Cancer Models Research Articles

Development and validation of the antibody-dependent cellular phagocytosis-based signature: A prognostic risk model of gastric cancer

Development and validation of the antibody-dependent cellular phagocytosis-based signature: A prognostic risk model of gastric cancer

Construction of molecular subtype and prognostic model for gastric cancer based on nucleus-encoded mitochondrial genes

Construction of molecular subtype and prognostic model for gastric cancer based on nucleus-encoded mitochondrial genes

Abstract A006: Investigating the effects of fibroblasts derived from the primary versus the metastatic organ on 3D biomimetic models of pancreatic cancer

Abstract Pancreatic ductal adenocarcinoma (PDAC) is the 3rd leading cause of cancer death in the United States with a 5-year survival rate of only 13%. Early diagnosis is very difficult and thus 53% of patients are diagnosed after metastasis has already occurred, with the liver being the most frequently affected site. Both primary tumors and metastases have dense desmoplastic stroma due to a high percentage of fibroblasts within the tumor microenvironment (TME). Previously, we developed a tunable 3D biomimetic model of the liver metastatic niche (LMN) to investigate how local fibroblasts affect tumor growth and chemoresistance in PDAC liver metastasis. This study aims to investigate the contributions of fibroblasts at the primary versus metastatic sites. We used matched primary PDAC and liver metastatic (LM) organoids derived from the Kras+/LSL-G12D; Trp53+/LSL-R172H; Pdx1-Cre (“KPC”) genetically engineered mouse model. This allows us to compare the effects of primary PDAC cancer associated fibroblasts (CAFs) and liver metastasis associated fibroblasts (MAFs) on tumor cell growth and chemoresistance. Rheometry analyses were conducted to study the impact of local fibroblasts on the extracellular matrix (ECM) stiffness. Our results showed that both storage and loss moduli were enhanced only when PDAC CAFs were present in the co-cultured gels compared to gels with MAFs. Additionally, the 3D biomimetic model showed fibroblasts increased tumor growth and chemoresistance to gemcitabine, only when they were derived from the same site as the tumor cells. This highlighted the importance of studying the organ-specific microenvironment to develop better treatment options for patients with metastatic PDAC. To delve deeper into the molecular basis of these observations, we conducted RNA-sequencing to identify and compare the gene expression profiles in primary and metastatic tumor organoids exposed to conditioned media from CAFs and MAFs using a transwell membrane co-culture model. Our results showed significant differences in gene expression based on the type of fibroblasts co-cultured with the organoids. Moreover, we investigated the role of MAF-derived exosomes on LM growth and chemoresistance using exosome depletion and direct exosome addition to LM organoids. Lastly, we performed exosomes size and distribution characterizations using dynamic light scattering (DLS) analysis. Taken together, these findings highlight the critical role of the organ-specific microenvironment in tumor progression and the necessity of targeted therapies to improve patient outcomes in metastatic PDAC. Our results underscore the importance of developing a tunable 3D biomimetic model of the LMN, as it enables the testing of novel therapeutic strategies designed to disrupt interactions between MAFs and tumor cells, and potentially advancing treatments for metastatic PDAC. Citation Format: Mahsa Pahlavanneshan, Weikun Xiao, Eileen Fung, Vaidhyanathan Mahaganapathy, Chae Young Eun, Chang-Il Hwang, Shannon Mumenthaler, Reginald Hill. Investigating the effects of fibroblasts derived from the primary versus the metastatic organ on 3D biomimetic models of pancreatic 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 A006.

Abstract A009: PIEZO1 driven tumor aggressiveness in an organ-on-chip model of colorectal cancer

Abstract Mechanical forces have long been known to affect the progression of cancer, however exact study of the specific consequences of these forces has been hampered by currently available model systems. Traditional cell culture models often lack the ability to incorporate physiologically relevant mechanical forces, and animal models offer too much complexity to be able to effectively isolate and study the mechanical forces. Organ-on-chip (OOC) technology allows for the integration of human relevant physiological forces in a setting conducive to their study. Here, we explore how the early metastatic spread of colorectal cancer (CRC) can be influenced by physiological mechanical forces. Specifically, we investigated the ability of peristaltic motions, responsible for natural bowel motility, to enhance the invasive capability of colon tumor cells. Our microfluidic OOC model comprises of an epithelial channel and endothelial channel separated by a porous membrane allowing for biological and chemical crosstalk between them. Vacuum channels spanning the length of the structure allow force to applied in a cyclic manner mimicking peristaltic contraction and relaxation. Our OOC model supports the addition of tumor microenvironment (TME) components in a piece-wise manner to better understand how specific factors influence the behavior of tumor cells. Analyzing gene and protein expression levels, we have found that peristaltic-like motions induce changes in the Hippo signaling and epithelial-to-mesenchymal (EMT) pathways resulting in greater invasion of tumor cells into the endothelial compartment as observed by on-chip confocal imaging. Moreover, knock down studies have demonstrated that the response to peristaltic-like stretch is driven through a PIEZO1-mediated mechanism. Furthermore, to increase the physiological relevance of our model, we administered peripheral blood mononuclear cells (PBMCs) to the endothelial channel to simulate aspects of the immune TME. Preliminary studies revealed that the recruitment of PBMCs can be altered by the presence of peristaltic-like stretch. Our findings demonstrate that mechanical forces in the CRC TME can dramatically alter tumor behavior as shown in our CRC-OOC model. Citation Format: Curran A. Shah, Carly R. Strelez, Aaron Schatz, Hannah Jiang, Rachel Perez, Shannon M. Mumenthaler. PIEZO1 driven tumor aggressiveness in an organ-on-chip model of colorectal 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 A009.

Abstract PR014: DNA associated with EVs is uniquely chromatinized and prevents metastasis by enhancing anti-tumor immunity

Abstract Cells release extracellular vesicles (EVs) loaded with functional biomolecules that facilitate intercellular communication in health and disease. These EVs contain DNA (EV-DNA), mirroring the mutational profile of parental cells, yet the mechanism of DNA packaging onto EVs and its role in diseases like cancer remain unclear. Using advanced imaging and biochemical techniques, we discovered that EV-DNA predominantly resides on the vesicle surface, bound to modified histones. Through genome-wide CRISPR knockout screens in cancer cell lines, we identified immune-related pathways and genes crucial for EV-DNA loading, such as APAF1 and NCF1. In several cancer models, loss of APAF1 reduced EV-DNA packaging, and enhancing metastasis, thus implicating EV-DNA in immune surveillance against cancer spread. We demonstrated that EV-DNA uptake by liver macrophages triggers DNA damage response, altering cytokine production and promoting immune activation in pre-metastatic sites. Moreover, quantifying EV-DNA in colorectal cancer biopsies revealed its potential as a predictive metastatic risk biomarker. Our findings shed light on EV-DNA packaging mechanisms and its significance, suggesting that elevated levels of tumor-derived EV-DNA bolster anti-tumor immunity and inhibit metastasis. Citation Format: Inbal Wortzel, Han-Sang Kim, David C. Lyden. DNA associated with EVs is uniquely chromatinized and prevents metastasis by enhancing anti-tumor immunity [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 PR014.

Abstract B031: Lean adipocyte-derived lipid decreases metastatic potential of breast cancer cells

Abstract Obesity rates are increasing globally, making it of critical importance to study obesity-linked diseases. Breast cancer is the most common cancer in women, and obesity is associated with both increased incidence and metastatic progression of breast cancer. Metastasis formation depends on a cancer cell leaving the primary site, migrating through the bloodstream, and establishing new growth in a distant site. Both metastasizing cell-intrinsic and metastatic site-dependent factors can help to regulate the effectiveness of this process; however, it is unknown whether obesity-linked metastasis depends on changes to the metastasizing cell and/or changes to the distant metastatic site. This study aims to characterize how the lean versus obese tumor microenvironment impacts breast cancer metastasis and identify adipocyte-derived molecules that modulate the metastatic potential of breast cancer cells. We and others have shown that obesity leads to increased metastasis formation in mouse models of orthotopic breast cancer. However, my preliminary data show that an obese metastatic site is not sufficient to increase metastasis formation in an intravenous injection model of metastasis, emphasizing the importance of the primary tumor microenvironment in programming breast cancer cells for metastasis. Cancer cell stemness helps to mediate metastasis formation and can be assessed in vitro with the mammosphere assay. Importantly, my data demonstrate that a secreted lipid from lean, but not obese, adipocytes potently inhibits the ability of breast cancer cells to form mammospheres. Furthermore, this inhibition induces a G1/S cell cycle arrest. Together, these data suggest that lean adipocytes in the breast cancer tumor microenvironment act in a paracrine manner to decrease the metastatic potential of breast cancer cells. My work demonstrates the role of adipocytes in the regulation of metastasis in breast cancer and provides important insight into the role of the tumor microenvironment in mediating metastasis in lean versus obese conditions. Citation Format: Abigail E. Jackson, Keren I Hilgendorf. Lean adipocyte-derived lipid decreases metastatic potential of breast cancer cells [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 B031.

Abstract B035: Reciprocal macrophage - T cell interactions regulate anti-tumor immunity

Abstract Cancer immunotherapy (including immune checkpoint blockade (ICB)) has shown great promise in the treatment of some solid cancers, but responses in breast cancer patients are limited. While breast cancer is generally considered poorly immunogenic, the abundance of CD8+ T cells correlates with clinical response. CD8+ T cells are critical mediators of anti-tumor immunity and the main target for ICB. However, the onset of terminal functional T cell exhaustion poses a major challenge. Although T cell exhaustion has been linked to persistent antigen exposure, it remains unclear how the immune composition of the breast tumor microenvironment (TME) contributes to this dysfunctional T cell state. Breast cancers are heavily infiltrated with tumor-associated macrophages (TAMs) and their abundance correlates with T cell exhaustion and poor prognosis. Previously, we discovered a spatiotemporal co-dependency between exhausted T cells (TEX) and TAMs in mouse models of melanoma and breast cancer. We showed that TEX actively recruit monocytes to the TME and shape their differentiation trajectory into TAMs. Reciprocally, these TAMs ‘capture’ T cells in long-lived synaptic interactions that contribute to functional T cell exhaustion. Our current work is focused on studying the TEX-derived chemokines that regulate these TAM – T cell interactions in the breast TME with the ultimate goal to alleviate immune evasion and improve responsiveness of breast cancer to immunotherapy. Citation Format: Meenakshi Sudhakaran, Sofia Lombardi, Sophie Ayma, Matthew F. Krummel, Kelly Kersten. Reciprocal macrophage - T cell interactions regulate anti-tumor immunity [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 B035.

Abstract B040: Investigating the impact of tumor EMT states on immune cell infiltration in breast cancer

Abstract Breast cancer is one of the most frequently diagnosed cancers and the second leading cause of women’s cancer death. Although the five-year survival rate for women in the United States with nonmetastatic invasive breast cancer is 90%, this rate drops to less than 30% for those with tumors that have metastasized to distant organs. Epithelial-to-Mesenchymal Transition (EMT) plays a critical role in tumor metastasis by enabling the loss of epithelial characteristics and the gain of mesenchymal traits, leading to increased cell motility, invasion, and resistance to therapy. Consequently, targeting the EMT process may prevent tumor cell migration and improve patient outcomes. Rather than being a binary switch from an epithelial to a mesenchymal state, cells undergoing EMT can assume a spectrum of intermediate states, some of which may reshape the tumor microenvironment by recruiting pro-tumor immunosuppressive cells, such as regulatory T cells, M2-like macrophages, and myeloid-derived suppressor cells. However, the impact of EMT on the immune composition of the tumor microenvironment and the causative mechanisms remain poorly understood. Using multi-omics approaches in a mouse model of triple-negative breast cancer, we assessed the interaction between tumor and immune cells in the tumor microenvironment driven by the EMT. A heterogeneous mouse breast cancer cell line (4T1) was used to isolate five distinct single-cell-derived clonal populations residing in distinct states within the EMT spectrum. These EMT clones, along with the parental 4T1 cell line, were orthotopically transplanted into the mammary fat pads of BALB/c mice. Primary tumors were subsequently harvested and dissociated for single-cell RNA-sequencing (scRNA-seq) and DNA methylation analysis. Lungs were histologically evaluated for metastases. Tumors derived from an intermediate EMT clone exhibited increased tumor growth kinetics and a higher incidence of metastasis compared to epithelial or mesenchymal clones. In scRNA-seq data, tumors derived from different EMT clones largely retained their original EMT states in vivo and recruited distinct immune cell profiles. DNA methylation analysis further revealed that these tumors displayed unique methylation patterns in EMT-related CpGs. This study introduced a model that captures the complexity of the tumor microenvironment across the EMT spectrum. This was accomplished through immunophenotyping using scRNA-seq and identifying unique epigenetic patterns through DNA methylation. Our findings highlight the potential for distinct immune cell populations to be recruited to tumors in different EMT states, thereby influencing survival and metastasis outcomes. Furthermore, our results open new opportunities for developing cancer combination treatment strategies that target specific tumor-immune cell interactions. Citation Format: Hanxu Lu, Meisam Bagheri, Todd Miller, Diwakar Pattabiraman, Brock Christensen. Investigating the impact of tumor EMT states on immune cell infiltration 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 B040.

Abstract PR004: Age-induced chronic accumulation of glucocorticoids drives therapy resistance in lung cancer

Abstract Non-small cell lung cancer (NSCLC), a highly aggressive cancer, is the leading cause of cancer- related deaths in the U.S. While chemotherapy and targeted therapy are the main treatment modalities in the clinic, many patients do not respond to these treatments. Strikingly, the median age for lung cancer diagnosis is 71. Yet, preclinical and clinical research have largely been skewed towards young mice and patients. Here, we address this gap in knowledge and evaluate if old age affects the response to standard of care NSCLC therapies in KRAS-driven NSCLC. Using human sera from young and old healthy subjects to treat NSCLC cell lines, we show that age-driven circulatory changes are sufficient to drive a state of profound resistance to both chemotherapies as well as KRASG12C targeted therapies. We confirmed the relevance of our findings in vivo, by transplanting cancer cells derived from the K-rasLSL-G12D/+; p53fl/fl genetically engineered mouse model of lung cancer into young and old C57BL/6 mice. Using this model we showed that unlike young lung tumor-bearing mice on chemotherapy, old tumor-bearing mice do not respond to treatment and have a poor prognosis. Mechanistically, we found that old age drives a transcriptional reprogramming that favors drug resistance and identified the glucocorticoid receptor as a major driver of these transcriptional changes. We traced this to an age-induced chronic accumulation of glucocorticoids in circulation and within the tumor interstitial fluid. Chronic treatment with age-relevant concentrations of cortisol alone was sufficient to drive glucocorticoid receptor activation and induce resistance to therapies mirroring the effects of old age. Further supporting a driving role for glucocorticoids in driving age- induced drug resistance, blocking the glucocorticoid receptor genetically or pharmacologically rescues the drug resistance state imposed by old age in NSCLC cells. Lastly, using TCGA patient data we show an inverse correlation between glucocorticoid receptor activation (GR score) and progression-free survival of lung cancer patients. Together, our work demonstrates a role for age-induced glucocorticoids in circulation in promoting therapy-resistance in NSCLC patients and supports the use of therapeutic agents that block the glucocorticoid receptor as a strategy to increase therapy efficacy in NSCLC patients. Citation Format: Devesh Raizada, Felicia Lazure, Stanislav Drapela, Nadir Sarigul, Joanne Tejero, Didem Ilter, Ana Da Silva Gomes. Age-induced chronic accumulation of glucocorticoids drives therapy resistance in lung 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 PR004.

Abstract C035: Spatially limited stroma-mediated resistance potentiates targeted therapy resistance through an integration of multiple juxtacrine and paracrine mechanisms

Abstract Despite the ability to induce strong clinical responses, therapies that target mutational drivers of oncogenic signaling are not curative in advanced cancers, as a subset of cancer cells is capable of surviving therapy and evolving resistance. While therapy resistance is commonly viewed as a cell-intrinsic phenomenon, multiple factors produced by tumors can also confer strong therapy resistance. In contrast to the detailed elucidation of molecular mediators of cell-intrinsic and stroma-mediated (SM) resistance, the relative importance of cell-intrinsic and SM resistance to in vivo therapeutic responses remains poorly defined. To address this gap of knowledge, we used a well-characterized experimental model of ALK+ lung cancer H3122 cell line that exemplifies a duality observed across common models of targetable cancers. Under standard stroma-free in vitro cultures, H3122 cells can survive under therapeutically relevant concentrations of ALK inhibitors (ALKi), eventually acquiring cell-intrinsic therapy resistance. At the same time, co-culture with stromal fibroblasts drastically reduces the sensitivity of H3122 cells to ALKi, indicating the relevance of SM resistance. To understand the impact of SM resistance on in vivo responses, we sought to identify the mechanism(s) responsible for the therapy-protective effects of stromal fibroblasts, subsequently interrogating the impact of the disruption of this mechanism on in vivo therapeutic responses. Our in vitro studies with a large panel of primary stromal fibroblast isolates identified the HGF-cMET axis as the major mechanism responsible for ALKi desensitization. Surprisingly, xenograft validation studies demonstrated a weak effect of HGF-cMET modulation. Histological analyses of tumor tissues revealed that this relative weakness is attributable to a strong, spatially limited HGF-independent component of SM resistance. Mechanistic follow-up demonstrated that the HGF-independent component of SM resistance integrates the effect of multiple well-known juxtacrine and paracrine-acting mechanisms. Whereas the multifactorial nature of stroma-mediated resistance prevented a clear assessment of its relative contribution to in vivo therapy responses, our spatial analyses indicate that SM resistance dominates the ability of tumors to avoid therapeutic elimination. Surprisingly, we found that SM resistance was also a substantial contributor to tumor relapse, indicating that in vivo therapy resistance can integrate both cell-intrinsic and cell-extrinsic effects. This duality of therapy resistance and the multifactorial underpinning of both cell-intrinsic and stroma-mediated resistance present a challenge to therapeutic strategies focused on identifying and targeting specific resistance mechanisms. Our studies suggest that this limitation can be overcome by shifting the therapeutic focus towards shared orthogonal therapeutic sensitivities of tumor cells within residual disease. Citation Format: Bina Desai, Tatiana Miti, Sandhya Prabhakaran, Daria Miroshnychenko, Menkara Henry, Viktoriya Marusyk, Chandler Gatenbee, Marilyn Bui, Jacob Scott, Philipp M. Altrock, Eric Haura, Alexander R.A. Anderson, David Basanta, Andriy Marusyk. Spatially limited stroma-mediated resistance potentiates targeted therapy resistance through an integration of multiple juxtacrine and paracrine mechanisms [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 C035.

Abstract B018: Multifaceted pro-metastatic role of IL-17 signaling in modulating the tumor microenvironment of colorectal cancer

Abstract Colorectal cancer (CRC) ranks second in mortality and advanced CRCs are resistant to current immunotherapies and prone to metastasis, which necessitates research into enhancing innate and adaptive anti-cancer immune responses. Chronic inflammation mediated by cytokines like IL6 and notably, IL17 activates the oncogenic pathways in cancer cells, promoting sporadic and inflammatory CRC. What is unknown, is the ability of cytokines to control tumor microenvironment (TME) via cell type specific mechanisms to increase cancer progression, metastasis and/or therapy resistance. Increased levels of IL17A in CRC portends poor prognosis indicating its potential involvement into metastasis. However, the role of IL17 signaling in TME in the process of CRC progression and metastasis remains enigmatic. We utilized different models of CRC progression and metastasis, as well as variety of genetic mice models and therapeutic interventions. First, using a model of colitis-associated cancer we found that “late” IL17A neutralization decreases tumor burden, possibly acting through regulation of ferroptosis, NK cells mediated cytotoxicity, as well as myeloid cells and chemokine network essential for the control of immunosuppressive TME. Next, models of CRC metastasis, including those based on MC38 cells and APTAK cancerous organoids, showed that IL17A neutralization reduces metastasis growth. Also, FACS analysis revealed that IL17A promotes the recruitment of tumor- associated macrophages and other key myeloid subsets into the metastatic liver environment. Further research, using mice with conditional knockout of IL17RC receptor in myeloid cells (Il17rc f/f -LysMCre) or hepatocytes (Il17rc f/f -AlbCre) also showed significance of IL17 signaling activation in CRC metastasis through two distinct mechanisms. Employing different techniques, from FACS, immunohistochemistry, to RNAseq and scRNAseq data analysis, we observed that local hepatic activation of IL17RC signaling recruits neutrophils and reduces infiltration of cytotoxic CD8+T and NK cells to the metastatic niche supporting tumor growth, while myeloid IL17RC signaling reshapes TME, including macrophages and neutrophils, enhancing CRC metastasis. Our research indicates that IL17 signaling plays a multifaceted pathogenic role in CRC progression by operating in at least several cell types, providing new insights into the basic biology of CRC metastasis and potentially illuminating the design and improvement of CRC treatment strategies. Citation Format: Katarzyna Chojnacka, Katrina Mae Reyes, Hana Tomizawa, Sergei Grivennikov. Multifaceted pro-metastatic role of IL-17 signaling in modulating the tumor microenvironment of colorectal 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 B018.

Abstract C021: Tumor-associated microbiota suppresses anti-tumor immunity by driving cDC1 dysfunction in lung cancer

Abstract Type 1 conventional dendritic cells (cDC1s) are critical for initiating and sustaining tumor-reactive CD8 T cells; lack of functional cDC1s is a key driver for failed tumor immunosurveillance and immunotherapy. However, what factors cause the cDC1 insufficiency in the tumor microenvironment (TME) remain poorly understood. Commensal microbiota has emerged as a key regulator of TME and the efficacy of cancer immunotherapies. Nonetheless, most studies have focused on the intestinal microbiome; it remains underexplored whether and how the local microbiota within tumors influences the anti-cancer immunity. Using the autochthonous Kras LSL-G12D/+ ; p53 flox/flox (KP) mouse model of lung cancer, we found an increased local bacterial burden and altered bacterial composition associated with lung tumors. Importantly, this local microbiota suppresses the anti-tumor CD8 T cell response both at baseline and in response to ICB therapies. Specifically, single-cell RNA-seq analysis revealed that the microbiota shapes the functional subsets of tumor-reactive CD8 T cells. Bacterial depletion promotes the accumulation of stem-like Tpex cells (precursor of exhausted T cells) in the TME, which serve as a reservoir of effector CD8 T cells and mediate an effective response upon ICB treatment. To distinguish the function of the local microbiota within TME from the distal gut microbiota, we developed a new method of aerosolized antibiotic treatment, which selectively ablates the intra-tumoral lung microbiota while preserving the intact gut microbiota. Using this approach, we demonstrated that removal of the intra-tumoral lung microbiota markedly improves the tumor-reactive T cell response and sensitizing “cold” lung tumors to ICB therapies. Mechanistically, we identified cDC1s as a central player in microbiota-mediated suppression of anti-tumor immunity. Local microbiota diminishes cDC1 quality and quantity in the lung TME, resulting in impaired T cell priming and Tpex maintenance. At the molecular level, our data revealed that bacterial products derived from the local microbiota induce type I interferon expression in tumor-associated myeloid cells and enhance GM-CSF production from cancer cells: chronic type I interferon and GM-CSF signaling acts cooperatively to reduce the functional cDC1 population. Combining in vitro cDC1 assays, competitive bone marrow chimera experiments and cDC1-specific knockout models, we establish the causal relationships between the local microbiota, IFN-I and GM-CSF signaling in cDC1s, and the tumor response to ICB. Altogether, our study uncovered a dominant role of tumor-associated microbiota in inhibiting cDC1s and suppressing anti-tumor immunity through type I IFN and GM-CSF dependent pathways in lung cancer. Our findings not only identify the intra-tumoral microbiota as a critical therapeutic target for lung cancer treatment, but also provide new insights into the tissue-specific, context-dependent regulatory mechanisms of cDC1s in the TME. Citation Format: Qiang Dong, Chengcheng Jin. Tumor-associated microbiota suppresses anti-tumor immunity by driving cDC1 dysfunction in lung 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 C021.

Abstract C034: Investigating residual disease in its spatial context in BRCA1 p53-deficient mammary tumors

Abstract Although various effective anti-cancer treatments have become available over the last decades, resistance to all available therapies remains the major cause of death of cancer patients with disseminated tumors. Striking examples are patients with triple-negative breast cancer (TNBC), which are frequently defective in the repair of DNA double strand breaks, e.g. due to loss of BRCA1 function. Because of this defect, the patients initially respond very well to DNA damage-inducing chemotherapy. Unfortunately, disseminated tumors are usually not eradicated and resistant tumor cells are eventually selected from residual primary or metastatic tumor sites. It is therefore crucial to understand the molecular mechanisms underlying the drug tolerance of the residual tumor cells. To study residual disease, we used the K14cre;Brca1 F/F ;p53 F/F (KB1P) mouse model for hereditary breast cancer, which provides the unique opportunity to explore and target those mechanisms in a fully immunocompetent model. The mammary tumors that spontaneously develop highly resemble their human counterparts, both morphologically and in their therapy response. For example, tumors shrink in response to poly(ADP-ribose) polymerase inhibition, platinum-based treatment or the commonly used doxorubicin, docetaxel and cyclophosphamide (TAC) combination therapy. But despite repeated drug sensitivity, the KB1P mammary tumors are not eradicated, not even by a frequent dosing schedule. By combining single-cell RNA sequencing, spatial transcriptomics and imaging mass cytometry, we dissected the intratumoral heterogeneity and alterations in the tumor microenvironment of residual disease. We identified specific subpopulations of tumor cells that have a survival benefit after treatment, and these occurred together with an altered microenvironment characterized by a highly reactive stroma infiltrated with both anti-inflammatory and pro-tumoral immune cells. Interestingly, those structural and transcriptional changes are reversed in the relapsed tumors, highlighting the plasticity of drug tolerance. To investigate the mechanisms of the altered tumor-stroma interactions that are relevant for drug tolerance, we have designed a custom-made CRISPR/Cas9 library based on differential gene expression of the residual tumor cells. This library enables us to functionally test relevant mechanisms of drug tolerance in vivo and we expect that these analyses will provide useful insights into the tumor-stroma interactions that contribute to residual disease. Taken together, our detailed analyses demonstrate the substantial remodeling of tumor cells in their microenvironment upon treatment. To develop new therapeutic approaches to eradicate drug-tolerant tumor cells and thereby circumvent tumor relapse, it is essential to better understand the heterogeneous cellular composition of residual tumors in its spatial context. With this project, we hope to provide comprehensive data to develop better therapeutic strategies that target the tumor-stroma interaction and eradicate residual tumors. Citation Format: Morgane Decollogny, Demeter Túrós, Astrid Chanfon, Myriam Siffert, Ismar Klebic, Sven Rottenberg. Investigating residual disease in its spatial context in BRCA1 p53-deficient mammary tumors [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 C034.

Abstract IA019: Regulation of EMT tumor states by stromal cells

Abstract Epithelial-to-mesenchymal transition (EMT) is a reversible process during which epithelial cells lose their epithelial characteristics and acquire mesenchymal features, that are important for tumor initiation, progression, stemness, metastasis, and therapy resistance. Different EMT states, each with distinct functional properties, have been identified across various tumor models. These EMT states reside within specific physical niches, characterized by unique stromal cell populations. Understanding the cellular interactions within the tumor microenvironment (TME) and their influence on EMT could lead to novel therapeutic strategies. To understand how the TME regulates the distinct tumor states, we performed single-cell RNA sequencing of the tumor cells and their TME in mouse cancer models presenting EMT. We identified distinct subsets of cancer-associated fibroblasts (CAFs), macrophages, neutrophils, endothelial cells, pericytes, adipocytes, dendritic cells, mast cells, Schwann cells, and T cells in different tumor types. To unravel how TME-tumor cell interactions regulates EMT, we used different bioinformatic approaches to identify ligand-receptor pairs that are likely to organize the tumor niche and to regulate tumor transition states. In vitro treatment of tumor cells with some of these ligands demonstrated their EMT-promoting effects. These findings provide novel mechanistic insights on the crosstalk between tumor cells and the surrounding TME, that may have important implications for anti-cancer therapy. Citation Format: Cédric Blanpain. Regulation of EMT tumor states by stromal cells [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 IA019.

Abstract B023: Regulatory T (Treg) cell contributes to tumor cell dissemination via extracellular matrix (ECM) remodeling, which is driven by TAMs in an IFNg-dependent manner

Abstract Background: The extracellular matrix (ECM) is a highly organized non-cellular network consisting of structural proteins, growth factors, cytokines and other secreted molecules. The ECM is highly dynamic and is a critical player in the regulation of local invasion and metastasis. The ECM network is ever-changing and an important immunosuppressive component of the tumor microenvironment (TME). However, the reciprocal effects of the immune system on the tumor-associated ECM are elusive and largely unexplored. Regulatory T (Treg) cells function to enforce peripheral tolerance and are potent suppressors of tumor immunity. We have previously shown that Treg cells promote tumor growth in murine breast cancer models by favoring alternative activation of tumor-associated macrophages (TAMs) via suppression of IFN-g. Aims: In this work, we sought to assess whether Treg cell-mediated immune suppression is associated with changes in the ECM, and whether those ECM changes functionally impact metastatic dissemination. Further, we assessed the requirement of TAMs and IFN-g in the ECM remodeling. Design Methods: In this study, we used spontaneous and transplantable models of breast cancer susceptible to genetic ablation of Treg cells. We used a combination of histopathological analysis, tumor decellularization, bioengineering 3D-chip modeling, in vivo manipulations and bioinformatic analysis, to evaluate remodeling of the ECM, cancer cell invasive behavior and metastatic dissemination. Results Summary: Treg cell ablation resulted in significant ECM remodeling, with reduced amounts and organization of collagen fibers, and increased amounts of fibronectin and laminin. Tumor cells seeding on Treg cell ablated tumor- derived decellularized ECM matrices results in reduced epithelial-mesenchymal transition (EMT) transcription factors, and profound impairment of collective migration. In vivo, Treg cell ablation in a neo-adjuvant setting followed by primary tumor resection resulted in significant reduction of circulating tumor cells (CTC) and impairment of lung metastatic disease. Importantly, we demonstrated that Treg cell ablation-driven changes in the matrisome correlate with long-term improved survival in a cohort of breast cancer patient samples. Through genetic knock-out models and in-vivo neutralization, we observed that Treg cell-dependent changes in ECM-related phenotypes are dependent on IFN-g-signaling. Single-cell RNA-sequencing (scRNA-seq) of murine breast tumors revealed that the matrisome signature is highly upregulated among TAMs, compared to other TME cell types. Lastly, using conditional genetic knock-out models we show these IFN-g-dependent changes are mostly driven by TAMs. Conclusions: Altogether, we identified a novel metastasis-promoting effect of Treg cells in the breast cancer microenvironment through regulation of ECM dynamics beyond their described effects on primary tumor growth. Citation Format: Ailen D. Garcia-Santillan, Jessanne Y. Lichtenberg, He Shen, Jasmine M Rodriguez, Jonathan Barra, Nicholas M Clark, Wei Du, Leandro M Martinez, Ashley D Hadjis, Taylor Calicchia, Mikhail G Dozmorov, Jose J Bravo-Cordero, Amy L Olex, Priscilla Y Hwang, Paula D Bos. Regulatory T (Treg) cell contributes to tumor cell dissemination via extracellular matrix (ECM) remodeling, which is driven by TAMs in an IFNg-dependent manner [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 B023.

Abstract A033: Integrating spatial transcriptomics and second harmonic generation imaging to identify targets of supermere-associated Discoidin Domain Receptor 1 involved in collagen alignment

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 C047: AGX101: Preclinical evaluation of a TM4SF1-directed tubulin inhibitor conjugate with ongoing first-in-human trial

Abstract Introduction: TM4SF1 (Transmembrane-4 L-Six-Family-Member-1) is an endothelial marker with critical roles in angiogenesis, as well as a tumor cell antigen that contributes significantly to invasion and metastasis. TM4SF1 is upregulated 20-fold in angiogenic tumor vascular endothelium compared to normal vasculature endothelium and exhibits a unique nuclear internalization pathway. AGX101 is a novel tubulin inhibitor conjugate specifically directed against TM4SF1, delivering a potent maytansinoid payload directly to the nucleus of cells within the tumor microenvironment. Delivery to both the vascular and tumor cell compartments of the tumor results in three mechanisms of action (MoAs): (1) activation of tumor immune surveillance, (2) tumor blood supply deprivation, and (3) direct tumor cell killing. Methods: TM4SF1 expression was assessed across solid tumor samples using immunohistochemistry. Safety and pharmacokinetics of AGX101 were evaluated in non-human primates, with escalating doses to determine the highest non-severely toxic dose (HNSTD). Efficacy studies were also conducted in mouse models, enabling assessment of the minimum effective dose (MED) needed to engage each of the three MoAs. The combination of HNSTD and MED enables calculation of a therapeutic index (TI). Preclinical efficacy studies used either AGX101 (in human tumor xenograft models, to study the tumor cell killing MoA) or AGXB01, a rodent surrogate of AGX101, to study vascular and immune MoAs and all three MoAs in syngeneic mouse cancer models. The potential for synergy with immune checkpoint inhibitors (ICIs) was also investigated. A first-in-human study of AGX101 in patients with advanced solid tumors with the primary objective of safety and dose-limiting toxicities (DLTs) has initiated. Results: TMFS41 is broadly expressed across solid tumors with increasing scoring intensity in higher grade tumors. In non-human primates, AGX101 exhibited a favorable safety profile, being tolerated at relatively high doses and with dose dependent, monitorable, and reversible effects. In preclinical efficacy studies, AGXB01 and AGX101 as monotherapies demonstrated robust efficacy through each of the three MoAs in multiple syngeneic, xenograft, and orthotopic tumor models in mice and rats as well as non-tumor models of angiogenesis. Measured by exposure, TI was large. Additionally, AGXB01 was shown to potentiate the effects of ICIs in syngeneic mouse models (CT26, Renca, and B16-F10), suggesting a potential synergistic approach in cancer therapy. The first dose level of AGX101 monotherapy in humans has cleared without DLTs. Conclusion: AGX101, targeting the TM4SF1 antigen, represents a promising new approach in cancer therapy. The preclinical data suggest that AGX101 could provide a significant therapeutic benefit by novel and differentiated mechanisms of action, namely selectively targeting the tumor vasculature and potentiating immune-based therapies. Further clinical development of AGX101 is ongoing. Citation Format: Ildefonso Ismael Rodriguez Rivera, Meredith S. Pelster, Shou-Ching Jaminet, Paul Jaminet, Glen J. Weiss. AGX101: Preclinical evaluation of a TM4SF1-directed tubulin inhibitor conjugate with ongoing first-in-human trial [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 C047.

Abstract C023: P21-positive senescent stromal cells promote prostate cancer immune suppression and progression that can be reversed by senolytic therapy

Abstract Cellular senescence is historically viewed as a tumor-suppressive cell cycle arrest program to limit outgrowth of pre-malignant cells. However, emerging evidence suggests senescent cell persistence contributes to immune suppression and cancer progression. Using prostate cancer patient samples and murine models, we find that p16+ senescent cells accumulate throughout malignant progression and are associated with immune suppression and poor survival. p16 ablation in mice eliminated senescent epithelial cells and reversed immune suppression mediated by immature myeloid cells but not prostate tumorigenesis. Single cell sequencing revealed an additional population of senescent p21+ fibroblasts and myeloid cells. Targeting BCL-xL or PD-L1 induced during senescence could remove both p16+ epithelial and p21+ stromal senescent cells, reactivate T cell immunity, and block tumor initiation as well as progression in advanced prostate cancer models. Our findings demonstrate that targeting heterogenous senescent populations can not only prevent malignant transformation but also yield therapeutic benefits in advanced prostate cancers through activating anti-tumor immunity. Citation Format: Lin Zhou, Kelly D. DeMarco, Katherine C. Murphy, Zhenpeng Wu, Jinping Li, Junhui Li, Calvin Johnson, Zhong Jiang, Shi Bai, Tianyi Ye, Karl Simin, Lihua Julie Zhu, Jason R Pitarresi, Hong Wu, Marcus Ruscetti. P21-positive senescent stromal cells promote prostate cancer immune suppression and progression that can be reversed by senolytic therapy [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 C023.

Abstract C036: Pharmacological modulation of glutamine metabolism alters macrophage activity and tumor immune responses

Abstract As a critical component of innate and adaptive immunity, macrophages play an important role in shaping the tumor microenvironment (TME), which affects tumor initiation, progression, and response to treatment. Tumor-associated macrophages can display anti-tumor or pro-tumor activity, a cell fate attributed to macrophage polarization that depends on metabolomic regulation. Targeting macrophage metabolism could be a promising approach for cancer treatment by converting a pro-tumor TME into an anti-tumor TME. To examine in vivo mechanisms behind glutamine metabolism on macrophages, we treated immunocompetent murine ovarian cancer models with a clinical-grade glutamine prodrug, JHU083, and performed single-cell RNA sequencing (scRNAseq). In addition to the significant anti-tumor efficacy of JHU083, we found that JHU083 specifically suppressed the M2-like tumor macrophages while sparing M1-like macrophages. To better understand the molecular mechanism of how JHU083 causes macrophage polarization shift, we cultured an M1-like macrophage cell line with DON (6-Diazo-5-oxo-L-norleucine), the active component of JHU083, and performed bulk RNA sequencing. Using bulk RNAseq and scRNAseq transcriptome analyses on M1-like macrophages, glutamine inhibitor treatment significantly enhanced MHC class II genes, including CD74, H2-Aa, H2-Eb1, H2-Ea, H2-Ab1, and TNF family genes including Tnfsf12, and Tnfrsf14 which may promote T cell trafficking and cytotoxicity through reversing immunosuppressive tumor microenvironment. Moreover, DON-treated bone marrow-derived M1 macrophages promoted CD4+ T cell expansion. On the other hand, DON treatment significantly suppressed bone marrow-derived M2 macrophages. In conclusion, our findings suggest that glutamine metabolism reprogramming can promote anti-tumor functions in tumor macrophages. Therefore, targeting glutamine metabolism to regulate macrophage function and polarization can be a promising direction for future cancer therapy. Citation Format: Jiawei Fan, Sumeng Qi, Ie-Ming Shih, Tian-Li Wang. Pharmacological modulation of glutamine metabolism alters macrophage activity and tumor immune responses [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 C036.

Abstract C012: Dissemination of retrotransposable elements from the non-coding genome in tumor-derived extracellular vesicles target stromal and immune cells to induce local and systemic inflammation

Abstract The majority of the human genome (>70%) contains non-coding DNA consisting of retrotransposable elements (RTE), such as LINE-1, SINE/Alu elements, human endogenous retroviruses (HERV), and satellite repeat DNA (Hsat2 and Hsat3). The expression of these elements is suppressed in normal adult tissues but are abnormally expressed in many cancers. Another key mechanism in cancer initiation and progression is the release of tumor-derived extracellular vesicles (EV) that are long-distance communication vehicles propagating signals from tumors inducing metabolic changes, immune dysregulation and promoting metastases across the body. Our work has uncovered a link between RTE, HERV and Hsat expression in cancer and EV in driving tumor progression and immune dysregulation. W hole transcriptome sequencing of EV derived from several different cancer cell lines and patient samples, including Ewing sarcoma, osteosarcoma, prostate, pancreatic, and breast cancer found that RTE, HERV and Hsat2,3 transcripts are highly enriched in EV versus coding region transcripts and in much higher abundance than in the tumor cell themselves. Tumor-derived EV contained dsRNA, dsDNA and RNA:DNA hybrids from these non-coding regions. Plasma EV isolated from both metastatic and non-metastatic patients also showed an enrichment of these RTE, HERV and Hsat2,3 elements and clearly differentiated healthy, normal donor EV that had little or no detectable signal. Evidence of local dissemination of these non-coding elements in EV was also found in vivo in tumor xenografts that showed transfer of Hsat2,3 transcripts into the murine stroma that naturally lack these satellite repeats. Treatment of fibroblasts and myeloid cells with tumor-derived EV triggered innate immune responses via type I IFN and pro-inflammatory cytokines, including IL-1beta, IL-6, IL-8, and TNFalpha owing to the pathogen-like nucleic acid sequences (viral mimicry) of these elements. These EV-induced chronic inflammatory effects were mainly induced through the cGAS-STING nucleic acid sensing pathway. Evidence of DNA damage in stromal fibroblasts and induced senescence was also found as a result of EV treatment. A key element of RTE is the expression of LINE-1 and HERV derived reverse transcriptase (RT) that propagates the action of RTE via RNA:DNA hybrids, dsDNA and retrotransposition in the genome. In a spontaneous estradiol-driven breast cancer model in ACI rats, long-term treatment with an HIV RT inhibitor (lamivudine/3TC) inhibited breast tumor development associated with reduced RTE activation in the mammary gland and in circulating immune cells as well as reduced chronic systemic innate inflammation. Our results suggest that RTE, HERV and Hsat activation, together with their local and systemic dissemination in EV plays an important role in cancer initiation and progression associated with chronic inflammation. We also suggest that abnormal dissemination of these activated non-coding elements in EV may also play a role in "inflammaging" facilitating not only cancer but also other chronic diseases. Citation Format: Laszlo Radvanyi, Valentina Evdokimova, Peter Ruzanov, Zhenbo Zhang, Poul Sorenson, Hendrik Gassmann, Stefan Burdach, Lincoln D. Stein. Dissemination of retrotransposable elements from the non-coding genome in tumor-derived extracellular vesicles target stromal and immune cells to induce local and systemic inflammation [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 C012.