tbuckley/cabot-search huggingface dataset:
Abstract 5597: Clinical significance of RNA polymerase I inhibitor in pancreatic cancer therapy
Authors: Mudassier Ahmad
Journal: Cancer Research (2024)

Abstract Pancreatic cancer (PanCa) is the third leading cause of cancer-related deaths in the United States with limited therapeutic options available. Gemcitabine (GEM), a deoxycytidine nucleoside analog is currently considered the most effective therapy for PanCa. However, it shows only a marginal survival benefit of six months. Aberrant ribosome biogenesis occurs in most tumor types. We observed that PanCa cells are addicted to ribosome biogenesis (RiBi), which supports their highly aggressive metastatic phenotypes. Thus, strategically targeting RiBi process could be one of the ideal strategies for the prevention and treatment of PanCa. In this study, we elucidated the molecular mechanisms of POLR1A (RPA194) overexpression and how its targeting along with p53 status impacts RNA polymerase I inhibitor therapy against PanCa. The expression level of RPA194 was significantly elevated in pancreatic tumor tissues when compared with adjacent normal pancreatic tissues. BMH-21 is a potent pharmacological inhibitor of RNA Pol I, which is known to degrade RPA194 protein. Our results demonstrated that BMH-21 can selectively induce apoptosis in various PanCa cells but not in HPNE cells. We also found that the cytotoxic effect of BMH-21 was dependent on the expression pattern of RPA-194 and p53 status. We further examined the therapeutic efficacy of BMH-21 in orthotopic xenograft mouse models by using two different PanCa cells, AsPC1 which contains non-functional p53 and MIA PaCa-2 which contains functional mutant p53. We observed that BMH-21 significantly inhibited the growth of tumors derived from both cancer cell lines. Interestingly, BMH-21-mediated inhibition of tumor growth was more significant in tumors derived from MIA PaCa-2 cells compared to AsPC1 cells. Further examination revealed that the inhibition of tumor growth was correlated with RPA194 degradation followed by inhibition of cell proliferation. Overall, our results strongly suggest that BMH-21 is a promising non-toxic agent for the treatment of advanced PanCa and its therapeutic potential depends on RPA194 expression and p53 status in PanCa cells. Citation Format: Mudassier Ahmad. Clinical significance of RNA polymerase I inhibitor in pancreatic cancer therapy [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 5597.
Abstract 2831: Development and application of the NCG-hIL2 mouse model: A humanized platform for enhanced NK cell evaluation in ADCC efficacy testing
Authors: Yuan Fang, Hongyan Sun, Huiyi Wang, Jun Xing, Jialu Fan, Jing Zhao, Xiang Gao, Cunxiang Ju
Journal: Cancer Research (2024)

Abstract Natural Killer (NK) cells play a pivotal role in immune surveillance and antitumor responses, making them valuable targets in cancer immunotherapy. The assessment of therapeutic antibodies' efficacy, particularly in the context of Antibody-Dependent Cell-Mediated Cytotoxicity (ADCC), necessitates models that faithfully recapitulate human NK cell responses. Here, we introduce the NCG-hIL2 mouse model, designed to address these requirements and advance our understanding of NK cell development. The NCG-hIL2 mouse model was engineered to express human Interleukin-2 (IL2) cytokine, a critical factor in NK cell development and activation. This humanized platform allows for the robust reconstitution of human NK cells through the transplantation of peripheral blood mononuclear cells (PBMCs) or hematopoietic stem cells (HSCs). In this study, we validate the NCG-hIL2 model's exceptional capability in supporting the reconstitution of human NK cells, highlighting the indispensable role of IL2 in NK cell development. Moreover, we demonstrate its utility in the evaluation of therapeutic antibodies, specifically Trastuzumab and the ADCC-enhanced Margetuximab, in the context of ADCC efficacy testing. Our findings reveal that the NCG-hIL2 model provides a unique advantage for assessing the impact of IL2 on NK cell development, thus facilitating a deeper understanding of the complex interplay between NK cells and therapeutic antibodies. The NCG-hIL2 mouse model serves as a valuable tool for studying NK cell development and evaluating the efficacy of immunotherapies, particularly in ADCC. By reconstituting human NK cells and leveraging the role of IL2, this model offers an enhanced platform for preclinical evaluation of therapeutic antibodies, ultimately advancing our ability to harness NK cell-mediated antitumor responses. It is poised to contribute significantly to the field of cancer immunotherapy and drug development. Citation Format: Yuan Fang, Hongyan Sun, Huiyi Wang, Jun Xing, Jialu Fan, Jing Zhao, Xiang Gao, Cunxiang Ju. Development and application of the NCG-hIL2 mouse model: A humanized platform for enhanced NK cell evaluation in ADCC efficacy testing [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 2831.
Abstract 7205: PLK1 inhibition overcomes PARP inhibitor resistance in triple-negative breast cancer
Authors: Abdul K. Siraj, Pratheesh Kumar Poyil, Divya Padmaja, Sandeep Kumar Parvathareddy, Khadija Alobaisi, Rafia Begum, Osama Almalik, Fouad Al-Dayel, Khawla S. Al-Kuraya
Journal: Cancer Research (2024)

Abstract Patients with aggressive breast cancer (BC) subtypes usually do not have favorable prognosis despite improvements in treatment modalities. These cancers remain a major cause of morbidity and mortality in women globally. This has fostered a major effort to discover actionable molecular targets to treat these patients. Polo-like Kinase (PLK1) is one of these molecular targets that are under comprehensive investigation for the treatment of such tumors. However, its role in the pathogenesis of BC from Middle Eastern ethnicity has not been explored. Therefore, we examined the expression of PLK1 protein in a large cohort of more than 1500 Middle Eastern ethnicity BC by immunohistochemistry. Correlation with clinico-pathological parameters and the prognosis was performed. PLK1 overexpression was observed in 27.4% of all BC and was significantly associated with aggressive clinico-pathological markers. The antitumor effect of PLK1 and PARP inhibitors either alone or in combination was tested in two BRCA mutated, and one BRCA proficient TNBC cell lines. We showed that combined inhibition significantly reduced cell survival and induced apoptosis in TNBC cell lines. Furthermore, our data suggest that PLK1 inhibition overcomes PARP inhibitor resistance in TNBC cell lines. These findings would pave the way to explore the future use of PLK1 inhibitors in the clinical setting of PARPi-resistant patients. Citation Format: Abdul K. Siraj, Pratheesh Kumar Poyil, Divya Padmaja, Sandeep Kumar Parvathareddy, Khadija Alobaisi, Rafia Begum, Osama Almalik, Fouad Al-Dayel, Khawla S. Al-Kuraya. PLK1 inhibition overcomes PARP inhibitor resistance in triple-negative breast 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 7205.
Abstract 4377: AT rich interaction domain 5a promotes gastrointestinal tumorigenesis by regulating YAP and STAT3 pathways
Authors: Koji Taniguchi, Kazuya Hamada, Shugo Tanaka, Hiroyuki Kurosu, Issei Kawakita, Kentaro Kumagai, Kentaro Nakazono, Sari Iwasaki, Satoshi Tanaka
Journal: Cancer Research (2024)

Abstract Background: Chronic inflammation and an inflammatory cytokine, interleukin(IL)-6, play important roles in gastrointestinal tumorigenesis and metastasis. Recently, autocrine IL-6 has been reported to promote cancer development and progression in gastrointestinal cancer. However, it is still unknown how IL-6 level is regulated in gastrointestinal cancer cells. RNA-binding proteins (RBPs) are known to be one of the regulatory mechanisms of cytokine production, including IL-6, especially in immune cells. AT rich interaction domain 5a (Arid5a), one of the RBPs, has been reported to bind to IL6 3’UTR and regulates its stability and expression. Therefore, we aimed to elucidate the role of Arid5a in gastrointestinal cancer, especially gastric and colon cancer. Methods: Human gastric and colon cancer cell lines were used in this study. Arid5a knocked-down gastric and colon cancer cells were generated with lentiviral transduction of shRNAs targeting Arid5a and their phenotypes were investigated by several assays including MTT, apoptosis and sphere formation assays. Bulk RNA-seq analysis was performed using Arid5a knocked-down gastric and colon cancer cells. Results: In both human gastric and colon cancer cell lines, Arid5a knockdown suppressed cancer cell proliferation and spheroid formation, and increased apoptosis. Unexpectedly, IL6 mRNA expression was not correlated with Arid5a expression level. We found that Arid5a knockdown suppresses the activation of YAP and STAT3 by western blot analysis. We identified several new Arid5a target genes by bulk RNA-seq analysis. Conclusion: Arid5a plays an important role in the regulation of cancer cell proliferation, apoptosis and stemness in human gastric and colon cancer cells, perhaps independently of IL-6. Arid5a regulates YAP and STAT3 pathways by unknown mechanisms. We are now investigating how Arid5a regulates YAP and STAT3 pathways by focusing new Arid5a target genes. Citation Format: Koji Taniguchi, Kazuya Hamada, Shugo Tanaka, Hiroyuki Kurosu, Issei Kawakita, Kentaro Kumagai, Kentaro Nakazono, Sari Iwasaki, Satoshi Tanaka. AT rich interaction domain 5a promotes gastrointestinal tumorigenesis by regulating YAP and STAT3 pathways [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 4377.
Abstract 7547: Enhancers as targets for improvements in immunotherapy
Authors: Anand Singh, Veena Kochat, Emre Arslan, Suresh Satpati, Wentao Deng, Sandeep Yadav, Efthalia Bataki, Cassian Yee, Kunal Rai
Journal: Cancer Research (2024)

Abstract Role of epigenetic elements in mediating tumor immune interaction remains poorly understood. We previously identified enrichment of active enhancer states on a set of genomic loci in non-responders to immune checkpoint blockade (ICB) therapy. We noted that the activated non-responder enhancers marked a group of key regulators of in melanoma cells that are known to mediate resistance to ICB therapy and several checkpoint receptors in T cells. Through spatial epigenomics (Spatial ATAC and CUT&amp;Tag) approaches, we identified the tumor-immune niches harboring unique gene regulatory elements and transcription factors that could mediate melanoma-T cell interaction. Further, we aimed to identify functional epigenetic elements through custom CRISPRi screening of enhancers in patient tumor-derived melanoma and T cells. CRISPRi approaches identified novel functional enhancers that mediate T cell mediated killing. For example, we identified distal c-MET enhancers as important contributors to T cell mediated killing. In T cells, we identified enhancer hubs that target multiple genes. These hubs could be targeted to activate interferon gamma, reduce T cell exhaustion, and improve T cell mediated killing of melanoma cells. Such enhancer hubs could serve as targets in the ex vivo setting to improve adoptive T cell therapy. Overall, our results suggest that enhancers with unique spatial patterns in melanoma tumors contribute to the response to immunotherapy and could be novel targets for therapy. Citation Format: Anand Singh, Veena Kochat, Emre Arslan, Suresh Satpati, Wentao Deng, Sandeep Yadav, Efthalia Bataki, Cassian Yee, Kunal Rai. Enhancers as targets for improvements in immunotherapy [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 7547.
Abstract 4388: Tumor-associated RhoA mutants interact with effectors in both GDP- and GTP-bound states
Authors: Yuan Lin, Theresa A. Ramelot, Simge Senyuz, Attila Gursoy, Hyunbum Jang, Ruth Nussinov, Ozlem Keskin, Yi Zheng
Journal: Cancer Research (2024)

Abstract RhoA is the founding member of the Ras-homology (Rho) small GTPase family and is a master regulator for multiple cell functions. Recurrent RhoA mutations have been identified in several human cancers, particularly in leukemia/lymphoma and gastric cancer. Intriguingly, both gain-of-function and loss-of-function mutations of RhoA are present, suggesting that RhoA GTPase may have a more sophisticated role in cancer and requires more rigorous investigations. Here, we have focused on two of the gain-of-function RhoA mutations identified in Adult T cell Leukemia/lymphoma (ATLL) at residue A161 (A161P and A161V) and aim to reveal the underlying mechanistic basis for their function by biochemical and structural analyses. We found that in contrast to conventional gain-of-function RhoA mutants such as RhoAG14V and RhoAQ63L which affect the GTP-hydrolysis activity, RhoAA161P and RhoAA161Vare both fast-cycling with drastically increased nucleotide dissociation and association rates, but only slightly reduced GTP-hydrolysis activity. We solved the crystal structures of GDP-bound RhoAA161P and RhoAA161V and saw that while RhoAA161P displays impaired solvent-mediated interactions to the bound nucleotide, RhoAA161V has a more exposed nucleotide binding pocket compared to RhoAWT and RhoAA161P. Interestingly, RhoAA161P and RhoAA161Vcan interact with effector targets in the GDP-bound states. Further 1H-15N HSQC NMR study provides evidence of the active population in GDP-bound RhoAA161V. Molecule dynamics (MD) simulations show that the dynamic properties of RhoA switch regions are affected differently by the two mutations. Thus, RhoAA161V and RhoAA161P are fast-cycling mutants with distinct mechanisms, and both likely endow their GDP-bound state towards an active conformation. These findings provide a better understanding of the oncogenic role of RhoA mutations in cancer and shine light on how changes in RhoA protein dynamic properties caused by mutations may affect its function. Citation Format: Yuan Lin, Theresa A. Ramelot, Simge Senyuz, Attila Gursoy, Hyunbum Jang, Ruth Nussinov, Ozlem Keskin, Yi Zheng. Tumor-associated RhoA mutants interact with effectors in both GDP- and GTP-bound states [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 4388.
Abstract 879: The AVERON Notebook to discover druggable cancer dependencies through the mutant-directed protein-protein interactions
Authors: Hongyue (Nicole) Chen, Sean Yeung, Brian Revennaugh, Haian Fu, Andrey A. Ivanov
Journal: Cancer Research (2024)

Abstract Cancer is a devastating disease that takes more than 10 million lives every year. The genomic alterations, such as mutations in cancer driver genes, can disrupt the essential networks of protein-protein interactions (PPIs), dysregulating major oncogenic pathways and inducing the transformation. While some mutations can disrupt existing PPIs, others can create neomorph PPIs (neoPPIs), which are unnatural for wild-type counterparts. Discovery of such mutant-created neoPPIs is vital for understanding the molecular mechanisms of mutant-driven tumorigenesis and developing new personalized clinical strategies in cancer. However, systematic experimental interrogation of the clinical significance and biological functions of neoPPIs is highly challenging. To address this critical challenge, we develop a novel computational platform called AVERON Notebook for identifying new Actionable Vulnerabilities Enabled by Rewired Oncogenic Networks. The AVERON employs specially designed algorithms and statistical techniques to i) Assess and compare the levels of neoPPIs in cancer patients; ii) Examine their impact on clinical outcomes; iii) Identify distinctive sets of signature genes and oncogenic pathways regulated by individual neomorph PPIs; and iv) Discover clinically significant neoPPI-regulated genes with available clinical compounds and approved drugs. Together, the AVERON Notebook provides a powerful tool for exploring the functional consequences of tumor-driving mutations mediated through the neoPPI networks and sheds new light on previously unexplored clinically actionable dependencies enabled by neomorph PPIs in cancer patients. The AVERON Notebook is freely available onGitHub: https://github.com/aivanovlab/averon_notebook and Code Ocean: https://doi.org/10.24433/CO.7986101.v1 Acknowledgments: This work was supported in part by NCI’s Informatics Technology for Cancer Research (ITCR) Program (R21CA274620, A.A.I.), Mary Kay Foundation Grant for Cancer Research (A.A.I), NCI Emory Lung Cancer SPORE (P50CA217691, H.F.), NCI P01CA257906 (H.F.), Career Enhancement Program (A.A.I., P50CA217691), Winship Cancer Institute (NIH 5P30CA138292). Citation Format: Hongyue (Nicole) Chen, Sean Yeung, Brian Revennaugh, Haian Fu, Andrey A. Ivanov. The AVERON Notebook to discover druggable cancer dependencies through the mutant-directed protein-protein interactions [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 879.
Abstract 5584: Experimental ‘loss-of function’ annotation of STK11 mutations with prognostic and therapeutic implications (TNG260mutationfinder.com)
Authors: Leanne G. Ahronian, Preksha Shahagadkar, Lauren Flynn, Lauren Grove, Shangtao Liu, Samuel R. Meier, Binzheng Shen, Hannah Stowe, Hsin-Jung Wu, Yi Yu, Andre Mignault, Iga Sienczylo, Heather DiBenedetto, Silvia Fenoglio, None Teng
Journal: Cancer Research (2024)

Abstract Loss of function mutations in Serine Threonine Kinase 11 (STK11) occur in 15% of lung adenocarcinoma and have been shown to drive resistance to immune checkpoint blockade clinically, as well as in preclinical models. Though STK11 is commonly inactivated in human cancer with strong implications for treatment outcomes, few STK11 mutations identified from tumor samples have been functionally characterized. TNG260 is an inhibitor of CoREST that is currently being investigated in combination with pembrolizumab for the treatment of STK11-mutant cancer (NCT05887492). Patients are eligible for enrollment in the TNG260 phase 1/2 trial if their tumor contains a deleterious STK11 mutation. To begin classifying non-annotated variants, over 2,000 distinct mutations in the STK11 gene were identified from STK11 literature or public repositories of tumor sequencing data such as AACR Project GENIE and ClinVar. Where possible, loss-of-function annotations were captured from literature or predictive tools such as PolyPhen-2. However, many STK11 variants, particularly missense mutations, have never been functionally characterized. We developed a functional screening approach to characterize STK11 alterations using the lung adenocarcinoma cell line A549. A549 cells contain homozygous loss of STK11 via a truncation mutation at Q37, and re-expression of wild-type STK11 in these cells strongly impairs their growth in vitro and in vivo. We created a library of STK11 variant cDNAs, each containing a unique barcode. This library was expressed in A549, and cells were maintained in vitro or in vivo to allow for positive selection of STK11 loss-of-function variants and depletion of variants that behave like wild-type STK11. At the end of the screen, variants were quantified by NGS using each mutant cDNA’s unique barcode and compared to well-annotated controls. These data were assembled to generate TNG260mutationfinder.com – the first website to curate STK11 variants with functional annotations. Citation Format: Leanne G. Ahronian, Preksha Shahagadkar, Lauren Flynn, Lauren Grove, Shangtao Liu, Samuel R. Meier, Binzheng Shen, Hannah Stowe, Hsin-Jung Wu, Yi Yu, Andre Mignault, Iga Sienczylo, Heather DiBenedetto, Silvia Fenoglio, Teng. Experimental ‘loss-of function’ annotation of STK11 mutations with prognostic and therapeutic implications (TNG260mutationfinder.com) [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 5584.
Abstract 6365: The bispecific antibody KA-3008, targeting both EGFR and B7H3, increases internalization and minimizes on-target, off-tumor toxicity
Authors: Guojin Wu, Li Ding, Hao Peng, Feng Hao, Feng He, Jinying Ning
Journal: Cancer Research (2024)

Abstract EGFR and B7H3 are highly expressed in various solid tumors, as well as in different normal tissues. Targeting EGFR or B7H3 alone with inhibitory monoclonal antibodies or antibody-drug conjugates (ADCs) may result in on-target, off-tumor toxicity. In this study, we developed a bispecific antibody (BsAb) named KA-3008, targeting both EGFR and B7H3 using our common light chain antibody discovery platform. KA-3008, in IgG1 format, features a regular antibody structure with an identical light chain, developed through knob-into-hole technology. Compared to its parent antibodies, its affinities for both EGFR and B7H3 decrease by more than ten times. It binds to cell lines expressing EGFR or B7H3 alone with an EC50 of more than 10nM, while it binds to cell lines expressing both EGFR and B7H3 with an EC50 of less than 1nM. KA-3008 also blocks the binding of EGF to EGFR and increases internalization when binding to both EGFR and B7H3 compared to binding to EGFR or B7H3 alone. In human tumor mouse models, KA-3008 effectively suppresses the growth of NCI-H1568 tumors expressing both EGFR and B7H3, but does not affect the growth of MS751 tumors that only highly express EGFR with low expression of B7H3. Additionally, KA-3008 has a half-life of more than five days in the blood of Balb/c mice. Finally, we assessed the developability of this BsAb with different treatments such as high concentration, low pH, repeated freezing and thawing, and high temperature, and KA-3008 shows neither aggregation nor degradation. In conclusion, the BsAb KA-3008, developed with our common light chain antibody discovery platform, is stable and holds potential for the development of ADCs targeting both EGFR and B7H3. Citation Format: Guojin Wu, Li Ding, Hao Peng, Feng Hao, Feng He, Jinying Ning. The bispecific antibody KA-3008, targeting both EGFR and B7H3, increases internalization and minimizes on-target, off-tumor toxicity [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 6365.