tbuckley/cabot-search huggingface dataset:
Abstract 4431: RRM2-driven dNTP biosynthesis: a therapeutic vulnerability in temozolomide-resistant glioblastoma
Authors: Atique U. Ahmed, Karan Dixit, Ella N Perrault, Jack M Shireman, Priya Kumthekar, Roger Stupp. David C James
Journal: Cancer Research (2025)

Abstract Glioblastoma (GBM) remains one of the most aggressive and fatal cancers, with a median survival of only 12-18 months despite standard treatments, including surgical resection, temozolomide (TMZ) chemotherapy, and radiotherapy. Tumor recurrence and therapy resistance are significant barriers to improving patient outcomes. To address this, our lab investigated the molecular mechanisms driving resistance during TMZ therapy using a single-cell RNA-sequencing screen on a patient-derived xenograft (PDX) model. This approach enabled us to study tumor evolution pre-, during, and post-therapy. Our analysis identified 149 unique genes expressed during TMZ therapy, with the ribonucleotide reductase (RNR) family, particularly Ribonucleotide Reductase Regulatory Subunit 2 (RRM2), emerging as critical players. During TMZ treatment, GBM cells preferentially utilize RRM1-RRM2 interaction to support deoxynucleoside triphosphate (dNTP) biosynthesis, whereas post-therapy recurrent GBM shifts to RRM1-RRM2B complexes. Functional studies demonstrated that RRM2 knockdown sensitized GBM cells to TMZ, reducing DNA repair capacity, as evidenced by increased yH2AX fluorescence, while RRM1 or RRM2B knockdown conferred resistance (p&amp;lt;0.001). Metabolomic profiling revealed that RRM2 mediates dCTP and dGTP production during TMZ treatment, critical for chemoresistance. Supplementation with these dNTPs rescued TMZ susceptibility in RRM2-deficient cells, highlighting its pivotal role in DNA repair and therapeutic resistance. Recognizing the limitations of first-generation RNR inhibitors, we explored the second-generation inhibitor Triapine (3-AP). Preclinical studies showed that 3-AP effectively inhibits RRM2 activity, enhancing TMZ sensitivity and extending survival in PDX models (p&amp;lt;0.0001). Mice treated with a combination of 3-AP and TMZ demonstrated significantly longer survival compared to TMZ alone. These findings underscore the potential of targeting RRM2-mediated dNTP biosynthesis to overcome chemoresistance in GBM. We are conducting a Phase 1/1b clinical trial to assess the safety, toxicity, and maximum tolerated dose (MTD) of combining 3-AP with TMZ in recurrent GBM patients. Citation Format: Atique U. Ahmed, Karan Dixit, Ella N Perrault, Jack M Shireman, Priya Kumthekar, Roger Stupp. David C James. RRM2-driven dNTP biosynthesis: a therapeutic vulnerability in temozolomide-resistant glioblastoma [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 4431.
Abstract 5295: Tumor stromal fibroblasts constitute a biological immune barrier by inducing instant immune cell death
Authors: Jianing Chen, Wenfeng Zeng, Penghan Huang, Erwei Song
Journal: Cancer Research (2025)

Abstract The majority of low immune-reactive ‘cold’ tumors present an immune-excluded phenotype and it was proposed that stromal fibroblasts together with their collagen products constitute a physical barrier precluding lymphocytic infiltration into tumors. Here, we demonstrated a histopathological structure characterized by stromal fibroblasts embedded with dead lymphocytes in ‘cold’ tumors, named Crab-Nebula sign (CNs), indicating poor patient prognosis. Moreover, we identified a unique fibroblast subset in CNs-enriched structures overexpressing a sulfotransferase which triggers instant activation-induced cell death (AICD) in CTLs and NK cells. Mechanistically, we reveal that sulfonated HSPG receptor on activated immunocytes engaged by sulfonated HSPG inhibit p38-MAPK activation and reduce PI9 expression, leading to Granzyme B release into the cytosol and GSDME cleavage. Furthermore, sulfotransferase-knockout in fibroblasts or blocking sulfonated HSPG receptor in CTLs enhances anti-tumor effects of immune cell therapy in vivo. Collectively, we revealed that stromal fibroblasts construct a toxic biological barrier in ‘cold’ tumors and highlighted the therapeutic potential of disrupting the interaction between stromal fibroblasts and immunocytes in turning ‘immune-cold’ tumors hot. Citation Format: Jianing Chen, Wenfeng Zeng, Penghan Huang, Erwei Song. Tumor stromal fibroblasts constitute a biological immune barrier by inducing instant immune cell death [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 5295.
Abstract 6156: Engineering a PD-1 dependent 4-1BB agonist for combination immunotherapy
Authors: Alana Kramer, Damien Ruiz, Jonathan Marable, Payal Agarwal, Deepa Bedi, Maninder Sandey
Journal: Cancer Research (2025)

Abstract First-generation 4-1BB (CD137) monoclonal antibody (mAb)-based agonists demonstrated significant potential in early preclinical and clinical studies by eliciting robust anti-tumor responses. However, their clinical development was hampered by dose-limiting hepatotoxicity, attributed to the systemic activation of 4-1BB receptors on monocytes, which in turn recruited CD8+ T cells to attack hepatocytes. To address this challenge, next-generation therapies have focused on decoupling the hepatotoxic effects of 4-1BB activation from its anti-tumor activity. These strategies utilize bispecific molecules to precisely target and activate 4-1BB receptors within the tumor microenvironment (TME). By binding to tumor-associated antigens, these molecules localize to TME, facilitating the hyperclustering and trimerization required for 4-1BB activation. This approach enhances tumor-specific immune responses while minimizing systemic activation and off-target effects. In this study, we introduce, to the best of our knowledge, the first PD-1-targeted 4-1BB agonist that leverages the PD-1 receptor on exhausted T cells to facilitate 4-1BB hyperclustering and activation. Three distinct murine-specific bispecific constructs were developed in silico, each employing an anti-PD-1 nanobody for crosslinking and trimerization of the 4-1BB receptor. Construct 1 was designed to function as a weak agonist in the absence of PD-1, transforming into a strong agonist in its presence. In contrast, constructs 2 and 3 are entirely dependent on PD-1 for hyperclustering and subsequent 4-1BB activation. The constructs were expressed and purified using Expi293F-based stable cell lines. Flow cytometry confirmed their ability to bind specifically to the cognate 4-1BB and PD-1 receptors. A 4-1BB luciferase bioassay was employed to demonstrate the PD-1 dependency of Constructs 2 and 3. As expected, constructs 2 and 3 exhibited no 4-1BB activation in the absence of PD1-expressing cells but transformed into potent agonists in their presence. Construct 1 activated the 4-1BB receptor regardless of PD-1, with its activity being markedly enhanced in its presence. Additionally, constructs 2 and 3 were shown to effectively block the PD-1/PD-L1 interaction. Preliminary preclinical evaluations confirmed that all three constructs function as designed. Following the completion of in vitro studies, we are currently conducting in vivo analyses using mouse xenograft models to evaluate the therapeutic efficacy, toxicity, and biodistribution of these constructs. Citation Format: Alana Kramer, Damien Ruiz, Jonathan Marable, Payal Agarwal, Deepa Bedi, Maninder Sandey. Engineering a PD-1 dependent 4-1BB agonist for combination immunotherapy [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 6156.
Abstract 1664: Survivin degrader 7I14 synergizes with docetaxel in castration-resistant prostate cancer by disrupting survivin dimerization and inducing its proteasome-dependent degradation
Authors: Qingbin Cui, Caoqinglong Huang, Xunzhen Zheng, Zizheng Dong, Jing-Yuan Liu, Jian-Ting Zhang
Journal: Cancer Research (2025)

Abstract Survivin, the smallest member of the Inhibitor of Apoptosis Protein (IAP) family, forms homodimers and coordinates with other IAPs to inhibit apoptosis by suppressing pro-apoptotic caspase 3/9 activation, contributing to drug resistance. Due to its overexpression in cancer cells and lack of expression in normal adult tissues, survivin is an attractive cancer target. However, developing survivin-selective inhibitors has been challenging due to the absence of suitable active sites for targeting. Strategies have been pursued to inhibit survivin expression by targeting its upstream transcriptional regulators, notably leading to discovery of YM155, which unexpectedly suffers from poor pharmacokinetics and multiple targets, including the ubiquitous transcription factor Sp1. We recently developed a novel approach to directly target survivin for discovery of survivin degraders by disrupting its dimerization, exposing the hydrophobic interface, and promoting proteasome-mediated degradation. The compound 7I, a quinoxaline-based survivin degrader, likely interacts with key residues for survivin dimerization via π-π interactions. We hypothesized that electron-withdrawing groups on 7I enhance its binding to survivin. To test this hypothesis, we synthesized a series of 7I analogs and identified two improved leads, 7I10 and 7I14, with up to 20-fold greater activity, selectively degrading survivin in castration-resistant prostate cancer (CRPC) cell lines C4-2 and PC-3. Both 7I10 and 7I14 dose-dependently induced spontaneous apoptosis and synergized with docetaxel, a first-line therapy for metastatic CRPC. In a PC-3 xenograft model, 7I14 at 15 mg/kg administered via IP twice/week effectively suppressed tumor growth and enhanced docetaxel’s effects by degrading survivin, with no added toxicity, as assessed by body weight, white blood cell counts, and hemoglobin levels. Thus, targeting survivin's dimerization domain is a promising strategy for its degradation, and 7I10 and 7I14 have potential as single agents or in combination with docetaxel for treating metastatic CRPC. Citation Format: Qingbin Cui, Caoqinglong Huang, Xunzhen Zheng, Zizheng Dong, Jing-Yuan Liu, Jian-Ting Zhang. Survivin degrader 7I14 synergizes with docetaxel in castration-resistant prostate cancer by disrupting survivin dimerization and inducing its proteasome-dependent degradation [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 1664.
Abstract 5347: Transcriptome analysis for Merkel cell carcinoma patients testing positive (+) and negative (-) for polyomavirus
Authors: MiaSara Pérez Salvá, Nicole Muñoz, Fnu Srividya, Maryam Pirhoushiaran, Daniel Wang, Manuel Delgado Velez, José A. Lasalde Dominicci, Phyu P. Aung, Leomar Y. Ballester
Journal: Cancer Research (2025)

Abstract Merkel cell carcinoma is a rare, aggressive primary cutaneous malignancy with neuroendocrine differentiation. Approximately 3, 000 new cases are diagnosed annually in the United States, with incidence rates rising partly due to advancements in diagnostic methods. The exact cause of MCC is unknown, but several potential etiologies have been proposed, including exposure to ultraviolet radiation (UVR) and integration of Merkel cell polyomavirus (MCPyV). MCPyV has been detected in up to 80% of MCC tumors in the United States, and its presence is associated with a better prognosis, with a five-year overall survival (OS) rate of approximately 50%. This study aims to investigate the transcriptomic and methylomic profiles of skin samples from 27 patients with MCC, comparing those positive and negative for MCPyV. The objective involves identifying potential genetic biomarkers that could be targeted for therapeutic intervention for both MCPyV (+) and MCPyV (-) patients. Citation Format: MiaSara Pérez Salvá, Nicole Muñoz, Fnu Srividya, Maryam Pirhoushiaran, Daniel Wang, Manuel Delgado Velez, José A. Lasalde Dominicci, Phyu P. Aung, Leomar Y. Ballester. Transcriptome analysis for Merkel cell carcinoma patients testing positive (+) and negative (-) for polyomavirus [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 5347.
Abstract 4767: XON11, a novel multi-target antibody in pancreas cancer
Authors: Carine Ciron, Ophelie Dauphouy, Pierre-Joseph Royer, Gwenaelle Evanno, Odile Devaux, Firas Bassissi
Journal: Cancer Research (2025)

Abstract Background: Pancreatic cancer continues to be one of the most lethal cancer types, with a 5-year overall survival rate of only 12%. It poses one of the toughest challenges in oncology, as chemotherapy and immunotherapy have not significantly improved patient outcomes. Consequently, there is an urgent need for new therapeutic approaches. XON11 is a new polyclonal antibody targeting several pancreatic cancer antigens, including KrasG12D. The aim of these studies was to assess the tolerance and efficacy of XON11 in non-clinical pancreatic cancer models. Material and methods: XON11 ability to induce Complement Dependent Cytotoxicity (CDC) and apoptosis compared to gemcitabine was tested in a panel of human pancreas cancer cell (MiaPaca, Aspc1, Capan, Panc1) after 24h of incubation. The capacity of XON11 and gemcitabine to impair tumorsphere formation and growth was investigated in pancreatic cancer cells for 11 days. In vivo XON11 and gemcitabine tolerance and efficacy was evaluated in NMRI nude mice after intraperitoneal dosing at 40 mg/kg tri-weekly for 4 weeks. Results: XON11 showed potent and selective anti-proliferative activity in a panel of human pancreatic Kras muted cancer cell lines, including those resistant to gemcitabine. It induced specific tumor cell cytotoxicity (Mean EC50 = 25.85 µg/mL) without affecting healthy cells (PBMC) at this concentration. XON11 displayed significantly higher potency against pancreatic cancers compared to gemcitabine. It was able to kill up to 97% of the cancer cells, whereas gemcitabine's maximum effect reached 30%. XON11 induced both caspase 8 and caspase 9 (suggesting activation of both apoptosis pathways). Furthermore, it induced a dose- response loss of mitochondrial membrane potential and ROS generation in different pancreatic cell lines. In contrast to gemcitabine, XON11 significantly decreased Aspc1 tumorspheres viability after treatment (&amp;gt;75% of cytotoxicity). In addition, XON11 completely inhibited sphere formation from 33µg/ml. XON11 was significantly effective against tumor growth in two xenograft mouse models and well tolerated in mice after repeated intraperitoneal dosing at 40 mg/kg over 28 days. Conclusion: Based on its high potency and tolerance, XON11 can provide a novel and promising therapy for fighting recurrent pancreatic cancer. Citation Format: Carine Ciron, Ophelie Dauphouy, Pierre-Joseph Royer, Gwenaelle Evanno, Odile Devaux, Firas Bassissi. XON11, a novel multi-target antibody in pancreas 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 4767.
Abstract 5423: A focused shRNA library screening identifies MRPL38 as an oncogenic regulator of lung cancer via regulation of mitochondrial homeostasis
Authors: Jieun Seo, So Young Lee, Sangwon Byun, Kyung Chan Park
Journal: Cancer Research (2025)

To identify a novel gene that contributes to lung cancer progression, we performed RNA interference genetic screening combined with multi-omics analysis of never-smoker lung cancer cohort (GSE256091). As a result of the screening and MAGeCK analysis, mitochondrial ribosomal protein L38 (MRPL38) was identified as a positive regulator of lung cancer progression. Mitochondrial dysfunction and metabolic reprogramming are key features of lung cancer. Despite their significance, the precise underlying mechanisms of these processes and the role of MRPL38 in lung cancer progression have not been fully elucidated. A significant upregulation of MRPL38 was observed in lung cancer patient tissues, which was associated with advanced tumor stages and poor prognosis. Knockdown of MRPL38 significantly reduced cell viability and colony formation and increased apoptosis in human lung cancer cells. Moreover, MRPL38 has been found to be crucial for maintaining mitochondrial protein translation and homeostasis. Loss-of-function experiments targeting MRPL38 in various lung cancer cell lines resulted in alterations in oxidative phosphorylation (OXPHOS) complex proteins, oxygen consumption rate (OCR), and mitochondrial biogenesis. In MRPL38-deficient cells, the expression levels of proteins encoding subunits of the respiratory chain complexes were significantly reduced, and both basal and maximal mitochondrial respiration were decreased. Furthermore, the inhibition of MRPL38 was found to significantly reduce the mass and number of mitochondria associated with mitochondrial biogenesis. These results suggest that MRPL38, a novel regulator in lung cancer, may promote lung cancer progression by regulating mitochondrial homeostasis. Citation Format: Jieun Seo, So Young Lee, Sangwon Byun, Kyung Chan Park. A focused shRNA library screening identifies MRPL38 as an oncogenic regulator of lung cancer via regulation of mitochondrial homeostasis [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 5423.
Abstract 2459: Membrane stain-enhanced quantification of HCR™ Pro RNA-ISH using HALO image analysis software
Authors: Randy Chen, Anne Hellebust, Aneesh Acharya, Harry Choi
Journal: Cancer Research (2025)

Abstract Accurate quantification of RNA in situ hybridization (RNA-ISH) signals is critical for understanding spatial gene expression, particularly at the single-cell level. Traditional methods using Hematoxylin or DAPI staining often fall short due to their inability to clearly define cell boundaries, leading to inaccurate dot counting. In the context of digital pathology, this challenge can hinder precise interpretation of spatial gene expression data. Here, we demonstrate how the incorporation of membrane stains enhances RNA-ISH signal quantification by delineating cell borders, enabling precise dot counting with HALO image analysis software. Membrane stains were applied across both chromogenic and fluorescent HCR™ Pro RNA-ISH assays, facilitating robust signal detection in brightfield and fluorescent imaging modalities. This approach also enabled the integration of cell-type specific markers (e.g., CD3 and CD4) to provide insights into gene expression dynamics within distinct cell subpopulations relevant to pathology workflows. Comparative analysis revealed superior accuracy in dot quantification when using membrane-enhanced staining compared to traditional Hematoxylin/DAPI-expanded methods. These findings underscore the importance of combining membrane stains with advanced imaging analysis tools like HALO in digital pathology for precise and reproducible quantification of RNA-ISH signals. This advancement paves the way for more detailed studies of differential gene expression and cellular heterogeneity within clinical and research pathology settings. Citation Format: Randy Chen, Anne Hellebust, Aneesh Acharya, Harry Choi. Membrane stain-enhanced quantification of HCR™ Pro RNA-ISH using HALO image analysis software [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 2459.
Abstract 5126: Time-series single-cell RNA sequencing uncovers PLAU enhancing early lung metastatic seeding of esophageal squamous cell carcinoma
Authors: Yingchen Lyu, Ching Ngar Wong, Hongyu Zhou, Songna Wang, Xinyuan Guan
Journal: Cancer Research (2025)

Abstract Background: Metastasis continues to be the primary cause of cancer death even with recent advancements in cancer treatment. The initiating ability of metastatic growth bottlenecked in cancer development and could be a promising target. We have successfully captured the distinctive features of early metastatic cells through time-series scRNA-seq using the pulmonary metastatic model. Methods: To characterize the early metastatic tumor microenvironment (TME), we looked into the highly expressed genes encoding the secreted protein in early metastasis performing GO and KEGG pathway analysis. Clinical implication of PLAU overexpression was studied in ESCC patients. Multiplex immunohistochemistry staining of PLAU and previously identified metastatic initiating genes in ESCC patient samples were completed. Functional assays, including cell migration, invasion, wound healing, and foci formation were undertaken to evaluate the metastatic ability. PLAU knockdown ESCC cells were injected intravenously and subsequent in vivo lung imaging was obtained. Results: Through GO and KEGG pathway analysis of the single-cell profiling, the genes highly expressed in early metastatic lung exhibited a significant enrichment in processes related to coagulation and fibrinolysis (F3, THBS1, PLAU, SEPRINE1 and ANXA2). Among these genes, PLAU increased greatly in 6 hours and was maintained at a relatively high level during the early metastatic phase. We further explored the implications of PLAU. The analysis of the TCGA database reveals that PLAU is significantly upregulated in tumor tissues compared to non-tumor tissues .Multiplex immunohistochemistry staining of both ESCC cell lines and clinical samples demonstrated co-expression of PLAU and the previously identified metastatic initiating signature CD44 and TACSTD2. Knockdown of PLAU greatly impaired the ability of migration, invasion, wound healing and foci formation (p&amp;lt;0.05). In addition, the knockdown of PLAU led to significantly fewer surviving cancer cells in mice lungs in the early phase of metastasis (p&amp;lt;0.05). Conclusions: In all, the finding indicated that PLAU co-expressed with previously identified metastatic initiating genes and increased early dissemination of ESCC lung metastasis. Targeting PLAU could offer a promising approach to limit early metastatic progression in ESCC. Citation Format: Yingchen Lyu, Ching Ngar Wong, Hongyu Zhou, Songna Wang, Xinyuan Guan. Time-series single-cell RNA sequencing uncovers PLAU enhancing early lung metastatic seeding of esophageal squamous cell carcinoma [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 5126.