Biology subjects

Der, C. J.

Publications and source records attributed to Der, C. J..

13 recordsLinked to original sources

bioRxiv2026

Concurrent AXL inhibition enhances RAS and ERK inhibitor efficacy in KRAS-mutant pancreatic and lung cancer

Resistance limits the clinical efficacy of RAS inhibitors. We applied chemical and genetic screens and identified the AXL receptor tyrosine kinase as a driver of resistance to RAS-ERK inhibition. We determined that combination treatment with the AXL inhibitor bemcentinib (AXLi) together with the RAS(ON) multi-selective tri-complex inhibitor RMC-7977 (RASi) or the ERK-selective inhibitor SCH772984 (ERKi) significantly enhanced growth suppression in human KRAS-mutant pancreatic and lung cancer models. Combined AXLi and RASi treatment of human KRAS-mutant pancreatic cell line-derived xenograft tumors synergistically suppressed ERK activation and MYC expression, and caused tumor regression. Analyses of immunocompetent mouse allograft pancreatic tumor models revealed a largely tumor cell-intrinsic response to inhibitor treatment. We identified an unexpected mechanism whereby KRAS inhibition upregulated the AXL ligand GAS6, activating AXL but inducing an AXL-dependent adaptive resistance mechanism wherein AXL antagonizes RASi efficacy. Our observations support concurrent AXL inhibition as a strategy to enhance RAS inhibitor clinical efficacy. STATEMENT OF SIGNIFICANCEOur findings identify AXL as a driver of resistance to RAS inhibitors, establishing a combination strategy to overcome resistance and enhance RAS inhibitor therapeutic efficacy in KRAS-mutant cancer by maximally inhibiting oncogenic RAS signaling.

cancer biology↗

bioRxiv2026

Characterization and therapeutic suppression of KEAP1-NRF2-driven resistance to KRAS inhibitors in pancreatic and lung cancer

The recent approval of KRAS inhibitors supports the therapeutic value of targeting mutant KRAS cancers. However, clinical efficacy is hindered by both primary and treatment-associated acquired resistance. We applied a CRISPR-Cas9 loss-of-function screen and identified loss of KEAP1 as a resistance mechanism to the KRASG12D-selective inhibitor MRTX1133 and the RAS(ON) multi-selective inhibitor RMC-7977 in pancreatic cancer models. RNA-sequencing analyses revealed a KEAP1KO transcriptome that is distinct from the ERK-, MYC-, and YAP/TAZ-TEAD-dependent transcriptional programs that drive KRAS inhibitor resistance, demonstrating a distinct mechanism of resistance. We then established a PDAC KEAP1-deficient (PKD) gene signature that was enriched in patients and preclinical models insensitive to KRAS inhibitor treatment. Finally, we observed that KEAP1-deficient cells exhibited elevated glutamine metabolism, and combination treatment with the glutamine antagonist DRP-104 (sirpiglenastat) enhanced KRAS inhibitor suppression of pancreatic and lung tumors. SIGNIFICANCEKEAP1 loss is associated with reduced response to KRAS inhibitor therapy. We demonstrate that KEAP1 loss-associated resistance can be overcome by pharmacologic inhibition of the KEAP1 loss-induced glutamine dependency, establishing a combination to enhance RAS inhibitor clinical efficacy.

cancer biology↗

bioRxiv2025

p53 and YAP/TAZ-TEAD activities determine metaplastic heterogeneity in pancreatic cancer

BACKGROUND and AIMSPancreatic ductal adenocarcinoma (PDAC) initiation and progression is characterized by lineage plasticity across a continuum of metaplastic and malignant cell fates. This molecular heterogeneity influences disease progression and therapeutic response, yet the genetic and molecular interactions underlying cellular plasticity during PDAC progression remain poorly understood. Here we studied how p53, the most frequently inactivated tumor suppressor in PDAC, interacts with the YAP/TAZ-TEAD transcriptional effector arm of the Hippo pathway to determine cell fate and neoplastic heterogeneity in PDAC development. METHODSWe characterized differentiation states in mouse PDAC and pre-malignant cells in response to p53 activation or inactivation, respectively, and upon genetic, pharmacological, and physiological modulation of YAP/TAZ-TEAD activity. Differentiation was analyzed in vivo in an orthotopic PDAC model permitting independent, inducible control of p53 and TEAD function. We analyzed the effect of p53 and YAP/TAZ-TEAD activity on cell fate in mouse and human PDAC and analyzed markers of clinically relevant molecular subtypes in human PDAC cell lines treated with small molecule TEAD inhibitors. RESULTSRe-engaging wildtype p53 function in KrasMut pancreatic cancer cells increases TEAD activity through accumulation of its co-activator TAZ. Remarkably, increased YAP/TAZ-TEAD activity broadly suppresses the expression of overlapping markers of gastric pit-like (GPL) differentiation and the classical PDAC subtype that are promoted by p53. Accordingly, p53 and YAP/TAZ-TEAD activity inversely correlate with GPL and classical differentiation during PDAC development and modulation of both pathways determines expression of GPL and classical markers in vitro and in vivo. GPL differentiation is acutely sensitive to YAP/TAZ-TEAD activity including oncogenic perturbations of the Hippo pathway, actin dynamics, cell-to-cell contact, and adaptative YAP/TAZ accumulation in response to Ras/MAPK pathway inhibition. Functional repression of gastric-classical differentiation by TEAD persists in human PDAC where potent TEAD inhibition increases expression of GPL and classical markers. CONCLUSIONSWe find that p53 and YAP/TAZ-TEAD activities determine gastric plasticity during PDAC development highlighting the role that key cancer drivers and therapeutically targetable signaling pathways play in active maintenance of cellular identity during pancreatic cancer development.

cancer biology↗

bioRxiv2025

Dordaviprone/ONC201 Activation of the ClpP Mitochondrial Protease Inhibits the Growth of KRAS-Mutant Pancreatic Cancer and Overcomes RAS Inhibitor Resistance

Pancreatic ductal adenocarcinoma (PDAC) is characterized by KRAS-driven oncogenic signaling and tumor growth. Blockade of the KRAS ERK-MAPK pathway via small molecule direct RAS inhibitors has shown clinical promise, but intrinsic and acquired resistance limit the efficacy of these inhibitors as single agents. To identify potential combination strategies, we first assessed the ability of dordaviprone/ONC201, an FDA-approved agent, to inhibit PDAC cell and organoid growth. We observed that ONC201 reduced the growth of a broad panel of KRAS-mutant PDAC cell lines, and that the expression of mitochondrial protease ClpP was required for this efficacy. Mechanistically, we observed that treatment with ONC201 led to inhibition of mitochondrial respiration, causing a compensatory increase in glycolysis. Furthermore, ONC201 caused ClpP-dependent activation of PI3K-AKT-mTOR signaling and concurrent PI3K and mTOR inhibition further enhanced ONC201 growth suppression. ONC201 demonstrated an additive effect when combined with a RAS(ON) multi-selective inhibitor RMC-7977 in PDAC cells and organoids. Finally, PDAC cell lines with acquired resistance to RMC-7977 or KEAP1 loss-driven resistance retained sensitivity to ONC201. We propose that concurrent treatment with ONC201 may delay onset of resistance to RAS inhibitor therapy. Statement of SignificanceClpP activation by dordaviprone/ONC201 suppressed PDAC cell growth and overcame resistance to the RAS(ON) multi-selective inhibitor RMC-7977, providing support for investigating this combination as a potential combination treatment for KRAS-mutant pancreatic cancer.

cancer biology↗

bioRxiv2025

p53 activity licenses transcriptional regulation by YAP/TAZ-TEAD to shape expression landscapes during tumorigenesis

The tumor suppressor p53 is the most frequently disabled gene in cancer, where its inactivation promotes the transition between transcriptionally distinct pre-malignant and malignant disease. How p53 action shapes these stage-dependent expression landscapes is poorly understood. Using a mouse model where p53 function is restored in advanced pancreatic cancer, we demonstrate that p53 dependent gene expression is determined by regulation of YAP/TAZ-TEAD transcriptional complexes at multiple levels of molecular control. Restoration of p53 activity in pancreatic cancer cells expands transcriptional regulation by reorganizing TEAD binding at newly accessible enhancer landscapes, resulting in distinct TEAD-driven gene regulatory networks when p53 is inactivated versus engaged. Furthermore, p53 potentiates expression of newly licensed TEAD targets by increasing TAZ levels in response to the actin remodeling associated with cell cycle arrest and senescence. Thus, p53 activity controls the qualitative and quantitative output of YAP/TAZ-TEAD, including secretory programs involved in tumor-immune communication and remodeling of the microenvironment. Our work nominates regulation of YAP/TAZ-TEAD via p53 as a mechanism that determines stage dependent transcriptional landscapes during stepwise tumorigenesis.

cancer biology↗

bioRxiv2025

TRIP13 protects pancreatic cancer cells against intrinsic and therapy-induced DNA replication stress

Oncogene activation in normal untransformed cells induces DNA replication stress and creates a dependency on DNA Damage Response (DDR) mechanisms for cell survival. Different oncogenic stimuli signal via distinct mechanisms in every cancer setting. The DDR is also pathologically re-programmed and deployed in diverse ways in different cancers. Because mutant KRAS is the driver oncogene in 90% of Pancreatic Ductal Adenocarcinomas (PDAC), here we have investigated DDR mechanisms by which KRAS-induced DNA replication stress is tolerated in normal human pancreatic epithelial cells (HPNE). Using a candidate screening approach, we identify TRIP13 as a KRASG12V-induced mRNA that is also expressed at high levels in PDAC relative to normal tissues. Using genetic and pharmacological tools, we show that TRIP13 is necessary to sustain ongoing DNA synthesis and viability specifically in KRASG12V-expressing cells. TRIP13 promotes survival of KRASG12V-expressing HPNE cells in a Homologous Recombination (HR)-dependent manner. KRASG12V-expressing HPNE cells lacking TRIP13 acquire hallmark HR-deficiency (HRD) phenotypes including sensitivity to inhibitors of Trans-Lesion Synthesis (TLS) and Poly-ADP Ribose Polymerase (PARP). Established PDAC cell lines are also sensitized to intrinsic DNA damage and therapy-induced genotoxicity following TRIP13-depletion. Taken together our results expose TRIP13 as an attractive new and therapeutically-tractable vulnerability of KRAS-mutant PDAC.

cancer biology↗

bioRxiv2023

Tumor-selective effects of active RAS inhibition in pancreatic ductal adenocarcinoma

Broad-spectrum RAS inhibition holds the potential to benefit roughly a quarter of human cancer patients whose tumors are driven by RAS mutations. However, the impact of inhibiting RAS functions in normal tissues is not known. RMC-7977 is a highly selective inhibitor of the active (GTP-bound) forms of KRAS, HRAS, and NRAS, with affinity for both mutant and wild type (WT) variants. As >90% of human pancreatic ductal adenocarcinoma (PDAC) cases are driven by activating mutations in KRAS, we assessed the therapeutic potential of RMC-7977 in a comprehensive range of PDAC models, including human and murine cell lines, human patient-derived organoids, human PDAC explants, subcutaneous and orthotopic cell-line or patient derived xenografts, syngeneic allografts, and genetically engineered mouse models. We observed broad and pronounced anti-tumor activity across these models following direct RAS inhibition at doses and concentrations that were well-tolerated in vivo. Pharmacological analyses revealed divergent responses to RMC-7977 in tumor versus normal tissues. Treated tumors exhibited waves of apoptosis along with sustained proliferative arrest whereas normal tissues underwent only transient decreases in proliferation, with no evidence of apoptosis. Together, these data establish a strong preclinical rationale for the use of broad-spectrum RAS inhibition in the setting of PDAC.

cancer biology↗

bioRxiv2022

Mediator Kinase Inhibition Impedes Transcriptional Plasticity and Prevents Resistance to ERK/MAPK-Targeted Therapy in KRAS-Mutant Cancers

Acquired resistance remains a major challenge for therapies targeting oncogene activated pathways. KRAS is the most frequently mutated oncogene in human cancers, yet strategies targeting its downstream signaling kinases have failed to produce durable treatment responses. Here, we developed multiple models of acquired resistance to dual-mechanism ERK/MAPK inhibitors across KRAS-mutant pancreatic, colorectal, and lung cancers, and then probed the long-term events enabling survival against this novel class of drugs. These studies revealed that resistance emerges secondary to large-scale transcriptional adaptations that are diverse and tumor-specific. Transcriptional reprogramming extends beyond the well-established early response, and instead represents a dynamic, evolved population-level process that is refined to attain a stably resistant phenotype. Mechanistic and translational studies reveal that resistance to dual-mechanism ERK/MAPK inhibition is broadly susceptible to manipulation of the epigenetic machinery, and that Mediator kinase, in particular, can be co-targeted at a bottleneck point to prevent diverse, tumor-specific resistance programs.

cancer biology↗

bioRxiv2022

Characterization of TR-107, a Novel Chemical Activator of the Human Mitochondrial Protease ClpP

We recently described the identification of a new class of small molecule activators of the mitochondrial protease ClpP. These compounds synthesized by Madera Therapeutics showed increased potency of cancer growth inhibition over the related compound ONC201. In this study, we describe chemical optimization and characterization of the next generation of highly potent and selective small molecule ClpP activators (TR compounds) and demonstrate their efficacy against breast cancer models in vitro and in vivo. One of these compounds (TR-107) with excellent potency, specificity and drug-like properties was selected for further evaluation. Examination of TR-107 effects in triple-negative breast cancer (TNBC) cell models showed growth inhibition in the low nanomolar range, equipotent to paclitaxel, in a ClpP-dependent manner. TR-107 reduced specific mitochondrial proteins including OXPHOS and TCA cycle components, in a time, dose and ClpP-dependent manner. Seahorse XF analysis and glucose deprivation experiments confirmed inactivation of OXPHOS and demonstrated an increased dependence on glycolysis following TR-107 exposure. The pharmacokinetic properties of TR-107 were compared to other known ClpP activators including ONC201 and ONC212. TR-107 displayed excellent exposure and serum t1/2 after oral administration. The antitumor response to TR-107 was investigated using human TNBC MDA-MB-231 cell line-induced xenograft tumors. Oral administration of TR-107 resulted in reduction in tumor volume and extension of survival in the treated compared with vehicle control mice. In summary, we describe the identification of highly potent new ClpP agonists with improved efficacy against TNBC, through targeted inactivation of OXPHOS and disruption of mitochondrial metabolism.

pharmacology and toxicology↗

bioRxiv2021

Defining the KRAS-regulated kinome in KRAS-mutant pancreatic cancer

Oncogenic KRAS drives cancer growth by activating diverse signaling networks, not all of which have been fully delineated. We set out to establish a system-wide profile of the KRAS-regulated kinase signaling network (kinome) in KRAS-mutant pancreatic ductal adenocarcinoma (PDAC). We knocked down KRAS expression in a panel of six cell lines, and then applied Multiplexed Inhibitor Bead/Mass Spectrometry (MIB/MS) chemical proteomics to monitor changes in kinase activity and/or expression. We hypothesized that depletion of KRAS would result in downregulation of kinases required for KRAS-mediated transforming activities, and in upregulation of other kinases that could potentially compensate for the deleterious consequences of the loss of KRAS. We identified 15 upregulated and 13 downregulated kinases in common across the panel. In agreement with our hypothesis, all 15 of the upregulated kinases have established roles as cancer drivers (e.g., SRC, TGFBR1, ILK), and pharmacologic inhibition of the upregulated kinase, DDR1, suppressed PDAC growth. Interestingly, 11 of the 13 downregulated kinases have established driver roles in cell cycle progression, particularly in mitosis (e.g., WEE1, Aurora A, PLK1). Consistent with a crucial role for the downregulated kinases in promoting KRAS-driven proliferation, we found that pharmacologic inhibition of WEE1 also suppressed PDAC growth. The unexpected paradoxical activation of ERK upon WEE1 inhibition led us to inhibit both WEE1 and ERK concurrently, which caused further potent growth suppression and enhanced apoptotic death than WEE1 inhibition alone. We conclude that system-wide delineation of the KRAS-regulated kinome can identify potential therapeutic targets for KRAS-mutant pancreatic cancer.

cancer biology↗

bioRxiv2021

Engineering Threshold-Based Selection Systems

Using model organisms to identify novel therapeutic targets is frequently constrained by pre-existing genetic toolkits. To expedite positive selection for identification of novel downstream effectors, we engineered conditional expression of activated CED-10/Rac to disrupt C. elegans embryonic morphogenesis, titrated to 100% lethality. The strategy of engineering thresholds for positive selection using experimental animals was validated with pharmacological and genetic suppression and is generalizable to diverse molecular processes and experimental systems.

genetics↗

bioRxiv2020

Silencing of oncogenic KRAS by mutant-selective small interfering RNA

Oncogenic mutations in the KRAS gene are well-established drivers of cancer. While the recently developed KRASG12C inhibitors offer a targeted KRAS therapy and have shown success in the clinic, KRASG12C represents only 11% of all KRAS mutations. Current therapeutic approaches for all other KRAS mutations are both indirect and non-mutant-selective, largely focusing on inhibition of downstream KRAS effectors such as MAP kinases. Inhibition of KRAS downstream signaling results in a system-wide down-modulation of the respective targets, raising concerns about systemic cell toxicity. Here, we describe a custom short interfering RNA (siRNA) oligonucleotide (EFTX-D1) designed to preferentially bind mRNA of the most commonly occurring KRAS missense mutations in codons 12 and 13. We determined that EFTX-D1 preferentially reduced the mutant KRAS sequence versus wild-type at the levels of both transcription and translation, and reversed oncogenic KRAS-induced morphologic and growth transformation. Furthermore, EFTX-D1 significantly impaired the proliferation of several KRAS mutant cancer cell lines in 2-D as well as 3-D assays. Taken together, our data indicate a novel use of RNA interference (RNAi) to target oncogenic KRAS-driven cancers specifically.

cancer biology↗

bioRxiv2018

Facile real time detection of membrane colocalization of RAS superfamily GTPase proteins in living cells

Members of the RAS family of GTPases (KRAS4A, KRAS4B, HRAS, and NRAS) are the most frequently mutated oncogenes in human cancers. The CAAX motif in the C-terminal hypervariable region (HVR-CAAX domain) contains the cysteine residue that is critical for protein prenylation that enables RAS protein membrane localization, homodimer/oligomer formation, and activation of effector signaling and oncogenic activity. However, it remains unclear if RAS can interact with other prenylated proteins, and if so, how this impacts RAS function. Here we use a newly developed quantifiable Recombinase enhanced Bimolecular Luciferase Complementation strategy (ReBiL2.0) to investigate some of the requirements for RAS superfamily small GTPase protein interactions, and whether this requires cell membrane localization. ReBiL enables such analyses to be done at physiologic expression levels in living cells. Our results confirm that the C-terminal prenylated HVR-CAAX domain is sufficient to direct KRAS and heterologous proteins to colocalize in the cell membrane. We discovered that KRAS also colocalizes with a subset of small GTPase superfamily members including RAC1, RAC2 and DIRAS3 in a prenylation-dependent manner. KRAS colocalization or co-clustering with heterologous proteins can impact KRAS downstream signaling. ReBiL2.0 thus provides a rapid, simple and straightforward method to identify and characterize the colocalization of membrane-associated proteins and to discover agonists and antagonists thereof.

cancer biology↗