinical indications, including in hematologic malignancies, it is still unclear whether PI3K plays an important role in normal HSC function. Upon environmental stresses like chemotherapy or infection, quiescent HSCs must enter the cell cycle to re-establish homeostasis and promote emergency myelopoiesis. To test for redundancy between p110α and p110δ in HSCs, we generated p110α and p110δ double knockout (DKO) mice, with germline deletion of p110δ and conditional deletion of p110α. DKO mice have leukopenia, anemia, and decreased numbers of lymphoid-primed multipotent progenitors (LMPPs) in the bone marrow, though HSC numbers are unchanged. In competitive repopulation assays, B-cell maintenance was severely impaired, while the myeloid and T-cell lineages were relatively preserved. This suggests that HSC function is not impaired at steady state. We performed transcriptome analysis of DKO, p110δ, and p110α KO HSCs and LMPPs after bone marrow transplantation. Gene set enrichment analysis revealed downregulation of gene sets associated with cell cycle progression. Interestingly, we also observed negative enrichment of inflammatory response gene sets in both p110δ KO and DKO HSCs and LMPPs. To examine the roles of p110δ and α in the hematopoietic stress response, we injected p110δ, DKO, and WT mice with 5-fluorouracil. We observed significantly decreased survival of 5-FU-treated DKO mice due to impaired hematopoietic recovery, associated with the failure of HSCs to enter the cell cycle. Consistent with this finding, we also observed a decrease in myeloid reconstitution by DKO HSCs in secondary competitive transplantation, suggesting that p110α and p110δ play redundant roles in emergency myelopoiesis. We also observed defects in downstream signaling in DKO HSCs and progenitors in response to IL1β or TNFα stimulation. Our results suggest that p110α and δ act in a redundant fashion to transduce specific inflammatory signals in HSPCs in response to hematopoietic stress. Our results have important implications for the use of PI3K inhibitors in combination with chemotherapy and in other hematopoietic stress conditions. Citation Format: Shayda Hemmati, Taneisha Sinclair, Meng Tong, Boris Bartholdy, Rachel Okabe, Kristina Ames, Leanne Ostrodka, Tamanna Haque, Imit Kaur, Anupriya Agarwal, Jean Zhao, Thomas Roberts, Kira Gritsman. The PI3K isoforms in myeloid leukemia and hematopoietic stem cells [abstract]. In: Proceedings of the AACR Special Conference on Targeting PI3K/mTOR Signaling; 2018 Nov 30-Dec 8; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(10_Suppl):Abstract nr IA18.