tbuckley/cabot-search huggingface dataset:
Abstract B002: Dynamic response and evolving adaptation of pancreatic cancer cells to the prolonged acidic pH microenvironment
Authors: Wun-Shaing Wayne Chang
Journal: Cancer Research (2024)

Abstract Solid tumor cells are often immersed in an acidic microenvironment. While many previous studies have investigated the short-term effects of extracellular acidity on tumor cells, little is known about how they adapt to the prolonged acidic microenvironmental stress and then advance to more aggressive stages. By challenging pancreatic tumor cells as an example with continuously and gradually acidified extracellular pH, a variety of cellular characteristics including phenotypic regulation, proliferation rates, autophagic control, metabolic plasticity and metastatic potentials were identified. More detailed evidence regarding the mitochondrial network dynamics and mechanistic control of pancreatic tumor cells in response to the extracellular acidosis will be presented at this conference to emphasize the critical effects of this stress factor as a selection force for tumor adaptation and progression. These findings not only highlight the importance of dynamic response and evolving adaptation of solid tumor cells to the chronic microenvironmental acidity, but also the potential of targeting the 'acid-mediated tumor malignancy' for anticancer therapy. Citation Format: Wun-Shaing Wayne Chang. Dynamic response and evolving adaptation of pancreatic cancer cells to the prolonged acidic pH microenvironment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr B002.
Abstract A005: Patient-derived cancer associated fibroblasts induce varying rates of colorectal cancer cell invasion using an organ-on-chip model
Authors: Bethany Haliday
Journal: Cancer Research (2024)

Abstract Colorectal cancer (CRC) is one of the most common cancers in the United States, with metastatic CRC having an especially poor prognosis. Because of this, significant effort has been put into understanding the metastatic cascade. However, very little is still understood about how the tumor microenvironment (TME) influences this process. Recent studies have implicated cancer associated fibroblasts (CAFs), a major component of the TME, to be involved in tumor cell invasion. CAFs have been reported to be highly heterogeneous, with classification into several subtypes, including inflammatory CAFs (iCAFs) and myofibroblastic CAFs (myCAFs), based on “-omics” based studies. However, there has been limited exploration into the specific functionality of these subtypes in contributing to cancer progression. Therefore, we have worked to develop an organ-on-chip model to study CAF influence on tumor invasion in CRC (CRC-on-chip). This microfluidic device simulates the fluid flow and peristalsis-like motions that occur in the gut and is composed of two extracellular matrix-coated overlapping channels separated by a porous membrane. CAFs and GFP-labelled tumor cells are seeded into the top “epithelial” channel and endothelial cells are seeded in the bottom “vascular” channel. Confocal microscopy is used to track and quantify GFP+ tumor cells intravasating into the vascular channel and determine rates of invasion. The CAFs are derived from our biobank of diverse CRC patient tumor samples. From previous work, we observed patient-specific differences in CAF-induced CRC invasion when exposing human CRC cells on-chip to CAF-conditioned media. Through physical co-cultures, we similarly observed that some CAF lines increased invasion while others did not change invasion. Bulk RNA-sequencing and flow cytometry analysis of the CAF lines revealed varied expression of invasion-related genes and trends toward specific CAF subtype signatures, such as the iCAF and myCAF subtypes. These results suggest that there may be specific CAF phenotypes that induce tumor invasion which could give insight into determining the invasive potential of a primary CRC tumor at diagnosis. Citation Format: Bethany Haliday. Patient-derived cancer associated fibroblasts induce varying rates of colorectal cancer cell invasion using an organ-on-chip model [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr A005.
Abstract B010: Improving pancreatic cancer image classification with transfer learning: CD45 vs. PANCK
Authors: Miracle Thomas
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is known for its high aggressiveness and is the fourth most common cause of death of cancer-related death in the United States. It is highly malignant and often goes undiagnosed until advanced stages due to its late-onset symptoms, resulting in poor prognosis. Using quantitative analyses of histological features, such as the expression of prognostic biomarker, can provide valuable insight to guide treatment decisions, monitor disease progression and predict outcomes. Previous researchers have found that CD45 and PANCK play a huge role in characterizing the tumor microenvironment of PDAC. One study using single-cell RNA sequencing compared the microenvironments of healthy pancreata and pancreatic tumors, revealing differences in cellular composition. Tumor samples showed a higher proportion of immune cells, including CD45+ cells, compared to heathy samples and utilized PANCK to differentiate between epithelial and non-epithelial cells. This study aims to enhance the accuracy of classifying pancreatic cancer pathological images based on prognostic markers using transfer learning techniques. We curated and pre-processed a dataset of pancreatic cancer pathological images with different prognostic markers. Using the pre-trained convolutional neural network (CNN) model VGG16, we fine-tuned it with our dataset to better differentiate between two prognostic markers, CD45 and PANCK. The model's performance was evaluated using a similarity matrix to illustrate distinctions among the two prognostic markers. Our results demonstrate that the transfer learning approach significantly improves classification accuracy, achieving confusion matrix validation results of 90% between CD45 and PANCK prognostic markers. SSIM values were relatively low, highlighting the ability of our model to differentiate between the two prognostic markers. The low SSIM value also shows variability within the two prognostic markers, indicating heterogeneity in structural changes due to pancreatic cancer. These findings indicate that transfer learning can be a powerful tool for improving the classification of pathological images and that there is notable variability in the structural features associated with different prognostic markers in pancreatic cancer. Citation Format: Miracle Thomas. Improving pancreatic cancer image classification with transfer learning: CD45 vs. PANCK [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr B010.
Abstract B027: ISG15 modulate cancer cell mechanics and metastasis in breast cancer
Authors: Mohamed Haloul, Priya Shah, Vinay Pai, Faruk Hossen, James James Lee, Ekrem Emrah Er
Journal: Cancer Research (2024)

Abstract Metastasis in breast cancer is a major challenge for prognosis and effective treatment, primarily because cancer cells can create an immune-suppressive microenvironment that supports their progression and spread. The physical properties of cancer cells significantly influence their metastatic potential and their interaction with the environment. Identifying targets that impact both the physical characteristics of cancer cells, and their microenvironment is crucial for tackling metastatic disease. Interferon-stimulated gene 15 (ISG15), a ubiquitin-like protein, is often overexpressed in breast cancer tissues and is associated with poor prognosis, higher tumor grade, and increased invasiveness. Despite these associations, the precise role of ISG15 and its post-translational modification, ISGylation, in cancer cell behavior and interactions with their microenvironment remains unclear. To explore this, we interrogated the biophysical role of ISG15 by using mouse modeling and in vitro loss of function approaches. We utilized whole- body ISG15-deficient mice and conducted a series of experiments to assess the impact of ISG15 on cancer cell properties and their surrounding environment. Our preliminary results indicate that cells lacking ISG15 exhibit altered physical traits, such as increased stiffness and size, which may influence their metastatic behavior. Additionally, targeting ISG15 or disrupting ISGylation enhances the susceptibility of cancer cells to immune cell-mediated destruction. In ISG15- deficient mice, we observed significantly reduced tumor growth and metastasis compared to wild-type controls. These findings suggest that ISG15 modulates critical aspects of cancer cell behavior and their interactions with the microenvironment, contributing to immune evasion and metastatic spread. Our research highlights ISG15 as a promising therapeutic target and provides a foundation for developing new strategies to prevent and treat metastatic cancer Citation Format: Mohamed Haloul, Priya Shah, Vinay Pai, Faruk Hossen, James James Lee, Ekrem Emrah Er. ISG15 modulate cancer cell mechanics and metastasis in breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr B027.
Abstract B005: Exploring breast cancer heterogeneity in the context of metastatic tumour microenvironments and therapy resistance
Authors: Sreeja Reddy Gadipally, Jean Berthelet, Samuel C. Lee, Dharmesh D. Bhuva, Michael Roach, Farrah El-Saafin, Caroline Bell, Yunjian Wu, David Baloyan, Christphe Ginestier, Charafe Jauffret Emmanuelle, Melissa Davis, Robin L. Anderson, Luciano Martelotto, Belinda Yeo, Delphine Merino
Journal: Cancer Research (2024)

Abstract Breast tumors comprise several sub-populations of cells, so-called “clones”, with specific cellular and molecular characteristics. Some cancer clones can be more ‘aggressive’ than others in particular tumor microenvironments (TMEs), contributing to metastatic progression and drug resistance. Understanding the specific genes/pathways deregulated in these aggressive cancer cells is essential for developing new tailored treatment strategies. To accomplish this, we optimized the use of a lentiviral-based barcoding technique (Berthelet, J., et.al., Sci Adv 2021, Serrano, A., et.al., Nat Rev Cancer 2022) where cancer cells from cell lines and patient-derived xenografts are tagged with optical barcodes and transplanted into the mammary fat pads of immunodeficient mice. Upon resection of tumors and collection of metastatic organs at the experimental endpoint, we analyzed clonal fate and fitness using flow cytometry and imaging. The subsequent molecular characterization of individual clones was determined by bulk and single-cell RNA sequencing. We also leverage the use of these barcoded models to investigate the mechanisms of innate and acquired resistance to Sacituzumab Govitecan (SG), a drug recently approved for the treatment of patients with advanced breast cancer. Our studies revealed unique gene signatures and pathways associated with preferential organ tropism (in the lungs, liver and brain TMEs) and SG resistance. This comprehensive analysis, currently validated using autopsy samples and patient databases, will support the design of new predictive markers and targeted therapies for metastatic breast cancer. Citation Format: Sreeja Reddy Gadipally, Jean Berthelet, Samuel C. Lee, Dharmesh D. Bhuva, Michael Roach, Farrah El-Saafin, Caroline Bell, Yunjian Wu, David Baloyan, Christphe Ginestier, Charafe Jauffret Emmanuelle, Melissa Davis, Robin L. Anderson, Luciano Martelotto, Belinda Yeo, Delphine Merino. Exploring breast cancer heterogeneity in the context of metastatic tumour microenvironments and therapy resistance [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr B005.
Abstract A041: Deciphering the crosstalk between cancer cells and stroma that drives EMT- coupled fibrosis
Authors: Elena Spina, Liangji Li, Junho Lee, Joan Massaguè
Journal: Cancer Research (2024)

Abstract In the tumor microenvironment (TME) cancer cells engage dynamically with the stromal component in promoting tumor progression and metastasis formation that are accompanied by intratumor fibrosis. Extensive extracellular matrix (ECM) remodeling and stiffness boost fibrosis which co-occurs with poor immune infiltration. Very little is known about the cross-interactions between tumor cells and stroma. A better understanding of this dynamic relationship may advance the development of new therapies. Transforming growth factor (TGF)-β signaling in both cancer epithelial cells and stroma is crucial for the establishment of intratumor fibrosis that enhances tumor progression. We previously discovered that in cancer cells, TGF-β signaling synergizes with RAS signal to regulate classical EMT transcription factors (Snail, Zeb1) and fibrogenic factors (Il11, Pdgf, Ctgfb, Wisp and others). This synergistic program is required for metastasis formation in pancreatic and lung adenocarcinoma (LUAD) models. However, how this dual program is affecting the stromal population in vivo remains unknown. Additionally, the role of each TGF-β dependent fibrogenic factor in regulating the stroma is still unclear. Using metastasis in vivo assays, we tested the metastatic ability of LUAD cells wild-type in comparison to Knock-Out cells targeting each one of the TGF-β dependent fibrogenic factors. We found that these factors are drivers of metastasis. More interestingly, these fibrogenic factors have a preferential effect depending on the metastatic site, suggesting that survival of the cancer cells in a certain tissue is dependent on the stromal niche within the site, which will act in favor or not of their growth. We also deeply characterize the stroma of micro-metastatic lesions by using high-throughput multiplex immunofluorescence to analyze the whole tissue TME at single cell resolution and found that lack of any of these fibrogenic factors compromise the establishment of a robust ECM at the very beginning of the metastatic colonization, to favor immune infiltration and consequently lead to cancer cell clearance. Together, these findings shed light on the potential role of these specific fibrogenic factors in metastasis, how their absence impacts the TME and how targeting these factors could be beneficial in metastatic disease. Citation Format: Elena Spina, Liangji Li, Junho Lee, Joan Massaguè. Deciphering the crosstalk between cancer cells and stroma that drives EMT- coupled fibrosis [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr A041.
Abstract A033: Integrating spatial transcriptomics and second harmonic generation imaging to identify targets of supermere-associated Discoidin Domain Receptor 1 involved in collagen alignment
Authors: Maxwell S. Hamilton, Oleg Tutanov, Harsimran Kaur, Alan J. Simmons, Clark Massick, Kasey Vickers, Ken S. Lau, Ambra Pozzi, Robert J. Coffey
Journal: Cancer Research (2024)

Abstract Immune checkpoint blockade has been shown to be an effective treatment for colorectal cancers (CRCs) highly infiltrated by CD8+ T cells. However, there is a paucity of CD8+ T-cell infiltration in the majority of CRCs. We previously identified the collagen-activated receptor Discoidin Domain Receptor 1 (DDR1) as a member of a four-gene signature associated with T-cell exclusion in CRC. The cleaved ectodomain (cECD) of DDR1 induces collagen alignment, leading to T-cell exclusion in a breast cancer model. We found that almost all DDR1 cECD is found in supermeres, a novel secreted nanoparticle identified by our lab, and that DDR1 cECD is required for supermere signaling in recipient cells. We hypothesized that supermere-associated DDR1 cECD signals to CRC stromal cells, leading to collagen alignment. To test this hypothesis, we developed a method to determine which genes are associated with collagen alignment and DDR1 expression. To do this, 30 μm thick CRC sections are imaged using a Nikon AX multiphoton microscope by second harmonic generation imaging, which permits label-free imaging of collagen fibers. Spatial heatmaps of the collagen alignment are generated from the resulting images. Spatial transcriptomics is performed on a serial tumor section using the Visium v2 platform and the gene expression matrix is integrated with the collagen alignment heatmap data. As proof-of-principle, two CRC tumors have been analyzed using this method. Highly aligned regions were found to be associated with expression of genes involved in extracellular matrix organization, keloidal collagen and specific fibroblast subtypes. Genes which may be regulated by DDR1 cECD and be involved in collagen alignment will be confirmed at the protein level by multiplexed immunofluorescence on serial sections and in vitro experiments. This method will provide a rich dataset to elucidate the roles of supermeres and DDR1 cECD in T-cell exclusion and collagen fiber alignment and may support the discovery of new strategies to overcome immune exclusion in CRC. Citation Format: Maxwell S. Hamilton, Oleg Tutanov, Harsimran Kaur, Alan J. Simmons, Clark Massick, Kasey Vickers, Ken S. Lau, Ambra Pozzi, Robert J. Coffey. Integrating spatial transcriptomics and second harmonic generation imaging to identify targets of supermere-associated Discoidin Domain Receptor 1 involved in collagen alignment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr A033.
Abstract A028: Direct interaction between cancer cells and fibroblasts drives epithelial- to- mesenchymal plasticity (EMP) and chemotherapy resistance
Authors: Nilu Dhungel, Ana-Maria Dragoi
Journal: Cancer Research (2024)

Abstract The tumor microenvironment (TME), composed of immune cells and fibroblasts, blood vessels, signaling molecules and extracellular matrix, provides important cues that govern epithelial-to- mesenchymal transition (EMT) and facilitate the acquisition of aggressive traits such as chemotherapy resistance by cancer cells. Cancer cells exist in multiple hybrid epithelial/mesenchymal (E/M) states, ensuring survival in the ever-changing environment during tumor development and metastasis. How are these hybrid states generated and maintained is not fully understood. Using small cell lung carcinoma (SCLC) and lung fibroblasts model, we show that direct interaction between SCLC and lung fibroblasts induces a hybrid E/M phenotype in cancer cells in which several mesenchymal genes involved in receptor interaction with the extracellular matrix (ECM) and ECM remodeling are upregulated while epithelial genes such as E-cadherin remain unchanged. We also demonstrate that several core EMT-regulating transcription factors (EMT-TFs) are upregulated in cancer cells during direct contact with fibroblasts, including Yes-associated protein (YAP1), a major regulator of the Hippo pathway. Furthermore, we demonstrate that the upregulation of YAP1 in cancer cells, which occurs only during the direct interaction with fibroblasts, renders the cancer cells more resistant to chemotherapeutic agents resulting in more aggressive phenotypes. The cells become sensitive to chemotherapeutic agents when YAP1 is inhibited. Altogether, our results provide evidence that tumor cells’ direct contact with the fibroblasts in the TME initiates a signaling cascade responsible for hybrid E/M states of cancer cells. These hybrid states are maintained during the interaction and contribute to therapy resistance via YAP1 pathway, while interference with direct contact will result in slow recovery and a switch to the initial states. Citation Format: Nilu Dhungel, Ana-Maria Dragoi. Direct interaction between cancer cells and fibroblasts drives epithelial- to- mesenchymal plasticity (EMP) and chemotherapy resistance [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr A028.
Abstract C008: New insights from a novel mouse model of synovial sarcoma
Authors: Hesham Mohei, Donn Van Deren, Irene S. Molina, Malay Haldar
Journal: Cancer Research (2024)

Abstract Mouse models are the basis of preclinical and translational research in solid tumors. Multiple methods exist to induce tumor formation in mice, including genetically engineered mouse models, chemotoxic agents, injection of tumor cells, and xenograft approaches. Synovial sarcoma, a rare highly malignant soft-tissue tumor, poses a serious threat to patients due to its aggressive nature and associated high rates of mortality and morbidity. This disease's underlying cause and development remain poorly comprehended, and existing treatment approaches have yielded unsatisfactory outcomes. In the last two decades, numerous effective animal models of soft tissue sarcoma (STS) have been created, primarily utilizing genetically engineered mice and zebrafish, however long latency of tumor development for several months in these models creates a barrier for practical in-vivo experiments for drug testing or manipulating the cellular composition of the tumor microenvironment. In studying cancer immunotherapy, it is important to consider aspects of antitumor immune responses and to produce a model that mimics the complexity of the immune system We have generated a new mouse model of synovial sarcoma of exceptionally fast tumor development. Intramuscular delivery of Cre recombinase protein in mice which drives conditional knockdown in PTEN, stabilization of β-catenin, and formation of fusion oncogenes of SS18-SSX2 was sufficient to initiate high-grade synovial sarcomas with myofibroblastic differentiation in 3 weeks. As immunotherapy is increasingly applied to sarcomas, our mouse model will serve as a great tool for preclinical data. Flow cytometry-based analysis of peripheral blood shows significant changes in immune cell populations as early as five days after Tat-Cre injection and continues throughout the development of synovial sarcoma. These results suggest a significant systemic phenotypic alteration of circulating immune cells, which may impact other major organs in this genetic mouse model of synovial sarcoma. Single- cell RNA sequencing of the CD45+ leukocytes in the tumor microenvironment reveals subsets that may promote tumor progression. Our work promises to significantly enhance our understanding of the pathogenesis of this disease and establish a reliable preclinical platform for devising and assessing therapeutic interventions. Citation Format: Hesham Mohei, Donn Van Deren, Irene S. Molina, Malay Haldar. New insights from a novel mouse model of synovial sarcoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr C008.