tbuckley/cabot-search huggingface dataset:
Abstract 1894: Correlative multiscale 3D spatial proteomics
Authors: Jingtian Zheng, Seung Young Lee, Yi-Chien Wu
Journal: Cancer Research (2025)

Abstract Tissues and organisms are complex systems, characterized by 3D structures, interconnected distinct functional subregions, and cellular heterogeneity, particularly in diseased states. To comprehensively understand the cellular and molecular mechanisms underlying disease, like tumor or neurodegenerative disease, it is crucial to construct a complete 3D map of tissues that integrates microanatomical structures, spatial cell composition, and molecular expression landscape, providing a holistic view of tissue pathophysiology. Existing tissue imaging methods can provide 2D spatial cellular and molecular information in tissue slices; however, only a fraction of the full 3D tissue architecture, leaving critical spatial and contextual information about the tissue microenvironment unresolved. To address this gap, we developed a novel methodology that integrates spatial proteomics with multiscale 3D optical tissue microscopy. The workflow begins with an overall 3D imaging of the tissue by light-sheet microscopy (LSFM), utilizing immunofluorescence (IF) or autofluorescence (AF) to visualize whole tissue morphology, cells, and molecules, providing a preview to identify Regions of Interest (ROIs). Using a tracking-based approach, macrosections containing these ROIs are physically isolated for subsequent 3D multiplex IF staining by cyclic staining and confocal microscopy (CLSM), allowing detailed, high-resolution cellular-level image and analysis. These sections are then subjected to thin-slicing and Super-Resolution Microscopy or Laser Capture Microdissection (LCM), which precisely extracts tissue regions for spatial proteomics analysis. Finally, the spatial proteomics data are aligned with multiscale 3D imaging data to provide a comprehensive, integrated analysis of the tissue. This integrated pipeline not only bridges 3D tissue imaging with molecular profiling but also enables selective analysis of ROIs, significantly saving time and resources while maintaining spatial and molecular fidelity, offering new insights into complex biological systems and disease mechanisms. Citation Format: Jingtian Zheng, Seung Young Lee, Yi-Chien Wu. Correlative multiscale 3D spatial proteomics [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 1894.
Abstract 2725: Noncanonical regulation of genes by KMT5C-H4K20me3 in EGFR inhibitor resistant non-small cell lung cancer
Authors: Alexandra Glaws, Jihye Son, Andrea Kasinski
Journal: Cancer Research (2025)

Abstract Lung cancer is the leading cause of all cancer-related deaths, with non-small cell lung cancer (NSCLC) making up ∼85% of lung cancer cases. Activating mutations in the epidermal growth factor receptors (EGFR) are associated with NSCLC development, comprising ∼32% of patients. Standard treatment for NSCLC patients involves targeting EGFR mutations with EGFR inhibitors (EGFRi), yet most patients develop resistance to EGFRi over time. Approximately 55% of the mechanisms involved in EGFRi resistance involve EGFR T790M secondary mutations; however, nearly 15% of these mechanisms are unknown. We have previously shown that the loss of KMT5C drives resistance to EGFRi in EGFR-mutant NSCLC cells. Patient data further supports that the KMT5C transcript level is downregulated following resistance. KMT5C is a histone methyltransferase that catalyzes the trimethylation of H4K20 (H4K20me3), a repressive modification historically known for the involvement of heterochromatin formation and maintenance. KMT5C recruitment through H4K20me3 to heterochromatic regions is a well-known mechanism occurring in H3K9me3-dependent manner. Our preliminary data also suggests KMT5C-H4K20me3 is associated with the regulation of gene-rich euchromatin regions; yet the mechanism of recruitment remains unknown. We hypothesize that recruitment of KMT5C to euchromatin is distinct from the mechanism involved in KMT5C recruitment to heterochromatin. Here, we study the interactome of KMT5C using an unbiased proximity labeling technique, BioID, and aim to identify factors that form a novel complex with KMT5C to enable the recruitment of KMT5C to its target genes in euchromatic regions that drive resistance to EGFRi. Citation Format: Alexandra Glaws, Jihye Son, Andrea Kasinski. Noncanonical regulation of genes by KMT5C-H4K20me3 in EGFR inhibitor resistant non-small cell lung 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 2725.
Abstract 3229: Investigating the transcriptomic signature of HHLA2-mediated suppression of NK cell activity
Authors: Nahuel Perrot, Nikolaos Kalavros, Deepthi Chowbene, Shoushuo Wang, Yered Pita-Juarez, Antonella Arruda de amaral, David McDermott, Gordon Freeman, Ioannis Vlachos, Kathleen Mahoney
Journal: Cancer Research (2025)

Abstract Determining how immune checkpoint inhibitors (ICI) alter functional characteristics of lymphocytes can improve our understanding of ICI. HERV-H LTR-associating 2 (HHLA2, B7-H7) is an immune checkpoint expressed by many tumors. Multiple HHLA2:KIR3DL3 blocking antibodies are currently in Phase I clinical trials and enrolling cancer patients (NCT05958199, NCT06240728), but little is known about how different subsets of NK cells are affected by HHLA2 expression. Our group previously found that in addition to an activating receptor, TMIGD2, HHLA2 has an inhibitory receptor, KIR3DL3. The KIR family of receptors is expressed in NK cells as well as T cells. Through co-culture experiments of CD56+ NK cells in the presence of K562 cells, we sought to investigate the mechanisms of NK cell engagement. Additionally, we generated transgenic K562 cell lines, over-expressing HHLA2, validated through flow cytometry, to maximize our ability to glean insight into HHLA2-KIR3DL3 mediated activation of NK cells. To this end, we generated a high quality scRNA-seq dataset of more than 100, 000 cells, comprising of more than 90, 000 NK cells, with approximately 30, 000 cells either cultured alone, co-cultured with K562 or K562 over-expressing HHLA2 tumor cells, allowing unprecedented granularity. In conjunction with published NK cell states and newly identified ones through this study, we recapitulate important known cytokines, growth factors and other regulators underlying NK cell maturation and substates that are differentially affected by treatment, in abundance, expression, and regulation. Furthermore, we shed some light on the complex interplay of positive and negative regulators, including CD48 - 2B4 and CD56 related interactions in CCL4 and XCL2 high NK cells, as well as TGFb related pathways. Uncovering NK cell activity modulators, such as amphiregulin, NKG7, FAM49B, and TXNIP, we then focused on NK cells in the context of KIR3DL or TMIGD2 expression. We add to previous efforts to understand immune checkpoint inhibition by the HHLA2-KIR3DL3 axis and in a concerted effort with blocking antibodies, provide evidence of enhanced NK cell efficacy. Better understanding of how HHLA2 pathway affects the function of different subsets of lymphocytes could determine which patients may best benefit from targeting this pathway. Citation Format: Nahuel Perrot, Nikolaos Kalavros, Deepthi Chowbene, Shoushuo Wang, Yered Pita-Juarez, Antonella Arruda de amaral, David McDermott, Gordon Freeman, Ioannis Vlachos, Kathleen Mahoney. Investigating the transcriptomic signature of HHLA2-mediated suppression of NK cell activity [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 3229.
Abstract 4494: Structure, dynamics and therapeutic potential of fatty acid synthase
Authors: Naimul Hasan, Alexander Keszei, Matthew Waas, Thomas Kislinger, Razq Hakem, Mohammad Mazhab-Jafari
Journal: Cancer Research (2025)

Abstract De novo lipid synthesis is facilitated by the multifunctional enzyme fatty acid synthase (FASN), a hallmark of cancer associated with chemotherapeutic resistance and poor prognosis. Human FASN (hFASN) is a dynamic protein that undergoes significant conformational changes during catalysis, posing challenges for structural characterization. To date, no structural information is available for full-length hFASN, hindering our understanding of its catalytic mechanism and complicating rational drug design.Here, we report the structure of hFASN resolved using electron cryo-microscopy (cryoEM). The modifying region of hFASN was determined at near-atomic resolution using a recombinant expression system bound to the first-in-class inhibitor Denifanstat, enabling structure-based small molecule discovery. Additionally, we solved the full-length structure of endogenous hFASN from MCF7 cells, revealing an interaction with the small heat shock protein HSP27. In some 2D classes of hFASN from cryoEM data, we found partial unfolding of the modifying region, evidence of potential protein degradation. However, HSP27 knockdown in breast cancer cell lines did not alter overall hFASN levels, indicating that this interaction may be transient or involve additional partners.Mass spectrometry-based post-translational modification analysis further identified dihydroxylation of proline, arginine, and tyrosine residues in hFASN from MCF7 cells, likely reflecting oxidative stress. These modifications may play a role in protein stabilization or regulation under stress conditions, highlighting a potential mechanism for hFASN activity modulation. Together, these findings provide critical structural and regulatory insights, paving the way for targeted therapeutic development. Citation Format: Naimul Hasan, Alexander Keszei, Matthew Waas, Thomas Kislinger, Razq Hakem, Mohammad Mazhab-Jafari. Structure, dynamics and therapeutic potential of fatty acid synthase [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 4494.
Abstract 3230: Preclinical double humanized CD47/SIRPΑ mouse model and MC38 cell line expressing human CD47 for efficacy and safety assessment of anti-CD47/SIRPΑ-targeting therapies
Authors: Philippe De La Rochère, Angela Pappalardo, Gaëlle Martin, Yacine Cherifi, Patricia Isnard-Petit, Fabiane Sonego, Kader Thiam
Journal: Cancer Research (2025)

Abstract CD47 is overexpressed on many human tumor cells and interacts with its ligand, the signal-regulating protein alpha (SIRPα), a protein expressed on macrophages and dendritic cells, to induce a “don’t eat me” signal. CD47 and its interaction with phagocytes is therefore a promising therapeutic target to treat cancer (S.B. Willingham et al., Proc Natl Acad Sci U S A. 2012). Herein, we describe a double humanized CD47/SIRPα model for efficacy and safety assessment of human CD47/SIRPα-targeting therapies in immunocompetent mice. The double humanized CD47 and SIRPα mouse model (hCD47/hSIRPα) was generated by intercrossing hCD47 and hSIRPα mice. Both hCD47 and hSIRPα are humanized and their model design enables expression of all human isoforms. hCD47 and hSIRPα are expressed at physiological levels, which enabled the biodistribution assessment of anti-SIRPα nanobodies, used as tracers in non-invasive in vivo imaging of tumors (T.R. Wagner et al., Front.Immunol. 2023). Activity of anti-CD47-targeting compounds were investigated in the model and a MC38 tumor cell line expressing hCD47 was developed to reproduce as much as possible the interactions between hCD47 and hSIRPα upon tumor engraftment in the mouse model. Tumor growth inhibition studies in the hCD47/hSIRPα model with the corresponding cell line have shown significant reduction of tumor growth in mice treated with Magrolimab (Hu5F9-G4). Furthermore, safety assessment of Magrolimab in MC38-hCD47-bearing hCD47/hSIRPα mice in tumor context recapitulates the clinical findings (C.K. Brierley et al., Transfusion. 2019), with a decline in hemoglobin and red blood cells post treatment. Altogether, these data suggest that the hCD47/hSIRPα model enables assessment of efficacy and safety of CD47 and/or SIRPα-targeting agents. The model is currently being upgraded to express humanized FcγR to enable assessment of Fc-mediated function of human antibodies targeting human CD47 and/or SIRPα. Citation Format: Philippe De La Rochère, Angela Pappalardo, Gaëlle Martin, Yacine Cherifi, Patricia Isnard-Petit, Fabiane Sonego, Kader Thiam. Preclinical double humanized CD47/SIRPΑ mouse model and MC38 cell line expressing human CD47 for efficacy and safety assessment of anti-CD47/SIRPΑ-targeting therapies [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 3230.
MVP-LCN2 axis triggers evasion of ferroptosis to drive hepatocarcinogenesis and sorafenib resistance
Authors: Jiawen Xu, Bo Wang, Qiaoyu Liu, Sheng Guo, Chen Chen, Jun Wu, Xiaoya Zhao, Mengmeng Li, Zhuang Ma, Shimeng Zhou, Yun Qian, Yijin Huang, Zhangding Wang, Chuanjun Shu, Qingxiang Xu, Jingjing Ben, Qiang Wang, Shouyu Wang
Journal: Drug Resistance Updates (2025)
Abstract 4944: Role of a planetary health diet in survival following breast cancer diagnosis
Authors: Andrea Romanos-Nanclares, Michelle D. Holmes, Wendy Y. Chen, Walter C. Willett, Bernard A. Rosner, A. Heather Eliassen
Journal: Cancer Research (2025)

Abstract Introduction: Whilst the current trend recommendation for breast cancer survivors to follow a healthy plant-centric diet seems prudent, evidence supporting this remains limited. Furthermore, diets that address both human health and environmental sustainability remain a research priority, and the EAT-Lancet Commission's 2019 "Planetary Health Diet" has offered a framework for this approach. Our study aimed to investigate whether a Planetary Health Diet Index (PHDI), quantifying adherence to these targets, is associated with overall and breast cancer-specific mortality. Methods: For 7, 639 women with stage I-III breast cancer from the Nurses' Health Study (NHS) and Nurses' Health Study II (NHSII), we calculated the cumulative average PHDI, using repeated measures of post-diagnostic diet assessed by food frequency questionnaires (FFQ). The PHDI index included a variety of high-quality plant-based foods (whole grains, fruits, vegetables, nuts and legumes) and low amounts of animal-based foods, refined grains, added sugars, and unhealthy fats. Deaths were ascertained by report from family members or by searching the National Death Index. Hazard ratios (HRs) and 95% confidence intervals (CI) were estimated using Cox proportional hazards models and adjusted for multiple time-varying and fixed-time covariates (measured prior to or at the time of diagnosis) and clinical factors. Results: Participants were followed up for a median of 12 years after breast cancer diagnosis. We documented 2, 983 deaths, including 788 due to breast cancer. In the multivariable-adjusted model, we observed a statistically significant inverse association for cumulatively averaged post-diagnosis PHDI and all-cause mortality (HRQ5vs.Q1 0.85 [0.73, 0.99], p-trend &amp;lt;0.01), but not breast cancer specific mortality. Findings for overall mortality were similar for PHDI measured at other timings/settings, including the first post-diagnosis dietary assessment (HRQ5vs.Q1 0.88 [0.76, 1.01], p-trend &amp;lt;0.01). Conclusions: High adherence to a diet consistent with both human and planetary health after a breast cancer diagnosis is associated with lower risk of all-cause, but not breast cancer-specific, mortality. As the number of breast cancer survivors grows and environmental sustainability becomes more urgent, strategies to reduce mortality should focus on the win-win benefits of dietary changes for both population and planetary health. Citation Format: Andrea Romanos-Nanclares, Michelle D. Holmes, Wendy Y. Chen, Walter C. Willett, Bernard A. Rosner, A. Heather Eliassen. Role of a planetary health diet in survival following breast cancer diagnosis [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 4944.
Abstract 3537: Development and validation of humanized HLA-A11.1 mouse model for preclinical evaluation of novel peptide vaccines
Authors: James Jin, Zhenlan Niu, Ying Zhao, Shuaiqiang Zhang, Zhi Zhang, Hui Xu
Journal: Cancer Research (2025)

Abstract The Major Histocompatibility Complex (MHC) is responsible for presenting diverse antigenic peptides and initiating T cell-mediated immune responses. Given the significant genetic differences between animal MHC systems and the human leukocyte antigen (HLA) system, HLA humanized mouse models offer an efficient in vivo system for HLA-A-related vaccine development and for studying HLA-A-restricted response mechanisms in humans. In this study, we present a novel B-HLA-A11.1 mouse model and have thoroughly investigated its phenotypic and immunological attributes. Our findings indicate that the blood routine and biochemistry of B-HLA-A11.1 mice are comparable to those of wild-type mice, suggesting that the humanization of HLA-A11.1 does not adversely alter blood cell composition or morphology, nor does it affect the health status of organs such as the heart, liver, or kidneys. Collectively, these data demonstrate that B-HLA-A11.1 mice develope normally and do not exhibit any evidence of spontaneous pathology due to the humanization of HLA-A11.1. To gain a deeper understanding of the role of MHC molecules, we extended our research using a humanized mouse model to assess immune responses against various cancer target peptides. In summary, our data indicate that humanized HLA-A11.1 mice provide a powerful preclinical model for in vivo/ex vivo evaluation of novel peptide and mRNA vaccines. Citation Format: James Jin, Zhenlan Niu, Ying Zhao, Shuaiqiang Zhang, Zhi Zhang, Hui Xu. Development and validation of humanized HLA-A11.1 mouse model for preclinical evaluation of novel peptide vaccines [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 3537.
Abstract 6137: Inhibition of FXR signaling in tumor-associated myeloid cells protects against melanoma progression
Authors: Shiun Chang, Darwin C. Chang, Rachel V. Jimenez, Rosa A. Sierra-Mondragon, Julio A. Vazquez Martinez, Paulo C. Rodriguez
Journal: Cancer Research (2025)

Abstract Our study delves into the complex interplay between the tumor microenvironment and immune cell regulation, with a particular focus on myeloid-derived suppressor cells (MDSCs). A key discovery of our research is the accumulation of bile acids (BAs) within the tumor microenvironment and tumor-infiltrating myeloid cells. BAs significantly enhance the suppressive function of MDSCs and M2 macrophages via activation of Farnesoid X Receptor (FXR).Using melanoma as our primary model. We demonstrate that modulation of MDSCs' suppressive function can be achieved through the targeting FXR using specific agents like GW4064 and z-Guggulsterone (z-GS). Myeloid-specific elimination of FXR via Lysozyme M Cre led to a significant delay in tumor progression. This was accompanied by the reduction of PMN-MDSC and an increased infiltration of CD45 positive immune cells and a surge in the presence of anti-tumor specific T cells. Administration of FXR inhibitor, z-GS, through oral gavage also reduced tumor size in vivo. Additionally, targeting FXR by z-GS or myeloid specific genetic ablation enhances adoptive T cells transfer therapy efficacy. MDSCs with impaired FXR signaling result in reduced mitochondria activity and downregulation of Arg1. Furthermore, an enhanced antigen presentation function is observed in MDSCs and dendritic cells treated with z-GS. Our research presents a compelling case for targeting FXR signaling in myeloid cells as a novel therapeutic strategy and open new pathways for enhancing anti-tumoral immunity. Citation Format: Shiun Chang, Darwin C. Chang, Rachel V. Jimenez, Rosa A. Sierra-Mondragon, Julio A. Vazquez Martinez, Paulo C. Rodriguez. Inhibition of FXR signaling in tumor-associated myeloid cells protects against melanoma progression [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 6137.
Abstract 3536: Synergistic effects of combined PD-L1 and B7-H3 fusion protein vaccination in a mouse model of pancreatic cancer
Authors: Kenneth Nansheng Lin, Melvin Toh, Hong Wang
Journal: Cancer Research (2025)

Abstract Background: Expressing immune checkpoint ligands is a mechanism for cancer cells to escape immune surveillance. Inhibiting these checkpoints effectively disrupts their escape mechanisms, improving cancer treatment outcomes. Various strategies have been developed to induce immune checkpoint inhibition. In this study, we developed cancer vaccines targeting checkpoint regulators, PD-L1 and B7-H3, and studied the anti-cancer activity in a syngeneic mouse cancer model using Panc02 cancer cells, known for their expression of both PD-L1 and B7-H3. Methods: Vaccines targeting PD-L1 and B7-H3 were recombinant proteins consisting of immune enhancers fused with mouse PD-L1 and B7-H3 extracellular domains, respectively, and produced in E.coli. C57BL/6 mice were vaccinated multiple times with vaccine protein(s) adjuvanted with Poly(I:C) and Freund's Adjuvant. Vaccine-induced humoral responses were measured by ELISA using serum samples collected from the mice. Anti-cancer activity was investigated using mice vaccinated four times followed by subcutaneous implantation of Panc02 cells and additional four vaccinations. Tumor growth was recorded. Tumor-infiltrated immune cells were characterized by immunofluorescence staining. Results: PD-L1 and B7-H3 vaccines induced specific antibodies against PD-L1 and B7-H3. Serum samples collected from PD-L1-vaccinated mice displayed neutralizing activity, blocking the binding of PD-L1 to PD-1. In mice inoculated with Panc02 cells, vaccination with PD-L1, B7-H3, and PD-L1/B7-H3 mixture inhibited tumor growth by 10%, 30%, and 66%, respectively. In the tumors, vaccination with the PD-L1/B7-H3 mixture increased CD4+ T cells significantly, indicating that vaccine-induced immune cell infiltration plays a critical role in tumor inhibition. Conclusions: Our results demonstrate that vaccination is an effective strategy for inducing neutralizing antibodies that inhibit immune checkpoints in cancer treatment. The most significant tumor growth inhibition observed with the combination of PD-L1 and B7-H3 vaccination underscores the necessity of simultaneously targeting multiple checkpoint regulators in cancers that express these proteins. Citation Format: Kenneth Nansheng Lin, Melvin Toh, Hong Wang. Synergistic effects of combined PD-L1 and B7-H3 fusion protein vaccination in a mouse model of pancreatic 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 3536.