tbuckley/cabot-search huggingface dataset:
Abstract 3336: Regulation of liver X receptor protein stability by novel ligands in pancreatic cancer cells
Authors: Abhinav Bagchi, Kasuni T. Gamage, Scott R. Gilbertson, Chin-Yo Lin
Journal: Cancer Research (2024)

Abstract Liver X Receptors (LXRs) are nuclear receptors that act as ligand-modulated transcription factors. LXRs are overexpressed in various cancers, including pancreatic cancer, and targeting LXR with small molecule ligands has emerged as a promising therapeutic strategy in cancer. Current small molecule LXR ligands were originally developed for the treatment of atherosclerosis and other metabolic diseases. To identify ligands specifically targeting cancer cells, we screened a focused library of drug-like molecules predicted to bind to LXR using molecular docking. In the screen, novel LXR ligand GAC0001E5 (1E5) exhibited significant anti-proliferative effects in human pancreatic ductal adenocarcinoma (PDAC) cell lines. Functionally, 1E5 is an LXR inverse agonist which decreases LXR target gene expression and a “degrader” of LXR proteins following prolonged treatment. We posit that this novel ligand inhibits PDAC cells by downregulating the expression of LXR target genes. To test this hypothesis, we treated cancer cells with the previously described LXR inverse agonist SR9238 and examined its effect on cancer cell proliferation. Interestingly, treatments with SR9238 had no effect on pancreatic cancer cell proliferation as compared to the novel ligand 1E5 and the 1E5 derivative KD-95, suggesting that LXR inverse agonism was insufficient to inhibit cell proliferation. To determine whether SR9238 has similar effects on LXR protein levels as novel ligands, we performed western analysis of protein expression following ligand treatment. In contrast to the novel ligands 1E5 and KD-95, treatments with SR9238 increased LXR protein levels. Furthermore, time-course studies in cycloheximide treated cells indicated that novel ligands decreased protein stability whereas SR9238 had the opposite effect. Inhibition of proteasomal degradation and autophagy abolished the effects of 1E5 and KD-95 in a cell line-dependent manner. Related to these observations, previously published data revealed that knockdown of LXR expression greatly diminished PDAC cell proliferation. Taken together, these findings indicate that LXR expression is essential in pancreatic cancer cells and suggest that the novel ligands may disrupt its involvement in protein-protein interactions and non-genomic mechanisms. Citation Format: Abhinav Bagchi, Kasuni T. Gamage, Scott R. Gilbertson, Chin-Yo Lin. Regulation of liver X receptor protein stability by novel ligands in pancreatic cancer cells [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 3336.
Abstract 5512: Cerebral endothelial FAK paradoxically inhibits brain metastasis <i>in vivo</i>
Authors: Shoko Noda-Narita, Atsu Aiba
Journal: Cancer Research (2024)

Abstract Introduction: In cancer metastasis in the trunk, the secreted proteins from tumors, such as VEGFs and TNF-α, activate focal adhesion kinase (FAK) in vascular endothelial cells (VECs). The activated FAK promotes VE-cadherin phosphorylation and the expression of cell adhesion molecules, and it facilitates the extravasation of cancer cells. In the cerebral blood vessels, the VECs maintain very strong cell adhesion supported by the surrounding pericytes and astrocytes. The strong barrier of cerebral VECs is called the blood-brain barrier (BBB) and is regulated differently from trunk VECs. Although the role of FAK in trunk metastasis is shown in many studies, its importance in brain metastasis is not verified. In this study, we focused on the role of the cerebral endothelial FAK and compared the role of FAK in brain metastasis with that in trunk metastasis. Methods: We generated tamoxifen-inducible VEC-specific FAK knockout (FAK-cKO) mice (VEcad-CreERT2; Ptk2-flox/flox) and brain metastatic (BrM) cell lines of Ex3LL (murine lung cancer cell line). We intracardially injected BrM cells of Ex3LL into the FAK-cKO mice and analyzed the tumor development using in vivo bioluminescence imaging and a CUBIC tissue clearing system. We also analyzed the intracranially injected mice of the parental and BrM cell lines to evaluate the tumor angiogenesis, which is reported to be promoted by the endothelial FAK. Results: Although FAK-cKO in VECs has been reported to inhibit lung metastasis, brain metastasis was accelerated in FAK-cKO mice compared with control mice. The number of brain metastatic sites increased in FAK-cKO mice, but there was no difference in the individual tumor size. It suggests that the brain metastasis was promoted by FAK-cKO, but that the proliferation of brain metastasis was not promoted by FAK-cKO. Blood vessel density was decreased with irregular shape in the brain tumors of FAK-cKO mice, suggesting that the angiogenesis was inhibited by FAK-cKO. It indicates that the angiogenic function of endothelial FAK in the brain vasculature was not different from that in the trunk. Conclusion: FAK-cKO in VECs exacerbated the brain metastasis of the BrM cells although it has been reported to inhibit the metastasis in the trunk. FAK-cKO in VECs decreased tumor angiogenesis both in the brain and the trunk. It suggests that the regulatory mechanism of cell adhesion and the FAK function in the brain vasculature is partly different from that in the other organs in the body trunk. We need further investigation to elucidate the function of endothelial FAK in brain metastasis. Citation Format: Shoko Noda-Narita, Atsu Aiba. Cerebral endothelial FAK paradoxically inhibits brain metastasis in vivo [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 5512.
Abstract 6958: CRIPTO-regulated extracellular vesicles mediate heterotypic cellular crosstalk in triple negative breast cancers
Authors: David W. Freeman, Brooke L. Gates, Mauri D. Spendlove, Benjamin T. Spike
Journal: Cancer Research (2024)

Abstract Tumor progression involves dynamic interaction between various cell types within the tumor microenvironment. Fibroblasts, which normally participate in wound healing, reciprocally communicate with breast cancer cells to promote tumor cell plasticity and heterogeneity. Gaining insights into the molecular mechanisms underlying this cell-to-cell communication, could unlock novel therapeutic avenues for inhibiting cellular plasticity, breast cancer progression and metastasis. The small GPI-anchored adaptor protein CRIPTO is a key player in this context though important molecular details remain to be elucidated. CRIPTO orchestrates TGF-β pathway signaling as well as growth factor-like signaling pathways that activate c-Src/MEK/AKT, in an autocrine and paracrine manner. CRIPTO is expressed during mammary development, wound healing, and breast cancer but is largely undetectable in homeostatic tissue, making it a promising therapeutic target. Our previous studies have demonstrated that the activity of CRIPTO is contingent upon cellular stress, with pronounced influence within pro-fibrotic, hypoxic domains of tumors. Importantly, we have shown that inhibition of CRIPTO using the soluble recombinant protein antagonist A4Fc effectively impedes the progression of triple negative breast cancer (TNBC) in murine xenograft models. Building upon these findings, we have been dissecting CRIPTO’s role in coordinating fibroblast activation and cell-state reprogramming in TNBC. We find that inhibition of CRIPTO with A4Fc suppresses cancer associated fibroblast (CAF) activation and collagen remodeling in vivo. Further, by modeling tumor cell:fibroblast crosstalk in vitro, we have demonstrated mechanistically that CRIPTO expression in tumor cells mediates subsequent extracellular vesicle (EV) uptake by fibroblasts, as well as fibroblast SMAD pathway activation and priming for reciprocal signaling back to tumor cells to promote transcriptional reprogramming and cellular invasion.The significance of these findings lies in their elucidation of key EV control mechanisms that could be exploited to intervene in essential tumor cell:fibroblast crosstalk or to enhance targeting of therapeutic moieties based on EV architecture and function in cancer and/or normative regenerative processes. Citation Format: David W. Freeman, Brooke L. Gates, Mauri D. Spendlove, Benjamin T. Spike. CRIPTO-regulated extracellular vesicles mediate heterotypic cellular crosstalk in triple negative breast 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 6958.
Abstract 4365: Mechanistic effects of N361 glycosylation in epidermal growth factor receptor protein
Authors: Dennis Lam, Ariel N. Liberchuk, Brandon Arroyo, Andrew L. Wolfe
Journal: Cancer Research (2024)

Abstract Glycosylation is a tightly regulated post-translational modification where structured sugar groups are added to protein amino acid backbones, most commonly on asparagine for N-glycosylation. The glycosylation-regulating metabolic enzyme uridine diphosphate-glucose pyrophosphorylase 2 (UGP2) is required in oncogene-transformed cancer cells, but not in normal cells. UGP2 heavily regulates glycosylation of epidermal growth factor receptor (EGFR) at asparagine 361 (N361), a key site near the ligand binding domain. EGFR is a transmembrane tyrosine kinase receptor that promotes cell proliferation via growth cascades. Mutations and amplifications in EGFR account for a significant fraction of non-small cell lung carcinomas and breast adenocarcinoma, with L858R being the most common oncogenic hotspot. Other glycosylation sites on EGFR have been implicated in ligand binding, dimerization, and phosphorylation of downstream targets. Molecular dynamic simulations suggested that N361 may be important for dimerization or ligand binding. However, the functional relevance of how glycosylation of EGFR at N361 impacts EGFR protein and cellular behaviors remains unclear. To determine the functional relevance of glycosylation at N361, we created glycosylation-defective EGFR N361A mutant, with or without an additional oncogenic EGFR L858R mutant. We expressed these constructs in MCF10A and 293T cells, which do not have pre-existing activation of this pathway. Immunofluorescence and flow cytometry showed that the mutants were each well expressed at the cell membrane. Proximity ligation assays measuring dimerization of EGFR in cells showed that EGFR N361A greatly increased dimerization relative to wildtype controls. Loss of glycosylation of EGFR N361 impacted cell viability when grown in dose courses of its high affinity ligand EGF or lower affinity ligand amphiregulin. Furthermore, EGFR N361A desensitized cells expressing the oncogenic EGFR L858R to inhibitors targeting the extracellular domain, possibly because the mutation alters the antibody binding interface. N361A sensitized EGFR L858R to inhibitors targeting the cytoplasmic domain of EGFR. These findings help us understand the intricate relationship between EGFR and N-glycosylation, reinforcing the critical functional relevance of post-translational modifications on oncogenes. Citation Format: Dennis Lam, Ariel N. Liberchuk, Brandon Arroyo, Andrew L. Wolfe. Mechanistic effects of N361 glycosylation in epidermal growth factor receptor protein [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 4365.
Abstract 7348: CytoCellDB: A gold standard database for classification and analysis of extrachromosomal DNA in cancer
Authors: Liz Brunk
Journal: Cancer Research (2024)

Abstract Extrachromosomal DNA (ecDNA), or double minute chromosomes, are established cytogenetic markers for malignancy and genome instability. More recently, the cancer community has gained a heightened awareness of the roles of ecDNA in cancer proliferation, drug resistance and epigenetic remodeling. A current hindrance to understanding the biological roles of ecDNA is the lack of available cell line model systems with experimental cytogenetic data that confirm ecDNA status. Although several recent landmark studies have identified numerous cell lines and tumor models with ecDNA, the current sample size limits our ability to detect ecDNA-driven molecular differences due to limitations in power. Increasing the number of model systems that are known to express ecDNA would provide new avenues for understanding the fundamental underpinnings of ecDNA biology and would unlock a wealth of potential targeting strategies for ecDNA-driven cancers. To bridge this gap, we created CytoCellDB, a resource that provides karyotype annotations, including ecDNA status, and leverages publicly available global cell line data from the Cancer Dependency Map (DepMap) and the Cancer Cell Line Encyclopedia (CCLE). We expanded the total number of cancer cell lines with ecDNA annotations to 632, or 34% of the cell lines in CCLE/DepMap. Of these, 154 cell lines express ecDNA, which is a 240% increase from the current sample size. We demonstrate that a strength of our framework is the ability to interrogate ecDNA, and the compendium of other chromosomal aberrations, in the context of cancer-specific vulnerabilities, drug sensitivities, and other multi-omic features (genomics, transcriptomics, methylation, proteomics). We anticipate that this resource will lower the barrier to systematic, population-scale discoveries related to ecDNA and will provide insights into strategies and best practices for determining novel therapeutics that overcome ecDNA-mediated drug resistance. Citation Format: Liz Brunk. CytoCellDB: A gold standard database for classification and analysis of extrachromosomal DNA in 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 7348.
Abstract 2333: Methylation based phylogeny and timing in cancer
Authors: Nataliya Guteneva, Eliezer Lichter, Ignaty Leshchiner
Journal: Cancer Research (2024)

Abstract Knowing the chronological sequence of genetic alterations during cancer development and progression is crucial for understanding the process of transformation of normal tissue into malignant tumors. This can offer insights into the etiology and intrinsic cellular mechanisms of the process, presenting opportunities for early detection and treatment of initial disease stages, as well as highlight key events as potential therapeutic. Current methods of establishing progression histories of cancers rely either on direct sequencing of premalignant lesions, which are seldom available for tumors or on computational inference timing methods capable of reconstructing the history from primary tumor data. These methods require genome or exome sequencing data from a relatively large cohort of tumors and provide limited resolution due to overall scarcity of somatic mutations. We utilize a different source of genetic information, genome methylation, that also “records” historic information about acquisition and development of mutations. Over 28 million methylated CpG sites exist in the genome with several percent of them differentially methylated (DMS) between tissue types and tumor vs adjacent normal tissue. The several orders of magnitude higher density of distinctly methylated sites provides unprecedented resolution, needs fewer tumors, can be merged with driver mutation data and co-analyzed with “methylation clock” information that allows to establish early development, phylogeny and progression at unprecedented resolution. We developed methods for whole genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS) and Oxford Nanopore Technologies native methylation sequencing data. Somatic DMS sites have distinct properties from somatic point mutations, can appear and disappear in the process of tumor evolution and development allowing for unique configuration of methylated islands. Our tools perform single sample and cohort level “timing”, multi-sample phylogeny reconstruction and cancer population reconstruction by integrating methylation and mutation information from the same sample. These new methods will significantly contribute to our understanding of cancer initiation and progression at a resolution not available previously. Citation Format: Nataliya Guteneva, Eliezer Lichter, Ignaty Leshchiner. Methylation based phylogeny and timing in 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 2333.
Abstract 527: Cancer cells in the resistant, endocycling cell state exhibit centrosome amplification
Authors: Madison Purkerson, Sarah Amend, Kenneth J. Pienta
Journal: Cancer Research (2024)

Abstract Therapy resistance is one of the most common underlying causes of poor prognosis in cancer patients, ultimately driving fatal outcome. We have previous demonstrated that following chemotherapeutic stress, a subset of cancer cells undergo a mitotic skip and enter an endocycle, causing whole-genome duplication without division. This endocycling cell state is resistant to cytotoxic therapies and thus is an actuator of therapy resistance. Cells in the endocycling state eventually undergo depolyploidization and repopulate the tumor, observed clinically as a recurrence. We also demonstrated that the minus-end directed motor protein KIFC1, a mediator of centrosome clustering, has higher expression in cells following treatment. Centrosome amplification (CA) involves aberrations in centrosome number, where cells have 3 centrosomes. Cells with extra centrosomes create a multi-polar spindle during mitosis, which presents high risk for cell death and arrest, but cancer cells with CA avoid this by clustering extra centrosomes to create a pseudo-bipolar spindle. Based upon this data, we hypothesize that studying centrosome dynamics and abnormalities presents a window into better understanding endocycle biology and this novel mechanism of therapy resistance. Cancer cells were treated with LD50 dose of cisplatin and released from treatment for varying lengths of time. CA in endocycling cells increased from 59.2% to 100% during the treatment recovery period while maintaining identical levels of clustering. Endocycling cancer cells have a nearly 5-fold increase in declustered centrosomes compared to proliferative cells. Centrosomes in endocycling cells are displaced from the perinuclear region and toward the cell periphery. We hypothesize that centrosome number may indicate the number of times a cell has endocycled and provide insight into the timing and mechanism of mitotic bypass. Centrosomes play a major role in microtubule nucleation, affecting cell motility and polarity, and act as signaling platforms, enhancing signaling activation and specificity. Because of this, we hypothesize that CA may be a critical mechanism for endocycling cancer cells to survive and maintain this resistant cell state. Citation Format: Madison Purkerson, Sarah Amend, Kenneth J. Pienta. Cancer cells in the resistant, endocycling cell state exhibit centrosome amplification [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 527.
Abstract 657: Discovery of a novel brain penetrant SHP2 allosteric inhibitor with anti-tumor effects
Authors: Miyeon Kim, Dongsu Kim, Yeejin Jeon, Kyeong Jin Yoon, Anna Jang, Mijung Lee, Dahye Jeon, Soyeon Jang, Jinhwan Kim, Eunji Kim, Jihoon Park, Victor Hong, Hayoun Jung, Sungpil Choi
Journal: Cancer Research (2024)

Abstract KRAS is the most frequently dysregulated oncogene with high prevalence in non-small cell lung cancer (NSCLC), colorectal cancer (CRC), and pancreatic ductal adenocarcinoma (PDAC). Currently, FDA-approved sotorasib and adagrasib provide ground breaking through therapies for cancer patients harboring KRAS G12C mutation. However, there is still high unmet medical needs for inhibitors targeting broader KRAS-driven tumor, especially a substantial unmet medical need for agents that can penetrate BBB to control the brain metastases. SHP2, a key activator of KRAS located in the upstream of RAS pathway, facilitates the conversion of GDP-bound KRAS (off) state to GTP-bound KRAS (on) state serving as a key mechanism of KRAS activation. Therefore, SHP2 could be a promising therapeutic target to shut down the oncogenic RAS pathway as a broad combination partner with RAS/RAF/MEK/ERK pathway inhibitors. Here we report a highly potent and selective brain penetrant SHP2 inhibitor that is designed to target solid tumors metastazied to brain. KT-01766 showed excellent potency against SHP2 protein in various biochemical and cellular assays and showed the robust synergistic effect with RAS pathway inhibitors. KT-01766 as a mono therapy and in combination with KRAS G12C inhibitors demonstrated great anti-tumor efficacy with no apparent toxicity in mouse xenograft models harboring KRAS mutations. Furthermore, robust anti-tumor acitivty was confirmed in intracranial brain tumor model, supporting its potential to control brain-metastasized tumors. The present data suggest that KT-01766 is a potential candidate for combination therapy with agents targeting RAS pathway, as it is able to effectively suppress tumor growth both systemically and within the brain in KRAS mutated cancers. Citation Format: Miyeon Kim, Dongsu Kim, Yeejin Jeon, Kyeong Jin Yoon, Anna Jang, Mijung Lee, Dahye Jeon, Soyeon Jang, Jinhwan Kim, Eunji Kim, Jihoon Park, Victor Hong, Hayoun Jung, Sungpil Choi. Discovery of a novel brain penetrant SHP2 allosteric inhibitor with anti-tumor effects [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 657.