tbuckley/cabot-search huggingface dataset:
Abstract 4604: Implications of genomic alterations in RNF43 and RSPO3 for the response of BRAFV600E metastatic colorectal cancer to anti-EGFR+BRAF combinatory therapy
Authors: Jakob M. Stenersen, Max Z. Totland, Luís Nunes, Ina A. Eilertsen, Vilde C. Elster, Tuula A. Nyman, Ragnihild A. Lothe, Anita Sveen, Kushtrim Kryeziu, Edward Leithe
Journal: Cancer Research (2025)

Abstract The BRAFV600E mutation, present in 8 - 10% of colorectal cancers (CRCs), is associated with poor patient outcome and has limited treatment options. Recent studies have shown that mutations in the E3 ubiquitin ligase RNF43 predict response to anti-EGFR/BRAF combinatory therapy in patients with BRAFV600E metastatic CRC. Gene expression analysis of CRCs with the BRAF/RNF43 co-mutation exhibit significantly higher expression levels of MAP2K1 and MAPK3 compared to their wild-type counterparts. This implies an unknown but clinically significant molecular relationship between RNF43 loss-of-function and the MAPK signaling pathway. RNF43 attenuates WNT signaling by promoting the endocytosis and lysosomal degradation of Frizzled receptors to desensitize the cells to WNT ligands. RNF43 itself is in turn negatively regulated by the R-spondin (RSPO) family of proteins. Activating fusions involving RSPOs and inactivating mutations in RNF43 are found in ∼2% and ∼5% of CRCs, respectively. The aim of the present project is to better understand how gene alterations affecting the R-spondin/RNF43 signaling module influence the response to EGFR/BRAF inhibitor combination treatment. We use patient-derived organoids with different genomic alterations in BRAF and RNF43, APC, or RSPO3 as preclinical models to elucidate signaling dynamics before and after treatment with EGFR and BRAF inhibitors alone or in combination. This analysis includes various omics approaches such as mass spectrometry, RNA sequencing and kinome profiling. Here, we present preliminary results from this study, showing how these treatments differentially affect MAPK and WNT signaling depending on the mutational profile of the organoids Citation Format: Jakob M. Stenersen, Max Z. Totland, Luís Nunes, Ina A. Eilertsen, Vilde C. Elster, Tuula A. Nyman, Ragnihild A. Lothe, Anita Sveen, Kushtrim Kryeziu, Edward Leithe. Implications of genomic alterations in RNF43 and RSPO3 for the response of BRAFV600E metastatic colorectal cancer to anti-EGFR+BRAF combinatory therapy [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 4604.
Abstract 257: The E3 ligase HECTD4 regulates COX-2 dependent tumor progression and metastasis
Authors: Joanna Vuille, Cem Tanriover, Douglas S. Micalizzi, Richard Y. Ebright, Sambhavi Animesh, Robert Morris, Soroush Hajizadeh, Zachary J. Nicholson, Hunter C. Russell, Eric F. Zaniewski, Ben S. Wittner, Ben K. Wesley, Julian Grünewald, Regan N. Szalay, Ezgi Antmen, Douglas B. Fox, Min Yang, Jae Keith Joung, Doga C. Gulhan, Andrew E. Elia, Wilhelm Haas, Eugene Oh, Shyamala Maheswaran, Daniel A. Haber
Journal: Cancer Research (2025)

Abstract E3 ubiquitin ligases mediating turnover of proteins engaged in cancer progression point to key regulatory nodes. To uncover modifiers of metastatic competency, we conducted an in vivo genome-wide CRISPR-inactivation screen using cultured breast circulating tumor cells, following intravascular seeding and lung colonization. We identified HECTD4, a previously uncharacterized gene encoding a conserved potential HECT domain-containing ubiquitin transferase, as a potent tumor suppressor. We show that purified HECTD4 mediates ubiquitin conjugation in vitro, and proteomic studies combined with ubiquitin remnant profiling identify a major degradation target as the prostaglandin synthetic enzyme cyclooxygenase-2 (COX-2; PTGS2). In addition to COX-2 itself, HECTD4 targets its regulatory kinase MKK7. In breast cancer models, HECTD4 expression is induced as cells lose adherence to the matrix, and its depletion massively increases COX-2 expression, enhancing anchorage-independent proliferation and tumorigenesis. Genetic or pharmacologic suppression of COX-2 reverses the pro-tumorigenic phenotype of HECTD4-depleted cells. Thus, HECTD4 encodes an E3 ubiquitin ligase that downregulates COX-2 suppressing anchorage-independence in epithelial cancer cells. Citation Format: Joanna Vuille, Cem Tanriover, Douglas S. Micalizzi, Richard Y. Ebright, Sambhavi Animesh, Robert Morris, Soroush Hajizadeh, Zachary J. Nicholson, Hunter C. Russell, Eric F. Zaniewski, Ben S. Wittner, Ben K. Wesley, Julian Grünewald, Regan N. Szalay, Ezgi Antmen, Douglas B. Fox, Min Yang, Jae Keith Joung, Doga C. Gulhan, Andrew E. Elia, Wilhelm Haas, Eugene Oh, Shyamala Maheswaran, Daniel A. Haber. The E3 ligase HECTD4 regulates COX-2 dependent tumor progression and metastasis [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 257.
Abstract 5651: Discovery of AS03157 as a highly potent and orally active antagonist of inhibitor of apoptosis proteins (IAPs)
Authors: Yan Xiong, Zhou Yu, Jiantao Hu, Jianyong Chen, Xiao Han, Zhiyan Liang, Yifan Zhai, Dajun Yang
Journal: Cancer Research (2025)

Abstract Background: Overexpression of antiapoptotic proteins, such as cellular inhibitor of apoptosis proteins 1 (cIAP1) and 2 (cIAP2) and X-linked IAP (XIAP), occurs in various hematologic and solid cancers and is associated with drug resistance and poor prognosis. Several small molecules are being investigated clinically as monotherapy or in combination therapy in solid tumors. AS03157, a novel and structurally distinct IAP antagonist, was identified with enhanced specificity towards cIAP1 and XIAP, and its pharmacological profiles were characterized in vitro and in vivo. Methods: Homogeneous time-resolved fluorescence assays were used to measure the binding of the compound to its target. Detroit 562 cell line was used to test the target degradation. MDA-MB-231 and EVSA-T breast cancer cell lines were used for antiproliferation assay. In vivo efficacy was evaluated in MDA-MB-231-derived xenograft model. Results: AS03157 strongly bound to cIAP1-BIR3 and XIAP-BIR3 at half-maximal inhibitory concentration (IC50) values of 4.3 nM and 13.7 nM, respectively. AS03157 inhibited cIAP1 with a half-maximal degradation concentration (DC50) of 1.38 nM after treatment for 2 hours in a Detroit 562 pharyngeal carcinoma cell line in vitro. AS03157 demonstrated potent growth inhibitory activities in MDA-MB-231 and EVSA-T breast cancer cell lines, with IC50 values of 20 nM and 2 nM, respectively. In addition, AS03157 exhibited high aqueous solubility, metabolic stability, as well as high oral bioavailability in both rodent and non-rodent species. Of interest, AS03157 10 and 20 mg/kg administered orally daily demonstrated dose-dependent antitumor activity in an MDA-MB-231-X1 human breast cancer xenograft model, with T/C values of 69.81% and 26.67% on Day 22, respectively. Conclusions: AS03157 showed promising in vitro and in vivo activity in preclinical cancer models, and these data provide a rationale for further clinical studies. Citation Format: Yan Xiong, Zhou Yu, Jiantao Hu, Jianyong Chen, Xiao Han, Zhiyan Liang, Yifan Zhai, Dajun Yang. Discovery of AS03157 as a highly potent and orally active antagonist of inhibitor of apoptosis proteins (IAPs) [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 5651.
Abstract 6853: A standardized drug selectivity profiling platform with a proteome coverage of more than 5,000 proteins
Authors: Tomas Friman, Tuomas Tolvanen, Tove Boström, Ying Sun, Alexey Chernobrovkin, Yasmin Andersson, Christina Velasco, Daniel Martinez Molina
Journal: Cancer Research (2025)

Abstract Drug hunters typically rely on a combination of biophysical/biochemical binding and efficacy assays to find and prioritize hit compounds in their drug discovery efforts. These activities are pivotal for success where the right assay combination can correlate productive binding (target engagement) with a biological effect. The earlier such correlations can be established, the better, as that speeds up the prioritization process and builds confidence in the lead series that are progressed to lead optimization. Currently, at that stage, selectivity assays for specific protein classes, typically including safety panels of up to 200 proteins, are applied. However, a limited number of proteins will result in a biased selectivity assessment. Instead, an unbiased and proteome-wide selectivity profiling assay, employed early in the drug discovery process, contributes to the correct prioritization of lead compounds. Pelago Bioscience has established a standardized assay for selectivity profiling, based on the Cellular Thermal Shift Assay (CETSA) with mass spectrometry (MS) detection, which enables discrimination between selective and more promiscuous molecules at the proteome level. As an example, we have profiled over 100 different drugs and probes used in clinical oncology and tumor biology research. Investigated drug classes include antimetabolites, alkylating agents, DNA intercalating agents, epigenetic modifiers, kinase inhibitors, and microtubule inhibitors. In the work presented here, we will show how compounds with similar structures and mode of action also display similar CETSA protein shift profiles with regards to intended targets and off-targets. Such reference data allows comparison of novel chemical hits to compounds with an established mode of action. High throughput and data quality, with an assessment of more than 5, 000 proteins, enables large compound batches to be assayed also during early phases of drug discovery. This speeds up the process and increases the confidence in lead series and future lead candidates. Citation Format: Tomas Friman, Tuomas Tolvanen, Tove Boström, Ying Sun, Alexey Chernobrovkin, Yasmin Andersson, Christina Velasco, Daniel Martinez Molina. A standardized drug selectivity profiling platform with a proteome coverage of more than 5, 000 proteins [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 6853.
Abstract 1554: Harnessing the Beacon® optofluidic platform for streamlined discovery of internalizing antibodies
Authors: Brittany Benlian, Leqian Liu, Alexander Mastroianni, Minha Park, Vincent Pai, Alireza Salmanzadeh
Journal: Cancer Research (2025)

Abstract Antibody drug conjugates (ADCs) are an innovative class of biopharmaceuticals which combine the potency of cytotoxic molecules with the targeted specificity of monoclonal antibodies. The success of a traditional ADC not only hinges on tumor antigen-specific binding but internalization to maximize cytotoxicity from the payload and minimize off-target damage to healthy tissue. The development of an ADC therapy is a complex, multistep process that involves identifying a target antigen, discovering an ideal antibody, selecting the cytotoxic payload and linker, and optimizing the conjugation chemistry - all of which can take years from initial research to therapeutic application. One significant bottleneck within this process is the lack of early phase assays to guide the down-selection of functional antibodies from hundreds of antigen binding clones. Therefore, developing an efficient high-throughput assay for antibody internalization is crucial for accelerating ADC development. The Beacon® optofluidic platform from Bruker Cellular Analysis is an advanced solution for this problem that enables researchers to identify valuable monoclonal antibodies within a week, bypassing the time consuming and laborious process of hybridoma library generation and screening. With this platform, tens of thousands of single primary cells can be isolated using Opto-Electronic Positioning (OEP) technology and assayed for antibody secretion, antigen binding, and receptor-specific internalization in live reporter cells within a single day. This cutting-edge technology is the only platform capable of screening and measuring &amp;gt;10, 000 antibodies simultaneously for rapid internalization (1-2 hours). We showcase the ability to streamline early-phase discovery of internalizing antibodies, going beyond mere antigen specificity to enable high-throughput, real-time evaluation of functional antibodies. The Beacon optofluidic platform significantly reduces hands-on time and resource expenditure, focusing efforts on the most promising ADC candidates for downstream characterization and optimization, ultimately expediting the progression of ideal antibodies into clinical applications. Citation Format: Brittany Benlian, Leqian Liu, Alexander Mastroianni, Minha Park, Vincent Pai, Alireza Salmanzadeh. Harnessing the Beacon® optofluidic platform for streamlined discovery of internalizing antibodies [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 1554.
Abstract 6302: A CellProfiler pipeline for RNAscope analyzing multiple markers across adjacent tissue sections spatially
Authors: Meng-Shin Shiao, Natini Jinawath, Katherine Copeland, Ariestya Indah Permata Sari
Journal: Cancer Research (2025)

Understanding the spatial distribution of cancer cells and how they interact with other cell types in the tumor microenvironment (TME) is crucial to elucidate the mechanisms of cancer development and progression. The identification of cell types in the TME relies on the distinct expression profiles of different cell types. Compared to sequencing-based spatial transcriptomics analysis, multiplex nucleic acid in-situ hybridization (ISH) at a single-molecule level is more focused and cost-effective. Based on ISH technology, RNAscope developed novel approaches to detect multiple gene expression profiles on tissue sections at a single-molecule level. It is highly sensitive and specific and can simultaneously quantify gene expression at sub-cellular levels. Although the technology has been applied to study spatial gene expression in various cancer types, few have applied it to elucidate the association between different markers in different cell compartments within the TME.This protocol describes an image analysis pipeline for multiplex fluorescent signals detected by RNAscope technology. It was developed based on a previous CellProfiler pipeline, facilitating spatial expression analyses across different cell compartments through a flexible, user-friendly interface for non-computational biologists. We describe specific steps to analyze the expression and spatial arrangement of four endogenous housekeeping genes as quality controls (QCs): POLR2A, PPIB, HPRT1, and UBC. We further apply these pipelines to analyze target genes in breast cancer samples, comparing those with and without skin metastasis. The analyses were demonstrated in one sample each using formalin-fixed paraffin-embedded tissue (FFPET) and fresh-frozen tissue (FFT) sections with the ISH steps followed the manufacturer’s protocol. Citation Format: Meng-Shin Shiao, Natini Jinawath, Katherine Copeland, Ariestya Indah Permata Sari. A CellProfiler pipeline for RNAscope analyzing multiple markers across adjacent tissue sections spatially [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 6302.
Abstract 1548: Deletion of peroxisomal 3-ketoacyl-CoA thiolase promoted overall survival in the KPC mice
Authors: Mingyu Kang, Woosol Hong, Woojin Ham, Chaeyoung Kim, Ho Lee, Sang Myung Woo, Wonyoung Choi, Sung Hoon Sim, Jung Won Chun, Soo-Youl Kim
Journal: Cancer Research (2025)

Abstract Background: Fast-growing cancer cells obtained ATP from fatty acid oxidation (FAO). We found that medium-chain acyl-carnitines (MC-AC) were increased by carnitine acyl-carnitine carrier knockdown in pancreatic ductal adenocarcinoma. MC-AC can be produced only in the peroxisome. Therefore, we propose that ATP production in cancer cells may depend on the peroxisomal FAO in addition to mitochondrial FAO. Methods: We have tested whether peroxisomal FAO is reduced by knockdown of peroxisomal 3-ketoacyl-CoA thiolase (acetyl-CoA acyltransferase 1, ACAA1). We have examined effects on ATP level and tumor growth by ACAA1 knockdown in PDAC cells, and cancer survival by crossbreeding of KPC mice (KrasG12D/+; Trp53R172H/+; P48-Cre) and Acaa1+/- mice. Findings: Peroxisomal FAO target levels in PDAC patients are higher than in normal individuals. In in vitro experiments, ACAA1 knockdown in PDAC cells reduced 40% of ATP production. In in vivo experiments, xenograft mouse models using human PDAC cells with ACAA1 knockdown showed significantly reduced tumor formation. Crossbreeding of the KPC mice with Acaa1+/- mice significantly increased the survival rate. Interpretation: While normal cells rely on glucose oxidation, ATP production in PDAC cells is critically dependent on FAO in peroxisomes and mitochondria. This suggests that to achieve complete FAO inhibition in cancer, it is necessary to block FAO in both peroxisomes and mitochondria. Funding source: This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT to SK (NRF-2019M3A9G1104345) and by a grant from the National Cancer Center of Korea to SHS (NCC 24H1210-2) and JWC (NCC 2410892-2). Citation Format: Mingyu Kang, Woosol Hong, Woojin Ham, Chaeyoung Kim, Ho Lee, Sang Myung Woo, Wonyoung Choi, Sung Hoon Sim, Jung Won Chun, Soo-Youl Kim. Deletion of peroxisomal 3-ketoacyl-CoA thiolase promoted overall survival in the KPC mice [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 1548.
Abstract 3873: Uncovering key regulators of OSCC invasion: A pathway to novel therapeutic strategies
Authors: Guillermo Flores, Slyn Uaroon, Juan A. Raygoza Garay, Marisa R. Buchakjian
Journal: Cancer Research (2025)

Abstract Recurrence and metastasis are the primary drivers of poor prognosis in patients with Oral Squamous Cell Carcinoma (OSCC), even after aggressive surgical interventions. To uncover the genetic regulators of OSCC invasion and migration, we conducted a first-of-its-kind genome-wide CRISPR screen. This screen identified several key players involved in epithelial-mesenchymal transition (EMT), a critical process in tumor progression and metastasis. Among the top hits was EDIL3, a gene that codes for a secreted protein that promotes EMT and chemotherapy resistance by interacting with integrin receptors in the extracellular matrix. Though previously implicated in other cancers, EDIL3’s role in OSCC has not been described. Additionally, our screen highlighted NISCH as the top anti-invasion hit, a gene whose expression is positively correlated with survival in head and neck cancers, including OSCC. NISCH appears to inhibit EDIL3-driven invasion by interfering with integrin-mediated signaling, potentially via a FAK and WNT5a-dependent mechanism. Current work is focused on characterizing EDIL3 and NISCH knockouts to validate their roles in OSCC migration and invasion. Functional assays such as spheroid formation and wound healing experiments are being performed to assess the impact of these knockouts on tumor cell behavior. Additionally, we are investigating FDA-approved drugs targeting these pathways to explore immediate translational potential. This research represents a novel approach to identifying genetic drivers of cancer metastasis and offers promising avenues for the development of targeted therapies for OSCC to reduce recurrence and improve patient outcomes. Citation Format: Guillermo Flores, Slyn Uaroon, Juan A. Raygoza Garay, Marisa R. Buchakjian. Uncovering key regulators of OSCC invasion: A pathway to novel therapeutic strategies [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 3873.
Abstract 5226: CD47-Sirpαblockade enhances antitumor activity against mouse liver cancer by boosting cDC2 functions
Authors: Guan-Sian Low, Cheng-Zhe Jian, Yi-Chiao Tseng, Da-Liang Ou, Chiun Hsu, Chien-Kuo Lee
Journal: Cancer Research (2025)

Abstract The CD47-SIRPα axis functions as an immune checkpoint, transmitting a “don’t eat me” signal to prevent macrophage-mediated phagocytosis of tumor cells. While CD47 is expressed on most immune cells and is highly induced in tumor cells, SIRPα is expressed on phagocytes, including macrophages and type II conventional dendritic cells (cDC2s). Blocking the binding between CD47 and SIRPα is shown to promote antitumor immunity. However, the mechanism of how CD47-Sirpα blockade regulates DC functions is still unclear. Here we demonstrated that anti-CD47 and/or anti-Sirpα antibodies increased the phagocytic activity and antigen presentation of MutuDC2, a cDC2 cell line, against Hepa1-6, a mouse hepatocellular carcinoma cell line expressing LCMV-GP protein. Moreover, CD47 blockade also enhanced BM-derived cDC2 functions in boosting the proliferation and cytotoxic activity of P14 CD8 T cells in vitro. More importantly, anti-CD47 antibodies reduced tumor growth in vivo and cDC2s and IFNγ+ functional CD8 T cells were enriched in the tumor microenvironment compared to isotype control. In conclusion, CD47-Sirpα blockade boosts cDC2 functions, including phagocytic activity, antigen presentation, and cross-presentation ability, eliciting a better antitumor activity in antigen-specific CD8 T cells and emphasizes the therapeutic benefits of immune checkpoint blockade through cDC2. Citation Format: Guan-Sian Low, Cheng-Zhe Jian, Yi-Chiao Tseng, Da-Liang Ou, Chiun Hsu, Chien-Kuo Lee. CD47-Sirpαblockade enhances antitumor activity against mouse liver cancer by boosting cDC2 functions [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 5226.