tbuckley/cabot-search huggingface dataset:
Abstract C011: Detection of circulating tumor cells for the early detection of pancreatic cancer
Authors: Dannel Yeo, Vera Klemm, Payal Saxena, Althea Bastian, Heidi Strauss, Charbel Sandroussi, Sara Wahlroos, Peter Grimison, John E.J. Rasko
Journal: Cancer Research (2024)

Abstract Introduction The majority of pancreatic cancer patients are diagnosed with advanced, metastatic disease. Biomarkers to detect pancreatic cancer at earlier stages could drastically improve the poor survival rates. Circulating tumor cells (CTCs) are tumor cells that disseminate or are shed into the vascular system and have been detected in patients at pre-malignant stages. However, detecting these rare cells accurately and reliably remains a challenge. The AccuCyte-CyteFinder system uses density-based enrichment of blood nucleated cells followed by detection of CTCs using fluorescence staining, whole slide scanning and automated image analysis. This study aimed to examine whether CTCs could be used to identify patients with pancreatic lesions likely to malignant. Methods 50 patients undergoing an endoscopic ultrasound procedure for a pancreatic mass were recruited at the Royal Prince Alfred Hospital, Sydney, Australia or Chris O’Brien Lifehouse, Sydney, Australia. Peripheral blood was collected prior to the procedure and processed for CTCs on the AccuCyte-CyteFinder platform using a CK+ EpCAM+ CD45- staining panel. Results 28% (14/50) were found to have an intraductal papillary mucinous neoplasm (IPMN), 10% (5/50) pancreatic ductal adenocarcinoma (PDAC), 6% (3/50) pancreatic neuroendocrine tumor (PNET), 42% (21/50) non-neoplastic pancreatic cyst, and 14% (7/50) normal (no mass found). CTCs were highest in the PDAC group with an average of 5 cells/ml, followed by the IPMN (3 cells/ml), pancreatic cyst (2.5 cells/ml), and PNET (0 cells/ml). 86% (12/14) of IPMN patients had detectable CTCs. 2 IPMN patients with CTC counts of more than 5 cells/ml resulted in a resected sample having high-grade dysplasia while 3 IPMN patients with no/low CTC counts resulted in a resected sample having low-grade dysplasia. There was no correlation with the size of the pancreatic mass and CTC number. Conclusions CTCs could be detected in patients with pre-malignant pancreatic cancer and could determine malignancy. CTCs could potentially be used to detect pancreatic cancer early however, larger patient numbers and longer follow-up are required to validate these findings. Citation Format: Dannel Yeo, Vera Klemm, Payal Saxena, Althea Bastian, Heidi Strauss, Charbel Sandroussi, Sara Wahlroos, Peter Grimison, John E.J. Rasko. Detection of circulating tumor cells for the early detection of 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 C011.
Abstract B064: Redefining phenotypic heterogeneity of pancreatic ductal adenocarcinoma: A bottom-up approach
Authors: Marc Hilmi, Flore Delecourt, Jerôme Rafenne, Taib Bourega, Nelson Dusetti, Juan Iovanna, Yuna Blum, Magali Richard, Cindy Neuzillet, Anne Couvelard, Louis De Mestier, Vinciane Rebours, Rémy Nicolle, Jérôme Cros
Journal: Cancer Research (2024)

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) tumor inter-patient heterogeneity has been well described with two major subtypes (classical and basal-like). An important intra-patient heterogeneity has not yet been extensively studied due to the lack of standardized and easily accessible high throughput methods compatible with clinical routine. Material and Methods: To build an immunohistochemical (IHC) tool capable of differentiating classical and basal-like tumors, relevant antibodies were selected using a multi-step process. The successive stages of an in-silico selection from the bulk transcriptome of 309 PDACs and 30 patient-derived xenografts followed by the validation on tissue microarrays in a cohort of PDAC (n=50) were conducted. We used our final IHC panel on whole slides of serial histology sections in 95 resected PDACs. After image registration, we performed a tile-based-analysis in tumoral and pre-neoplastic areas and a k-means clustering to identify relevant marker combinations. Results: Our final selection of the IHC panel included GATA6, CLN18, TFF1, MUC16, S100A2, KRT17, PanBasal. Among the 44,042 tumor tiles analyzed, 4 different phenotypes were identified: 1 classical (CLN18+, TFF1+, GATA6+), 1 intermediate (KRT17+) and 2 basal-like (MUC16+ vs S100A2+) with specific biological properties. A minor basal contingent drastically reduced overall survival (OS) in the multivariate analysis (HR=2.36, p=0.01). In contrast, the presence of the intermediate and classical clusters did not impact OS. However, among patients with PDAC expressing the classical cluster, a tremendous difference of OS was observed according to the co-occurence of a basal cluster (HR=0.34, p=0.003). These prognostic associations have been validated in an independent cohort of 150 patients with PDAC on tissue microarrays. By analyzing preneoplastic lesions, we showed the evolution process of pancreatic carcinogenesis going from a classical toward a basal through an early intermediate phenotype. Conclusion: Our restricted panel of antibodies could help pathologists to predict the high degree of PDAC heterogeneity, ultimately leading to an improvement of patient management. Citation Format: Marc Hilmi, Flore Delecourt, Jerôme Rafenne, Taib Bourega, Nelson Dusetti, Juan Iovanna, Yuna Blum, Magali Richard, Cindy Neuzillet, Anne Couvelard, Louis De Mestier, Vinciane Rebours, Rémy Nicolle, Jérôme Cros. Redefining phenotypic heterogeneity of pancreatic ductal adenocarcinoma: A bottom-up approach [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 B064.
Abstract A054: PP2A activation alters macropinosome processing in pancreatic cancer cells leading to metabolic stress and cancer cell death
Authors: Garima Baral, Claire M. Pfeffer, Indiraa Doraivel, Brittany L. Allen-Petersen
Journal: Cancer Research (2024)

Abstract The majority of pancreatic ductal adenocarcinoma (PDAC) patients present with late-stage, metastatic disease that is often resistant to therapeutics, resulting in the lowest survival rate of all major cancers. Metabolic rewiring in response to oncogenic signals plays a critical role in PDAC cell survival, tumor growth, and metastasis. In contrast to normal epithelial cells, these metabolic alterations make PDAC tumors dependent on glutamine for survival, highlighting a unique metabolic vulnerability that can be therapeutically exploited. However, during times of nutrient stress, PDAC cells can circumvent this vulnerability by engulfing extracellular fluids to replenish amino acids, including glutamine, in a process called, macropinocytosis. Macropinocytosis occurs downstream of oncogenic KRAS, a small GTPase that is almost universally mutated in PDAC patients. The inhibition of macropinocytosis in vivo reduces PDAC tumor growth, underscoring the importance of this pathway to cancer cell survival. However, the signaling mechanisms that regulate this process and the contribution of macropinocytic signaling to aggressive cancer phenotypes remains poorly understood. Protein phosphatase 2A (PP2A) is a heterotrimeric complex that regulates a wide variety of cell signaling pathways, including KRAS, and is commonly deregulated in human PDAC tumors. Recently, PP2A has been implicated as an important regulator of macropinocytosis, but the mechanism by which this occurs is unknown. We demonstrate that the genetic loss of the specific PP2A subunit, B56a, accelerates the formation of KRAS-driven pancreatic lesions in an in vivo mouse model, implicating this subunit as a critical negative regulator of KRAS phenotypes during PDAC progression. Here, we show that acute PP2A-B56a activation prevents the fusion of macropinosomes with lysosomes, robbing PDAC cells of critical metabolic nutrients and driving cell death. Consistent with these findings, PP2A activation also reduces glutamine levels and suppresses oxidative phosphorylation. Finally, we determined that PP2A activating compounds can function synergistically with metabolic inhibitors, supporting a new therapeutic strategy in this aggressive and deadly cancer. Together, our results implicate PP2A as a critical suppressor of PDAC metabolic plasticity and highlight the use of PP2A activating compounds to prevent PDAC nutrient scavenging. Citation Format: Garima Baral, Claire M. Pfeffer, Indiraa Doraivel, Brittany L. Allen-Petersen. PP2A activation alters macropinosome processing in pancreatic cancer cells leading to metabolic stress and cancer cell death [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 A054.
Abstract A107: MAPK signaling is a conserved mechanism explaining phenotypic heterogeneity across diverse drivers of epithelial-mesenchymal transition in pancreas cancer
Authors: Michelle C. Barbeau, Matthew J. Lazzara
Journal: Cancer Research (2024)

Abstract Epithelial-mesenchymal transition (EMT) is a developmental process that is aberrantly activated in cancers such as pancreatic ductal adenocarcinoma (PDAC) to promote disease progression and chemoresistance. EMT occurs heterogeneously among PDAC ductal cells, which frustrates efforts to identify the underlying signaling regulatory mechanisms. We hypothesize that cell-to-cell variation in the activities of specific signaling pathways explains EMT heterogeneity. To test this, we developed a workflow integrating: 1) iterative indirect immunofluorescence imaging (4i) to quantify the activities of up to seven purported EMT-regulating pathways with single-cell resolution and 2) a multivariate mutual information computational model to predict the pathways that are most informative of the EMT phenotype. In cultured PDAC cells, EMT was induced by treating cells with growth factors present in the tumor microenvironment (hepatocyte growth factor, epidermal growth factor, transforming growth factor β1, or two combinations) or with chemotherapeutics (gemcitabine or 5-fluorouracil). EMT phenotypic markers and signaling pathway proxies were assessed daily for up to 96 hr. A mutual information analysis of the aggregated data identified ERK as the most important signaling node explaining EMT heterogeneity across the diverse set of agonists investigated. Kinase inhibition and siRNA studies confirmed the implied role of ERK but also revealed a compensatory, EMT-driving JNK activation in the context of MEK inhibition that explains a cooperative effect of simultaneous MEK and JNK inhibition on EMT antagonism. Importantly, a model based on cell population-level measurements nominated JNK as more informative than ERK for determining EMT state in response to growth factors. We are implementing this approach in vivo using pancreas cancer tissue sections to determine generalizability of these findings in different microenvironmental contexts. Overall, our results demonstrate the pervasive importance of ERK for diverse drivers of EMT and the need to account for the effects of heterogeneous signaling pathway activation in the determination of EMT. Citation Format: Michelle C. Barbeau, Matthew J. Lazzara. MAPK signaling is a conserved mechanism explaining phenotypic heterogeneity across diverse drivers of epithelial-mesenchymal transition in pancreas 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 A107.
Abstract B039: Hypoxia promotes an inflammatory phenotype of fibroblasts in pancreatic cancer
Authors: Tenzin Ngodup, Ashley Mello
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is notable for its dense desmoplastic stroma, consisting of extracellular matrix, cancer-associated fibroblasts (CAFs), and immune cells. Another notable feature of the PDAC microenvironment is hypoxia, a condition of insufficient oxygen availability. Although hypoxia leads to adaptive responses in both cancer cells and stromal cells, the effects of hypoxia on the PDAC stroma and tumor-stroma interactions are not fully understood. Cancer-associated fibroblasts (CAFs) are a predominant and heterogeneous stromal cell type in PDAC, and single-cell transcriptomics of human and mouse PDAC has recently revealed a distinct CAF subpopulation, inflammatory CAFs (iCAFs). These inflammatory fibroblasts produce high levels of cytokines and chemokines in PDAC and have the potential to contribute to its immunosuppressive microenvironment and tumorigenesis. By injecting a hypoxia probe into PDAC mouse models, we recently found that iCAFs predominantly reside in hypoxic tumor regions. We also observed that the hypoxia-related gene signature is positively enriched in iCAFs in human PDAC samples. By exposing 3D cocultures of pancreatic tumor cells and fibroblasts to either hypoxia or normoxia, we demonstrated that hypoxia promotes iCAF formation via IL1ɑ secreted from tumor cells. Importantly, the presence of hypoxic fibroblasts further elevated IL1ɑ levels in tumor cells, implicating hypoxia as a modulator of bidirectional interactions between tumor cells and fibroblasts. Efforts are ongoing to understand the mechanism by which hypoxia promotes iCAF formation by modulating bidirectional interactions between tumor cells and fibroblasts in PDAC. Together, our study identifies hypoxia as a key environmental cue for inducing an iCAF phenotype, thus highlighting an instructive role of hypoxia in shaping the stromal microenvironment. Citation Format: Tenzin Ngodup, Ashley Mello. Hypoxia promotes an inflammatory phenotype of 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 B039.
Abstract A094: LIN28B/HMGA2 axis accelerates PDA by promoting oncogenic protein synthesis
Authors: Stephanie Dobersch, Sarah Cavendar, Naomi Yamamoto, Liberales Debraj Boila, Cindy Wladyka, Martine Roudier, Faiyaz Notta, Robert Eisenman, Andrew Hsieh, Sita Kugel
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal human malignancies and is projected to be the second leading cause of cancer deaths in the United States by 2030. Molecular characterization studies have described two major transcriptional subsets, called 'classical’ and ‘basal’. Basal PDAs (~25% of PDAs) have the worst overall survival and are the only class to act as an independent poor prognostic factor. The imminent entry of KRAS inhibitors into the clinic to treat PDA is poised to change this, but genetic experiments have predicted that the basal subtype of pancreatic cancer will be intrinsically resistant to these inhibitors. Therefore, there is an urgent need to understand basal PDA development and identify its unique vulnerabilities. We have discovered that the expression of the oncofetal RNA-binding protein LIN28B and its downstream target, the chromatin protein and high-mobility group (HMG) AT-hook 2 (HMGA2), are highly expressed in the basal subtype of PDA. We find LIN28B dramatically accelerates KRAS-driven PDA and acts as a potent oncogene in genetically engineered mouse models (GEMMs) of PDA. We find that HMGA2, downstream of LIN28B, controls cell growth and orchestrates the pathogenesis of basal PDA by hijacking a precise node of mRNA translation machinery. This raises the intriguing possibility that the aberrant activation of HMGA2 increases mRNA translation and may be one mechanism by which PDA attains the highly aggressive basal phenotype. Mechanistically, we observed that loss of HMGA2 results in decreased phosphorylation of S6K and EIF4B. Interestingly, this was independent of changes in MTOR activity. Loss of function studies using siRNA or inhibitors against PP2A restored pS6K and pEIF4B levels, and mRNA translation when HMGA2 was lost. It is known that reduction in pEIF4B levels leads to a reduction in mRNA translation of difficult-to-transcribe transcripts, such as the MYC oncogene. Indeed, loss of HMGA2 leads to a dramatic reduction in MYC protein levels but no changes to transcription or protein stability. Thus, our work has unveiled a new axis in LIN28B/HMGA2 high basal PDA that controls mRNA translation independent of MTOR, is reliant on PP2A, and controls cell growth through MYC translation. This work has the potential to identify innovative therapeutic strategies to combat this deadly subtype of PDA. Citation Format: Stephanie Dobersch, Sarah Cavendar, Naomi Yamamoto, Liberales Debraj Boila, Cindy Wladyka, Martine Roudier, Faiyaz Notta, Robert Eisenman, Andrew Hsieh, Sita Kugel. LIN28B/HMGA2 axis accelerates PDA by promoting oncogenic protein synthesis [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 A094.
Abstract C036: Restoration of T effector cells function by targeting senescent cancer-associated fibroblast in tumor microenvironment of stroma-rich cancers
Authors: Yao Wang, Hara Apostolopoulou, Arjun Sanyal, Hong Sun, Cynthia Sieland, Kavya Gupta, Jiayu Ye, David Gibbs, Paul Wong, Ntranos Vasilis, Sui Huang, James Gardner, Ajay Maker, Thea Tlsty, Anil Bhushan, Tamara Alliston
Journal: Cancer Research (2024)

Abstract The stroma that surrounds the tumor in many solid cancers exhibits potent immunosuppressive activity to promote tumor progression and confer resistance to immune-based therapies. Cancer associated fibroblasts (CAFs) encompassing functionally distinct populations are key components of the stroma that are emerging as a key cell type in regulating an immune response. However, the mechanisms by which CAFs can directly suppress the immune activity to promote tumor growth is not clear. Here, we identify that a subset of CAF in both rodent and human stromagenic cancers that displays characteristics of senescent fibroblasts and referred to as sCAFs. We show that sCAFs secrete a decoy protein that interferes with cytotoxic activity of activated T effector (Teff) cells. In mouse models for stroma-rich pancreatic cancer, administration of an antibody that blocked the decoy protein resulted in recalibration of the stromal fibroblast by promoted the formation of interferon-licensed-fibroblast cells at the expense of sCAFs. This switch not only enhanced infiltration of tumor-infiltrating T cells but also alleviated their direct suppression resulting in enhanced effector function and tumor regression. Collectively, these results point to the potent immunosuppressive activity of sCAFs mediated by decoy protein as a mechanism by which stroma can promote tumor progression. As stromagenic-cancers are resistance to current therapies, the development of treatments involving blocking of decoy protein may inhibit tumor growth and improve patient survival. Citation Format: Yao Wang, Hara Apostolopoulou, Arjun Sanyal, Hong Sun, Cynthia Sieland, Kavya Gupta, Jiayu Ye, David Gibbs, Paul Wong, Ntranos Vasilis, Sui Huang, James Gardner, Ajay Maker, Thea Tlsty, Anil Bhushan, Tamara Alliston. Restoration of T effector cells function by targeting senescent cancer-associated fibroblast in tumor microenvironment of stroma-rich 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 C036.
Abstract A102: Secreted frizzled related-protein 2 is prognostic for survival in pancreatic cancer
Authors: Lillian Hsu, Julie Siegel, Patrick Nasarre, Rupak Mukherjee, Meghan Gormley, Bailey Richardson, Jordan Morningstar, Imran Khan, Eleanor Hilliard, John O’Bryan, Krist Helke, Laura Spruill, Nathan Dolloff, Nancy Klauber-Demore
Journal: Cancer Research (2024)

Abstract INTRODUCTION: Secreted frizzled-related protein 2 (SFRP2) is overexpressed in several tumor types and blocks tumor apoptosis, increases angiogenesis, and promotes T-cell exhaustion. It has also been shown to be associated with fibrosis in non-neoplastic pathologies. We hypothesize SFRP2 is prognostic for survival and associated with PDAC fibrosis and mesenchymal transformation. METHODS: SFRP2 gene expression and protein levels in patients with PDAC were analyzed using NCI’s The Cancer Genome Atlas (TCGA) data and data from resected tumors analyzed for protein levels by western blot. Disease free survival (DFS) and overall survival (OS) were analyzed using Kaplan Meier test. The association of stroma content and SFPR2 RNA expression in human PDAC was studied using Spearman correlation between the ESTIMATE algorithm stromal score and TCGA data. The GEPIA tool was used to compare SFRP2 mRNA levels between PDAC and normal pancreas tissue. Immunohistochemistry (IHC) for SFRP2 in KPC PDAC tumors were correlated with fibrosis stains Picrosirus red and Massone trichome. The role of SFRP2 in mesenchymal transformation was assessed by western blot in fibroblasts. RESULTS: TCGA RNAseq analysis of SFRP2 expression showed highest SFRP2 mRNA levels in pancreatic cancer out of 32 cancer types. GEPIA analysis of PDAC (n=179) and normal pancreas (n=177) mRNA data showed higher levels of SFRP2 mRNA in PDAC compared to normal pancreas (p&amp;lt;.01). High SFRP2 mRNA levels were associated with decreased disease-free survival hazard ratio = 2.6; p=0.0097). PDAC tissue showed higher SFRP2 protein compared to matched normal-adjacent tissue (n=24, p=0.0003). High SFRP2 expression was associated with decreased OS (p=0.0158. The ESTIMATE stromal score correlated with SFRP2 expression in human PDAC (Spearman correlation coefficient 0.81). Fibrosis levels in KPC PDAC tumors correlated with SFRP2 IHC (Spearman correlation coefficient 0.75). Fibroblasts treated with SFRP2 and TGFβ showed higher mesenchymal markers compared to untreated control. CONCLUSIONS: SFRP2 is increased in PDAC, associated with tumor fibrosis, and prognostic for survival. SFRP2 is a novel therapeutic target in PDAC. Citation Format: Lillian Hsu, Julie Siegel, Patrick Nasarre, Rupak Mukherjee, Meghan Gormley, Bailey Richardson, Jordan Morningstar, Imran Khan, Eleanor Hilliard, John O’Bryan, Krist Helke, Laura Spruill, Nathan Dolloff, Nancy Klauber-Demore. Secreted frizzled related-protein 2 is prognostic for survival 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 A102.