tbuckley/cabot-search huggingface dataset:
Abstract 170: A novel protease-free workflow for spatial multiomics analysis of the tumor microenvironment in breast cancer
Authors: Patrick Savickas
Journal: Cancer Research (2025)

Abstract Introduction: Spatial multiomics is revolutionizing our understanding of the tumor microenvironment (TME) by enabling simultaneous analysis of multiple analytes within their tissue context. Combining in situ hybridization with immunofluorescence enables detection of key RNA and protein markers, together, on the same section. However, traditional ISH protocols that use enzyme-based pretreatment were incompatible with certain IHC/IF antibodies. Here, we present a novel protease-free workflow for a spatial multiomics panel, applied to human breast cancer samples, to investigate the interplay between immune cell infiltration and tumor cell signaling. Methods: Formalin-fixed paraffin-embedded (FFPE) breast cancer tissue sections underwent a protease-free staining protocol. The panel comprised three protein markers: CD3 (all T cells), CD8 (cytotoxic T cells), and PanCK (tumor cells). The RNAscope™ Multiomic LS in situ hybridization (ISH) assay was employed to detect IFNG (T cell activation), CXCL9 (chemokine produced by tumor cells), and CXCR3 (receptor for CXCL9 on CD8+ T cells). Spatial analysis algorithms were used to quantify co-expression and proximity of these markers. Results: Our protease-free workflow enabled simultaneous visualization of protein and RNA targets with high sensitivity and specificity. Preliminary data demonstrate distinct spatial patterns of immune cell infiltration and activation within the breast TME. We observed correlations between IFNG expression in CD8+ T cells and CXCL9 expression in PanCK+ tumor cells, suggesting a potential mechanism of T cell recruitment and activation. Conclusions: This novel protease-free spatial multiomics panel provides a powerful tool for dissecting the complex interactions between tumor cells and the immune system in breast cancer. By preserving both protein and RNA integrity, this approach offers valuable insights into the spatial organization of the TME and may identify novel therapeutic targets and biomarkers. Citation Format: Patrick Savickas. A novel protease-free workflow for spatial multiomics analysis of the tumor microenvironment 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 170.
Abstract 2816: Lipid composition differentiates ferroptosis sensitivity between in vitro and in vivo systems
Authors: Vivian S. Park, Lauren E. Pope, Justin Ingram, Grace A. Alchemy, Julie Purkal, Eli Y. Andino-Frydman, Sha Jin, Sanjana Singh, Anlu Chen, Priya Narayanan, Sarah Kongpachith, Darren C. Phillips, Scott J. Dixon, Relja Popovic
Journal: Cancer Research (2025)

Abstract Ferroptosis is a regulated non-apoptotic cell death process characterized by iron-dependent lipid peroxidation. This process has recently emerged as a promising approach for cancer therapy. Peroxidation of polyunsaturated fatty acid-containing phospholipids (PUFA-PLs) is necessary for the execution of ferroptosis. Ferroptosis is normally suppressed by glutathione peroxidase 4 (GPX4), which reduces lipid hydroperoxides to lipid alcohols. Some evidence indicates that GPX4 may be a useful target for drug development, yet factors that govern GPX4 inhibitor sensitivity in vivo are poorly understood. We find that pharmacological and genetic loss of GPX4 function was sufficient to induce ferroptosis in multiple adherent (“2D”) cancer cell cultures. However, reducing GPX4 protein levels did not affect tumor xenograft growth when these cells were implanted in mice. Furthermore, sensitivity to GPX4 inhibition was markedly reduced when cells were cultured as spheroids (“3D”). Mechanistically, growth in 3D versus 2D conditions reduced the abundance of PUFA-PLs. 3D culture conditions upregulated the monounsaturated fatty acid (MUFA) biosynthetic gene stearoyl-CoA desaturase (SCD). SCD-derived MUFAs appear to protect against ferroptosis in 3D conditions by displacing PUFAs from phospholipids. Various structurally related long chain MUFAs can inhibit ferroptosis through this PUFA-displacement mechanism. These findings suggest that growth-condition-dependent lipidome remodeling is an important mechanism governing GPX4 inhibitor effects. This resistance mechanism may specifically limit GPX4 inhibitor effectiveness in vivo. Disclosure Statement: V.S.P., J.P., S.J., S.S., A.C., P.N., S.K., D.C.P. and R.P. are employees of AbbVie and may own stock. J.I. was an employee of AbbVie at the time of the study. S.J.D., L.E.P., G.A.A. and E.Y.A are affiliated with Stanford University. The design, study conduct, and financial support for this research were provided by AbbVie. AbbVie participated in the interpretation of data, review, and approval of the publication. Citation Format: Vivian S. Park, Lauren E. Pope, Justin Ingram, Grace A. Alchemy, Julie Purkal, Eli Y. Andino-Frydman, Sha Jin, Sanjana Singh, Anlu Chen, Priya Narayanan, Sarah Kongpachith, Darren C. Phillips, Scott J. Dixon, Relja Popovic. Lipid composition differentiates ferroptosis sensitivity between in vitro and in vivo systems [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 2816.
Abstract 603: Repurposing the plant-derived compound apigenin in anticancer and antiaging pipelines
Authors: Yu Sun, Hongwei Zhang, Qixia Xu, Rong Sun, James L. Kirkland
Journal: Cancer Research (2025)

Abstract Cellular senescence is a cell fate triggered by inherent or environmental stress and characterized by stable cell cycle arrest accompanied by a hypersecretory feature, termed as the senescence-associated secretory phenotype (SASP). Senescent cell burden increases with natural aging, functionally contributing to age-related organ dysfunction and multiple disorders including various malignancies. In this study, we performed a large scale screening of a natural product library for senotherapeutic candidates by assessing their effects on human senescent cells. Apigenin, a dietary flavonoid previously reported with antioxidant and anti-inflammatory activities, exhibited a prominent capacity in targeting senescent cells as a senomorphic agent. In senescent cells, apigenin blocks the interactions between ATM/p38 and HSPA8, thus preventing transition of the acute stress-associated phenotype (ASAP) towards the SASP. Mechanistically, apigenin targets peroxiredoxin 6 (PRDX6), an intracellular redox-active molecule, suppressing the iPLA2 activity of PRDX6 and disrupting downstream reactions underlying the SASP development. Without reversing cellular senescence, apigenin deprives cancer cells of malignancy acquired from senescent stromal cells in culture, while reducing chemoresistance upon combination with chemotherapy in anticancer regimens. In preclinical trials, apigenin administration improves physical function of animals prematurely aged after whole body irradiation, alleviating physical frailty and cognitive impairment. Overall, our study demonstrates the potential of exploiting a naturally derived compound with senomorphic capacity to achieve anticancer and geroprotective effects by modulating the SASP, thus providing a research platform for future exploration of novel natural agents against age-related pathologies, including but not limited to cancers. Citation Format: Yu Sun, Hongwei Zhang, Qixia Xu, Rong Sun, James L. Kirkland. Repurposing the plant-derived compound apigenin in anticancer and antiaging pipelines [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 603.
Abstract 245: Preclinical development of HDM2020, a novel ADC targeting FGFR2b, in gastric cancer (GC) and squamous non-small cell lung cancer (sq-NSCLC) xenograft models
Authors: Tingyang Wang, Liubin Guo, Kuan Lu, Hao Pan, Yang Chen, Zhaoxing Yu, Yayun Zhao, Shengxing Zhao, Qingli We, Ruizhe Wang, Yan Xia, Hongwen Li, Dongzhou Jeffrey Liu
Journal: Cancer Research (2025)

Abstract Introduction: FGFR2b is a novel protein biomarker detected by IHC with the overexpression rate of ∼30% (any 2+/3+) in gastric or gastroesophageal junction cancer(GC/GEJC) patients, and among those patients ∼40% are not eligible for currently approved targeted therapies (HER2, PD-L1, MMR and CLDN18.2)1. HDM2020 is a topoisomerase Inhibitor based DAR8 ADC developed using a novel Ab targeted against FGFR2b, which has the potential to treat FGFR2b overexpressing tumor with reasonable safety window2. Methods: In vivo cell line (CDX) and patient derived xenograft (PDX) models were conducted to validate the therapeutic potential of HDM2020 against GC and sq-NSCLC. FGFR2b expression were detected by IHC using various tumor paraffin sections. Results: Combination of HDM2020 and avastin or paclitaxel demonstrated a synergistic effect in GC CDX model. Single-agent therapeutic activity of HDM2020 was demonstrated in two FGFR2b-positive GC PDX models with TP53 or BCOR gene mutation and at least 1st line chemotherapy. At a dose of 10mg/kg, the maximum tumor growth inhibition rate were 98% and 99%. In FGFR2b middle expressed sq-NSCLC PDX model, complete response was observed at single dose of 10mg/kg. The minimum effective doses were between 2.5-3mg/kg in above three models. FGFR2b is overexpressed in GC, sq-NSCLC, TNBC and may other tumor types. Conclusion: Based on the clinical validation of FGFR2b in GC and signs of early preclinical activity in sq-NSCLC with significant unmet need, HDM2020 might has promising efficacy in these indications. HDM2020 is expected to enter clinical development in 2025. References:1: Seiya Sato, Shannon L Rhodes, et al. Fibroblast Growth Factor Receptor 2 Isoform IIIb (FGFR2b) Protein Overexpression and Biomarker Overlap in Patients With Advanced Gastric or Gastroesophageal Junction Cancer(GC/GEJC). ESMO, 2024.2: Tingyang Wang, Liubin Guo, et al. Development of a novel FGFR2b-targeting ADC with robust anti-tumor efficacy in preclinical evaluation. World ADC SAN DIEGO 2024. Citation Format: Tingyang Wang, Liubin Guo, Kuan Lu, Hao Pan, Yang Chen, Zhaoxing Yu, Yayun Zhao, Shengxing Zhao, Qingli We, Ruizhe Wang, Yan Xia, Hongwen Li, Dongzhou Jeffrey Liu. Preclinical development of HDM2020, a novel ADC targeting FGFR2b, in gastric cancer (GC) and squamous non-small cell lung cancer (sq-NSCLC) xenograft models [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 245.
Abstract 190: Effects of bisphenol compounds on gene expression and cellular outcomes in MDA-MB-231 breast cancer cells mediated via the G protein-coupled estrogen receptor
Authors: Norman R. Estes, Cameron Sheeler, Olivia Merriam
Journal: Cancer Research (2025)

Abstract Bisphenol A (BPA) is used in the manufacturing of various consumer products such as plastic bottles, epoxy resins in food cans, thermal printed paper, and dental sealants. BPA has been identified as an endocrine disruptor due to its ability to mimic estrogen by activating estrogen receptor signaling pathways and regulating estrogen-responsive genes through a classical estrogen receptor-mediated pathway. Concerningly, BPA is linked to health risks, such as hormone-dependent cancers, metabolic diseases, and developmental defects. What remains unclear is the effect BPA and BPA alternatives have on gene expression and cellular outcomes via interaction with a membrane-bound estrogen receptor that functions as a G protein-coupled receptor (GPER). MDA-MB-231 triple-negative breast cancer cells (TNBC) express GPER but lack the classical estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). These studies seek to determine if BPA or alternatives, functioning through GPER, differentially affect gene expression, cell proliferation, and cell migration through GPER. Preliminary studies using total RNA sequencing (RNA-Seq) identified differential gene expression patterns in cells treated with BPA or 17β -estradiol including changes in cancer-related pathways, CREB signaling, and G-protein coupled receptor-mediated pathways. Cell migration assays performed in MDA-MB-231 cells treated with BPA, BPB, BPC, or 17β -estradiol suggest that treatment with these compounds differentially affects migration, with the highest degree of migration being induced by BPC. These studies indicate that BPA and BPA alternatives differentially affect gene expression and cell migration in triple negative MDA-MB-231 breast cancer cells and exposure to these compounds may affect therapeutic outcomes in TNBC patients. Future studies will seek to clarify the role of select genes and related pathways as identified through RNA-Seq analysis in TNBC cells treated with BPA or BPA alternatives in order to clarify the role of GPER-mediated signaling in TNBC cells. Citation Format: Norman R. Estes, Cameron Sheeler, Olivia Merriam. Effects of bisphenol compounds on gene expression and cellular outcomes in MDA-MB-231 breast cancer cells mediated via the G protein-coupled estrogen receptor [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 190.
Abstract 194: Angiopoietin-like 4 induces proliferation and migration of head and neck squamous cell carcinoma cells via p38 kinase and NRP1/ABL1/PXN pathway
Authors: Ajay Kumar
Journal: Cancer Research (2025)

Abstract Background: The molecular mechanisms in which angiopoietin-like 4 (ANGPTL4), a pluripotent protein implicated in cancer development, contribute to head and neck squamous cell carcinoma (HNSCC) growth and dissemination are unclear. Methods: We analyzed ANGPTL4 expression in human normal oral keratinocytes (NOKs), dysplastic oral keratinocytes (DOKs), oral leukoplakia cells (LEUK1), and HNSCC cell lines, HN13, HN6, HN4, HN12, and CAL27, as well as in tissue biopsies from patients with oral dysplasia, and primary and metastatic HNSCC. We further examined the contribution of ANGPTL4 cancer progression in an HNSCC orthotopic floor-of-mouth tumors model and upstream and downstream signaling pathways linking ANGPTL4 to cancer cell proliferation and migration. Results: ANGPTL4 expression was upregulated in premalignant DOKs and HNSCC cell lines compared to NOKs as well as in tissue biopsies from patients with oral dysplasia, and primary and metastatic HNSCC. Downregulation of ANGPTL4 expression inhibited primary and metastatic cancer growth in an HNSCC orthotopic tumor model. Interestingly, ANGPTL4 binding to the neuropilin 1 (NRP1) receptor led to phosphorylation of the focal adhesion protein, paxillin (PXN), and tumor cell migration; this was dependent on the tyrosine kinase ABL1. Further, we examined theextracellular signaling associated with ANGPTL4 expression in HNSCC. Intriguingly, amphiregulin (AREG), an epidermal growth factor receptor ligand, induced ANGPTL4 expression in NOKs and DOKs. AREG-induced activation of cell proliferation was dependent on ANGPTL4. We show that the proliferative potential of AREG in HNSCC is, in part, mediated by ANGPTL4. We also observed a role for p38 MAPK as an important downstream effector for the pro-tumorigenic effects ofANGPTL4 and an upregulation of a wide array of proliferative, proangiogenic, and proinflammatory factors upon treatment of NOKs with this adipokine. This suggests that ANGPTL4 may induce HNSCC tumorigenesis through both autocrine and paracrine pathways. Conclusion: Our findings identify novel opportunities for the development of therapies targeting the ANGPTL4-induced signaling pathways for the treatment of patients with HNSCC. Citation Format: Ajay Kumar. Angiopoietin-like 4 induces proliferation and migration of head and neck squamous cell carcinoma cells via p38 kinase and NRP1/ABL1/PXN pathway [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 194.
Abstract 604: Punicic acid from pomegranate seed oil induces cytotoxicity and oxidative stress in MCF-7 breast cancer cells
Authors: Braden Quitmeyer, Shelley A. Phelan
Journal: Cancer Research (2025)

Abstract Punicic Acid is an omega-5 long chain saturated fatty acid found in abundance in the oil of pomegranate seeds. While already known to provide various health benefits from a dietary perspective, punicic acid (PA) has also been shown to be an anti-proliferation agent in various cancer cell lines such as colorectal cancer and breast cancer. In this study, we examined the effects of PA on the MCF-7 breast cancer cell line as compared to the non-cancerous MCF-10A breast epithelial cell line. We found that PA induces dose-dependent cytotoxicity on both lines, with higher cytotoxicity in MCF-10A cells at all concentrations. MCF-7 cells exhibited relatively strong resistance to PA at the 0.4 μg/ml concentration, but increased cytotoxicity at 2 and 10 μg/ml. By contrast, there was notable cell death at all three concentrations within the non-cancerous cell line. Examination of apoptosis confirmed its role in both cell line responses to punicic acid, with significantly higher levels of apoptosis in MCF-10A cells. In order to examine the antioxidant response to punicic acid, we used qPCR to measure the expression of the Peroxiredoxin gene family (Prdx1, Prdx2, Prdx3, Prdx4, Prdx5, and Prdx6) after 48 hours of punicic acid treatment in both lines. We observed significant induction of all six Prdx genes in MCF-7 cells, with over a 4-fold increase in Prdx1, Prdx2 and Prdx6 at the 10ug/ml concentration. Interestingly, MCF-10A cells exhibited considerably higher induction of all six Prdx mRNAs at 10 μg/ml, exceeding a 30-fold induction of Prdx1, Prdx2 and Prdx5. Current work in our lab is focused on determining the role of oxidative stress in the PA-induced cytotoxicity in MCF-7 cells. Our data suggests a dose-dependent increase in mitochondrial superoxide production after 48hrs of punicic acid treatment. Analysis of other ROS markers is ongoing. Together, our data provide important new insights into the mechanisms and cell-specific effects of punicic acid, and its potential preventative and treatment efficacy in breast cancer. Citation Format: Braden Quitmeyer, Shelley A. Phelan. Punicic acid from pomegranate seed oil induces cytotoxicity and oxidative stress in MCF-7 breast cancer cells [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 604.
Abstract 2177: Spatial transcriptomic and functional analysis of HLA/PD-1/CTLA4 multi-gene edited CD19 CAR-iNK cells targeting pericytes in the glioblastoma tumor microenvironment to inhibit tumor migration and growth
Authors: Kyung-Sun Kang
Journal: Cancer Research (2025)

Abstract Targeting glioblastoma (GBM) stem cell-derived pericytes in the perivascular niche offers a promising strategy to overcome intratumoral heterogeneity and inhibit tumor migration. By targeting CD19-positive pericytes, CD19 chimeric antigen receptor (CAR)-expressing natural killer (NK) cells can mitigate off-tumor toxicity; however, their interactions within the GBM tumor microenvironment (TME) require further investigation. In this study, we developed a GBM TME xenograft model by transplanting GBM-blood vessel assembloids (GBVA) into immunodeficient mice to study the effects of CD19 CAR-expressing iPSC-derived NK (CAR-iNK) cells on pericytes and their interactions within the TME. Additionally, we enhanced the efficacy of CD19 CAR-iNK cells by knocking out PD1 and CTLA4, enabling these cells to better target GBM within an immunosuppressive TME. As a result, GBVA xenografts recapitulated the GBM TME including human pericytes and macrophages, providing a robust in vivo platform for validating CD19 CAR-iNK cell efficacy against GBM. Optimization of CAR-iNK cell dosing and efficacy resulted in significant antitumor effects. Spatial transcriptome analysis using SLACS (Spatially Linked Antibody and cDNA Sequencing) revealed that CD19 CAR-iNK cell infiltration altered gene expression in the TME, elucidating mechanisms of GBM lysis, migration inhibition, and evasion of immunosuppressive influences. These findings underscore the therapeutic potential of CD19 CAR-iNK cells for GBM treatment through precise targeting of pericytes and modulation of the TME. Citation Format: Kyung-Sun Kang. Spatial transcriptomic and functional analysis of HLA/PD-1/CTLA4 multi-gene edited CD19 CAR-iNK cells targeting pericytes in the glioblastoma tumor microenvironment to inhibit tumor migration and growth [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 2177.
Abstract 655: Spatiotemporally deciphering the response dynamics of micro-satellite stable rectal cancer to neoadjuvant short-course radiotherapy and PD-1 blockade
Authors: Jingwen Wang, Zhen Zhang
Journal: Cancer Research (2025)

Abstract Neoadjuvant chemoradiotherapy is the stand of care for patients with locally advanced rectal cancer (LARC). For microsatellite-stable (MSS) LARC patients, combining immune checkpoint inhibitors (ICIs) with radiotherapy has shown improved tumor regression, though the mechanisms behind tumor response remain unclear. Here, we analyzed 60 pre-, mid- and post-treatment tumor samples from 39 LARC patients in the TORCH clinical trial, utilizing single-cell sequencing and spatial transcriptomics to explore cell dynamics and their association with therapeutic efficacy. In well responders, combination therapy expanded the CD8+ and CD4+ memory T cell pool, which interacted with type 2 dendritic cells and clustered around non-malignant epithelial cells, forming part of tertiary lymphoid structures, as validated by spatial transcriptomics. In poor responders, the tumor microenvironment was enriched with immunosuppressive cells clustering around cancer-associated fibroblasts. This study uncovers mechanisms underlying the efficacy of radiotherapy combined with ICIs and provides valuable resources for identifying targets in MSS LARC patients. Citation Format: Jingwen Wang, Zhen Zhang. Spatiotemporally deciphering the response dynamics of micro-satellite stable rectal cancer to neoadjuvant short-course radiotherapy and PD-1 blockade. [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 655.