tbuckley/cabot-search huggingface dataset:
Abstract 5488: Identifying novel Ewing sarcoma therapeutics using a high-throughput chromatin accessibility assay
Authors: Darian Williams, Andrew McFadden, Austin Hepperla, Min Shen, Tino Sanchez, Gordon Stott, Mark Henderson, Ian Davis, Samantha Pattenden
Journal: Cancer Research (2025)

Abstract Chromatin dysregulation has been implicated in the development of a wide range of diseases, including cancer, as well as therapeutic resistance. Genetic alterations in chromatin regulatory factors and aberrant activity of transcriptional regulators alter chromatin states and drive tumor growth in cancer. One example of a cancer that is driven by alterations in chromatin landscape is Ewing sarcoma, a highly aggressive pediatric cancer of bones and soft tissues. Ewing sarcoma is driven by an oncoprotein generated by the translocation of the EWSR1 and FLI1 genes, resulting in the fusion oncoprotein (EWSR1::FLI1), which activates noncanonical enhancers and alters the expression of critical genes associated with the disease. EWSR1::FL1 is challenging, if not impossible, to target directly with small molecules, and viable therapeutic targets for Ewing sarcoma have been slow to emerge. To broaden the search for druggable targets we developed a target agnostic screening approach that exploits oncoprotein-specific chromatin accessibility states as a relevant and direct functional readout for identifying novel therapeutics. We developed and optimized a 384-well, high throughput (HT) version of the Assay for Transpose-Accessible Chromatin assay (HT-ATAC-seq) that was applied to 500 EWSR1::FLI1-regulated chromatin regions. Using Ewing sarcoma-derived A673 cells, we conducted a pilot screen of 12,000 small-molecule compounds comprising approved drugs, investigational agents, and bioactive compounds. The screen identified 285 compounds that partially reversed Ewing sarcoma chromatin abnormalities. The set of active compounds included Panobinostat, which is currently in preclinical development for Ewing sarcoma. This pilot screen supports the HT-ATAC-seq assay as a robust approach to identify novel compounds that reverse the chromatin alterations associated with Ewing sarcoma. This approach and assay can be adapted to investigate other cancers or pathologies associated with chromatin state alterations. Citation Format: Darian Williams, Andrew McFadden, Austin Hepperla, Min Shen, Tino Sanchez, Gordon Stott, Mark Henderson, Ian Davis, Samantha Pattenden. Identifying novel Ewing sarcoma therapeutics using a high-throughput chromatin accessibility assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5488.
Abstract 7027: Mass spectrometry-based proteomics for accelerating PROTAC and molecular glue drug discovery
Authors: Michael J. Ford, Ravi Amunugama, David L. Allen, Richard C. Jones
Journal: Cancer Research (2025)

Abstract Targeted protein degradation (TPD) platforms, including PROTACs and molecular glues, have revolutionized drug discovery as transformative therapeutic strategies. Recent advancements in mass spectrometry-based proteomics have dramatically improved assay speed and sensitivity, providing actionable insights into degradation profiles and drug efficacy on timescales compatible with discovery chemistry. This study evaluates the practical utility of advanced proteomic assays in supporting TPD research, focusing on their role in streamlining drug discovery pipelines. State-of-the-art proteomic workflows were employed to quantify the proteome-wide effects of PROTACs and molecular glues across diverse cellular models. Assay sensitivity, reproducibility, and throughput were rigorously assessed to determine their real-world applicability. Our findings reveal that these enhanced technologies generate robust, high-resolution datasets, capturing the dynamic interplay between target degradation, protein interactions, and cellular responses. This enabled the rapid identification of optimal degrader candidates and informed structure-activity relationship (SAR) studies. Mass spectrometry-based proteomics has emerged as an essential tool for advancing TPD strategies. By combining heightened sensitivity with operational feasibility, these assays offer critical insights that accelerate the development of PROTACs and molecular glues, bridging the gap between foundational research and clinical application. Citation Format: Michael J. Ford, Ravi Amunugama, David L. Allen, Richard C. Jones. Mass spectrometry-based proteomics for accelerating PROTAC and molecular glue drug discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7027.
Abstract 4053: Dynamic combinatorial p53 post-translational modifications regulate temporal transcription program and cell fates
Authors: Dan Lu
Journal: Cancer Research (2025)

Abstract The tumor suppressor p53 is activated by a range of cellular stresses including DNA damage, oncogenic signals, and nutrient deprivation. Upon activation, p53 transcriptionally upregulates an extensive repertoire of genes including those affecting cell fates such as cell cycle arrest, senescence, and apoptosis. What remains unclear is how information is conveyed through p53 to elicit the appropriate downstream responses according to the nature of the upstream stress. Changes in p53 temporal expression dynamics as well as specific p53 post-translational modifications (PTMs) are known to differentially regulate target gene induction. However, with over 100 known PTMs possible on p53, technical limitations have restricted the ability to detect the combinations of modifications on whole p53 molecules. Using a state-of-the-art mass spectrometry method (I2MS) which enabled the first measurement of individual intact human p53 proteins, we have begun to uncover the landscapes of combinatorial PTMs from different p53 activation regimes in cancer cell lines. Together with complementary p53 modification specific antibodies we identified changes in PTM patterns which were both stimuli and time dependent. For example, we found that in response to double-strand DNA breaks, p53 exhibits pulses of expression. Furthermore, p53’s post-translational modification state is altered between successive pulses, which we ascertained the most prominent temporal change in p53 PTMs in response to DNA damage to be a reduction of multiple p53 lysine acetylations. Inhibition of the deacetylase HDAC1, but not SIRT1, prevented the reduction in p53 acetylation, causing overexpression of senescence and apoptotic genes, and corresponding cell fates. Finally, we abrogated lysine acetylation by generating KR (lysine to arginine) mutations at single or multiple sites on p53, and found that acetylation sites are functionally non-redundant, with specific combinations exerting unique transcriptional effects on p53 target gene inductions. These results demonstrate an interplay between dynamics and modifications as a mechanistic strategy for cellular hubs like p53 to temporally organize multiple processes in individual cells. In addition, it highlights the importance of accounting for dynamical combinations of p53 PTMs in order to achieve the desired cellular response and efficacy of p53-mediated cancer therapies. Citation Format: Dan Lu. Dynamic combinatorial p53 post-translational modifications regulate temporal transcription program and cell fates [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4053.
Abstract 6784: Effect of novel gold(I) compounds on cell proliferation and signaling protein expression in MDA-MB-231 breast cancer cells
Authors: Alexis Pawlak, Talitha T. Rajah
Journal: Cancer Research (2025)

Abstract Gold(I) compounds have been gaining prominence in research as alternative metallo-chemotherapeutic strategies against chemo-resistant tumors. However, the cellular and molecular mechanisms by which gold(I) compounds disrupt cellular processes critical to breast cancer cell proliferation are largely unknown. Our study evaluated the effect of eight novel gold(I) chloride compounds (Table 1) on MDA-MB-231 breast cancer cell proliferation and their mechanistic action on signaling proteins (Bax, Bcl2, pERK1/2). Cell proliferation was assessed by the MTT assay for 24 to 72 hours, and protein expression was analyzed by western blotting and immunodetection after exposure to gold(I) chloride compounds at their respective IC50 concentrations. Our results indicate that except for PEt3AuCl, all compounds inhibited cell proliferation across all exposure times. PCy3AuCl, PiPr3AuCl, PPh3AuCl and PMe3AuCl exhibited the greatest efficacy at low micromolar doses. PPh3AuCl (2-fold) and PBu3AuCl (2.5-fold) displayed high Bax/Bcl2 ratios suggesting proapoptotic effects. All other compounds showed either decreased or unaltered Bax/Bcl2 ratios. Each compound inhibited pERK1/2, with PiPr3AuCl (70%), PMe3AuCl (64%), and PCy3AuCl (52%) showing the greatest inhibition. Overall, our results suggest PCy3AuCl, PiPr3AuCl, and PMe3AuCl inhibited cell proliferation at low micromolar doses most effectively in MDA-MB-231 cells and the cellular mechanism of action likely varies by compound. These could be through altered status of the cell proliferative pERK1/2 protein and/or the apoptotic proteins Bax or Bcl2 in this cell line. This study provides new insights into the cellular mechanism by which these gold(I) compounds may exert their effects in this triple negative human breast cancer cell line and contributes to the growing evidence supporting the potential of gold(I) compounds in cancer therapeutics. Table 1 Effect of Gold(I) Compounds on Cell Proliferation Gold(I) Compound Name Concentration Range Tested (μM) 48 Hour IC50 (μM) Proliferation Inhibition (48 hours) (%) PMe3AuCl 0.1 - 7.5 0.94 ± 0.19 15.8 - 88.4 PEt3AuCl 1 - 300 - 0 - 1.9 PiPr3AuCl 0.1 - 7.5 0.56 ± 0.36 7 - 99.2 PBu3AuCl 0.01 - 2.5 6.3 ± 0.39 0 - 45.7 PtBu3AuCl 0.1 - 7.5 2.3 ± 1.2 0 - 98.6 (PTA)AuCl 1 - 100 69 ± 0.78 0 - 68.3 PCy3AuCl 0.1 - 7.5 0.37 ± 0.21 16.3 - 98.6 PPh3AuCl 1 - 15 1.78 ± 0.40 15.4 - 99.5 Citation Format: Alexis Pawlak, Talitha T. Rajah. Effect of novel gold(I) compounds on cell proliferation and signaling protein expression in MDA-MB-231 breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6784.
Abstract 6346: The chromatin remodeler SMARCA5 selectively shapes nuclear receptor signaling in African American prostate cancer
Authors: Shahid Hussain, Debasis Nayak, Sajad A. Wani, Isra Elhussin, Michael R. Freeman, Christopher C. Coss, Solomon O. Rotimi, Adam R. Murphy, Clayton Yates, Moray J. Campbell
Journal: Cancer Research (2025)

Abstract SMARCA5 is found in distinct chromatin remodeling complexes where it regulates ATP hydrolysis to control nucleosome positioning required for gene expression and DNA repair. Previously, we established the chromatin remodeling enzyme SMARCA5 is significantly down-regulated in African American (AA) compared to European Americans (EA) prostate cancer (PCa). We have now explored how SMARCA5 distorts the epigenome and impacts transcription, as well as cell phenotypes. Firstly, we revealed that the H3K27ac cistrome had significantly different distributions between AA (RC43N) and EA (HPr1AR) normal cells, and AA (RC43T) and EA (LNCaP) PCa cells. Motif enrichment in H3K27ac revealed significant differences with Helix-Loop-Helix motifs enriched in RC43N compared to HPr1AR; and STAT motifs enriched in RC43T compared to LNCaP. Similarly, nuclear receptor (NR) motifs were distinct with vitamin D receptor (VDR) and orphan receptors (e.g., RORG) enriched in RC43T compared to LNCaP. Next we up-regulated SMARCA5’s using dCas9-VP64-activator in the same cells and tested the impact on gene expression with RNA-Seq following treatment with the VDR ligand (1, 25(OH)2D3, 100nM). SMARCA5 regulated ∼1200 genes in both RC43T and RC77T, and only ∼200 genes in LNCaP. The SMARCA5-dependent genes in AA PCa cells models were significantly enriched for luminal-differentiation genes. Likewise, in the AA compared to EA PCa models, GSEA analyses revealed enrichment for inflammation responses, and distinct NR signaling, such as progesterone signaling. Likewise LISA analyses revealed enrichment in the SMARCA5-dependent genes in AA PCa for progesterone signaling. Finally, we also identified a subset of miRNA related to differentiation that were uniquely regulated in AA PCa models by 1, 25(OH)2D3 and a significant number were also SMARCA5-dependent. Ongoing studies are addressing the effect of SMARCA5 on chromatin accessibility using ATAC-Seq. Overall, these studies support the concept the epigenome is shaped by genomic ancestry. The epigenomic-regulator SMARCA5 is significantly downregulated in AA PCa and impacts NRs, including VDR signaling. These findings suggest that African ancestry shapes SMARCA5 functions, NR signaling, and tumor outcomes. Citation Format: Shahid Hussain, Debasis Nayak, Sajad A. Wani, Isra Elhussin, Michael R. Freeman, Christopher C. Coss, Solomon O. Rotimi, Adam R. Murphy, Clayton Yates, Moray J. Campbell. The chromatin remodeler SMARCA5 selectively shapes nuclear receptor signaling in African American prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6346.
Abstract 4849: MYC-mediated resistance to immune activation by SWI/SNF mutation or chemical inhibition
Authors: Shitian Li, Diana Hargreaves
Journal: Cancer Research (2025)

Abstract ARID1A is a critical subunit of the SWI/SNF chromatin remodeling complex, frequently mutated in several cancers. We have shown that loss of ARID1A induces an accumulation of R-loops, leading to cytosolic release of RNA:DNA hybrids and single stranded DNA (ssDNA) and cGAS/STING-dependent activation of Type I interferon (IFN-I) stimulated genes (ISGs). SWI/SNF ATPase inhibitors (FHD-286, BRD98, and BRM014) and degraders (ACBI1) similarly induce ISGs through a cGAS/STING-dependent mechanism. Consequently, ARID1A mutant tumors are more highly infiltrated with cytotoxic CD8+ T cells and exhibited enhanced tumor immunity and sensitivity to immune checkpoint blockade (ICB)1. These results provide a molecular mechanism for the enrichment of ARID1A mutations among ICB responders. However, co-occurring oncogenic mutations in ARID1A mutant cancers, such as MYC, KRAS, and β-catenin, have been associated with immunosuppression in some cases through suppression of IFN-I signaling and ISG expression. It is not known how such co-occurring mutations affect the ARID1A mutant ISG response or whether such mutations would counteract ISG activation by SWI/SNF inhibitors. In this study, we investigate the impact of MYC overexpression on IFN-I responses induced by ARID1A loss or SWI/SNF inhibition in cancer cells. Our data reveal that MYC overexpression impairs the ability of these cells to induce IFN-I response genes (ISGs) when cells are directly stimulated with IFN-I or treated with inhibitors targeting the SWI/SNF complex, including FHD-286 and BRM014. Through bulk RNA-seq, we characterize the molecular mechanisms underlying this resistance, with a focus on IFN-I related genes. This study highlights the suppressive effect of MYC overexpression on IFN-I responses in ARID1A-deficient cancers and suggests a potential link to therapeutic resistance in MYC-high tumors. While the precise molecular mechanisms remain to be fully elucidated, these findings provide a foundation for future studies aimed at understanding the interplay between oncogenic drivers and immune signaling pathways, with implications for developing more effective therapeutic strategies. Reference: (1). Maxwell, M. B., et al. ARID1A Suppresses R-Loop-Mediated STING-Type I Interferon Pathway Activation of Anti-Tumor Immunity. Cell 2024, S0092867424004513. https://doi.org/10.1016/j.cell.2024.04.025. Citation Format: Shitian Li, Diana Hargreaves. MYC-mediated resistance to immune activation by SWI/SNF mutation or chemical inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4849.
Abstract 6446: <i>Yap1</i> and CD276/B7-H3: key players in Sex-biased SHH medulloblastoma immune evasion
Authors: Nourhan Abdelfattah, Sivaraman Natarajan, Han Nhat Tran, Thomas Wong, Jose Maldonado, Rachael McMinimy, Hannah Borland, Shu-hsia Chen, Fernando Camargo, James Olson, Joshy George, Kyuson Yun
Journal: Cancer Research (2025)

The molecular mechanisms driving sex disparities in cancer prevalence, progression, and treatment outcomes represent a crucial yet understudied area with significant implications for cancer therapy. Medulloblastoma (MB), exhibits a pronounced sex bias in incidence and survival rates, with males experiencing higher incidence and poorer prognoses compared to females. This study focused on the role of Yap1 in Sonic Hedgehog medulloblastomas (SHH MBs), which revealed an unanticipated sex-biased role of Yap1 in MB immune evasion. Hippo/Yap pathway is one of the top 10 most dysregulated pathways in human cancer. Our in vivo studies uncovered that Yap1 deletion in a spontaneous SHH MB model significantly extended survival, providing genetic evidence that Yap1 is a critical oncogene in MB formation. Notably, Yap1 deletion/inhibition benefitted males, but not females, revealing its sex-biased function for the first time. Integrated multi-omics analyses showed Yap1 is essential for maintaining MB stem/progenitor cells by activating stemness genes (Sox2) and repressing differentiation genes (Neurod1, Zic1/2) in both sexes. However, Yap1 plays a more pivotal role in immune evasion in males, particularly by regulating the immune checkpoint molecule; Cd276/B7-H3. In males, either CD276 blockade or Yap1 deletion reverses T cell suppression. In contrast, in females, CD276 blockade or Yap1 deletion is not sufficient to overcome T cell suppression, and it requires both interventions to activate T cells. Furthermore, our newly discovered transcriptional target gene signatures of YAP1 predict survival in male but not female patients across multiple human cancers, indicating a highly conserved mechanism across species and cancer types. This study highlights sex-specific differences in tumor:immune interactions downstream of YAP1/CD276. In addition, it reveals a novel sex-biased role of YAP1 transcriptional programs, providing molecular entry points for future research on sex differences in immune response. These results underscore the importance of considering sex as a major variable in mechanistic and therapeutic studies involving Yap1 and CD276, with broader implications for targeted cancer therapies. Citation Format: Nourhan Abdelfattah, Sivaraman Natarajan, Han Nhat Tran, Thomas Wong, Jose Maldonado, Rachael McMinimy, Hannah Borland, Shu-hsia Chen, Fernando Camargo, James Olson, Joshy George, Kyuson Yun. Yap1 and CD276/B7-H3: key players in Sex-biased SHH medulloblastoma immune evasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6446.
Abstract 6873: Discovery and characterization of novel ULK1/2 inhibitors and their ability to degrade ATG13, inhibit autophagy, and treat lung cancer
Authors: Patrick Martin Hagan, Allison Limpert, Douglas Sheffler, Huiyu Ren, Nicholas Cosford
Journal: Cancer Research (2025)

Abstract Lung cancer is the leading cause of cancer-related mortality across all populations. Autophagy (ATG) is a cell survival process by which dysfunctional cellular components are removed and recycled to maintain homeostasis through a lysosomal dependent degradation mechanism. ATG upregulation is implicated as a bad actor in several diseases, particularly K-Ras driven non-small cell lung cancer (NSCLC), where it provides nutrients to lung cancer cells in the nutrient poor and hypoxic tumor microenvironment. ATG also contributes to chemotherapeutic resistance, making it a viable pathway for therapeutic intervention. However, the only clinically available drugs targeting ATG are chloroquine and hydroxychloroquine, which are not ATG-specific and have multiple adverse side effects. ATG is an intricate, multistep process beginning with the Unc-51-like autophagy-activating kinases 1 and 2 (ULK1/2) initiation complex. The supramolecular assembly of this complex relies on the adaptor protein ATG13, which binds ULK1/2. Knockout of ATG13 significantly reduces the viability of lung cancer cell lines, indicating that ATG13 is a viable therapeutic target for lung cancer. Furthermore, our group has characterized other autophagy inhibiting compounds that also robustly degrade ATG13 in cells and tissues, leading to cancer cell death. We have developed and optimized a high throughput screening (HTS) assay whereby ATG13 is HiBit tagged in A549 NSCLC cells (ATG13 HiBit assay) to allow identification of compounds that induce ATG13 protein loss, and therefore inhibit ATG. We have also developed a testing funnel that employs multiple assays to characterize compounds that degrade ATG13 independent of cellular toxicity (cell viability assay), confirm their activity against our protein of interest (In Cell Western blot ATG13 assay), measure their ability to inhibit autophagy (GFP-LC3-RFP-LC3∆G ATG flux assay) and eliminate compounds that cause assay interference (HiBit counterscreen). Using these assays we have identified a novel lead compound which degrade ATG13 and inhibits autophagy resulting in cell death in NSCLC. Citation Format: Patrick Martin Hagan, Allison Limpert, Douglas Sheffler, Huiyu Ren, Nicholas Cosford. Discovery and characterization of novel ULK1/2 inhibitors and their ability to degrade ATG13, inhibit autophagy, and treat lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6873.