tbuckley/cabot-search huggingface dataset:
Abstract 2772: Comparison of three single-cell CRISPR-Seq protocols on the 10X Genomics platform
Authors: Donato Tedesco, Tianbing Liu, Mikhail Makhanov, Nadya Isachenko, Dongfang Hu, Paul Diehl, Alex Chenchik
Journal: Cancer Research (2025)

Different methodologies exist for single-cell CRISPR (scCRISPR) screens, each with its own requirements concerning sgRNA scaffold, sgRNA library vector design, instrumentation, and reagents. This study compares the performance of three distinct scCRISPR protocols: 10X Genomics 3’ scCRISPR, CROP-Seq (using a modified 10X 3’ scCRISPR protocol), and 10X Genomics 5’ scCRISPR. 10X 3’ scCRISPR relies on the CS1 capture sequence inserted in the sgRNA tracr to detect expressed sgRNAs. CROP-Seq protocol requires the sgRNA sequences to be embedded in an expressed mRNA for detection. 10X Genomics 5’ scCRISPR detects sgRNAs without the need for scaffold modifications or inclusion in a mRNA transcript. A modification of the 10X 5’ scCRISPR protocol also allowed us to incorporate sc-targeted RNA-seq, decreasing NGS costs and potentially leading to better transcriptional profiling data. The findings of the study showed that while the CROP-Seq and 10X-CS1 approaches are equally effective for single-cell sgRNA detection and gene expression profiling, the CROP-seq approach was superior in the sgRNA’s ability to induce the expected phenotype. The 10X 5’ scCRISPR protocol proved to be superior to both CROP-Seq and 10X-CS1 in sgRNA detection, and comparable if not better to CROP-seq in gene expression profiling and sgRNA activity. Also, the 5’ scCRISPR targeted RNAseq approach proved to be technically successful, although it did not provide the expected transcriptional profiling improvement. Given the ease of use, the quality of the results, and the lack of need for specialized sgRNA scaffold or library design, 10X 5’ scCRISPR should be the protocol of choice for scCRISPR screens utilizing the 10X Genomics platform. Citation Format: Donato Tedesco, Tianbing Liu, Mikhail Makhanov, Nadya Isachenko, Dongfang Hu, Paul Diehl, Alex Chenchik. Comparison of three single-cell CRISPR-Seq protocols on the 10X Genomics platform [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 2772.
Abstract 4715: Depletion of mMDSCs using a CCR2-directed cytotoxicity targeting chimera (CyTAC) leads to remodeling of the tumor microenvironment and immune mediated tumor regression
Authors: Brandon J. Turunen, Beth Knapp-Reed, Craig Leach, Peiling Chen, Matthew Sender, Joseph Marino, Cunyu Zhang, Yao Chen
Journal: Cancer Research (2025)

Abstract mMDSCs (monocytic myeloid derived suppressor cells) are recruited to solid tumors and serve as potent inhibitors of T-cell mediated antitumor immunity. Therapeutic depletion of mMDSCs presents an exciting opportunity to increase the frequency and durability of anti-tumor clinical responses achieved with immune checkpoint inhibition. Currently, no marketed or investigational agents function by specific mMDSC depletion and no specific markers for therapeutic targeting of these cells have been clinically validated. We demonstrate that mMDSCs express high and homogeneous levels of the chemokine receptor CCR2. Because of this, we have developed a CCR2 targeting Cytotoxicity Targeting Chimera, which potently binds CCR2 on cells, and when combined with the CyTAC platform antibody, eliminates target cells via enhanced effector mediated killing. We demonstrate that the CCR2 CyTAC can deplete CCR2+ monocytes and mMDSCs from the periphery and intratumorally both ex vivo and in vivo. In the MC38 syngeneic tumor model this depletion leads to T-cell dependent anti-tumor activity and increases the levels of CD8 T-cells within the tumor microenvironment. We show across multiple additional syngeneic tumor models that depletion of CCR2+ cells remodels the tumor microenvironment causing an increase in tumor infiltrating CD8 T-Cells and a decrease in regulatory T-cells and mMDSCs. These PD changes were observed in both responding and non-responding tumor models where response can be enhanced with anti-PD1. Significance: We have applied our CyTAC technology to specifically target CCR2 expressing cells and depletion of mMDSCs and demonstrate that this can lead to remodeling of the tumor microenvironment from a pro-tumor to pro-inflammatory phenotype. This agent has potential for treating tumors with high mMDSC content regardless of tumor type. Note: Human biological samples were sourced ethically, and their research use was in accord with the terms of the informed consents under an IRB/REC approved protocol. All studies conducted according to GSK's Policy on the Care, Welfare and Treatment of Lab Animals and reviewed by the Institutional Animal Care and Use Committee at GSK or by the ethical review process at the institution where the work was performed. Citation Format: Brandon J. Turunen, Beth Knapp-Reed, Craig Leach, Peiling Chen, Matthew Sender, Joseph Marino, Cunyu Zhang, Yao Chen. Depletion of mMDSCs using a CCR2-directed cytotoxicity targeting chimera (CyTAC) leads to remodeling of the tumor microenvironment and immune mediated tumor regression [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 4715.
Abstract 2964: SCR-A002, a novel FGFR2b-targeting ADC for solid tumors
Authors: Yayuan Fu, Yuanjie Ge, Xiaohui Shao, Qi Deng, Chunlei Xia, Renhong Tang
Journal: Cancer Research (2025)

Abstract Background: FGFR2b (fibroblast growth factor receptor 2 IIIb), an isoform of transmembrane tyrosine kinase FGFR family, is overexpressed in various cancers, including gastric, esophageal, breast, hepatocellular, pancreatic, ovary, uterine, cervical, endometrial, lung, colorectal cancers. Bemarituzumab (FPA144) is an afucosylated humanized IgG1 monoclonal antibody targeting FGFR2b with enhanced ADCC activity, which had promising clinical efficacy in phase 2 study of FGFR2b-selected gastric or gastroesophageal junction adenocarcinoma. Simcere Zaiming has developed a potential first-in-class FGFR2b-targeting ADC (SCR-A002) at IND-enabling status, displaying significantly superior anti-tumor potency compared to Bemarituzumab. Methods: Using hybridoma technique, anti-FGFR2b antibody was generated from immunization of FGFR2b protein in mice. SCR-A002 was comprised of a humanized anti-FGFR2b IgG1 monoclonal antibody conjugated through a cleavable linker to proprietary TOPO1 inhibitor payload (DAR 8). Binding activity and cytotoxicity were assessed in FGFR2b+ tumor cell line. And anti-tumor efficacy was evaluated in several CDX and PDX models. Results: SCR-A002 specifically bound to FGFR2b on tumor cells and could be internalized, and the TOPO1 inhibitor could be cleaved intracellularly and then exhibited potent cytotoxicity to tumor cells. And tumor regression was achieved after single-dose administration of SCR-A002 in different FGFR2b expression level CDX and PDX models, even with big-size tumor or Bemarituzumab resistance. Conclusion: SCR-A002 showed remarkable anti-tumor efficacy in preclinical data, suggesting that SCR-A002 is expected to provide a new treatment option as single agent or combo with SoC for patients with FGFR2b-overexpressing solid tumor. Citation Format: Yayuan Fu, Yuanjie Ge, Xiaohui Shao, Qi Deng, Chunlei Xia, Renhong Tang. SCR-A002, a novel FGFR2b-targeting ADC for solid tumors [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 2964.
Abstract 1228: High throughput phenotyping and drug discovery using the TumorGraft3D co-culture platform and flow cytometry
Authors: Sumanun Suwunnakorn, Fu-Ju Chou, Elena Bruni, Karolina Pilipow, Xiangyang Zhang, Chelsea Riveley, Mara Gilardi, Stefano Cairo, Brandon Walling
Journal: Cancer Research (2025)

Abstract Many anticancer drugs fail in clinical trials due to issues resulting from inadequate efficacy and/or high toxicity emphasizing the need for improving clinically relevant, preclinical models for high throughput drug screening. Currently, 3D models have emerged as a highly promising tool for initial drug screening that closely mimics in vivo tumors through preserved morphology and molecular mechanisms. To further recapitulate the in vivo models, interactions between immune and tumor cells can be performed via co-culture models. As the complexity of the models has increased, the analytical methods have had to evolve as well. In this work, we have developed a high throughput flow cytometry (FlowHT) assay using Champions' TumorGraft3D (CTG3D) models. CTG3D are 3D organoids derived from our highly characterized and clinically annotated Patient Derived Xenograft (PDX) models. We have developed a method of TumorGraft3D dissociation which preserves cell viability and epitope stability. We further optimized a robust FlowHT workflow that allows for the detection of low-frequency targets and the characterization of unique subpopulations in modular multicolor panels to distinguish immune cells and CTG3D in mixed populations. Using this method, we have validated that the CTG3D models retain their original phenotype with minimal differences observed between source PDX tumors and expanded ex-vivo 3D models. At co-culture endpoints, our assay was highly sensitive to immune cell-mediated tumor killing as well as SOC drug responses. Interrogation in an allogenic PBMC coculture revealed the ability to detect cytotoxic T cells (Tc) and helper T cells (Th) activation and immune checkpoint markers such as CD69, TIM-3, and PD-1 among others. Collectively, we have developed a quantitative, sensitive, and robust assay that can be utilized as an analytical endpoint for both monoculture and coculture studies to enhance the interrogation of immune-oncology agents for tumor killing, ADCC effects, increasing T cell activation, reversal of T cell exhaustion and identifying specific markers across multiple cell types. Citation Format: Sumanun Suwunnakorn, Fu-Ju Chou, Elena Bruni, Karolina Pilipow, Xiangyang Zhang, Chelsea Riveley, Mara Gilardi, Stefano Cairo, Brandon Walling. High throughput phenotyping and drug discovery using the TumorGraft3D co-culture platform and flow cytometry [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 1228.
Abstract 2047: Homologous recombination deficiency in lung cancer in the INSPIRE study
Authors: Katherine G. Roth, Kevin J. McDonnell, Ernest Nadal, Joseph D. Bonner, Arman Seuylemezian, Suravi Nahar, Lawrence Shaktah, Jonathan Salazar, Sidney Lindsey, Xiaoyu Xia, Sara A. Byron, Jonathan J. Keats, Allen Mao, Adrien Larsen, Bryce Turner, Ravi Salgia, Stacy W. Gray, Stephen B. Gruber
Journal: Cancer Research (2025)

Abstract Introduction: Evaluating genomic signatures may improve prognostic information and outcomes for patients with lung cancer. Objective: To determine if homologous recombination deficiency (HRD) is associated with clinical features or overall survival in patients with lung cancer. Methods: This is a retrospective cohort study derived from City of Hope’s Implementing Next-Generation Sequencing for Precision Intervention and Risk Evaluation (INSPIRE) study. Study participants with histologically confirmed lung cancer and adequate tissue for comprehensive paired tumor-normal whole exome sequencing were eligible for analysis. 197 patients were sequenced, excluding 14 with rare histologies. Clinical and treatment variables were obtained from cancer registries and the electronic medical record and were recorded by experienced data curation and abstraction specialists. HRD scores were calculated using the scarHRD R package. Mutational signatures were analyzed using SigProfiler and SigEstimation. Associations between clinical variables and HRD status were measured using univariate and multivariate methods. Unsupervised analysis was performed to identify genes in HRD-high (sum score greater than or equal to 42) and HRD-low samples (sum score less than 42). Overall survival was quantified using non-parametric Kaplan-Meier statistics and multivariate Cox-proportional hazards models. Results: Of the 183 lung cancer samples analyzed, 63 (34.4%) samples were HRD-high. Of these, 43 had a TP53 alteration and 20 did not; 120 (65.6%) samples were HRD-low, 50 with a TP53 alteration and 70 without (OR 3.01 (95%CI 1.58, 5.72), p=0.0008). Conclusion: TP53 alterations were strongly associated with high HRD scores. Overall survival was improved in patients with HRD-high tumors treated with platinum therapy, although this difference did not reach statistical significance. Citation Format: Katherine G. Roth, Kevin J. McDonnell, Ernest Nadal, Joseph D. Bonner, Arman Seuylemezian, Suravi Nahar, Lawrence Shaktah, Jonathan Salazar, Sidney Lindsey, Xiaoyu Xia, Sara A. Byron, Jonathan J. Keats, Allen Mao, Adrien Larsen, Bryce Turner, Ravi Salgia, Stacy W. Gray, Stephen B. Gruber. Homologous recombination deficiency in lung cancer in the INSPIRE study [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 2047.
Abstract 3069: Inhibition of PGE2 signaling by an EP2/4 dual antagonist OCT-598 prevents acquisition of therapy-resistance and tumor relapse
Authors: Youngrae Lee, Haein Choi, Jong-Won Lim, Sung Eun Lee, Yeeun Kim, Changhoon Choi, Taeyoung Yoon
Journal: Cancer Research (2025)

Abstract Conventional antitumor drug discovery focuses primarily on selective killing of cancer cells. However, more often than not, cancer cells become resistant to the therapy and tumors eventually relapse in a more malignant form, potentially even accelerating disease progression afterwards. Therefore, it is of paramount importance to curtail the process by which cancer cells adapt to the therapeutic pressure to re-invent themselves and regenerate. Prostaglandin E2 (PGE2) is widely recognized as an important mediator of wound healing and tissue regeneration after injury by orchestrating reparative immune responses and mobilizing tissue stem cells. Likewise, in cancer, the PGE2 pathway has been shown to promote tumor growth, immune evasion, angiogenesis, and cancer stem cell (CSC) survival. Thus, upon cytotoxic insults, the apoptotic signal in dying cells induces PGE2 production, which enables, in a paracrine manner, the surviving cells to persist and eventually repopulate. Therefore, blockade of the PGE2 signals concurrently with cell-killing is anticipated to prevent tumors from acquiring therapy resistance. Of the known PGE2 receptors EP1-4, EP2 and EP4 are best known to convey its pro-tumor and immune-evasive signals. OCT-598 is a potent and selective dual antagonist of EP2 and EP4 with Ki values of 23 nM and 0.2 nM vs EP2 and EP4, respectively. OCT-598 has been shown previously to elicit complete regression in a mouse syngeneic TC-1 tumor model when used in conjunction with the standard of care chemo-immunotherapy regimen (Abstract 3234, AACR 2023). In this study, we present “anti-resistance” activities of OCT-598. In vitro, chemotherapy-induced cell deaths are followed by a dormant period, where the ‘un-dead’ cells show enlarged morphology and hyperploidy, and subsequently by repopulation of smaller, proliferative para-diploid cells. Addition of OCT-598 along with the chemotherapeutic agent decreased the number of the transient, enlarged cells and inhibited eventual repopulation in a dose-dependent manner. In vivo, OCT-598 abrogated tumor relapse after irradiation in CT26 mouse syngeneic tumor model, leading to complete remissions. Based on these observations, a clinical trial is set to be initiated to test the “anti-resistance” activity of OCT-598 as an adjuvant to the standard-of-care treatment in patients with advanced solid tumors. Citation Format: Youngrae Lee, Haein Choi, Jong-Won Lim, Sung Eun Lee, Yeeun Kim, Changhoon Choi, Taeyoung Yoon. Inhibition of PGE2 signaling by an EP2/4 dual antagonist OCT-598 prevents acquisition of therapy-resistance and tumor relapse [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 3069.
Abstract 2518: Implementing an AI triage platform for identification and management of patients suspected of cancer risk to improve elective recovery post pandemic
Authors: Miles Payling, Seema Dadhania, Michael Moss, Judith Gordon, Bea Bakshi
Journal: Cancer Research (2025)

Abstract Background: The COVID-19 pandemic caused a significant backlog in the UK National Health Service (NHS), with 7.6 million patients awaiting consultant appointments as of August 2024. A major consequence of this was a surge in urgent suspected cancer (USC) referrals, which rose by 27% compared to pre-pandemic levels without a proportional increase in cancer detection rates. General Practitioners (GPs) often default to USC referrals, bypassing initial investigations, which strains secondary care services. C the Signs, an AI-led cancer prediction platform, supports GPs to improve cancer triage by identifying high-risk patients for appropriate pathways (such as direct access diagnostics or non-urgent referrals) without increasing referral volumes. This system optimizes USC referrals, reserving them for patients truly requiring intensive diagnostic resources, reducing pressure on secondary care. Methods: From January 2020 to September 2024, data from 1, 084 GP practices using C the Signs were analyzed, covering 235, 662 risk assessments. The platform stratified patients into categories: urgent admission, USC referral, non-urgent referral, and direct access diagnostics (e.g. blood tests, FIT, X-ray). Patients not at risk were safely excluded from cancer pathways. Results: C the Signs redirected 21.7% of patients away from the USC pathway, safely excluding 21, 449 (9.1%), triaging 18, 063 (7.7%) to tests and diagnostics, and 11, 587 (4.9%) to non-urgent referrals—reducing USC pathway pressure by 61, 099 patients. Meanwhile, 184, 487 patients (78.3%) were appropriately referred for USC, ensuring focus on high-risk cases. Only 1.5% of assessments resulted in multiple USC referrals, and just 76 patients (0.0%) required urgent admission. A total of 13, 585 cancers were diagnosed, yielding a 7.3% conversion rate—20.9% higher than the NHS England average of 6.0%. Conclusion: C the Signs effectively stratifies suspected cancer patients, excluding low-risk individuals from USC pathways and directing others to appropriate care. This enhances NHS resource efficiency and supports elective recovery while maintaining diagnostic safety. If implemented nationally, C the Signs could reduce USC referrals by 505, 196 (17.5%) without compromising safety or outcomes. Longitudinal studies could further assess the platform’s impact on healthcare outcomes and efficiency. Citation Format: Miles Payling, Seema Dadhania, Michael Moss, Judith Gordon, Bea Bakshi. Implementing an AI triage platform for identification and management of patients suspected of cancer risk to improve elective recovery post pandemic [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 2518.
Abstract 5100: Mediator subunit <i>Med4</i> enforces metastatic dormancy in breast cancer
Authors: Seong-Yeon Bae, Hsiang-Hsi Ling, Yi Chen, Hong Chen, Dhiraj Kumar, Jiankang Zhang, Aaron Viny, Ronald A. DePinho, Filippo G. Giancotti
Journal: Cancer Research (2025)

Long term survival of breast cancer patients is limited due to recurrence from metastatic dormant cancer cells. However, the mechanisms by which these dormant breast cancer cells survive and awaken remain poorly understood. Our unbiased genome-scale genetic screen in mice identified Med4 as a novel cancer-cell intrinsic gatekeeper in metastatic reactivation. MED4 haploinsufficiency is prevalent in metastatic breast cancer patients and correlates with poorer prognosis. Syngeneic xenograft models revealed that Med4 enforces breast cancer dormancy. Contrary to the canonical function of the Mediator complex in activating gene expression, Med4 maintains 3D chromatin compaction and enhancer landscape, by preventing enhancer priming or activation through the suppression of H3K4me1 deposition. Med4 haploinsufficiency disrupts enhancer poise and reprograms the enhancer dynamics to facilitate extracellular matrix (ECM) gene expression and integrin-mediated mechano-transduction, driving metastatic growth. Our findings establish Med4 as a key regulator of cellular dormancy and a potential biomarker for high-risk metastatic relapse. Citation Format: Seong-Yeon Bae, Hsiang-Hsi Ling, Yi Chen, Hong Chen, Dhiraj Kumar, Jiankang Zhang, Aaron Viny, Ronald A. DePinho, Filippo G. Giancotti. Mediator subunit Med4 enforces metastatic dormancy in breast 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 5100.
Abstract 3057: Telomerase and G-quadruplex dual-targeting chimera inhibits melanoma via telomere disruption
Authors: Yutong Sui, qi xu, mingsheng liu, jinyu liu, geng qin
Journal: Cancer Research (2025)

Abstract Interference with telomerase and telomere maintenance have historically been viewed as a highly attractive target for anticancer therapies by restraining proliferative capacity via telomere length. A range of screens have identified many small molecule inhibitors of telomerase, but these inhibitors have all encountered obstacles in the early stages of preclinical studies primarily due to their limited potency and delayed onset of cytotoxic effects. Ligand-induced stabilization of telomeric G-quadruplexes (G4s) formation have been thought to be negative regulators of telomerase activity. However, given that G4-forming sequences are pervasive in human genome, G4 ligands display quite limited intra-G4 selectivity, resulting in a risk of side effects in therapeutic use. Here, we introduce an innovative telomere targeting strategy leveraging telomerase and G4 dual-targeting chimera. We design and synthesize such chimera by connecting telomerase inhibitor BIBR1532 to G4 ligands pyridostatin via a linker. On one hand, pyridostatin can enhance the anticancer potency of BIBR1532 by targeting telomere G4 structures. On the other hand, BIBR1532 can recruit pyridostatin to the telomere region by directly interacting with telomerase, thereby mitigating its off-target effects. As expected, the chimeric compound is capable of telomerase inhibition and suppress melanoma progression in vitro and in patient-derived xenograft (PDX) model with no observable toxicity. Notably, the anti-melanoma effects of the chimeric compound outperform that of BIBR1532 or pyridostatin alone. Our study provides a more effective strategy for telomerase inhibition, and the telomerase and G4 dual-targeting chimera is a promising candidate for anticancer therapy. Citation Format: Yutong Sui, qi xu, mingsheng liu, jinyu liu, geng qin. Telomerase and G-quadruplex dual-targeting chimera inhibits melanoma via telomere disruption [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 3057.