tbuckley/cabot-search huggingface dataset:
Abstract 4414: Targeting CCL5 signaling pathway in endocrine resistant breast cancer therapy
Authors: Dominick Lomonaco, Kideok Jin
Journal: Cancer Research (2025)

Estrogen receptor (ER) is the primary transcription factor driving ∼75% of all breast cancers and serves as the target for endocrine therapies. However, resistance to endocrine therapy remains a critical clinical challenge, particularly in metastatic ER-positive breast cancers harboring ESR1 point mutations in the ligand-binding domain, such as Y537S and D538G. These mutations are frequently identified in metastatic tumors and circulating tumor DNA (ctDNA) from patients undergoing endocrine treatment. Despite the efficacy of endocrine therapies combined with CDK4/6 inhibitors, resistance mechanisms and therapeutic vulnerabilities in ESR1-mutated metastatic breast cancer remain poorly understood. Our preliminary studies explored the crosstalk between endocrine-resistant breast cancer (ERBC) cells and stromal cells. By co-culturing seven ERBC cell lines, including genome-edited models of ESR1 mutations, with four stromal cell types, we screened 28 secretome combinations using cytokine antibody arrays. This analysis identified significant upregulation of CCL5 and endoglin in the tumor-stromal microenvironment. We hypothesize that CCL5 mediates endocrine therapy resistance and facilitates the metastatic transition of ERBC cells through interactions with stromal components. To test this, we used CRISPR-Cas9 to generate CCL5 knockout EO771 cells and validated the loss of CCL5 expression via qRT-PCR and ELISA. Functional assays revealed significantly reduced proliferation and migration in CCL5 KO cells compared to wild-type cells. In vivo studies using an orthotopic mouse model demonstrated decreased CCL5 KO tumor growth and metastasis, and treatment with maraviroc (a CCR5 inhibitor) selectively reduced wild-type cell viability. These findings establish CCL5 as a critical regulator of ERBC growth and metastasis, supporting its potential as a therapeutic target. This research provides a foundation for designing clinical trials targeting CCL5-mediated resistance mechanisms in endocrine-resistant breast cancer. Citation Format: Dominick Lomonaco, Kideok Jin. Targeting CCL5 signaling pathway in endocrine resistant breast cancer 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 4414.
Abstract 5388: Metastasis suppressor RKIP modulates mitochondrial metabolism in triple-negative breast cancer
Authors: Joana Pinheiro, Dongbo Yang, Madeline Henn, Long Chi Nguyen, Olga Martinho, Brandon Faubert, Marsha Rich Rosner
Journal: Cancer Research (2025)

Abstract Triple-negative breast cancer (TNBC) remains the most aggressive subtype of breast cancer, with a high propensity for metastasis. Tumor cell heterogeneity has been closely linked to metastatic progression, therapy resistance, and disease recurrence in solid tumors, including TNBC. Within tumors, metabolic heterogeneity emerges as cancer cells adapt to diverse environmental pressures, further driving tumor aggressiveness. However, the role of metastasis suppressors, such as Raf Kinase Inhibitory Protein (RKIP), in regulating metabolic heterogeneity is not yet fully understood. Analysis of RNA sequencing data from breast cancer patients revealed a strong correlation between RKIP expression and oxidative phosphorylation (OXPHOS) genes. Together with this, by performing gene set enrichment analysis of bulk RNA sequencing of mouse xenografts we observed an enrichment of hallmark of OXPHOS in RKIP-overexpressing tumors compared to controls. Consistent with these findings, RKIP was shown to modulate oxygen consumption rates in vitro. Using stable isotope tracing with [U-13C] glucose in vivo, we observed higher glucose contribution to citrate labeling in RKIP-overexpressing tumors compared to controls. Through single-cell RNA sequencing, we demonstrate that RKIP reduces overall transcriptional heterogeneity, particularly by decreasing the variability of genes involved in mitochondrial respiration. Importantly, treatment with the OXPHOS inhibitor metformin selectively inhibited the growth of RKIP-overexpressing tumors, while control tumors were unaffected. This study suggests that RKIP or drugs that mimic its action have the potential to promote OXPHOS in tumor cells, presenting an opportunity to suppress tumor growth by subsequent therapeutic targeting of mitochondrial respiration in TNBC. Citation Format: Joana Pinheiro, Dongbo Yang, Madeline Henn, Long Chi Nguyen, Olga Martinho, Brandon Faubert, Marsha Rich Rosner. Metastasis suppressor RKIP modulates mitochondrial metabolism in triple-negative 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 5388.
Abstract 4211: Studying WRN inhibitors with dSTRIDE-WRN assay
Authors: Olga Wójcikowska, Magdalena Bartyńska, Maja Białecka, Magdalena Kordon-Kiszala, Kamil Solarczyk
Journal: Cancer Research (2025)

Abstract The Werner syndrome helicase (WRN) is a critical enzyme involved in resolving replication stress and repairing double-strand DNA breaks, particularly in microsatellite instability-high (MSI-H) cancers. WRN inhibitors, such as HRO761, exploit the synthetic lethality of MSI-H cancers by trapping WRN on DNA, inducing genomic instability, and selectively killing tumor cells. Understanding the precise molecular mechanisms of WRN inhibition and its role in DNA repair pathways is essential for developing targeted therapies. Here, we introduce a newly developed assay for measuring WRN activity, specifically focusing on its exonuclease domain. This novel assay leverages the STRIDE platform technology, enabling direct and sensitive detection of single- and double-strand DNA breaks in situ within fixed cells. The dSTRIDE-WRN assay detects double-strand DNA breaks in close proximity to the WRN protein, providing a direct readout of its enzymatic activity. HCT116, a colorectal carcinoma cell line displaying high-level microsatellite instability (MSI-H) was chosen for optimization and validation of the assay. Two antibodies were tested initially, both producing satisfactory immunofluorescence staining; however, only one provided reliable readouts once incorporated into the STRIDE assay. The selected antibody generated consistent results across technical replicates and exhibited minimal signal in negative controls, confirming the assay's specificity and reproducibility. The assay’s ability to inform about WRN inhibition was evaluated by treating cells with HRO761, a selective inhibitor of WRN, with readouts collected at 1, 2, 4, and 6 hours post-treatment. A marked decrease in the dSTRIDE-WRN assay signal was observed at 4 and 6 hours, suggesting that HRO761 also influences WRN activity during DNA strand-breaks repair. These findings establish the dSTRIDE-WRN assay as a sensitive and reliable tool for quantifying WRN activity and its inhibition in the context of DNA damage repair. By providing a direct readout of WRN’s enzymatic function, the assay offers valuable insights into the molecular mechanisms underlying WRN-targeting therapies. This platform holds the potential for advancing the development and evaluation of WRN inhibitors in MSI-H cancers and beyond. Citation Format: Olga Wójcikowska, Magdalena Bartyńska, Maja Białecka, Magdalena Kordon-Kiszala, Kamil Solarczyk. Studying WRN inhibitors with dSTRIDE-WRN assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4211.
Abstract 7259: An in vivo humanized mouse model for human dendritic cell reconstitution to evaluate efficacy of tumor immunotherapy by B-NDG Flt3 KO mice
Authors: Fengqian Chen, Shujin Zhang, Fengxing Gu, Shaozu Fu, Yanling Wang
Journal: Cancer Research (2025)

Abstract Fms-like tyrosine kinase receptor 3 (Flt3) is a membrane protein that is strongly expressed on hematopoietic stem cells (HSCs). FLT3LG (FLT3 ligand) is a growth factor that can stimulate the proliferation, differentiation, and survival of these cells when it binds to its receptor FLT3. The Flt3/Flt3L signaling axis indeed plays an important role in the production of conventional dendritic cells (cDCs) and plasmacytoid dendritic cells (pDCs). Knockout of mouse Flt3 results in a reduction of mouse dendritic cells (DCs), which increases the availability of mouse Flt3L to the human receptor after human HSCs transplantation, thereby supporting the development of human immune cells, particularly dendritic cells. Biocytogen developed B-NDG Flt3 KO mice by knocking out the Flt3 gene in the NDG background. mFLT3 was detectable in DCs and CD117+ cells of B-NDG mice, but not in homozygous B-NDG Flt3 KO mice. To determine whether the knockout of Flt3 will affect the expression of FLT3LG. Serum were isolated from B-NDG mice and homozygous B-NDG Flt3 KO mice. Expression level of mouse FLT3L were analyzed by ELISA. Mouse FLT3L was detectable in B-NDG mice and homozygous B-NDG Flt3 KO mice. Levels of mFLT3L were substantially elevated in homozygous B-NDG Flt3 KO mice compared to B-NDG mice. To evaluate whether the knockout of Flt3 impacts the frequency of leukocyte subpopulations, Bone marrow cells were isolated from B-NDG mice and homozygous B-NDG Flt3 KO mice, Frequencies of T cells, B cells, NK cells, granulocytes, monocytes, macrophages in B-NDG Flt3 KO mice were like those in B-NDG mice. Frequencies of DCs in B-NDG Flt3 KO mice were lower than those in B-NDG mice. In summary, the significant decrease of DCs in B-NDG Flt3 KO mice creates an opportunity for the successful reconstruction of human DCs, which could have a significant positive impact on tumor immunotherapy. Citation Format: Fengqian Chen, Shujin Zhang, Fengxing Gu, Shaozu Fu, Yanling Wang. An in vivo humanized mouse model for human dendritic cell reconstitution to evaluate efficacy of tumor immunotherapy by B-NDG Flt3 KO 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 7259.
Abstract 7264: AI-guided engineering and preclinical characterization of anti-PD1/IL15 mutein bifunctional fusion proteins
Authors: Yun Zhang, Liang Tian, Chenpeng Su, Xiangyu Sun, Ran Hao, Tianhong Li, Dandan Liu, Jiyuan Tian, Xiaoqian Chen, Jian Peng, Zhenping Zhu
Journal: Cancer Research (2025)

Abstract IL15, a cytokine of the IL2 family, is pivotal for activating natural killer cells and effector/memory CD8 T cells. Clinical application with various IL15 formulations for cancer therapy, however, has been greatly hindered by its pharmacokinetics and dose-dependent systemic toxicity. A promising approach involves the fusion of IL15 with an anti-TAA antibody or an immune checkpoint antibody, in an attempt to specifically target IL15 to the tumor and its microenvironment while reducing peripheral exposure and toxicity. In this study, we generated a panel of stable IL15 variants (IL15v), utilizing an internally developed AI algorithm, with attenuated binding affinity to IL2Rβ and biological activity. We then engineered a panel of fusion proteins each comprising of a disulfide-bond stabilized IL15v, the IL15Ra sushi domain, and an anti-PD1 antibody IgG. Several lead molecules were produced with good expression level, stability and drugability. These anti-PD1/IL15v fusions not only fully retained their PD1-blocking activity, but also were significantly more potent in promoting the activation of PD1-expressing T cells, comparing to those of PD1-negative cells. In vivo pharmacokinetics and antitumor activity of these anti-PD1/IL15v fusions are currently being investigated. Anti-PD1 targeted delivery of stabilized and attenuated IL15v may provide an effective approach, with an improved safety profile, to reverse the suppressive state of tumor-infiltrating antigen-specific PD1-expressing CD8 T cells. Citation Format: Yun Zhang, Liang Tian, Chenpeng Su, Xiangyu Sun, Ran Hao, Tianhong Li, Dandan Liu, Jiyuan Tian, Xiaoqian Chen, Jian Peng, Zhenping Zhu. AI-guided engineering and preclinical characterization of anti-PD1/IL15 mutein bifunctional fusion 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 7264.
Abstract 4120: A systematic design of multiplex methylation-specific qPCR for CRC biomarkers
Authors: Michelle Y. Lee, Joy Wang, Brian B. Lin, Katelyn Y. Chao, Annie X. Wu
Journal: Cancer Research (2025)

Abstract Analysis of circulating cell-free DNA (cfDNA) methylation abnormalities has emerged as a promising strategy for detecting various diseases, including cancer. While single-biomarker approaches may lack sensitivity, comprehensive next-generation sequencing (NGS) can be cumbersome and expensive. Multiplex methylation qPCR assays offer a practical intermediate solution by providing accurate, accessible, and affordable methylation biomarker detection. In this study, we demonstrated a process for developing a multiplex methylation-specific qPCR assay using colorectal cancer (CRC) methylation biomarkers as a case study. Starting with a set of CRC methylation biomarkers, we developed the Multiplex Methylation-specific qPCR (MMqPCR) algorithm to scan differentially methylated regions (DMRs) for methylation-specific PCR primer and probe design. We then established a systematic process to eliminate assay cross-reactions, reduce background noise, and assess multiplex compatibility. Using a low concentration of hypermethylated DNA (0.1%) in a digital analysis, we demonstrated a 95.8% detection rate with the multiplex strategy, significantly outperforming the singleplex approach (47.9%). The multiplex qPCR development principles and automated primer design algorithm presented here provide valuable tools for developing disease screening, detection or monitoring methods based on methylation analysis. Citation Format: Michelle Y. Lee, Joy Wang, Brian B. Lin, Katelyn Y. Chao, Annie X. Wu. A systematic design of multiplex methylation-specific qPCR for CRC biomarkers [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 4120.
Abstract 4273: Discovery of first in class, polyphenolic inhibitors of CKAP4 and their antitumor activity in ovarian and endometrial cancer
Authors: Eugenio Gaudio, Viktor Ivasishin, Paulina Biniecka, Christian Kleusch, Cosimo Kropp, Benjamin Zimmer, Kamilla Pawlicka, Helena Almqvist, Alexey Chernobrovkin, Janneke Melis, Guido Zaman, Dan F. Stoicescu
Journal: Cancer Research (2025)

While some plant-derived polyphenolic compounds exhibit anticancer activity, their complex mechanism of action is generally hindering the efforts to produce clinically useful derivatives. Here we present several compounds that are, to the best of our knowledge, the first known inhibitors of cytoskeleton associated protein 4 (CKAP4) a transmembrane protein associated with resilient forms of cancer. Since CKAP4 is overexpressed in ovarian cancer the compounds were evaluated in the experimental models below as proof of concept. Target deconvolution using CETSA was followed by spectral shift binding, TRIC and ITC validation. In vitro studies assessed anti-proliferative activity (ATPLite, Revvity), with Oncolines Profiler analysis comparing the IC50 fingerprints with those of 213 pre-profiled reference drugs. Bioprinted human tissue organoids tested the efficacy of the new chemical entities. Tumor microenvironment characterization was performed using immunofluorescence imaging.From our proprietary physical library of 400 new chemical entities SND 106, 108, 562, 581, 584 and 586 were selected based on their strong binding to CKAP4. They were highly active in the ovarian and endometrial cell lines: PA-1, ES-2, AN3-CA, OVCAR-3 with IC50s in the low nanomolar range. Furthermore, the results of the organoid assays showed a significantly improved efficacy of the new compounds compared with the standard of care drug carboplatin.Novel, first-in-class small molecules inhibitors of CKAP4 were discovered, showing strong antitumor activity in ovarian and endometrial cancer. Future studies will determine whether they can be developed into new drugs. Citation Format: Eugenio Gaudio, Viktor Ivasishin, Paulina Biniecka, Christian Kleusch, Cosimo Kropp, Benjamin Zimmer, Kamilla Pawlicka, Helena Almqvist, Alexey Chernobrovkin, Janneke Melis, Guido Zaman, Dan F. Stoicescu. Discovery of first in class, polyphenolic inhibitors of CKAP4 and their antitumor activity in ovarian and endometrial 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 4273.
Abstract 2481: Employing joint modeling to support clinical interpretation of ctDNA dynamics during the treatment of advanced colorectal cancer
Authors: Christopher R. Pretz, Jiemin Liao, Aaron Hardin, Amar Das
Journal: Cancer Research (2025)

Abstract Background: Recent evidence suggests dynamic changes in cell-free circulating tumor DNA (ctDNA), defined as the maximum variant allele fraction (maxVAF), is predictive of overall survival (OS) in colorectal cancer (CRC) patents. As such, we leverage an advanced statistical approach, joint modeling of longitudinal and time-to-event data (JM), to associate ctDNA dynamics and OS. Contrasting with traditional methods, a unique advantage of JM is results assume the form of patient-specific adaptive dynamic predictions, where utilizing these predictions can enhance clinical decision-making in longitudinal monitoring. Methods: We applied JM to a retrospective cohort of patients with advanced CRC who received chemotherapy (chemo). The cohort was extracted from GuardantINFORM, a real-world clinico-genomics database. Patients analyzed had baseline Guardant360 (G360) ctDNA tests within 14 days before chemo initiation and &amp;gt;2 G360 tests on treatment. JMs are comprised of two sub-models: a hierarchical cubic spline random effects sub-model evaluated the serial ctDNA measures and a Cox-regression sub-model examined OS. Covariates incorporated into each sub-model included: age, gender, smoking status, and the Charlson Comorbidity Index. JMs, based on different association structures (AS) designed to connect information between sub-models, were investigated. ASs included the biomarker’s estimated value, instantaneous rate of change, and cumulative effect. Results: In total, 137 patients with 759 ctDNA time points were analyzed using three different JMs, one for each AS. After controlling for confounders, each AS demonstrated a significant relationship between ctDNA progression and OS (respective p-values &amp;lt; 0.005). As results are best interpreted graphically, various dynamic predictions are provided, each accentuating how the AS modifies the relationship between ctDNA and OS. Conclusions: To our knowledge, using JM to link dynamic ctDNA changes and OS in CRC patients is novel. In this study we demonstrate that a biomarker’s updated estimated value, instantaneous rate of change, or cumulative effect can forecast OS. As such, JM may afford healthcare providers different options to monitor patient progression and update prognosis as new ctDNA information becomes available on clinical reports. In sum, these results establish a foundation for integrating serial ctDNA measures for prognostic clinical interpretation. Citation Format: Christopher R. Pretz, Jiemin Liao, Aaron Hardin, Amar Das. Employing joint modeling to support clinical interpretation of ctDNA dynamics during the treatment of advanced colorectal 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 2481.
Abstract 4690: Radio-sensitizing activity in apoptosis pathway in HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC)
Authors: Loren D. Lopez Rivera, Elizabeth Boeree, Kwang P. Nickel, Zafer Gurel, Randall J. Kimple
Journal: Cancer Research (2025)

Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common cancer worldwide, presenting as two distinct diseases: HPV-positive HNSCC driven by high-risk human papillomavirus (HPV) infections; and HPV-negative HNSCC associated with heavy tobacco and alcohol use. Poor prognosis in HNSCC is partly attributed to therapy resistance, which differs between the two subtypes and is influenced by their underlying mechanism. Accumulating evidence points to dysregulation of the apoptotic pathway in HNSCC tumors via overexpression of Inhibitor of Apoptosis Proteins (IAPs). This results in evasion of cell death and makes these proteins critical therapeutic targets. Second mitochondria-derived activator of caspases (SMAC) mimetics, or IAP antagonists, are being explored as anti-cancer agents, especially in combination with radiation therapy. This study evaluates the efficacy of the IAP inhibitor AT406, alone and with radiation, in both HPV positive (UM-SCC47 and UD-SCC2) and HPV-negative (Cal27 and DET562) HNSCC cell lines. Preliminary findings suggest AT406 reduces cell viability in both subtypes, with HPV-positive cells exhibiting greater sensitivity, particularly in combination with radiation. On the other hand, HPV-negative cells show less pronounced reductions in cell viability, suggesting subtype-specific resistance mechanism. This trend underscores the potential of AT406 as a radio-sensitizing agent and highlight differences in therapeutic response between HPV-positive and HPV-negative HNSCC. Ongoing studies aim to confirm these findings and elucidate the molecular mechanism driving these differential responses. Apoptotic activity will be assessed through Caspase-3/7 activity, and expression of IAP proteins (cIAP1, cIAP2 and XIAP) will be evaluated using western blotting. In addition, Liquid Chromatography- Mass Spectrometry (LC-MS/MS) is being utilized to profile changes in protein expression under different treatment conditions to identify molecular contributors to resistance mechanisms. These studies aim to provide mechanistic insights into IAP inhibition and inform the development of combination therapies outcomes in HNSCC. Citation Format: Loren D. Lopez Rivera, Elizabeth Boeree, Kwang P. Nickel, Zafer Gurel, Randall J. Kimple. Radio-sensitizing activity in apoptosis pathway in HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC) [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 4690.