tbuckley/cabot-search huggingface dataset:
Abstract 3215: Cystatin F changes in melanoma patients during therapy with immune checkpoint inhibitors
Authors: Milica M. Perisic Nanut, Emanuela Senjor, Tanja Mesti, Simona Miceska, Janja Ocvirk, Janko Kos
Journal: Cancer Research (2025)

Abstract Although immune checkpoint inhibitors (ICI) have achieved undeniable success in the treatment of metastatic melanoma, primary and secondary resistance to ICI therapy continues to pose a significant challenge for melanoma patients. Around 40-60% of patients respond to immunotherapy, achieving long-term benefits, but over two-thirds experience immune-related adverse events (irAEs) with ICIs. About 10% show pseudoprogression, marked by transient inflammation, while up to 30% experience hyperprogression with rapid cancer advancement. Despite irAEs, treatment interruption often leads to better outcomes and prolonged survival. The lack of clinically validated predictive biomarkers remains a major factor contributing to the unpredictable effects of immunotherapy. Implementing biological markers in clinical practice is essential to enhance personalized treatment and predict responses. We have identified a protease inhibitor cystatin F as a potent down regulator of cytotoxic efficacy of cytotoxic T lymphocytes (CTLs). Its expression was shown to be increased in hypo responsive and exhausted CTLs but also in the cancer tissue in several types of cancer. In order to elucidate its role in CTLs of patients with melanoma and correlation its expression with response to treatment we have examined cystatin F expression, along with the CTL PD-1 expression and IFNγ in peripheral blood CTLs form patients with advanced melanoma (TNM classification, stage IIID and IV) receiving first-line therapy with ICIs. Study-specific data were collected at three different time points: up to 4 weeks before the start of treatment, at the 12th (+/−2 weeks) and 28th week (+/−2 weeks) and the expression of markers on whole blood preparations or isolated CTLs was analysed using flow cytometry. We characterized the cellular sources of cystatin F in tumor tissue using multicolor immunofluorescence staining and confocal analysis on formalin-fixed melanoma tissue samples. Our findings reveal cystatin F expression in predominantly in non-lymphoid cells within the tumor microenvironment. Analysis of cystatin F in peripheral blood CTLs shows higher expression in non-responders and patients with irAEs, suggesting its potential as a marker for enhancing personalized treatment and predicting treatment responses. Citation Format: Milica M. Perisic Nanut, Emanuela Senjor, Tanja Mesti, Simona Miceska, Janja Ocvirk, Janko Kos. Cystatin F changes in melanoma patients during therapy with immune checkpoint inhibitors [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 3215.
Abstract 2838: Modeling putative oncogenic variants of human topoisomerase II by genome editing of a near haploid cell line
Authors: Karin C. Nitiss, Brigid Conroy, Maureen N. McCoy, John L. Nitiss
Journal: Cancer Research (2025)

DNA topoisomerases (Topos) carry out changes in DNA structure by introducing transient breaks in DNA. These breaks are needed to change DNA conformation, and the enzyme mechanisms minimize possible genome instability from a failure to resolve the cleaved DNA intermediates. Nonetheless, small molecules can interfere with the Topo reaction, leading to elevated DNA cleavage, genome instability and cell death, and this property is the basis of the action of important anti-cancer drugs. Recent work has led to the identification of mutations in eukaryotic Top2 that also result in high levels of Top2 cleavage; including Lys743Asn in the Top2 alpha isoform which was observed in multiple human cancers. Hyper cleavage Top2 mutants are genome destabilizing in yeast and have been shown to induce 2-5 nucleotide de novo duplications, as well as other genetic changes. To generate mammalian cell lines expressing hyper cleavage Top2 mutants, we used Piggybac mediated scarless editing in the haploid mammalian cell line eHap. We accomplished successful editing of both Top2 alpha and Top2 beta in this cell line. Successful editing was assessed by sequencing Top2 cDNAs as well as sequencing of the edited genomic loci. Two independent successfully edited cell lines resulted in changes of Lys600Thr in Top2 beta and Lys579Thr in Top2 alpha; allowing us to compare the effects of mutations at orthologous positions in the two mammalian Top2 isoforms. Both edited cell lines show strong constitutive induction of DNA damage responses with elevated levels of DNA-PKcs and histone H2AX phosphorylation. Interestingly, elevated levels of ubiquitylated H2AX were also seen, suggesting that H2AX ubiquitylation may be indicative of constitutive topoisomerase induced damage. These cell lines are being used to measure genetic changes induced by topoisomerase induced damage and will be a unique tool to identify pathways that repair Topo-induced DNA damage. These cells will also provide insights into topoisomerase mediated mechanisms of oncogenesis. Citation Format: Karin C. Nitiss, Brigid Conroy, Maureen N. McCoy, John L. Nitiss. Modeling putative oncogenic variants of human topoisomerase II by genome editing of a near haploid cell line [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 2838.
Abstract 2820: Intracellular calcium dynamics affect ferroptosis sensitivity
Authors: Veronica T. Brooks, Ronan Talty, Simon F. Roy, Marcus W. Bosenberg
Journal: Cancer Research (2025)

Abstract Background: Melanoma is the deadliest form of skin cancer, and its incidence continues to rise. While advances in immunotherapy, in the form of anti-PD-1, anti-CTLA-4, and anti-LAG-3 immune checkpoint inhibitors, have led to extended cancer-free outcomes for many patients with advanced disease, most patients do not have durable responses. Therefore, improvements in long-term treatment of melanoma will depend on the identification of methods to enhance existing immunotherapy regimens. Recent studies highlight ferroptosis, an iron-dependent form of regulated cell death, as a necessary component of immunotherapy-induced tumor clearance. Cytosolic calcium influx is a key aspect of ferroptosis, preceding cell bursting and linking increased plasma membrane permeability with the activation of membrane repair mechanisms. Design: This study investigated the ability of calcium modulators to alter sensitivity to ferroptosis in cancer cells. SKF96365, an inhibitor of calcium release-activated channel (CRAC) activity and store-operated calcium entry (SOCE) channels, was selected for its effects on cellular calcium homeostasis and its limited exploration as an anti-melanoma agent and ferroptosis regulator. The ability of SKF96365 to sensitize melanoma cells to ferroptosis induction was assessed by evaluating key ferroptotic hallmarks, including cell death, lipid peroxidation and reduced glutathione levels. To further elucidate the underlying mechanism, three additional calcium modulators—GSK7975A, 2-Aminoethoxydiphenyl borate (2-APB), and Ruthenium Red (RR)—were tested. Results: SKF96365 enhanced sensitivity to ferroptotic cell death, but not apoptosis or autophagy. Melanoma and colon adenocarcinoma cells treated with SKF96365 had increased levels of lipid peroxides and decreased reduced glutathione levels. GSK7975A similarly sensitized cells, supporting the role of store-operated calcium entry (SOCE) channels in ferroptosis. In contrast, 2-APB, which shows a dose-dependent bimodal effect on SOCE, increased resistance to ferroptosis despite elevating lipid peroxides and reducing glutathione. RR, a mitochondrial calcium uniporter inhibitor, also sensitized cells to ferroptosis. Conclusion: SKF96365, GSK7975A, and RR enhance ferroptosis sensitivity, whereas 2-APB confers resistance. These results provide a foundation for further exploration of calcium signaling pathways in ferroptotic cell death. Citation Format: Veronica T. Brooks, Ronan Talty, Simon F. Roy, Marcus W. Bosenberg. Intracellular calcium dynamics affect ferroptosis sensitivity [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 2820.
Abstract 2843: Neoantigen evaluation in viably cryopreserved dissociated tissue via large scale proteomic profiling
Authors: Shawn P. Fahl, Casey Smith, Kerri Colwell, Jessica Moore, Jaison Arivalagan, Danielle Gutierrez
Journal: Cancer Research (2025)

Abstract Genomic instability is a hallmark of cancer where the acquisition of numerous genetic alterations leads to transformation and carcinogenesis. These alterations result in the generation of potentially immunogenic neoantigens, and the clinical success of checkpoint inhibitor therapies has highlighted the importance of neoantigens in cancer immunotherapy. Evaluation of the next generation of neoantigen therapies is complicated by the difficulty in sourcing primary patient material. During tumor resection and pathology review, the tissue is fixed, which prevents the ability to test in vitro model systems for therapy efficacy. While fresh tissue is amendable to in vitro culture, it is not possible to perform large scale genomic and proteomic screens in a timeframe for the culture to occur. By leveraging viably cryopreserved dissociated tissue, the tumor can be analyzed for genetic alterations and then, when novel neoantigens are determined, cultured at a later date. To test this workflow, we profiled dissociated tissues from cancer indications with a high degree of genomic instability for microsatellite instability (MSI). Consistent with previous studies, 17-55% of endometrial, colorectal, and gastric cancer samples were MSI-high. MSI-high and microsatellite stable (MSS) samples were further analyzed for peptide identification using LC-MS/MS (Orbitrap Astral) and over 10,000 protein groups and 80,000 peptides were identified. Samples were also amendable to T cell receptor (TCR) repertoire sequencing to uncover tumor-reactive T cell clones. These deep molecular analyses provided the foundation for the development of short-term spheroid and long-term tumoroid culture systems to understand immune responses using autologous tumor-infiltrating and peripheral lymphocytes. Collectively, this workflow provides a scalable system to identify neoantigens and evaluate the immune response to these antigens in a robust and reproducible pipeline. Citation Format: Shawn P. Fahl, Casey Smith, Kerri Colwell, Jessica Moore, Jaison Arivalagan, Danielle Gutierrez. Neoantigen evaluation in viably cryopreserved dissociated tissue via large scale proteomic profiling [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 2843.
Abstract 3178: Discovery and characterization of small molecules to enhance NK cell cytotoxicity against solid tumors
Authors: Indrani Das, Olubukola Abiona, Riufu Liu, David N. Wald
Journal: Cancer Research (2025)

Abstract Adoptive cell therapies (ACT), such as CAR-T and NK therapy, have transformed hematologic cancer treatment but show limited efficacy against solid tumors. NK cell therapies in particular have an excellent safety profile due to their specific, innate recognition of cancer cells, but fail to elicit adequate and sustained tumor clearance in vivo. To address this hurdle, we developed a high-throughput phenotypic small molecule screen to identify novel compounds that can enhance NK cell cytotoxicity against tumor cells. We screened 300, 000 compounds for their ability to enhance NK cytotoxicity against ovarian cancer cells (OVCAR-3). Our primary screen and subsequent hit validation identified 11 lead compounds that increase NK cell killing of OVCAR-3 cells (&amp;gt;10% increase over vehicle-treated control). We performed secondary screening using a flow cytometry-based assay on 5 of these 11 compounds to date, confirming that 3 significantly enhance NK cytotoxicity against OVCAR-3. After completing the secondary screening of the remaining 6 compounds, we will identify the most promising lead compound(s) through a series of secondary and orthogonal assays to characterize the biological activity and toxicity profile of validated hits. We will then pursue medicinal chemistry efforts to increase potency of our best lead compound, coupled with mechanistic studies for how the compound promotes NK cytotoxic activity. Ultimately, we hope to translate our findings into NK cell therapy clinical trials to achieve greater efficacy against solid cancers. Citation Format: Indrani Das, Olubukola Abiona, Riufu Liu, David N. Wald. Discovery and characterization of small molecules to enhance NK cell cytotoxicity against 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 3178.
Abstract 3275: Reprogramming of MDSCs by ST316, a clinical peptide antagonist of b-Catenin/BCL9, enhances anti-tumor immuno- and chemotherapy
Authors: Claudio Scuoppo, Julia Diehl, Ricardo Ramirez, Barry J. Kappel, Abi Vainstein-Haras, Jim A. Rotolo
Journal: Cancer Research (2025)

Abstract Myeloid-derived suppressor cells (MDSCs) are a diverse group of immune cells that play critical roles in mediating immune-suppression. They are often associated with poor responses in various cancer types and represent an attractive target for immunotherapy. Challenges in defining the genetic dependencies of MDSCs have hindered the development of effective therapeutic strategies aimed at targeting them. The Wnt/β-catenin signaling pathway is a key oncogenic driver that has been implicated in immune-exclusion, although additional roles in immune-suppression remain unclear. ST316 is a clinical-stage peptide antagonist of the interaction between β-catenin and its co-activators, BCL9 and BCL9L. Currently, ST316 is being evaluated in a Phase 2 study (NCT05848739) in patients with advanced colorectal cancer (CRC) in combination with standard-of-care agents. We demonstrated in a Phase 1 dose escalation study that ST316 suppresses MDSC expansion in the peripheral blood of treated patients and corroborated these findings in non-clinical CRC murine models. Here, we characterize the role of the Wnt/β-catenin/BCL9 pathway in MDSC programming and investigate the mechanism by which ST316 reduces MDSC expression and immuno-suppressive activity. Transcriptional profiling of MDSCs from tumor-bearing mice indicates that β-catenin and other Wnt pathway components are highly expressed in these cells. Our findings indicate that exposure to ST316 reduces the expression of receptor systems linked to MDSC-mediated T-cell suppression, thereby activating T-cell responses in vivo. In combination studies, ST316 significantly enhances the anti-tumor efficacy of anti-PD-1 immunotherapy and standard-of-care chemotherapies for advanced CRC such as FOLFIRI. Moreover, while anti-PD-1 and FOLFIRI alone each resulted in expansion of immunosuppressive MDSCs, combination with ST316 prevented this expansion. Our results reveal a novel role for Wnt/β-catenin signaling in MDSC biology and demonstrate that ST316 can suppress the increase of therapy-driven MDSCs in vivo. These data suggest that therapeutically targeting the BCL9/β-catenin interaction may be an effective strategy to enhance both chemotherapy and immunotherapy in Wnt-driven tumors that respond poorly to monotherapy. Citation Format: Claudio Scuoppo, Julia Diehl, Ricardo Ramirez, Barry J. Kappel, Abi Vainstein-Haras, Jim A. Rotolo. Reprogramming of MDSCs by ST316, a clinical peptide antagonist of b-Catenin/BCL9, enhances anti-tumor immuno- and chemotherapy [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 3275.
Abstract 2839: The functional role of tumor suppressor WW domain-containing oxidoreductase in maintaining genome integrity
Authors: Li-Jin Hsu
Journal: Cancer Research (2025)

The induction of DNA damage response (DDR) to ensure accurate duplication of genetic information during DNA replication is crucial for maintaining genome integrity. Cellular senescence is a DDR mechanism that prevents the proliferation of cells with deleterious DNA damage to avoid mitotic anomalies and inheritance of the damage over cell generations. A decreased ability of the cells to undergo senescence has been suggested to be associated with cancer development. Using Wwox knockout models, we determined that Wwox knockout mouse embryonic fibroblasts (MEFs) failed to undergo replication stress-induced cellular senescence after multiple passages in culture. Importantly, accelerated cell cycle progression and increased apoptosis were detected in Wwox knockout MEFs at late passages. Increased γH2AX-positive cells and microsatellite instability were examined in late-passage Wwox knockout MEFs, indicating massive accumulation of DNA damages in these cells. We detected significantly reduced expression of p53 and CDK inhibitors p16INK4A and p21cip1/waf1 in late-passage Wwox knockout MEFs. Inhibition of oxidative stress during en vitro passage culture reversed p16INK4A and p21cip1/waf1 downregulation and induced senescence in Wwox knockout MEFs. Importantly, we demonstrated that WWOX protein expression was upregulated in cells during DNA replication. Significantly enhanced phosphorylation of Chk-1 protein was detected in proliferating WWOX-knockdown HEK-293T cells and Wwox knockout MEFs, suggesting that WWOX plays an important role in regulating DDR signaling for maintaining genome stability upon replication stress. Our findings delineate the regulatory role of WWOX in DDR and have great impact on our understanding of molecular pathogenesis of cancer and senescence-related diseases. Citation Format: Li-Jin Hsu. The functional role of tumor suppressor WW domain-containing oxidoreductase in maintaining genome integrity [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 2839.
Abstract 3758: Discovery of a bridged proteolysis targeting chimera (PROTAC) recruiting the SPOP E3 ubiquitin ligase for targeted protein degradation
Authors: Jerrel Lewis Catlett, Zhijie Deng, Youngeun Lee, Yan Xiong, Husnu Ü. Kaniskan, Jian Jin
Journal: Cancer Research (2025)

Abstract Proteolysis Targeting Chimeras (PROTACs) are promising therapeutic modalities for eliminating disease-causing proteins, particularly in oncology. However, the widespread applicability of PROTAC technology is limited by the paucity of suitable E3 ubiquitin ligases available for targeted protein degradation (TPD) despite the existence of over 600 such ligases in the human genome. Many E3 ligases lack small-molecule ligands, rendering them inaccessible to recruitment by traditional PROTAC design methodology. To overcome this challenge, we instead leverage a high-affinity binder of the histone methyltransferase GLP, an endogenous substrate of the yet unharnessed E3 ligase SPOP, to facilitate PROTAC discovery and targeted degradation of the epigenetic regulator BRD4. Through the application of this novel substrate-bridged PROTAC strategy we discovered the compound MS479, which represents the first molecule of its class capable of recruiting SPOP for TPD and the first to do so by taking advantage of the endogenous interaction between an E3 ligase and one of its protein substrates. This approach successfully facilitates the polyubiquitination of BET-family proteins (i.e., BRD4/3/2) and their subsequent degradation of by the 26S proteasome. In particular, MS479 demonstrates significant efficacy in reducing the post-translational expression of BRD4 short isoform in HT29 cells in a time-, concentration-, GLP-, SPOP-, and ubiquitin-proteasome system- (UPS) dependent manner. Additionally, MS479 exhibits potent inhibition of colorectal cancer (CRC) cell proliferation. Our substrate-bridged PROTAC strategy will ultimately increase the available repertoire of E3 ligases that are tractable for TPD, serving as proof-of-concept for a novel and generalizable platform to target the large suite of E3 ubiquitin ligases that lack pharmacological ligands. Citation Format: Jerrel Lewis Catlett, Zhijie Deng, Youngeun Lee, Yan Xiong, Husnu Ü. Kaniskan, Jian Jin. Discovery of a bridged proteolysis targeting chimera (PROTAC) recruiting the SPOP E3 ubiquitin ligase for targeted protein 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 3758.
Abstract 3192: GT316: a next-generation TIL therapy identified through genome-wide CRISPR screening with promising efficacy in advanced solid tumors
Authors: Jingwei Sun, Yao Sheng, Jingman Wang, Jiahui Jin, Zhao Xu, JIng Yu, Jing Guo, Zhongping Cheng, Pin Wang, Yarong Liu
Journal: Cancer Research (2025)

Abstract Adoptive cell therapy using tumor-infiltrating lymphocytes (TILs) has demonstrated therapeutic efficacy in late-stage melanoma patients. However, expanding its applicability to other solid tumors and improving clinical outcomes remain significant challenges. To address these limitations, we developed ImmuTFinder, a genome-wide CRISPR/Cas9 screening platform designed to identify key immunoregulatory targets that enhance TIL functionality and broaden their therapeutic potential. Functional validation of over 120 top candidate targets was performed in TCR-T cells using a high-throughput 96-well array. Promising targets were further tested for combinatorial effects in TILs through in vitro assays and in vivo models. A dual knockout of GT304 and GT312, termed GT316, emerged as the most effective combination, significantly improving TIL proliferation, cytokine production, tumor eradication in CDX and PDX mouse models, and long-term persistence with reduced dependency on IL-2. Specific and highly efficient sgRNAs for these targets were selected, and a scalable manufacturing process for GT316 TILs, named KOReTIL, was developed. A first-in-human trial of GT316 demonstrated good tolerability and encouraging preliminary antitumor activity in patients with advanced solid tumors. Notably, a patient with treatment-refractory cervical cancer achieved a confirmed complete response (CR) four weeks post-infusion, with the response persisting for 50 weeks to date (RECIST 1.1). Another patient with ovarian cancer, previously treated with nine lines of systemic therapy, achieved a confirmed partial response (PR) at six weeks post-infusion, with a response lasting over 50 weeks (RECIST 1.1). Data collection on additional responses is ongoing. In summary, these findings highlight the utility of the ImmuTFinder platform for discovering novel immunoregulatory targets and demonstrate the potential of GT316 as a next-generation TIL therapy for advanced solid tumors. Citation Format: Jingwei Sun, Yao Sheng, Jingman Wang, Jiahui Jin, Zhao Xu, JIng Yu, Jing Guo, Zhongping Cheng, Pin Wang, Yarong Liu. GT316: a next-generation TIL therapy identified through genome-wide CRISPR screening with promising efficacy in advanced 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 3192.