tbuckley/cabot-search huggingface dataset:
Abstract C107: Use of spatial transcriptomics to identify molecular features associated with African American heritage in pancreatic cancer
Authors: Yuesong Wu, Aoqi Xie, Ian Loveless, Madison George, Kendyll Gartrelle, Julie Clark, Daniel Salas-Escabillas, Rupen Shah, David Kwon, Ralph Francescone, Débora B. Vendramini Costa, Howard Crawford, Brian Theisen, Yuehua Cui, Ling Huang, Nina G. Steele
Journal: Cancer Research (2024)

Abstract Pancreatic cancer is the third leading cause of cancer-related deaths in the US, with a 5-year survival rate of 12%. Black or African American patients (BAA) have a 20% higher incidence of pancreatic cancer, and recent studies suggest that there are biological factors that may influence this disparity, in addition to complex socioeconomic factors. Pancreatic tumors are highly enriched with stroma and exhibit significant inter- and intra-patient morphological and molecular heterogeneity. To improve the care for all patients, we need to better understand the disease mechanisms by comprehensively mapping different spatial locations within individual patients’ tumors and determining whether there are common patterns of pathogenesis across diverse patient populations. In this study, we utilized the 10X Visium spatial transcriptomics platform on eight treatment-naïve primary pancreatic tumors. We tested multiple published bioinformatic packages, including SpatialDE, SPARK-X, Spatial PCA, and Cottrazm, and optimized a multi-sample integrated analysis pipeline that allows us to automatically segment tumor lesions, infer major cell types in regions of interest on tissues, detect spatially variant genes, and assess associations between tissue morphological phenotypes and transcriptomic features. Importantly, our study cohort includes four White patients and four BAA patients. Through the comparison of spatial transcriptomes between White and BAA patients, we identified several genes displaying differential expression in tumor lesions of distinct racial groups, including Trefoil Factor 1 (TFF1) and CYP3A5. These genes present potential candidates for further investigation to elucidate the biological mechanisms underlying racial disparities in pancreatic cancer. Citation Format: Yuesong Wu, Aoqi Xie, Ian Loveless, Madison George, Kendyll Gartrelle, Julie Clark, Daniel Salas-Escabillas, Rupen Shah, David Kwon, Ralph Francescone, Débora B. Vendramini Costa, Howard Crawford, Brian Theisen, Yuehua Cui, Ling Huang, Nina G. Steele. Use of spatial transcriptomics to identify molecular features associated with African American heritage in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C107.
Abstract C023: PTEN/STAT3 pathway in cancer-associated fibroblasts in Pancreatic Cancer
Authors: Samaneh Saberi, Cameron Bumbleburg, Victoria Jordan, Julia E. Lefler, Sudarshana Sharma, Michael C. Ostrowski
Journal: Cancer Research (2024)

Abstract Pancreatic cancer is a devastating disease with a high mortality rate with a five-year survival rate of 12%. Recent studies have shed light on the crucial role of cancer-associated fibroblasts (CAFs) in shaping the tumor microenvironment. Our group demonstrated PTEN loss occurs in CAFs in ~25% of PDAC patient samples, which leads to increased activation of signaling pathways in CAFs, including the STAT3 pathway. Conditional deletion of STAT3 in CAFs in a dual flpO/cre recombinase PDAC model correlated with increased survival, decreased M2-like macrophages and increased T-cell infiltration. In the present study we aimed to test the hypothesis that direct interactions between PTEN and STAT3 in cancer CAFs contributes to an immuno-suppressive tumor microenvironment in pancreatic ductal carcinoma (PDAC). To address this hypothesis, we utilized CAFS isolated from the dual recombinase PDAC model. Proximity ligation assays with these CAFS demonstrated that PTEN-STAT3 are in a complex in the cell cytosol that translocate to the nucleus upon IL6 treatment. This finding was validated by co-immunoprecipitation experiments. ChIP-seq analysis of CAFs with PTEN and pSTAT3/STAT3 antibodies revealed a significant overlap in PTEN and pSTAT3/STAT3 occupation of gene promoters. Integrative analysis of PTEN-STAT3 bound genes with corresponding RNA-seq data revealed that the PTEN/STAT3 complex targets cytokines and ligands that directly affect T-cell function, contributing to an immune suppressive microenvironment. Analysis of human PDAC samples support the relationship between STAT3 activation and T-cell activity. Identifying PTEN/STAT3 targets in CAFs may provide new avenues for overcoming the anti-tumor immune responses in PDAC. Citation Format: Samaneh Saberi, Cameron Bumbleburg, Victoria Jordan, Julia E. Lefler, Sudarshana Sharma, Michael C. Ostrowski. PTEN/STAT3 pathway in cancer-associated fibroblasts in Pancreatic Cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C023.
Abstract B096: Acquired resistance to KRAS inhibition modulates the pancreatic cancer tumor microenvironment
Authors: Kevin Christian Montecillo Gulay, Jay Patel, Isabella Ng, Tatiana Hurtado de Mendoza, Herve Tiriac, Andrew Lowy
Journal: Cancer Research (2024)

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with dismal patient outcomes. Acquired resistance to chemotherapeutics is a major barrier to successful pancreatic cancer treatment. MRTX-1133 is a potent, selective KRAS G12D inhibitor that is in early-phase clinical trials. While initially effective, clinical experience with KRAS G12C inhibitors has shown tumors rapidly acquire therapeutic resistance. The tumor microenvironment (TME) plays a pivotal role in resistance development by activating prosurvival pathways, promoting epithelial-mesenchymal transition (EMT) and stemness, and inhibiting apoptosis. In this study, we sought to understand changes in the PDAC TME associated with acquired resistance to KRAS G12D inhibition. Methods: In order to investigate resistance to KRAS G12D inhibition in PDAC, we developed various mouse and human MRTX-1133 resistant (MRTXR) cell models (FC1199, FC1242, FC1245, and SUIT2). Intriguingly, these models also displayed resistance to several pan-RAS(ON) inhibitors. We utilized flow cytometry analysis to investigate the dynamic changes occurring in the TME following resistance to MRTX-1133, and we employed cytokine array and RNA-seq analyses to elucidate the impact of cancer cells on gene and protein expression of TME cells. Results: A comparative analysis between parental PDAC cells and MRTXR tumors revealed significant alterations within the TME. We found a significant decrease (p=0.013, p=0.045, respectively) in the number of inactivated and naïve CD8 T cells (CD8+/CD69+ and CD44-/CD62L+ cells) in MRTXR tumors. We also observed an upregulation of CXCL1, CCL20, and CXCL2 secretion in MRTXR cells compared to parental cells. Conclusions: Pancreatic cancer cells with acquired resistance to KRAS inhibitors modulate their tumor microenvironment uniquely. Ongoing studies aim to identify the critical pathways responsible for these alterations and to develop alternative treatment strategies for KRAS therapy-resistant tumors. Citation Format: Kevin Christian Montecillo Gulay, Jay Patel, Isabella Ng, Tatiana Hurtado de Mendoza, Herve Tiriac, Andrew Lowy. Acquired resistance to KRAS inhibition modulates the pancreatic cancer tumor microenvironment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B096.
Abstract A025: Autotaxin-lysolipid signaling suppresses a CCL11- eosinophil axis to promote pancreatic cancer progression
Authors: Sohinee Bhattacharyya, Chet Oon, Holly Sandborg, Terry Morgan, Mara H. Sherman
Journal: Cancer Research (2024)

Abstract Among all cancer types, pancreatic ductal adenocarcinoma (PDAC) has one of the worst outcomes. In recent studies, metabolic and microenvironmental reprogramming in PDAC has been shown to facilitate tumor progression by promoting immune escape mechanisms, however these mechanisms are still poorly understood. Recently, our lab established that autotaxin (ATX) - lysophosphatidic acid (LPA) signaling in PDAC enhances tumorigenicity, but the immunomodulatory function of this signal pathway remains largely unexplored. We now show that ablation of the LPA-producing enzyme autotaxin (ATX) in PDAC cells can reduce tumor burden in mice and reprogram the tumor immune microenvironment by increasing tumor eosinophil infiltration. The functional role of eosinophils in the context of PDAC is a poorly understood area. The presence of eosinophils in pancreatic cancer has been reported in a few case reports: for example, prior studies identified neutrophils and eosinophils together as a group, expressing high levels of CD66b. We confirmed the presence of eosinophils in PDAC in mice as well as patients, and we found that rare patient samples with the highest intratumoral eosinophil abundance had the longest survival rates. Genetic or pharmacologic ATX inhibition increased intratumoral eosinophils, which promote tumor cell apoptosis locally and suppress tumor progression. When eosinophils were present, primary tumor growth was modestly reduced, but metastatic spread was greatly reduced. Mechanistically, ATX suppresses eosinophil accumulation via an autocrine feedback loop wherein ATX-LPA signaling negatively regulates activity of AP-1 transcription factor c-Jun, in turn suppressing expression of potent eosinophil chemoattractant CCL11 (Eotaxin-1). This is the first study that highlights the anti-tumor potential of eosinophils in pancreatic cancer. Citation Format: Sohinee Bhattacharyya, Chet Oon, Holly Sandborg, Terry Morgan, Mara H. Sherman. Autotaxin-lysolipid signaling suppresses a CCL11- eosinophil axis to promote pancreatic cancer progression [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A025.
Abstract B063: Tertiary lymphoid organogenesis and lymphocyte activation in human organ chips
Authors: Yunhao Zhai, Pranav Prabhala, Lucas Barck, Min Wen Ku, Aditya Patil, Viktor Horvath, Russell A. Gould, Donald E. Ingber, Girija Goyal
Journal: Cancer Research (2024)

Abstract The rates of tertiary lymphoid organ (TLO) formation in pancreatic cancer are very low but patients with TLO have dramatically better survival rates. Our goal is to understand how pancreatic cancer suppresses TLO so that we can improve patient survival and reduce recurrence. We integrated human cell lines from pancreatic and lung cancer with either high or low PDL1/L2 expression into our previously described lymphoid follicle (LF) chip (Goyal et al., Adv. Sci, 2022), where peripheral blood mononuclear cells are induced to form 3D TLO-like structures. The hot lung cancer cell line, which expressed high levels of PDL1/L2 and a “hot” phenotype in published murine studies, produced a high levels of cytokines and stimulated increased TLO formation in the LF chip. In contrast, the cold lung and pancreatic cell lines did not induce the cytokine signature or TLOs. Importantly, TLO formation correlated with increased B cell activation, anti-tumor CD8 activity and tumor cell death. We have coupled this in vitro study with analysis of the pancreatic cancer transcriptome from the Cancer Genome Atlas to identify therapeutic targets to promote TLO formation in pancreatic cancer. In ongoing studies, we are assessing the functionality of the lung cancer TLO in vitro and in vivo and identifying therapeutics that may improve TLO formation in pancreatic cancer. Citation Format: Yunhao Zhai, Pranav Prabhala, Lucas Barck, Min Wen Ku, Aditya Patil, Viktor Horvath, Russell A. Gould, Donald E. Ingber, Girija Goyal. Tertiary lymphoid organogenesis and lymphocyte activation in human organ chips [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B063.
Abstract B030: Spatial coupling of microbes and immune cells shapes the tumor microenvironment in human cancers
Authors: Yan Li, Renee B. Chang, Meredith L. Stone, Yuqing Xue, Heather Coho, Kelly Markowitz, Dhruv Patel, Veronica M. Herrera, Joey H. Li, Devora Delman, Liti Zhang, Shaanti Choi-Bose, Michael Giannone, Jae W. Lee, Gregory Beatty
Journal: Cancer Research (2024)

Abstract Microbes play a crucial role in the tumor microenvironment, yet the factors governing their presence within tumors remain poorly understood. In this study, we employed advanced in situ spatial-profiling technologies to investigate the relationship between microbial and immune cell heterogeneity in human lung and pancreas cancers. We observed a spatial coupling between microbes and immune cells, which was also replicated in mouse models of pancreatic cancer. Within the tumor, distinct niches characterized by T cell abundance or scarcity exhibited varied microbial diversity and compositions associated with immunologically active and quiescent phenotypes. Interestingly, gut microbiome are similar between mice bearing T cell- enriched or T cell-poor pancreas tumors. Depletion of intra-tumoral bacteria resulted in reduced tumor growth specifically in T cell-poor tumors and altered the phenotype and presence of myeloid and B cells in T cell-enriched tumors, without affecting T cell infiltration. Conversely, depletion of T cells disrupted the immunological state of tumors and led to a decrease in intra-tumoral bacteria. Our findings highlight a tight interplay between microbes and T cells in the tumor microenvironment, where spatially defined immune-microbial communities differentially influence tumor biology. Citation Format: Yan Li, Renee B. Chang, Meredith L. Stone, Yuqing Xue, Heather Coho, Kelly Markowitz, Dhruv Patel, Veronica M. Herrera, Joey H. Li, Devora Delman, Liti Zhang, Shaanti Choi-Bose, Michael Giannone, Jae W. Lee, Gregory Beatty. Spatial coupling of microbes and immune cells shapes the tumor microenvironment in human cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B030.
Abstract B088: The macropinosome: Uncovering the molecular anatomy of an oncogene-driven organelle
Authors: Ambroise Manceau, Koen M.O. Galenkamp, Cheska M. Galapate, Cosimo Commisso
Journal: Cancer Research (2024)

Abstract As an integral aspect of the metabolic reprogramming that occurs in cancer, oncogenic KRAS mutations drive the stimulation of macropinocytosis, a type of endocytosis that mediates nonselective fluid-phase uptake. Using KRAS-driven models of pancreatic ductal adenocarcinoma (PDAC), we were the first to demonstrate that macropinocytosis functions in tumor cells as a nutrient acquisition pathway. Macropinocytosis triggers the internalization of extracellular proteins via discrete endocytic vesicles called macropinosomes. The incoming protein cargo is targeted for lysosome-dependent degradation, causing the intracellular release of amino acids. These protein-derived amino acids support metabolic fitness by contributing to the intracellular amino acid pools, as well as to the biosynthesis of central carbon metabolites. In this way, macropinocytosis represents a novel amino acid supply route that tumor cells use to survive the nutrient-poor conditions of the tumor microenvironment. While the tenets of the signal transduction events that drive macropinocytosis in cancer have emerged, a detailed picture of the macropinosome itself is not yet available. With the aid of nanotechnology, we have developed a methodology to isolate a pure fraction of macropinosomes from PDAC cells. Using a large-scale proteomic approach, we have been able to generate a list of proteins that reside in macropinosomes. The specificity of this approach was confirmed through the identification and validation of proteins known to specifically localize to these organelles in different contexts, such as Rab5 or SDC1. Thanks to this innovative method, we have demonstrated the involvement of two calcium channels, ATP2B1 and ATP2B4, in the formation of macropinosomes. By elucidating the molecular anatomy of KRAS-driven macropinosomes, we will gain further insight into the regulation and function of macropinocytosis in cancer. Moreover, having a clearer picture of the macropinosome will make us better positioned to exploit this pathway therapeutically and deliver breakthroughs to patients. Citation Format: Ambroise Manceau, Koen M.O. Galenkamp, Cheska M. Galapate, Cosimo Commisso. The macropinosome: Uncovering the molecular anatomy of an oncogene-driven organelle [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B088.
Abstract A013: Uptake and predictors of Covid-19 vaccination among United States’ cancer populations
Authors: Tayla Greene, Kikelomo Olaosebikan, Osahon Idolor, James Appiah-Pippim
Journal: Cancer Research (2024)

Abstract The COVID-19 pandemic led different stakeholders to call for measures to reduce the morbidity and mortality associated with it. However, following the development of a vaccine, United States adults were reluctant to get vaccinated against COVID-19. Our objective was to evaluate the uptake of COVID-19 vaccination among at risk adults with cancer, and to analyze the predictors of vaccination. Using 2021 data from the National Health Interview Survey, COVID-19 vaccination uptake among 2703 respondents representing 150 million United States adults with any type of cancer was explored, as well as the sociodemographic and comorbid predictors of the vaccination. Chi-square analysis was used to analyze differences between the vaccinated and unvaccinated respondents, and a multiple logistic regression analysis was used to determine the predictors of COVID-19 vaccination. Among 2703 respondents with any type of cancer, 2317 (83.8%) of them reported vaccination against COVID-19. As compared to those who were unvaccinated, those who were vaccinated were mostly 65+ years and above (88.7% vs 11.4%), females (81.9% vs 18.1%), whites (84.0% vs 16.0%), insured (84.7% vs 15.3%), and educated (92.0% vs 8.0%). With regards to the sociodemographic and comorbid predictors of COVID-19 vaccination. As compared to those less than 40 years of age, those between 40-64 years (AOR 2.55, CI 1.45 – 4.48; p=0.001) and 65 years and above (AOR 4.82, CI 2.65 – 8.79; p=&amp;lt;.001) were more likely to be vaccinated, the insured were more likely be vaccinated as compared to the uninsured (AOR 2.85, CI 1.42 – 5.71; p=0.003), and those who were educated were more likely to be vaccinated (AOR 3.10, CI 2.22 - 4.32; p=&amp;lt;.001) as compared to those who were uneducated. However, being a current smoker of cigarettes was associated with reduced odds of being vaccinated against COVID-19 infection compared to non-smokers (AOR 0.67, 0.47 – 0.97; p=0.035) While there appears to be a reasonable uptake of the COVID-19 vaccine among US adults with any type of cancer, efforts are needed to increase vaccine uptake among those who smoke cigarettes. In addition, younger, uninsured, and less educated adults with any type of cancer may be at a higher risk of contracting COVID-19 infection, and therefore measures to increase uptake in these groups are also. Citation Format: Tayla Greene, Kikelomo Olaosebikan, Osahon Idolor, James Appiah-Pippim. Uptake and predictors of Covid-19 vaccination among United States’ cancer populations [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A013.
Abstract A047: ARID1A mutations drive metastasis of pancreatic neuroendocrine tumors and pancreatic adenocarcinomas by activation of NTN1/UNC5B signaling
Authors: Chris Harris, Muhammad Sadeqi Nezhad, Asra Asad, Wade Narrow, Orjola Prela, Darren Carpizo
Journal: Cancer Research (2024)

Abstract ARID1A, a component of the SWI/SNF DNA chromatin remodeling complex, is recurrently mutated in many types of cancer. In pancreatic ductal adenocarcinomas (PDACs), mutations in ARID1A are found in 6-15% of cases, and ARID1A expression has previously been shown to associate with poor patient outcome. But the effect of ARID1A mutations on pancreatic neuroendocrine tumors (PNETs) has not been previously studied, and we observed that ARID1A mutations were 15-fold more common in patients with metastatic PNETs than in patients with localized disease, indicating the importance of ARID1A mutations in driving the progression of what is normally an indolent disease. We have studied ARID1A mutations in models of both PDACs and PNETs and observe that in both diseases ARID1A mutations associated with several properties common to metastatic cells including epithelial-mesenchymal transition, in vitro invasiveness, and insensitivity to anoikis. Mutation of ARID1A activated expression of the axonal guidance protein NTN1 in both PDACs and PNETs, and interaction between the NTN1 ligand and its dependence receptor UNC5b were required for the metastatic properties of ARID1A mutant cells. Treatment with a NTN1 inhibitor, NP137, overcame insensitivity to anoikis, while deletion or knockdown of UNC5b caused ARID1A mutant cells to undergo a mesenchymal-epithelial transition. In vivo, metastasis of PDACs was blocked by NP137 treatment, or by deletion of UNC5b. NP137 is currently in clinical trials for many tumor types including PDACs, and our data strongly indicate that NP137 should also be tested in patients with metastatic PNETs. Citation Format: Chris Harris, Muhammad Sadeqi Nezhad, Asra Asad, Wade Narrow, Orjola Prela, Darren Carpizo. ARID1A mutations drive metastasis of pancreatic neuroendocrine tumors and pancreatic adenocarcinomas by activation of NTN1/UNC5B signaling [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A047.