tbuckley/cabot-search huggingface dataset:
Abstract 3289: APOBEC3A drives tumor evolution through activation of ERVs in non small cell lung cancer
Authors: Hideko Isozaki, Ramin Sakhtemani, Naveed Nikpour, Susanna Monroe, Michael Lawrence, Aaron Hata
Journal: Cancer Research (2024)

Abstract Acquired drug resistance to even the most effective anti-cancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified, the underlying molecular mechanisms shaping tumor evolution during treatment are incompletely understood. We recently demonstrated that lung cancer targeted therapies commonly used in the clinic induce the expression of cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug-tolerant cancer cells persisting during therapy. Preventing therapy-induced A3A mutagenesis by gene deletion decreased the chromosomal aberration events and delayed the emergence of drug resistance. Thus, inhibition of A3A may represent a potential therapeutic strategy to prevent acquired resistance. Understanding the regulatory mechanisms of A3A may provide alternative approaches to inhibit A3A mutagenesis. Using a panel drug screen, we found that DNA methyltransferase (DNMT) inhibitor remarkably induces A3A in non-small cell lung cancer cells. RNA-seq profiling revealed that targeted therapy as well as DNMT inhibitor treatment activate expression of distinct classes non-coding repetitive RNA elements, including endogenous retrovirus (ERVs), in drug-tolerant persister cells. Activation of intracellular viral sensing pathways by introduction of exogenous nucleic acids mimicking viral elements induced A3A expression. While the transcription factor NFkB was acutely activated by targeted therapy, TBK1-IRF3 signaling was activated at later time points. These findings suggest that reactivation of ERVs may underlie A3A mutagenic activity and tumor evolution during targeted therapy. Citation Format: Hideko Isozaki, Ramin Sakhtemani, Naveed Nikpour, Susanna Monroe, Michael Lawrence, Aaron Hata. APOBEC3A drives tumor evolution through activation of ERVs in non small cell lung 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 3289.
Abstract 2073: Human breast patient derived organoids: Development and characterization of a new tissue mimetic model
Authors: Rudra Bhowmick, Sudarshan Malla, Sameena Wani, Anirban Chatterjee
Journal: Cancer Research (2024)

Abstract Worldwide, breast cancer (BC), is the most frequently diagnosed cancer among women. In the US, 1 out of 8 women may expect to be diagnosed with BC In their lifetime. Current models for studying BC tumor biology and BC drug discovery include 2D cultured cell lines and patient derived xenografts (PDX). As 2D cultured cells do not represent the 3D complexity of human tissue, and PDX models are time consuming and cost prohibitive, better tissue mimetic models are needed. Organoids are self-assembled 3D cultured cellular units that may mimic the corresponding human tissue structurally and functionally (1). Patient derived organoids (PDO) are developed from tissue of specific patients and may resemble the source tissue in molecular features, including recapitulation of patient specific responses to therapies (2). Here, we report development and characterization of novel breast PDO lines from fresh (≤24h post-surgery) and cryopreserved (≤7 days post-surgery) tissue. Breast tumor and normal, tumor adjacent (NTA) tissue were sourced from consented patients. Breast PDO were generated following modifications to a published protocol (3). Briefly, tissue samples were minced, digested with collagenase, and filtered. The filtrate was resuspended in Matrigel (Corning) and small drops were added on cell culture plates. Both tumor and NTA PDO were cultured using the same media and organoids were monitored using brightfield microscopy (Olympus CK40) and live cell imaging (Muvicyte, Perkin Elmer). PDO lines were analyzed for expression and distribution of important breast-specific biomarkers using confocal microscopy (ImagExpress, Molecular Devices). PDO lines displayed hormone receptors (ER, PR), cell surface (EpCAM, CD49f), cytoskeletal (cytokeratin 14, 19, E-cadherin, vimentin) and cell proliferation (Ki67) markers. Transcriptome profiles were analyzed using vendor services (Azenta). PDO were also tested for their susceptibility to breast cancer drugs, e.g., Tamoxifen, chlorambucil and Docetaxel. We have successfully generated one NTA ER+/PR+/HER2− PDO line and one tumor ER+/PR+/HER2− PDO line from different donors. Our breast PDO lines would be highly useful in understanding tumor biology, BC progression, signal transduction, and drug discovery/testing. Future efforts would include process scaling up and development of BC specific assays. References:1.Zhao et al., 2022. STAR Protocols 2.Bleijs, M. et al., 2019. EMBO J3.Dekkers et al., 2021. Nature Protocols Citation Format: Rudra Bhowmick, Sudarshan Malla, Sameena Wani, Anirban Chatterjee. Human breast patient derived organoids: Development and characterization of a new tissue mimetic model [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 2073.
Abstract 1737: METTL3-mediated m6A modification promotes tumor progression in upper tract urothelial carcinoma
Authors: LI-JIE LIN, PEI-HUA PENG, KAI-WEN HSU
Journal: Cancer Research (2024)

Abstract Upper tract urothelial carcinoma (UTUC), comprising 5% of urothelial neoplasms, is a rare malignancy arising from the transitional epithelium of the renal pelvis and ureter. Its rarity and diverse histology pose diagnostic and therapeutic challenges, often lead to delayed diagnoses. The absence of targeted therapies, coupled with a limited understanding of molecular pathogenesis, underscores the ongoing research in urological oncology for effective UTUC management. N6-methyladenosine (m6A) is the predominant RNA methylation in mammalian cells, with its inscription primarily orchestrated by METTL3, a crucial methyltransferase. METTL3 has been implicated in various cancers, affecting critical processes like proliferation, migration, and tumor progression. However, the specific mechanisms and biological function of how METTL3/m6A regulates the progression of UTUC remain unclear. In our study, we found that m6A modification and METTL3 expression were elevated in aggressive UTUC, both are negatively correlated with unfavorable clinical outcomes and poor patient survival. By overexpressing METTL3 in less aggressive UTUC cell lines BFTC909 and KTCC28, the abilities of cell proliferation, migration, invasion, and colony formation increased. Notably, overexpression of METTL3 also increased tumor growth and metastasis in the in vivo orthotopic mouse model. In contrast, knockdown of METTL3 decreases tumor progression in a highly aggressive UTUC cell line KTCC28M. Furthermore, our comparative analysis of RNA-seq and m6A MeRIP-seq datasets unveiled the regulation of 1660 genes by METTL3. This diverse set includes genes associated with tumor growth and metastasis (such as MYC, JAK2, and STAT3), as well as RNA processing-related genes which their critical roles in modulating mRNA stability and splicing (such as GEMIN5 and PABPC1L). Together, we noticed METTL3/m6A is a crucial protagonist in the oncogenic landscape of UTUC, which suggested that it can be used as a target for novel therapeutic strategy for UTUC treatment. Citation Format: LI-JIE LIN, PEI-HUA PENG, KAI-WEN HSU. METTL3-mediated m6A modification promotes tumor progression in upper tract urothelial 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 1737.
Abstract 4486: Characterization of a novel mutant selective, EGFR sparing, ErbB2 inhibitor with activity across activating mutations in systemic and CNS tumors
Authors: Jennifer Fulton, Tanna Bettendorf, Abiezer Blandon, Karyn Bouhana, Richard K. Brizendine, LouAnn Cable, Mark J. Chicarelli, Michelle Crow, Brad Fell, John Fischer, Anna Guarnieri, Madison Hillman, Ravi Jalluri, Vijay Kumar, Cori A. Malinky, Rob Rieger, John Robinson, Lee Stunkard, Francis Sullivan, John I. Trujillo, Shannon Winski, Yeyun Zhou
Journal: Cancer Research (2024)

Abstract Alterations in ErbB2, including amplification, overexpression, insertions, and point mutations, are established oncogenic drivers in many solid tumors. These mutations are found in approximately 3-4% of breast cancers and 3% of advanced lung cancers and have emerged as mechanisms of acquired resistance to targeted therapies. ErbB2 alterations are also found in metastatic breast and lung cancers that have advanced to the brain and remain a major clinical challenge with limited therapeutic options. Currently approved ErbB2 tyrosine kinase inhibitors have inferior potency against these mutations and lack sufficient brain penetration to be an impactful treatment option for patients. Herein, we describe advanced preclinical profiling of our candidate series of brain-penetrant EGFR-sparing ErbB2 inhibitors with activity against prevalent point mutations and exon 20 YVMA insertions. Citation Format: Jennifer Fulton, Tanna Bettendorf, Abiezer Blandon, Karyn Bouhana, Richard K. Brizendine, LouAnn Cable, Mark J. Chicarelli, Michelle Crow, Brad Fell, John Fischer, Anna Guarnieri, Madison Hillman, Ravi Jalluri, Vijay Kumar, Cori A. Malinky, Rob Rieger, John Robinson, Lee Stunkard, Francis Sullivan, John I. Trujillo, Shannon Winski, Yeyun Zhou. Characterization of a novel mutant selective, EGFR sparing, ErbB2 inhibitor with activity across activating mutations in systemic and CNS tumors [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 4486.
Abstract 2059: An image-based real time method to measure antibody-dependent cellular phagocytosis
Authors: Jianyong Wang, Yongchang Shi, Yonglian Sun, James T. Koerber, Akiko Seki, Sascha Rutz
Journal: Cancer Research (2024)

Abstract Antibody-dependent cellular phagocytosis (ADCP) is an important mechanism of action of therapeutic antibodies. In vitro quantification of macrophage phagocytosis has been technically challenging. Flow cytometry assays were traditionally used for ADCP activity measurements, these methods were static measurements at certain time point, thus provide no information about engulfment kinetics. Moreover, the flow cytometry assays require lifting the macrophage cells from the labware which may affect macrophage activities. We have developed a real time ADCP assay using a live cell analysis system. The target cells labeled with a pH sensitive dye only fluoresce when they are engulfed in acidic phagosomes in the presence of specific antibodies. Our assay is a plate-based with a simple mix and read protocol without disturbing the macrophages. The new method is quantitative and robust, can be readily used for high-throughput screening for functional antibodies. By studying the ADCP activities of different subtypes of macrophages, we found M2 microphages showed the strongest ADCP activity compare to M0 and M1 macrophages, due to their different expression levels of FcgRs. The assay is highly sensitive to differentiate the antibody variants with enhanced Fc function. It can also be used to study the kinetics and mechanisms of ADCP. Citation Format: Jianyong Wang, Yongchang Shi, Yonglian Sun, James T. Koerber, Akiko Seki, Sascha Rutz. An image-based real time method to measure antibody-dependent cellular phagocytosis [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 2059.
Abstract 2655: Unexpected role of the NuRD component, Chd4, in Foxp3+ Treg cells and its relevance to tumor immunotherapy
Authors: Wayne W. Hancock, Liqing Wang, Martina Minisini, Eros di Giorgio, Ivan Babic, Elmar Nurmemmedov
Journal: Cancer Research (2024)

Abstract We are investigating basic questions like why do Foxp3+ T-regulatory (Treg) cells have at least 3 nuclear complexes involving Hdac1 and Hdac2 (CoREST, Sin3, NuRD), and how can the inhibitory effects of Foxp3+ Tregs on host anti-tumor immune responses be targeted therapeutically? Here, we report on the immune functions of chromodomain-helicase-DNA-binding protein 4 (Chd4), a key enzyme of the nucleosome remodeling and deacetylase complex (NuRD) complex. TCGA analysis showed increased Chd4 expression and Foxp3+ Tregs within lung tumors, leading us to assess the effects of conditional gene deletion within Foxp3+ murine Tregs. Chd4 knockout led to systemic autoimmunity and death of mice within 3 weeks of life and RNAseq studies showed Chd4 loss led to derepression of ~1400 genes and repression of &amp;gt;700 further genes resulting in a Treg signature markedly different from conditional deletion of Hdac1, Hdac2 or Mbd2 in Treg cells. Chd4 is an intrinsically disordered therapeutic target without a defined structure outside its physiological cell environment. To date, no specific inhibitors targeting Chd4 have been developed. We have identified Ch41, a novel and potent inhibitor of Chd4, using a novel cellular target engagement platform. Transcriptomic and mass-spec investigations showed that Ch41 impaired thymic Treg function and iTreg development, led to decreased CNS2 demethylation within the Foxp3 locus, and significantly impaired growth of lung tumors and hepatocellular carcinomas in immunocompetent but not in immunodeficient C57BL/6 mice (p&amp;lt;0.01). Following Chd4 inhibitor therapy, intratumoral conventional T cells had increased activation and cytokine production (IL-2, IFN-g) compared to intratumoral T cells in control tumor-bearing mice but, perhaps unexpectedly, treated mice did not show histologic or biochemical evidence of autoimmunity. We conclude that while tumor associated Tregs have unique properties that include their increased suppressive activity compared to non-tumor associated Treg cells, they are also more susceptible than the latter and conventional T cells to newly developed therapeutic interventions, including targeting of the Chd4 chromodomain of the NuRD complex. Citation Format: Wayne W. Hancock, Liqing Wang, Martina Minisini, Eros di Giorgio, Ivan Babic, Elmar Nurmemmedov. Unexpected role of the NuRD component, Chd4, in Foxp3+ Treg cells and its relevance to tumor 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 2655.
Abstract 7074: Perturbed RNA N6-methyladenosine methylome in SETD2 mutant clear cell renal carcinoma
Authors: Shafiq Shaikh, Ryan Wagner, Ryan Hlady, Keith D. Robertson
Journal: Cancer Research (2024)

Abstract Clear cell renal carcinoma (ccRCC), which arises from the epithelial cells of the proximal tubule represents 70% of all renal cell carcinoma. Mutations that drive ccRCC in conjunction with near ubiquitous and early VHL loss include, PBRM1 (33 - 45%), BAP1 (15%) and SETD2 (13%). Loss of SETD2 leads to diminished occupancy of H3K36me3 in active gene bodies, which is progressively deregulated in primary RCC and metastasis, linking loss of H3K36me to tumor progression and metastasis. N6-Methyladenosine (m6A) is an important post-transcriptional regulator of RNA transcript stability and half-life. Preliminary findings have shown H3K36me3 (deposited by SETD2), targeting the core m6A methyltransferase machinery (METTL3, METTL14 and WTAP) to the mRNA by virtue of its interaction to METTL14 subunit. The goal of this study is to investigate if H3K36me3 depletion as observed in SETD2 mutant ccRCC, leads to a deregulated m6A methylome. We further investigate how deregulated methylome in key pathways leads to cancer initiation and progression in ccRCC. To accomplish our goals, we generated isogenic ccRCC cell lines with H3K36me3 depletion by knocking out SETD2. RNA-immunoprecipitation and sequencing for m6A (MeRIP) showed global deregulation of m6A methylome in SETD2KO isogenic ccRCC cell lines. We also show a number of pro-tumorigenic genes and pathways including cell invasion, inflammation and stemness being differentially methylated and expressed in SETD2KO ccRCC cell lines. Furthermore, we show SETD2KO cells being more sensitive to METTL3 inhibition suggesting the relevance of m6A hypermethylated transcripts in promoting pro-tumorigenic and growth promoting processes in SETD2KO ccRCC cell lines. Citation Format: Shafiq Shaikh, Ryan Wagner, Ryan Hlady, Keith D. Robertson. Perturbed RNA N6-methyladenosine methylome in SETD2 mutant clear cell renal 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 7074.
Abstract 6064: Discovery of potent and selective EP300 degraders with anti-cancer activity
Authors: Mark Zimmerman, Ammar Adam, Hafiz Ahmad, Benjamin Adams, Ketaki Adhikari, Wesley Austin, Breanna Bullock, Julie Di Bernardo, Thomas Dixon, Danette Daniels, Claudia Dominici, GiNell Elliot, Brian Ethell, Anais Gervais, Md Imran Hossain, David Huang, Dave Lahr, Mei Yun Lin, David Mayhew, Karolina Mizeracka, Solymar Negretti, Tyler Nguyen, Olga Prifti, Darshan Sappal, Shawn Schiller, Brenna Sherbanee, David Terry, Nihan Ucisik, Elizabeth Wittenborn, Qianhe Zhou, Laura La Bonte
Journal: Cancer Research (2024)

Abstract E1A binding protein (EP300) and CREB binding protein (CBP) are paralog histone acetyltransferases involved in many cellular processes via their activity as transcriptional co-activators. Dysregulation of one or both proteins has been implicated in various cancers, and functional genomic screens have demonstrated a bidirectional synthetic lethal relationship between the two genes in tumor cells. Due to the high homology between EP300 and CBP, identifying chemical matter that selectively targets EP300 or CBP has proven challenging. Here, we describe a potent, highly selective heterobifunctional degrader of EP300 with biological activity in CBP-deficient and EP300-dependent tumor cells. Targeted degradation of EP300 protein resulted in a stronger suppression of cell growth and survival than targeting the bromodomain or HAT activity of EP300/CBP with small molecule inhibitors. Anti-proliferative effects have been demonstrated in multiple cancer types, including malignant lymphomas and castration-resistant prostate tumors, highlighting the essential role of EP300 in mediating oncogenic transcription required for tumor cell growth and survival. Degradation of EP300 in vivo attenuated androgen-driven transcription and inhibited tumor growth in VCAP (AR+) prostate tumor xenografts. Importantly, no evidence of overt toxicity or thrombocytopenia was observed at therapeutically efficacious doses. These findings indicate that selective targeting of EP300 with targeted protein degradation is a safe and effective treatment strategy for advanced tumors. Citation Format: Mark Zimmerman, Ammar Adam, Hafiz Ahmad, Benjamin Adams, Ketaki Adhikari, Wesley Austin, Breanna Bullock, Julie Di Bernardo, Thomas Dixon, Danette Daniels, Claudia Dominici, GiNell Elliot, Brian Ethell, Anais Gervais, Md Imran Hossain, David Huang, Dave Lahr, Mei Yun Lin, David Mayhew, Karolina Mizeracka, Solymar Negretti, Tyler Nguyen, Olga Prifti, Darshan Sappal, Shawn Schiller, Brenna Sherbanee, David Terry, Nihan Ucisik, Elizabeth Wittenborn, Qianhe Zhou, Laura La Bonte. Discovery of potent and selective EP300 degraders with anti-cancer activity [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 6064.
Abstract 1873: AST-05X: A novel GCN2 inhibitor as a promising anti-cancer approach for sarcoma
Authors: Youngki Choi, Jinback Lim, Hyo-Hyun Park, Jinho Kang, Hyosong Kim, Kumhee Yun, Hun Jung
Journal: Cancer Research (2024)

Abstract Background Integrated stress response (ISR) is an adaptive signaling pathway that responds to stress and plays an important role in cell fate determination. This pathway enables cellular adaptation and survival under stress conditions by activating specific genes that reduce protein synthesis. Tumors exist in a state characterized by heightened intrinsic and extrinsic stress, heavily relying on a balanced ISR to manage the metabolic demands for rapid growth. ISR (Integrated Stress Response) consists of four major kinases: GCN2, PERK, HRI, and PKR. GCN2 is activated by stress due to amino acid deprivation. Amino acids are crucial for cell survival, and cancer cells, require higher amounts than normal cells, particularly depending on conditionally essential amino acids like glutamine, asparagine, and arginine. GCN2 activation acts as a key mechanism for cancer cells to overcome amino acid deficiencies, making GCN2 a potential target, especially in conjunction with anticancer drugs like asparaginase. In this study, we aimed to identify a potential GCN2 inhibitor to explore a promising anti-cancer approach in sarcoma, a rare cancer with no new therapeutic alternatives. Method The activity verification of ISR kinases was characterized using in-vitro enzyme assays. In-vitro panel assays were employed to determine the selectivity profiling for oncology kinases. The modulation of the ISR pathway was validated using a sarcoma cell line (HT-1080) and a cell line derived from sarcoma patients. Western blot or ELISA assays were employed to measure phospho-GCN2, ATF4, phospho-eIF2a, and CHOP under both basal conditions and amino acid starvation conditions. Gene expression profiling (GEP) of sarcoma patient tissue samples(n=17) was conducted through RNA sequencing (RNAseq) analysis. Results AST-05X is a selective and potent GCN2 inhibitor. AST-05X inhibits the expression of GCN2 and ISR downstream factors (p-eIF2a, ATF, CHOP) in vitro cell-based experiments under amino acid deprivation. In addition, based on the results of ISR-related gene expression profiling GEP analysis, we identified potential CDx biomarkers for evaluating the diagnosis and treatment response of sarcoma. Conclusion This study is currently investigating the efficacy of the drug in sarcoma patient-derived xenograft models. AST-05X is a GCN2 inhibitor that has the potential to validate the inhibition of GCN2 as a promising anti-cancer approach for sarcoma, a rare cancer with limited therapeutic alternatives. Citation Format: Youngki Choi, Jinback Lim, Hyo-Hyun Park, Jinho Kang, Hyosong Kim, Kumhee Yun, Hun Jung. AST-05X: A novel GCN2 inhibitor as a promising anti-cancer approach for sarcoma [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 1873.