Combined MEK Research Articles

Drug-resistant BRAF V600E-mutant recurrent pleomorphic xanthoastrocytoma, CNS WHO Grade 3 successfully resolved with incidental discontinuation of combined BRAF and MEK inhibitor therapy

Background: Combination therapy with BRAF and MEK inhibitor holds promise for treating gliomas harboring the BRAF V600E mutation; however, the development of acquired resistance remains a challenge. Case Description: We describe a case of repeated recurrent BRAF-mutant pleomorphic xanthoastrocytoma (central nervous system World Health Organization grade 3) treated with combination therapy with BRAF and MEK inhibitor. The patient received dabrafenib (BRAF inhibitor) and trametinib (MEK inhibitor); however, she developed resistance to the combination therapy. Remarkably, incidental drug discontinuation contributed to the disappearance of the resistant tumor. The same phenomenon was repeatedly observed after that. Genetic analysis demonstrated that the resistant tumor had BRAF V600E amplification; the resistant tumor remained BRAF→MEK→ERK pathway dependent, and drug resistance might be due to elevated BRAF V600E expression. We speculated that ERK1/2 signal extremes caused by the discontinuation of the combination therapy affected the resistant tumor survival. Conclusion: This case study provides important insights into novel treatment strategies and their underlying mechanisms for gliomas with BRAF mutations.

Abstract B027: An Innovative cell-penetrating peptide-based RNAi Therapy to Overcome B-Raf/MEK Inhibitor Resistance in Melanoma

Abstract Small-molecule-targeted therapies have revolutionized cancer treatment, including for B-RafV600E-mutated melanoma, where B-Raf and combined B-Raf/MEK inhibitors (BRAFi/MEKi) prolong progression-free survival and overall survival. However, resistance to these therapies quickly develops, driven by mechanisms such as the expression of alternative spliced isoforms of B-RafV600E and mutated MEK1 variants. The need for novel strategies to overcome such resistance is critical. In this study, we developed and evaluated a novel RNAi-based therapeutic using our designed cell-penetrating peptide HE25 to specifically target and silence resistance-associated spliced isoforms of B-RafV600E, restoring the efficacy of existing treatments. In a recently published work (Tuttolomondo et al., 2024), we demonstrated that HE25 effectively reduced SARS-CoV-2 replication when complexed with siRNA targeting the virus's RNA-dependent RNA polymerase. HE25 facilitated siRNA internalization via multiple receptors involved in viral entry, including ACE2, integrins, and NRP1, through endocytosis, highlighting its versatility as a delivery platform with potential applications beyond cancer research. Initially, we established a vemurafenib-resistant A375 melanoma cell line (A375-VR), which revealed an alternatively spliced B-RafV600E isoform driving resistance to vemurafenib. Through cDNA Sanger sequencing, we confirmed that this alternatively spliced isoform lacks the regulatory domain, leading to constitutive B-Raf activation and rendering vemurafenib ineffective. Given these findings, we hypothesized that specifically silencing this isoform with our siRNA-HE25 complex could synergize with B-Raf inhibition, thereby overcoming vemurafenib resistance. The B-RafV600E-targeting siRNA encapsulated within HE25 significantly inhibited the proliferation of both A375 and A375-VR cells in vitro, with no toxic effects on non-cancerous melanocytes. In vivo, B-RafV600E siRNA-HE25 treatment significantly reduced tumor growth in A375 melanoma xenografts compared to a non-targeting siRNA control. We also developed A375-VTR cells resistant to combined vemurafenib and MEK inhibitor trametinib. This cell line also expressed the shortened B-RafV600E isoform and its silencing by the B-RafV600E siRNA/HE25 system was confirmed by Western blotting. Indeed, in A375-VTR cells, the combination of vemurafenib and B-RafV600E siRNA/HE25 was more effective than the combination of vemurafenib and trametinib. Our strategy holds promise for personalized cancer treatment by targeting resistance-related mutations or alternatively spliced isoforms. Future work will optimize this approach for broader clinical use and explore its efficacy in combination with existing therapies. These findings suggest that siRNA-based therapeutics via HE25 offer a promising solution for overcoming resistance in B-RafV600E-mutated melanoma and resistance mechanisms in other cancer types. This strategy should enable tailored treatments with broad applicability across cancer types. Citation Format: Martina Tuttolomondo, Mikkel Green Terp, Chiara Brienza, Morten Frier Gjerstorff, Henrik Jørn Ditzel. An Innovative cell-penetrating peptide-based RNAi Therapy to Overcome B-Raf/MEK Inhibitor Resistance in Melanoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B027.

Multiomic Analyses Reveal New Targets of Polycomb Repressor Complex 2 in Schwann Lineage Cells and Malignant Peripheral Nerve Sheath Tumors

Abstract Background Malignant peripheral nerve sheath tumors (MPNST) can arise from atypical neurofibromas (ANF). Loss of the polycomb repressor complex 2 (PRC2) is a common event. Previous studies on PRC2-regulated genes in MPNST used genetic addback experiments in highly aneuploid MPNST cell lines which may miss PRC2-regulated genes in NF1-mutant ANF-like precursor cells. A set of PRC2-regulated genes in human Schwann cells has not been defined. We hypothesized PRC2 loss has direct and indirect effects on gene expression resulting in MPNST, so we sought to identify PRC2-regulated genes in immortalized human Schwann cells (iHSCs). Methods We engineered NF1-deficient iHSCs with loss of function SUZ12 or EED mutations. RNA sequencing revealed 1,327 differentially expressed genes to define PRC2-regulated genes. To investigate MPNST pathogenesis we compared genes in iHSCs to consistent gene expression differences between ANF and MPNSTs. Chromatin immunoprecipitation sequencing was used to further define targets. Methylome and proteomic analyses were performed to further identify enriched pathways. Results We identified potential PRC2-regulated drivers of MPNST progression. Pathway analysis indicates many upregulated cancer-related pathways. We found transcriptional evidence for activated Notch and Sonic Hedgehog signaling in PRC2-deficient iHSCs. Functional studies confirm Notch signaling is active in MPNST cell lines, patient-derived xenografts, and transient cell models of PRC2 deficiency. A combination of MEK and γ-secretase inhibition shows synergy in MPNST cell lines. Conclusions We identified PRC2-regulated genes and potential drivers of MPNSTs. Our findings support the Notch pathway as a druggable target in MPNSTs. Our identification of PRC2-regulated genes and pathways could result in more novel therapeutic approaches.

Dual MAPK Inhibition Triggers Pro-inflammatory Signals and Sensitizes BRAF V600E Glioma to T Cell-Mediated Checkpoint Therapy.

BRAF V600E pediatric low-grade gliomas frequently transform into high-grade gliomas (HGG) and poorly respond to chemotherapy, resulting in high mortality. Although combined BRAF and MEK inhibition (BRAFi+MEKi) outperforms chemotherapy, ∼70% of BRAF V600E HGG patients are therapy resistant and undergo unbridled tumor progression. BRAF V600E glioma have an immune-rich microenvironment suggesting that they could be responsive to immunotherapy but effects of BRAFi+MEKi on anti-tumor immunity are unclear. Using patient tumor tissue before and after BRAFi+MEKi, two novel syngeneic murine models of BRAF V600E HGG, and patient-derived cell lines, we examined the effects of clinically relevant BRAFi+MEKi with dabrafenib and trametinib on tumor growth, cell states, and tumor-infiltrating T cells. We find that BRAFi+MEKi treatment: i) upregulated programmed cell death protein-1 (PD-1) signaling genes and PD-1 ligand (PD-L1) protein expression in murine BRAF V600E HGG by stimulating IFNγ and IL-27, ii) attenuated T cell activity by IL-23, IL-27 and IL-32 production, which can promote the expansion of regulatory T cells, and iii) induced glial differentiation linked to a therapy-resistant PD-L1+ compartment through Galectin-3 secretion by tumor cells. Murine BRAF V600E HGG shrinkage by BRAFi+MEKi is associated with the upregulation of interferon-gamma response genes, MHC class I/II expression, and antigen presentation and processing programs, indicative of increased anti-tumor immunity. Combined BRAFi+MEKi with therapeutic antibodies inhibiting the PD-1 and cytotoxic T-lymphocyte associated protein 4 (CTLA-4) immune checkpoints re-activate T cells and provide a survival benefit over single therapy in a T cell-dependent manner. The quadruple treatment overcame BRAFi+MEKi resistance by invigorating T cell-mediated anti-tumor immunity in murine BRAF V600E HGG. PD-L1 expression was elevated in human BRAF-mutant versus BRAF-wildtype glioblastoma clinical specimen, complementing experimental findings and suggesting translational relevance for patient care.

Marmoset and human trophoblast stem cells differ in signaling requirements and recapitulate divergent modes of trophoblast invasion

Early human trophoblast development has remained elusive due to the inaccessibility of the early conceptus. Non-human primate models recapitulate many features of human development and allow access to early postimplantation stages. Here, we tracked the pre- to postimplantation transition of the trophoblast lineage in superficially implanting marmoset embryos invivo. We differentiated marmoset naive pluripotent stem cells into trophoblast stem cells (TSCs), which exhibited trophoblast-specific transcriptome, methylome, differentiation potential, and long-term self-renewal. Notably, human TSC culture conditions failed to support marmoset TSC derivation, instead inducing an extraembryonic mesoderm-like fate in marmoset cells. We show that combined MEK, TGF-β/NODAL, and histone deacetylase inhibition stabilizes a periimplantation trophoblast-like identity in marmoset TSCs. By contrast, these conditions differentiated human TSCs toward extravillous trophoblasts. Our work presents a paradigm to harness the evolutionary divergence in implantation strategies to elucidate human trophoblast development and invasion.

Abstract C023: PDAC tumors from patients treated with combination MEK and autophagy inhibition reveal a treatment sensitive epithelial subtype that is enriched in murine models

Abstract Combining MEK and autophagy inhibitors in preclinical PDAC mouse models resulted in tumor regressions and improved rodent survival. These findings provided the rationale for clinical investigation of this combination. The phase 1 MEKiAUTO trial evaluated combination cobimetinib, HCQ, with or without atezolizumab in 14 patients (pts) with KRAS-mutated pancreatic adenocarcinoma (PDAC). The study was closed due to a lack of preliminary efficacy and poor tolerability; however, three patients experienced progression free survival (PFS) beyond 12 weeks (two with KRAS G12R , one with KRAS G12D ). Correlative analyses on twenty-one biopsies (8-paired FFPE and 6-paired fresh frozen specimens) with multiplex immunofluorescence (mIF) demonstrated decreased phosphorylation of ERK and accumulation of p62 indicating a pharmacodynamic effect. Reverse phase protein array (RPPA) also confirmed MAPK pathway inhibition, with a decrease in pERK, and autophagy inhibition, with decreased autophagy signature score, within the tumor compartment of on-treatment biopsies compared to baseline. Single nucleus RNAseq with protein expression activity extrapolated using ARACNe (Algorithm for the Reconstruction of Accurate Cellular Networks) and VIPER (Virtual Inference of Protein-activity by Enriched Regulon) pipelines identified five distinct tumor subpopulations. Comparing prevalence of tumor clusters before and after treatment identified differential responses to treatment. Gene set enrichment analysis revealed that the most sensitive tumor cluster, tumor cluster 2, was enriched in autophagy and MAPK signaling. Pre- treatment frequency of tumor cluster 2 was higher in patients who experienced a clinical benefit and independently correlated with PFS. Among the non-tumor cell clusters identified, patients with clinical benefit also had increased immune cell infiltration. To explain the discordance in efficacy with this combination in preclinical models and humans, we interrogated the preclinical tumor model systems for tumor heterogeneity. Single cell RNA-Seq analysis of tumors from Kras LSL.G12D/+ ; p53 LSL.R172H/+ ; Pdx1-Cre tg/+ (KPC) mice treated with the combination confirmed presence of similar treatment-sensitive and treatment-resistant clusters, with the former being enriched for MAPK and autophagy signatures. Parallel analysis of cell lines previously shown to be sensitive to combination MEK and autophagy inhibition, including MiaPACA2 and PANC1, showed they were mostly enriched in the treatment-sensitive human cluster 2 phenotype but not treatment-resistant clusters. Our results suggest that some preclinical models may overrepresent subtypes which are sensitive to MEK and autophagy inhibitors and thus do not recapitulate the extent of intertumoral heterogeneity in human PDAC. Observed preclinical responses likely represented elimination of treatment-sensitive cluster(s), with the remaining clusters responsible for maintained resistance. Citation Format: Brian W Labadie, Aleksandar Z Obradovic, Sarah Sta Ana, Michael May, Naomi Sender, Isabelle V Ross, Monica Rodriguez-Mendez, Urszula Wasko, Lorenzo Tomassoni, Li Li, Manan Vij, Sinan Abuzaid, Julia Wulfkuhle, Winston Wong, Ilenia Pellicciotta, Benjamin Izar, Emanuel F Petricoin, Aik Choon Tan, Kenneth P Olive, Alex G Raufi, Gulam A Manji. PDAC tumors from patients treated with combination MEK and autophagy inhibition reveal a treatment sensitive epithelial subtype that is enriched in murine models [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C023.

Tretinoin synergistically enhances the antitumor effect of combined BRAF, MEK, and EGFR inhibition in BRAFV600E colorectal cancer.

Patients with BRAF-mutated colorectal cancer (BRAFV600E CRC) are currently treated with a combination of BRAF inhibitor and anti-EGFR antibody with or without MEK inhibitor. A fundamental problem in treating patients with BRAFV600E CRC is intrinsic and/or acquired resistance to this combination therapy. By screening 78 compounds, we identified tretinoin, a retinoid, as a compound that synergistically enhances the antiproliferative effect of a combination of BRAF inhibition and MEK inhibition with or without EGFR inhibition on BRAFV600E CRC cells. This synergistic effect was also exerted by other retinoids. Tretinoin, added to BRAF inhibitor and MEK inhibitor, upregulated PARP, BAK, and p-H2AX. When either RARα or RXRα was silenced, the increase in cleaved PARP expression by the addition of TRE to ENC/BIN or ENC/BIN/CET was canceled. Our results suggest that the mechanism of the synergistic antiproliferative effect involves modulation of the Bcl-2 family and the DNA damage response that affects apoptotic pathways, and this synergistic effect is induced by RARα- or RXRα-mediated apoptosis. Tretinoin also enhanced the antitumor effect of a combination of the BRAF inhibitor and anti-EGFR antibody with or without MEK inhibitor in a BRAFV600E CRC xenograft mouse model. Our data provide a rationale for developing retinoids as a new combination agent to overcome resistance to the combination therapy for patients with BRAFV600E CRC.

BIOM-03. IMMUNO-ONCOLOGIC PROFILING OF PEDIATRIC BRAIN TUMORS REVEALS MAJOR CLINICAL SIGNIFICANCE OF THE TUMOR IMMUNE MICROENVIRONMENT

Abstract With the success of immunotherapy in cancer, understanding the tumor immune microenvironment (TIME) has become increasingly important; however in pediatric brain tumors this remains poorly characterized. Accordingly, we developed a clinical immune-oncology gene expression assay, including the 18-gene tumor inflammation signature (TIS) as a marker of overall immune activation, and validated this with immunohistochemistry for key cell-type markers. We used this assay, in conjunction with public data from the Pediatric Brain Tumor Atlas (PBTA), to profile a diverse range of 1382 samples in total with detailed clinical and molecular annotation. Overall among the main types of pediatric brain tumors, low-grade gliomas (LGG) had the highest inflammation levels (regardless of genetic driver alteration) and medulloblastomas the lowest. In LGG we identified three distinct patterns of immune activation with prognostic significance in BRAF V600E-mutant tumors, specifically that higher inflammation predicted worse outcomes. In high-grade gliomas (HGG), we observed immune activation and T-cell infiltrates in tumors that have historically been considered exclusively immune cold. There were genomic correlates of inflammation levels, with BRAF-V600E-mutant HGG having the highest inflammation levels and suggesting these may be candidates for combination MEK inhibition and immunotherapy. In mismatch repair deficient HGG, we found that high TIS was a significant predictor of response to immune checkpoint inhibition, and demonstrated the potential for multimodal biomarkers (TIS plus tumor mutation burden) to improve treatment stratification. Importantly, while overall patterns of immune activation were observed for histologically and genetically defined tumor types, there was significant variability within each entity, indicating that the TIME must be evaluated as an independent feature from diagnosis. In sum, in addition to the histology and molecular profile, this work underscores the importance of reporting on the TIME as an essential axis of cancer diagnosis in the era of personalized medicine.

Nab-paclitaxel and gemcitabine (modified) in combination with oral cobimetinib and encorafenib following FOLFIRINOX in patients with metastatic G12D and G12V pancreatic cancer.

e16330 Background: Pancreatic cancer is the only human cancer in which most of the tumors are KRAS mutated. A majority of the mutations occur in codon 12. Mutations percentages are as follows: G12D (50%), G12V (35%) and G12R(12%). We are reporting on a pilot study in patients with advanced pancreatic cancer who have failed, or have become resistant to FOLFIRINOX. Thereafter the patients were placed on Nab-paclitaxel and Gemcitabine in combination with oral Cobimetinib and encorafenib. Methods: Patients with advanced pancreatic cancers are typically offered modified FOLFIRINOX followed by Nab-paclitaxel and Gemcitabine. After obtaining a written informed consent, we conducted a single arm study of patients with pathologic proven unresectable metastatic pancreatic cancer. Patients who had failed FOLFRINOX were placed on a modified regimen of Gemcitabine (1000mg/m2) and Nab-paclitaxel (125 mg/M2) on days 1 and 15 every 28-day cycle. Oral medications, Cobimetinib 20 mg bid and encorafenib of 150 mg bid were given. The oral chemotherapies were administered weekdays only during the 28-day cycle. The primary end point was to determine the response rate from the time the patients were placed on Nab-paclitaxel and Gemcitabine and the oral medication. The secondary endpoint was to assess the overall survivorship from the beginning of the therapy, and overall toxicities of the combination therapy. Twelve patients with advanced metastatic pancreatic cancer were enrolled on this pilot study. Six patients were male, and the median age was 67 years. Liver metastases were present in eight patients. Treatment was continued as long as there was no disease progression. CBC, CMP, CA19-9 was performed every other week. CT and PET scan was ordered every eight weeks. Results: Overall follow up is from 5 to 19 months (median 14 months). Segmental median survival from the start of oral therapy in conjunction with Nab-paclitaxel and Gemcitabine is 5 months (2-9 months). As from now,all patients are alive and 10 of 12 patients are on therapy. One patient who achieved pathologic response in the liver was deemed operable, and pathologically the distal pancreatectomy demonstrated NO disease. The other patient has progressed and is not on treatment. Grade 3 non-hematological toxicities included nausea, vomiting and fatigue in 3 of 12 patients. Hematological toxicities included neutropenia and neutrophil support was needed in 6 out of 12 patients. Median survivorship has NOT been reached. In this small study, we have observed a rapid and dramatic reduction in tumor volume. Conclusions: The combination of MEK and BRAF inhibitors with chemotherapy may be potentially active in pancreatic tumors (G12D and G12V). Based on the data presented, Nab-paclitaxel and Gemcitabine in combination with oral Cobimetinib and encorafenib needs to be further explored in a larger cohort of patients.

A randomized phase 2 study of combination atezolizumab and varlilumab (CDX-1127) with or without addition of cobimetinib in previously treated unresectable biliary tract cancer.

4017 Background: Combined MEK inhibition (MEKi) and PD-L1 blockade significantly improved progression-free survival (PFS) versus PD-L1 monotherapy in patients with advanced biliary tract cancer (BTC) following first-line chemotherapy (NCT03201458). Further study has shown MEKi enhances tumor immunogenicity but impairs host T cell activation/priming. The addition of immune agonists, e.g. a CD27 agonist, can rescue T cell function in the setting of systemic MEKi in vivo and may be an effective strategy to optimize MEKi’s immunomodulatory potential when used in combination with checkpoint blockade. Methods: We conducted a randomized ph 2 trial (NCT04941287) evaluating Atezolizumab in combination with the CD27 immune agonist (CDX-1127 [Varlilumab]) with or without the addition of a MEKi (Cobimetinib) in patients with unresectable, previously treated, BTC. Adults with pathologically-confirmed BTC, s/p at least 1 prior line (no more than 2) of systemic therapy, measurable disease, and ECOG PS ≤1 were enrolled. Patients who had received previous PD-[L]1 were eligible. The study was planned for 64 evaluable subjects randomized in a 1:1 ratio, stratified by BTC site, to either AV (Atezolizumab [840mg IV days 1,15])+ Varlilumab [3mg/kg IV days 1, 15]) or CAV (Cobimetinib [60mg oral daily days 1-21, off 22-28] + Atezolizumab + Varlilumab). Overall response rate (ORR) and PFS were co-primary endpoints. The primary correlative outcome was treatment-related changes in CD8+ infiltrating T cells. Results: A preplanned interim analysis based on objective response rates did not meet the threshold for continuance in either treatment arm, so the trial was closed early for futility. In total, 57 patients were enrolled (n = 29 [CAV], n = 28 [AV], 67% had intrahepatic cholangiocarcinoma, and 33% had received previous PD-[L]1. Both CAV and AV regimens were well-tolerated without new safety signals. Adding CDX-1127 did not appear to meaningful increase immunotoxicity beyond established PD-L1 toxicity profiles. ORR was 0% (CAV) and 4% (AV). With a median follow up time of 6.2 months, median PFS was 2.2 (CAV) and 1.8 (AV) months (HR 0.71 [0.40,1.25]). In PD[L]1-experienced patients, median PFS was 3.6 (CAV) and 1.7 (AV) months (HR 0.44 [0.14,1.33]). Median OS was 10.2 (CAV) and 6.1 (AV) months (HR 0.76 [0.37,1.55]). In PD[L]1-experienced patients, median OS was 6.4 (CAV) and 4.4 (AV) months for CAV and AV (HR 0.68 [0.19,2.42]). Primary correlative endpoint and updated survival will be reported at time of meeting. Conclusions: The combination of Atezolizumab and Varlilumab with or without Cobimetinib was safe but did not improve clinical outcomes in advanced stage BTC patients treated in later lines. Though not statistically significant, treatment with CAV demonstrated numerically favorable PFS/OS compared AV among immunotherapy-experienced patients. Clinical trial information: NCT03201458 .

Abstract 1099: Combined MEK and RET inhibition overcomes resistance to single agent RET inhibition in medullary thyroid cancer

Abstract Medullary thyroid carcinoma (MTC) is a rare neuroendocrine cancer, caused by activating mutations in the RET proto-oncogene, contributing to 13% of all thyroid cancer mortalities. Patients with metastatic MTC treated with RET inhibitors (RETi) can develop resistance through mechanisms currently being investigated. We aim to understand the molecular mechanisms of acquired resistance to RETi and develop novel combination therapies to circumvent resistance to these drugs. We used TT, an MTC cell line, to develop vandetanib-resistant (VanR) lines, at two independent sites, the Medical College of Wisconsin (MCW) and the Pediatric Oncology Branch (POB) at the NCI. We applied a multiomic approach to investigate the mechanisms of resistance, including Spectral karyotyping (SKY) and multiplex interphase Fluorescence in situ Hybridization (miFISH) to study the karyotype, ploidy, and heterogeneity at a single-cell level. Whole exome and RNA-sequencing was done to identify genetic alterations such as acquired mutations, copy number variations, and gene expression changes. In parallel, we performed genome-wide CRISPR gene knockout (KO) in TT cells treated with selpercatinib or vehicle to develop potential synergistic targeted combination therapy with RETi. Additionally, we performed a cytotoxicity screening using the Mechanism Interrogation Plate (MIPE6.0) library containing 2803 investigational drugs, novel agents, and FDA-approved drugs with known mechanisms of action. SKY and miFISH results showed that, for the parental TT_POB cell line, there were 4 copies of chromosome 10 (location of the RET gene), whereas there were 3 copies in TT_POB VanR. This was associated with an increase in the RET variant allele frequency, indicating a loss of heterozygosity of the wildtype allele as a mechanism of resistance, which was confirmed by whole exome sequencing. For TT_MCW VanR, we identified a new RET solvent front (G810S), as well as an increased copy number of RET with an increase in expression. CRISPR KO demonstrated that the knockout of NF1 led to resistance and survival to selpercatinib treatment. The MIPE6.0 screening confirmed resistance to RETi in TT_MCW VanR and sensitivity to multiple MEK inhibitors. In vivo testing in a xenograft mouse model confirmed the synergistic/additive activity of combined selpercatinib with trametinib, a MEK inhibitor. In conclusion, using a multiomic approach, we show that resistance to RETi occurs by an adaptive increase in RET signaling through secondary mutations in RET, and an increase in expression or dose of the mutant RET allele. These genetic events are associated with an activation of RAS signaling, in VanR cell lines, through the ERK/MAPK pathway. Furthermore, we demonstrate that the combination of RET and ERK/MAPK inhibition is synergistic against RET-mutant MTC. Future plans include translating our findings through clinical trials at the NCI. Citation Format: Arwa Fallatah, Abdelrahman Rahmy, Sophia Khan, Hsien-chao Chou, Kerstin Heselmeyer-Haddad, Darawalee Wangsa, David Milewski, Yong Kim, Robert Hawley, Young Song, Xiaohu Zhang, Craig Thomas, Jun S. Wei, Jong-In Park, John Glod, Javed Khan. Combined MEK and RET inhibition overcomes resistance to single agent RET inhibition in medullary thyroid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1099.

Abstract 1925: Wild-type RAS signaling is an essential therapeutic target in RAS-mutated cancers

Abstract Single-agent targeting of RAS-mutated cancers using RAF/MEK/ERK or PI3K/AKT pathway inhibitors is ineffective; blocking one pathway relieves negative feedback control of RTK signaling and hyperactivates parallel effector pathways. While combined MEK and PI3K inhibition is effective in preclinical models, toxicity of this combination prevents its clinical use. Alternative strategies for treating RAS-mutated cancers are essential. Therapeutics directly targeting mutated RAS proteins have the potential to spare normal cellular function thereby lessening overall toxicity. Unfortunately, direct RAS inhibition as a monotherapy does not fully block RAS effector signaling. RAS proteins show differential activation of RAF and PI3K pathways: KRAS potently activates RAF but poorly activates PI3K, whereas HRAS effectively activates PI3K but poorly activates RAF. Further, mutant RAS inhibition relieves negative feedback controls leading to rapid hyperactivation of RTK−WT RAS signaling. A more comprehensive understanding of the interplay between mutant RAS and RTK−WT RAS signaling is essential to developing rational therapeutic approaches to treat RAS-mutated cancers. We found that WT RAS enhanced mutant RAS-driven transformation by activating RAS effectors poorly engaged by mutated RAS. Further, inhibition of RAS effectors activated poorly by mutant RAS synergized with and limited resistance to mutant HRAS and KRAS inhibitors. The mutant HRAS inhibitor tipifarnib blocked PI3K signaling and synergized with MEK inhibitors in HRAS-mutated cancer cell lines; covalent KRASG12C inhibitors blocked MEK signaling and synergized with PI3K inhibitors in KRASG12C- mutated cell lines. Synergy between inhibitors of mutant RAS and RAS effectors was dependent on intact RTK/WT RAS signaling and was lost in both RASless or SOSless MEFs. Dual knock-out of WT RAS isoforms in KRAS- and HRAS-mutated cancer cell lines reduced PI3K signaling in KRAS-mutant cell lines and MAPK signaling in HRAS-mutant cell lines and reduced proliferation, confirming our findings in MEF cells. Overall, our data highlight the critical role of WT RAS isoforms in supporting mutant RAS signaling and should be considered when designing combination therapies in RAS-mutated cancers. Citation Format: Nancy E. Sealover, Bridget Finniff, Jacob Hughes, Hyun Lee, Robert L. Kortum. Wild-type RAS signaling is an essential therapeutic target in RAS-mutated cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1925.

Abstract 5265: Targeting mtDNA dynamics enhances immunogenicity and sensitizes KRAS mutant cancers to PD-1 blockade

Abstract Mitochondrial DNA (mtDNA) can stimulate an innate immune response that potentiates the efficacy of cancer immunotherapy. However, mtDNA-targeting therapy has not been developed to enhance this innate immune system in specific cancer subtypes efficiently. Here we discover that mtDNA is enriched in KRAS mutant tumors where the DNA sensor machinery cGAS-STING signaling is primed for innate immune activation. Intriguingly, MEK inhibitor induces cytosolic mtDNA release to potently activate the cGAS-STING signaling, which in turn induces PRKN-mediated mitophagy in response to mitochondrial stress in KRAS mutant cancer cells. During the process of mitophagy, PRKN, as an E3 ubiquitin ligase, degrades BAX protein and attenuates mitochondrial pore formation, which is essential for mtDNA efflux upon MEK inhibition. Combined MEK and mitophagy inhibitors efficiently stimulate type I IFNs in both mtDNA- and STING-dependent manners, and this combination enhances the efficacy of PD-1 blockade in Kras mutant murine syngeneic tumors. In the clinic, PRKN is associated with a ‘cold tumor’ phenotype among KRAS mutant tumors. Together, targeting mtDNA dynamics by co-inhibition of MEK and mitophagy represents a promising strategy to convert ‘cold to hot tumor’ in mtDNA-enriched KRAS mutant cancers. Citation Format: Kosuke Tanaka, Yasuki Adachi, Miyuki Yoshiya, Takuya Owari, Tomoko Yamamori-Morita, Akihiro Ohashi, Susumu Kobayashi, Shohei Koyama, Hiroyoshi Nishikawa. Targeting mtDNA dynamics enhances immunogenicity and sensitizes KRAS mutant cancers to PD-1 blockade [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5265.

Abstract 3163: (Phospho)proteomic analysis reveals vulnerabilities in refractory metastatic colorectal cancer

Abstract Proteomic networks are crucial for cellular homeostasis maintenance and, indeed, their aberrant regulation is implicated in cancer development and progression. Understanding alterations underlying these pathways, provides a way to design therapeutic interventions in human cancer. Improvements in mass spectrometry analysis have unlocked our potential to unveil cancer vulnerabilities. Here, we performed (phospho)proteomic analysis and ex-vivo drug testing on a cohort of refractory metastatic colorectal cancer (mCRC) tissues and matched patients-Derived Organoids (PDO) to identify new putative druggable biomarkers. The comparison between the proteome and phosphoproteome of 10 mCRCs tissues with their matched PDOs normalized to a pool of 6 colon mucosa tissues highlighted a strong overall correlation (R= 0.57 and R=0.6, respectively) suggesting a good level of similarity. Applying GSEA on our proteomic dataset, we identified up-regulation in MYC, cell cycle and MTORC1 signaling pathways in mCRC tissues and PDO, while kinase enrichment analysis highlighted an increase in Casein Kinase II (CKII) activity, an important cell cycle regulator. Our ex-vivo experiments showed that silmitasertib-mediated CKII inhibition reduced the cell viability in our PDO models, but with an overall modest effect. Analysis revealed that, even though not statistically significant, high Wnt signaling score correlated with an higher resistance to silmitasertib treatment (R=0.61; p=0.08). Previous works highlighted that MAPK activity is increased after silmitasertib treatment and responsible for resistance mechanisms to CKII inhibition. Strikingly, the combined trametinib-mediated MEK blockade and CKII blockade resulted in a synergistic interaction leading to enhanced antitumor activity, especially in PDO harboring high Wnt (R=0.74; p=0.022) and cell cycle (R=0.69; p=0.04) pathway activity. Moreover, the combined treatment strongly reduced S6 activity and RAPTOR expression, overcoming the significant effect exerted by the single agents. Surprisingly, none of them altered baseline MAPK activity, suggesting that silmitasertib and trametinib synergize their activity via inactivating the MTORC1-S6 axis in an ERK-independent manner. We are currently integrating genomic and transcriptomic data to better characterize the observed drug synergy. Taken together, our findings propose the silmitasertib and trametinib combination as a new therapeutic opportunity for refractory mCRC patients and strengthen the use of PDO as a suitable model for drug screening. Citation Format: Mattia Marinucci, Gina Faye Boot, Lara Zaidi, Cinzia Esposito, Mairene Coto Llerena, Savas Soysal, Otto Kolmar, Charlotte K Y Ng, Salvatore Piscuoglio. (Phospho)proteomic analysis reveals vulnerabilities in refractory metastatic colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3163.

Abstract 5847: Characterizing mechanisms of BRAF/MEK inhibitor resistance in BRAF V600 mutant colorectal cancer vs. melanoma

Abstract Background: BRAF V600 mutations comprise ~80% of all oncogenic BRAF mutations in metastatic colorectal cancer (mCRC). While most cancers with BRAF V600 mutations can be effectively treated with combined BRAF and MEK inhibition, BRAF V600 mutant mCRC acquire resistance through EGFR-mediated signaling. The profound difference in response rates to BRAF/MEK inhibitors in BRAF V600 mutant mCRC (12%) vs. melanoma (63-68%) is not sufficiently explained by increased EGFR signaling in CRC. Therefore, we sought to characterize the differences that exist between BRAF V600 mutant CRC and melanomas that could explain the differential sensitivity to BRAF/MEK inhibition and identify more effective treatments for BRAF V600 mutant CRC. Methods: We assessed cell survival by clonogenic assay in the presence of small molecule inhibitors. In parallel, we mined TCGA RNAseq data to calculate the MAPK Pathway Activity Score (MPAS). RTK expression was assessed in TCGA data from patients with BRAF V600 mutant CRC vs. melanoma. We developed cells with acquired resistance to BRAF+MEK inhibitors (Encorafenib+Binimetinib; E+B) by culturing cells in increasing concentrations of drug over several months. RNA-sequencing and analysis was performed on parental and resistant cells treated with vehicle control or BRAF+MEK inhibitors. Results: When comparing the efficacy of BRAF+MEK inhibitors across BRAF V600 mutant cells, we found that BRAF V600 mutant CRC cell lines (n=2) were less sensitive than melanoma cell lines (n=2). MPAS scores were significantly lower in BRAF V600 mutant CRC (n=46) vs. melanoma (n=188) tumors. We interrogated protein array data from the DepMap and identified increased activation of several RTKs (EGFR, HER2, HER3) in BRAF V600 CRC (n=8) vs. melanoma (n=39) cell lines. Similarly, we established resistant HT29 (BRAF V600 CRC) cells and observed sustained MAPK pathway activity despite a lack of difference in EGFR activity in the presence of BRAF+MEK inhibitor treatment. Both HT29 parental and resistant cells showed re-establishment of MAPK signaling after 72 hours. Resistant SkMel28 (BRAF V600 melanoma) cells showed increased pERK levels compared to resistant HT29 cells. RNAseq revealed increased expression of multiple RTKs (PDGFRB, ERBB2, ERBB3) and ligands/growth factors for multiple RTKs (FGF3, PDGFA, HB-EGF) in resistant HT29 cells. Shp2 is a protein tyrosine phosphatase that regulates signaling of multiple RTKs to activate the MAPK pathway. Accordingly, we assessed the efficacy of an inhibitor of Shp2 (TNO155) overcoming MAPKi resistance in BRAF V600 CRC cells. We confirmed that E+B+TNO155 more effectively inhibited cell growth and MAPK pathway activity in BRAF V600 CRC cell lines (n=2) in vitro. Conclusion: Together, these data identify key, actionable drivers of MAPK inhibitor resistance in CRC and highlight Shp2 as a potential therapeutic target for BRAF V600 CRC. Citation Format: Jennifer Maxwell, Emmanuelle Rousselle, Lucy An, April Rose. Characterizing mechanisms of BRAF/MEK inhibitor resistance in BRAF V600 mutant colorectal cancer vs. melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5847.

Abstract 3581: IGFR1 and MEK inhibition synergize to mediate anti-tumor activity in adrenocortical carcinoma

Abstract Adrenocortical carcinoma (ACC) is an aggressive and rare endocrine malignancy with limited treatment options and poor prognosis. IGF2, the ligand for IGFR1, is highly expressed in ACC. However, linsitinib, an IGFR1 inhibitor, failed to improve overall survival over placebo in a randomized, phase 3 clinical trial of metastatic ACC. We hypothesized that combination therapy with IGFR1 inhibition may have greater anti-tumor efficacy in ACC than IGFR1 inhibition alone. To test this hypothesis, we performed high-throughput cell toxicity screening of 2803 clinical-stage compounds with linsitinib in an ACC cell line. MAPK inhibitors were among the top screening hits. MEK inhibitors were chosen for further evaluation given the safety, tolerability, and broad clinical activity of these FDA-approved agents. IGFR1 and MEK inhibitors were strongly synergistic in cytotoxicity across ACC cell lines, ACC organoid short-term cultures derived from surgical tissue resections (PDOs), and PDX-derived organoids (PDXOs). Genetic depletion of IGF2 significantly inhibited growth with cobimetinib and genetic depletion of MEK1 inhibited growth with linsitinib in ACC cell lines. Combination IGFR1 and MEK inhibition downregulated ERK phosphorylation and increased apoptosis compared to either IGFR1 or MEK inhibition alone. Linsitinib combined with cobimetinib significantly reduced tumor growth compared to either linsitinib or cobimetinib alone in an ACC xenograft model. Our study provides preclinical support for testing the combination of IGFR1 and MEK inhibition in patients with ACC. Citation Format: Suresh Kumar, Nai-Yun Sun, Yasuhiro Arakawa, Diana Varghese, Chuong D. Hoang, Jonathan M. Hernandez, Yves Pommier, Craig Thomas, Jaydira Del Rivero, Nitin Roper. IGFR1 and MEK inhibition synergize to mediate anti-tumor activity in adrenocortical carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3581.

Abstract 6555: scRNAseq and TCR repertoire analysis identifies immune correlates of response to combined BRAF/MEK/PD1 inhibition in a phase 2 trial

Abstract Background: Our recent clinical trial of combined BRAF, MEK, and PD-1 inhibition showed a 24% response rate in BRAF V600E mutant colon cancer (PMID: 36702949). Analysis of epithelial single-cell RNA sequencing data showed an increase in interferon-stimulated genes (ISG) and inhibition of the MAPK pathway in responders. MAPK inhibition in organoids also induced ISGs. These data suggest a synergy between MAPK inhibition and induction of immune responses. Methods: We analyzed over 100,000 immune and stromal cells from 23 paired scRNAseq profiles of pre- and day 15 on-treatment tumor biopsies. Progression free survival greater than 6 months was defined as a clinical response. We performed traditional differentially expressed gene and gene program analyses, and tracked TCR repertoire in tumor and blood. We developed a novel approach based on supervised clustering (PMID: 34675423) to identify fine-grained cell subtypes associated with response. We applied supervised clustering separately to T and myeloid cells, and tested the association of each cluster’s abundance with response. Results: We applied supervised clustering to T cells and identified a CD74+IFNG+ CD8 T cell cluster that increased in only responders (p=0.0078). In the myeloid compartment, we identified two populations of CXCL10+ macrophages: one whose abundance increased in all patients and a CCL3+CCL4+ activation state expanded (p=0.01) only in responders. Pathway analysis of the expanded populations suggests an enrichment of ISGs in both CD74+IFNG+ CD8 T cells and CXCL10+CCL3+CCL4+ macrophages, with specific enrichment of interferon-gamma responsive genes GBP1 and GBP4 in the macrophages. T cell analysis yielded two responders with marked clonal expansion within the CXCL13+ population, which likely represent tumor-specific T cells. Within the blood, these CXCL13+ clonotypes underwent a short-lived burst at day 15, yet represented only a minor population. We saw concomitant expansion of both CXCL13+ CD4 and CD8 populations within patients, suggesting CXCL13+ CD4s might provide help to the CXCL13+ CD8 T cells. The same two responders had increased stem-like TCF7+PD1+ CD8 T cells previously implicated in immunotherapy response and an increase in CCL19+ fibroblasts associated with stem-immunity hubs. Conclusions: Our analysis of pre- and on-therapy biopsy scRNAseq data from our clinical trial of MAPK and PD-1 inhibition found expansion of ISG enriched CD74+IFNG+ CD8 T cells and CXCL10+CCL3+CCL4+ macrophages in responders. Both populations are enriched in ISGs: this coordinated expansion may result from a shared, interferon-rich microenvironment. Ongoing work will explore this hypothesis using spatial transcriptomics to identify these activated cells and their microenvironments. Ethics approval "This study was approved by the DF/HCC IRB as protocol 18-144 (see also ClinicalTrials.gov NCT03668431). Citation Format: Hongcheng Yao, Vjola Jorgji, Alexander L. Tang, David Lieb, Sherry X. Chao, Daniel J. Stein, Maxwell Spurrell, Liad Elmelech, Jun Tian, Moshe Sade-Feldman, Karin Pelka, Ryan B. Corcoran, Nir Hacohen, Ilya Korsunsky, Jonathan Chen. scRNAseq and TCR repertoire analysis identifies immune correlates of response to combined BRAF/MEK/PD1 inhibition in a phase 2 trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6555.

Anaplastic thyroid cancer spheroids as preclinical models to test therapeutics

Anaplastic thyroid cancer (ATC) is the most aggressive thyroid cancer. Despite advances in tissue culture techniques, a robust model for ATC spheroid culture is yet to be developed. In this study, we created an efficient and cost-effective 3D tumor spheroids culture system from human ATC cells and existing cell lines that better mimic patient tumors and that can enhance our understanding of in vivo treatment response. We found that patient-derived ATC cells and cell lines can readily form spheroids in culture with a unique morphology, size, and cytoskeletal organization. We observed both cohesive (dense and solid structures) and discohesive (irregularly shaped structures) spheroids within the same culture condition across different cell lines. BRAFWT ATC spheroids grew in a cohesive pattern, while BRAFV600E-mutant ATC spheroids had a discohesive organization. In the patient-derived BRAFV600E-mutant ATC spheroids, we observed both growth patterns, but mostly the discohesive type. Histologically, ATC spheroids had a similar morphology to the patient’s tumor through H&E staining and proliferation marker staining. Moreover, RNA sequencing analysis revealed that the gene expression profile of tumor cells derived from the spheroids closely matched parental patient tumor-derived cells in comparison to monolayer cultures. In addition, treatment response to combined BRAF and MEK inhibition in BRAFV600E-mutant ATC spheroids exhibited a similar sensitivity to the patient clinical response. Our study provides a robust and novel ex vivo spheroid model system that can be used in both established ATC cell lines and patient-derived tumor samples to better understand the biology of ATC and to test therapeutics.

A Review of Current and Pipeline Drugs for Treatment of Melanoma.

Malignant melanoma is the most aggressive form of skin cancer. Standard treatment options include surgery, radiation therapy, systemic chemotherapy, targeted therapy, and immunotherapy. Combining these modalities often yields better responses. Surgery is suitable for localized cases, sometimes involving lymph node dissection and biopsy, to assess the spread of the disease. Radiation therapy may be sometimes used as a standalone treatment or following surgical excision. Systemic chemotherapy, while having low response rates, is utilized as part of combination treatments or when other methods fail. The development of resistance to systemic chemotherapies and associated side effects have prompted further research and clinical trials for novel approaches. In the case of advanced-stage melanoma, a comprehensive approach may be necessary, incorporating targeted therapies and immunotherapies that demonstrate significant antitumor activity. Targeted therapies, including inhibitors targeting BRAF, MEK, c-KIT, and NRAS, are designed to block the specific molecules responsible for tumor growth. These therapies show promise, particularly in patients with corresponding mutations. Combination therapy, including BRAF and MEK inhibitors, has been evidenced to improve progression-free survival; however, concerns about resistance and cutaneous toxicities highlight the need for close monitoring. Immunotherapies, leveraging tumor-infiltrating lymphocytes and CAR T cells, enhance immune responses. Lifileucel, an FDA-approved tumor-infiltrating lymphocyte therapy, has demonstrated improved response rates in advanced-stage melanoma. Ongoing trials continue to explore the efficacy of CAR T-cell therapy for advanced melanoma. Checkpoint inhibitors targeting CTLA-4 and PD-1 have enhanced outcomes. Emerging IL-2 therapies boost dendritic cells, enhancing anticancer immunity. Oncolytic virus therapy, approved for advanced melanoma, augments treatment efficacy in combination approaches. While immunotherapy has significantly advanced melanoma treatment, its success varies, prompting research into new drugs and factors influencing outcomes. This review provides insights into current melanoma treatments and recent therapeutic advances.

Abstract A026: EGF/EGFR signaling in priming for resistance to BRAF/MEK inhibitors in melanoma

Abstract Targeted therapies kill cancer cells very efficiently. However, the effectiveness of targeted therapies is limited by the eventual emergence of resistance, arising from a small subset of cells capable of surviving therapy. Our work has shown genetically homogeneous cells, in distinct transcriptomic states, are capable of surviving combination BRAF and MEK inhibition. In the presence of targeted therapies these rare cells transform into resistant cells, we therefore call these cells ‘primed’ for resistance. Our research has focused on characterizing these primed cells, however, the mechanisms of survival remain unknown. Since primed cells overexpress receptor tyrosine kinases (RTKs), which are associated with growth and survival, we tested if overexpression of the RTK EGFR could explain priming and subsequent resistance. While melanoma cells in which we artificially overexpressed EGFR had no significant increase in resistance, EGFR overexpressing cells in the presence of exogenous EGF are highly resistant to combination BRAF/MEK inhibition. While EGF is not overexpressed in primed cells, preliminary data suggests that while most cells reduce EGF expression in the presence of BRAF/MEK inhibition, primed cells maintain their baseline expression, potentially maintaining EGF/EGFR signaling in these colonies. We are therefore testing if EGF/EGFR signaling is necessary in vitro by knocking out EGF or EGFR. Furthermore, to test if EGF/EGFR signaling can create a primed state, we used flow cytometry to determine expression of the prime cell marker NT5E. In cells with confirmed EGFR overexpression we observed an increased fraction of NT5E overexpressing cells, suggesting that EGF/EGFR signaling could initiate aspects of primeness beyond simple survival. Further research will determine if EGF/EGFR signaling can initiate an overall primed transcriptional state. The heritability of any primeness as a consequence of EGF/EGFR signaling will inform us if this signaling is a potential cause of priming or a mechanism by which paracrine signaling and/or stromal protection can eventually result in independent resistance. Citation Format: Robert J. Vander Velde, Sydney M. Shaffer. EGF/EGFR signaling in priming for resistance to BRAF/MEK inhibitors in melanoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr A026.