tbuckley/cabot-search huggingface dataset:
Abstract B093: The evaluation of the gene expression profile of pancreatic ductal adenocarcinomas (PDACs) in 3D cell culture vs in vivo and development of new 3D PDACs' models for an evaluation of anti-cancer drug testing
Authors: Marcin Krzykawski, David Earnshaw, Krzysztof Kus, Artur Pirog, Sachin Kote, Mark Treherne, Justyna Kocik-Krol
Journal: Cancer Research (2024)

Abstract In the ever-evolving landscape of biomedical research, 3D Cell Culture (3DCC) systems have emerged as pivotal tools for mimicking in vivo environments and fostering more physiologically relevant cellular responses. Despite promises, 3DCC based drug discovery efforts didn’t fulfil the hopes. The classic way 3DCC is done, always starts with 2D cell culture (2DCC) followed by brief 3 day 3DCC and finally drug testing. Following those observations we decided to mimic much more than just brief 3DCC state but enhance the culture by constant 3DCC to 3DCC passages. We characterized the gene expression profiles and proteomic characteristics of pancreatic tumors concluding that prolonged 3DCC is the closest to an in vivo model. The protracted cultivation periods mimic the intricacies of the in vivo environment, enabling a more accurate representation of the molecular dynamics within pancreatic tumors. In our study, we identified a panel of genes characterized by similar expression levels between prolonged 3D cell culture and in vivo conditions, while displaying significant divergence between 2D cultures and short-term 3D cultures when compared to in vivo. These genes play a pivotal role in the progression and treatment of cancer, underscoring the potential of prolonged 3DCC of LifeGel® significance in understanding tumor biology and devising therapeutic strategies. Furthermore, we also investigated the implications of prolonged 3D in vitro cultures on evaluating anti-cancer drug activities. The findings highlight the significance of 3DCC in enhancing our understanding of pancreatic tumor biology and in refining drug screening methodologies for more effective therapeutic interventions. By providing a biomimetic microenvironment, our hydrogels facilitate the formation of complex cellular structures, enabling more accurate representation of tissue architecture and cellular interactions. We delivered LifeGel® platform which presents a myriad of opportunities for researchers seeking to enhance the fidelity and translatability of their in vitro studies into pre-clinial models. Citation Format: Marcin Krzykawski, David Earnshaw, Krzysztof Kus, Artur Pirog, Sachin Kote, Mark Treherne, Justyna Kocik-Krol. The evaluation of the gene expression profile of pancreatic ductal adenocarcinomas (PDACs) in 3D cell culture vs in vivo and development of new 3D PDACs' models for an evaluation of anti-cancer drug testing [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B093.
Abstract PR-16: Evaluating direct KRASQ61H inhibition in pancreatic cancer models
Authors: Szu-Aun Long, Amber M Amparo, Haley Todd, Grace Goodhart, Syed A Ahmad, Andrew M Waters
Journal: Cancer Research (2024)

Abstract KRASQ61 mutations are associated with the worst prognosis among the various KRAS mutational subtypes of pancreatic ductal adenocarcinoma (PDAC). RMC-7977 is a RAS(ON) multi-selective noncovalent inhibitor with broad spectrum activity against oncogenic RAS mutants and wild-type RAS. The related investigational agent RMC-6236 is currently undergoing clinical trials. Binary complexes of CypA: RMC-7977 bind equipotently to multiple KRAS mutational subtypes however RMC-7977 is less potent at inhibiting growth in KRASQ61H-mutant cell lines. In contrast, RM-047 is a preclinical RAS(ON) Q61H-selective inhibitor tool compound. We evaluated direct KRASQ61H inhibition using both RMC-7977 and RM-047 in cell culture models. We found that in KRASQ61H-rescued RASless mouse embryonic fibroblasts (MEFs), RM-047 inhibited ERK activity and suppressed growth more potently than RMC-7977. Conversely, in a panel of KRASQ61H-mutant PDAC cell lines, RM-047 was less potent than RMC-7977 in two out of three KRASQ61H-mutant PDAC cell lines. Furthermore, we discovered that ERK activity rapidly rebounded with treatment in KRASQ61H-mutant PDAC cell lines, whereas ERK activity remained suppressed in KRASQ61H-rescued RASless MEFS lacking WT RAS alleles. Our analysis of DepMap data indicated that among the KRAS mutational subtypes frequently found in pancreatic cancer, KRASQ61H is the least dependent on KRAS for survival. This suggests that in a KRASQ61H-mutant PDAC setting, additional factors such as WT RAS expression may mediate growth. From our KRAS drug-anchored CRISPR loss-of-function screens, we found that the loss of EGFR sensitized cells to KRAS inhibition, particularly in a KRASQ61H-dependent context. Therefore, we combined erlotinib, an FDA-approved EGFR inhibitor, with either RM-047 or RMC-7977, and found that the addition of erlotinib prevented ERK rebound activity and synergized with RM-047 or RMC-7977 to reduce growth in KRASQ61H-mutant PDAC cell lines. These data provide insights into mechanisms by which KRASQ61H-mutant PDAC may be less dependent on KRAS for survival and further support the clinical evaluation of combined EGFR and RAS(ON) inhibition as a potential therapeutic strategy in the treatment of PDAC patients harboring KRASQ61H mutations. Citation Format: Szu-Aun Long, Amber M Amparo, Haley Todd, Grace Goodhart, Syed A Ahmad, Andrew M Waters. Evaluating direct KRAS inhibition in pancreatic cancer models [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr PR-16.
Abstract C050: Vitamin B6 restriction impairs pancreatic cancer progression
Authors: Chunbo He, Kamiya Mehla
Journal: Cancer Research (2024)

Abstract Introduction: Cancer cells utilize altered metabolism to sustain their rapid growth, and understanding how these metabolic changes aid in tumor development could enhance current treatment approaches. Vitamins are essential micronutrients necessary in small quantities to support the proper functioning and metabolism of our organs and systems. Despite the recognized importance of vitamins in maintaining overall health, there is no direct evidence linking vitamin metabolism to pancreatic ductal adenocarcinoma (PDAC). Methods: PDAC animal models, organoid models, 3D-culture models, and LC-MS/MS-based metabolomic analysis were used to explore the role of vitamin B6 (VB6) in pancreatic cancer. Results: Our data showed that 1) Patients with PDAC exhibit lower levels of circulating vitamin B6 compared to healthy individuals of the same age. Additionally, vitamin B6 levels are reduced in the interstitial fluid of KPC (KrasG12D/+; p53R172H/+; Pdx1-Cretg/+) tumors and in the blood of mice with KPC tumors compared to healthy mice of the same age; 2) PDAC cells metabolize VB6 more rapidly than non-cancerous pancreatic epithelial cells; 3) VB6 restriction impairs PDAC cell proliferation in vitro and PDAC tumor growth in vivo; 4) VB6 depletion decreases key metabolites of the one-carbon pathway necessary for PDAC cell growth; 5) Inhibiting the one- carbon pathway mimics the effects of a vitamin B6 deficiency on PDAC cell proliferation. And knocking down VB6-dependent enzymes SHMT1/2 negates the pro-growth impact of VB6. Conclusion: Our research suggests that VB6 plays a key role in regulating various metabolic processes essential for the growth of PDAC cells. By focusing on inhibiting VB6-dependent enzymatic reactions, we may uncover new therapeutic strategies for treating PDAC. Citation Format: Chunbo He, Kamiya Mehla. Vitamin B6 restriction impairs pancreatic cancer progression [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C050.
Abstract C045: Targeting metabolic heterogeneity in pancreatic ductal adenocarcinoma
Authors: Taryn Morningstar, Cecily Anaraki, Lorenzo Scipioni, Giulia Tedeschi, Michelle Digman, Aimee Edinger, Claus Jorgensen, Melissa Fishel, Christopher J Halbrook
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer-related death in the US. This poor prognosis is related to the complex tumor microenvironment and tumor heterogeneity that drives resistance to chemotherapy. Here the heterogeneity of the stromal, immune, and malignant epithelial cell populations enables signaling and metabolic crosstalk mechanisms that drive immune suppression and resistance to therapy. Recently, our group unveiled that multiple distinct metabolic subclasses of cancer cells coexist within individual PDAC tumors. Among these, two PDAC clonal populations can engage in metabolic symbiosis that supports mitochondrial metabolism. One subtype has a constitutively high integrated stress response (ISR), enabling resistance to mitochondrial inhibitors. Further, these cells release asparagine that supports the mitochondrial metabolism of the other subtype that are more sensitive to mitochondrial inhibition. Given these observations, we are developing approaches to disrupt this metabolic symbiosis. Clonal PDAC cells with constitutively active ISR exhibit increased sensitivity to inhibition of the redox activity of Redox factor 1/Apurinic-apyrimidinic endonuclease 1 (Ref-1). Importantly, this can be leveraged to disrupt the support of the mitochondrial metabolism of clonal symbiotic pairs. Moreover, polyclonal PDAC cell lines representative of the heterogeneity seen in PDAC patients show a highly synergistic response to the combination of Ref-1 redox inhibitors with mitochondrial inhibitors. These data suggest this treatment combination will be synergistic in polyclonal tumors that exist in most PDAC patients. Overall, these data have the potential to lead to new avenues to directly target heterogenous populations of cancer cells to treat pancreatic cancer- an urgent clinical need. Citation Format: Taryn Morningstar, Cecily Anaraki, Lorenzo Scipioni, Giulia Tedeschi, Michelle Digman, Aimee Edinger, Claus Jorgensen, Melissa Fishel, Christopher J Halbrook. Targeting metabolic heterogeneity in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C045.
Abstract C067: Tuft cells transdifferentiate to neural-like progenitor cells in the progression of pancreatic cancer
Authors: Daniel J. Salas-Escabillas, Megan T. Hoffman, Sydney M. Brender, Jacee S. Moore, Hui-Ju Wen, Simone Benitz, Erick T. Davis, Daniel Long, Allison Wombwell, Nina G. Steele, Brittany Allen-Petersen, Rosalie C. Sears, Ichiro Matsumoto, Kathleen E. DelGiorno, Howard C. Crawford
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDA) is partly initiated through the transdifferentiation of acinar cells to metaplastic ducts that act as precursors of neoplasia and cancer. Tuft cells are solitary chemosensory cells not found in the normal pancreas but arise in metaplasia and neoplasia, diminishing as neoplastic lesions progress to carcinoma. Metaplastic tuft cells (mTCs) function to suppress tumor progression through communication with the tumor microenvironment, but their fate during progression is unknown. To determine the fate of mTCs during PDA progression, we have created a lineage tracing model that uses a tamoxifen-inducible tuft-cell specific Pou2f3CreERT/+ driver to induce transgene expression, including the lineage tracer tdTomato or the oncogene Myc. mTC lineage trace models of pancreatic neoplasia and carcinoma were used to follow mTC fate. We found that mTCs, in the carcinoma model, transdifferentiate into neural-like progenitor cells (NRPs), a cell type associated with poor survival in PDA patients. Using conditional knock-out and overexpression systems, we found that Myc activity in mTCs is necessary and sufficient to induce this Tuft-to- Neuroendocrine-Transition (TNT). Citation Format: Daniel J. Salas-Escabillas, Megan T. Hoffman, Sydney M. Brender, Jacee S. Moore, Hui-Ju Wen, Simone Benitz, Erick T. Davis, Daniel Long, Allison Wombwell, Nina G. Steele, Brittany Allen-Petersen, Rosalie C. Sears, Ichiro Matsumoto, Kathleen E. DelGiorno, Howard C. Crawford. Tuft cells transdifferentiate to neural-like progenitor cells in the progression of pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C067.
Abstract A039: Repeat RNA mediated disruption of cellular plasticity in pancreatic cancer
Authors: Eunae You, Patrick Danaher, Chenyue Lu, Siyu Sun, Luli Zou, Ildiko Phillips, Alexandra Rojas, Natalie Ho, Yuhui Song, Michael Raabe, Katherine Xu, Peter Richieri, Hao Li, Natalie Aston, Rebecca Porter, Bidish Patel, Linda Nieman, Nathan Schurman, Briana Hudson, Khrystyna North, Sarah Church, Vikram Deshpande, Andrew Liss, Tae Kim, Yi Cui, Youngmi Kim, Benjamin Greenbaum, Martin Aryee, David Ting
Journal: Cancer Research (2024)

Abstract Aberrant expression of repeat RNAs in pancreatic ductal adenocarcinoma (PDAC) mimics viral-like responses with implications for tumor cell state and the surrounding microenvironment. To better understand the relationship of repeat RNAs in human PDAC, we employed the NanoString CosMx™ spatial molecular imaging (SMI) platform, which utilizes a 1,000-plex RNA panel with custom repeat RNA probes targeting long interspersed nuclear element 1 (LINE-1) retrotransposon ORF1 and ORF2, HSATII satellite (SAT) repeat, and two human endogenous retroviruses (HERV-K and HERV-H) in 46 primary tumors. This analysis revealed correlations of high repeat RNA expression with alterations in the epithelial state of PDAC cells and the myofibroblast phenotype in cancer-associated fibroblasts (CAFs). The loss of cellular identity observed with dosing of extracellular vesicles (EVs) and individual repeat RNAs in PDAC and CAF cell culture models points to cell-cell intercommunication involving these viral-like elements. Differences in the PDAC and CAF response are driven by distinct innate immune signaling pathways through interferon regulatory transcription factor 3 (IRF3). Altogether, our data indicate that cell context-specific viral-like responses driven by tumor cells have broad impacts on single-cell heterogeneity within cancer cells and the pancreatic cancer microenvironment. Citation Format: Eunae You, Patrick Danaher, Chenyue Lu, Siyu Sun, Luli Zou, Ildiko Phillips, Alexandra Rojas, Natalie Ho, Yuhui Song, Michael Raabe, Katherine Xu, Peter Richieri, Hao Li, Natalie Aston, Rebecca Porter, Bidish Patel, Linda Nieman, Nathan Schurman, Briana Hudson, Khrystyna North, Sarah Church, Vikram Deshpande, Andrew Liss, Tae Kim, Yi Cui, Youngmi Kim, Benjamin Greenbaum, Martin Aryee, David Ting. Repeat RNA mediated disruption of cellular plasticity in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A039.
Abstract A011: Enhanced Radiosensitivity of Pancreatic Cancer Achieved through Inhibition of Cyclin-Dependent Kinase 1
Authors: Stetson Van Matre, Saaimatul Huq, Lokesh Akana, Oscar Zuniga, Henrique Rodrigues, Adam Wolfe
Journal: Cancer Research (2024)

Abstract Introduction: One of the major challenges in treating Pancreatic Ductal Adenocarcinoma (PDAC) is overcoming radioresistance. This study investigates the targeting of Cyclin-dependent kinase-1 (CDK1) through both genetic and pharmaceutical inhibition as a strategy to increase the radiosensitivity of PDAC cells. Methods: We conducted mass spectrometry and phosphoproteomics analyses to compare engineered radiation-resistant PDAC cell lines (MIA PaCa-2 and PANC-1) with their parental controls. Additionally, we examined the TCGA PDAC database to correlate clinical outcomes, such as overall survival (OS), with CDK1 mRNA expression levels in PDAC patients. Furthermore, we developed a microRNA-based TET-on inducible shRNA to specifically inhibit CDK1 expression in PDAC cell lines. In an orthotopic PDAC model, we evaluated the radiation sensitivity of PDAC tumors with or without doxycycline treatment. We also employed a selective CDK1 inhibitor, RO-3306, to target CDK1 activation, followed by in vitro experiments using immunoblotting, immunocytochemistry, and clonogenic assays. Results: Our phosphoproteomics analysis revealed a significant increase in phospho-CDK1 (Tyr15) levels in the radiation-resistant cell lines. High CDK1 expression was associated with poorer OS in PDAC patients. Additionally, we observed heightened CDK1 phosphorylation at the threonine tyrosine 14 (Tyr14) residue following radiation exposure. Through our in vivo and in vitro experiments, we demonstrated that CDK1 inhibition, in conjunction with radiation therapy, delayed tumor growth and enhanced radiosensitivity in PDAC cells. Treatment with RO-3306 caused a substantial shift of cells into the G2/M phase and disrupted DNA repair post-radiation exposure, further enhancing radiosensitivity. Conclusion: Our findings underscore the critical role of CDK1 in PDAC radioresistance. Targeting CDK1 in combination with radiotherapy shows promise for future exploration as a potential treatment strategy in PDAC. Citation Format: Stetson Van Matre, Saaimatul Huq, Lokesh Akana, Oscar Zuniga, Henrique Rodrigues, Adam Wolfe. Enhanced Radiosensitivity of Pancreatic Cancer Achieved through Inhibition of Cyclin-Dependent Kinase 1 [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A011.
Abstract A057: Investigating Fibroblast-Epithelial crosstalk in pre-malignant and cancerous microenvironment
Authors: Padma Kadiyala, Ahmed Elhossiny, Jianhua Liu, Alexander Bray, Katelyn Donahue, Arvind Rao, Jiaqi Shi, Yaqing Zhang, Filip Bednar, Timothy Frankel, Eileen Carpenter, Marina Pasca Di Magliano
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) originates from precursor lesions, the most common of which are known as pancreatic intraepithelial neoplasia (PanIN). PanIN formation and progression is accompanied by accumulation of a precursor microenvironment (PME) composed of desmoplastic stroma that plays an important role in promoting tumor growth and immune evasion. The crosstalk between tumor cells and stromal cells is an area of active investigation. While PanIN and the PME have been extensively studied in mouse models, their nature in humans have remained elusive as there is no clinical indication to sample healthy pancreas. Through a unique collaboration with the Gift of Life Organ and Tissue donation program, we performed transcriptomic analysis on normal pancreata declined for transplant. We noted that epithelial cells in the PanIN and cancer microenvironment were transcriptomically similar; however, their surrounding stromal fibroblasts were markedly distinct. Given that most precursor lesions remain quiescent while some progress to tumor, we sought out to elucidate how the transcriptional programs in epithelial cells influence fibroblast cell fate. To do so, we developed a 3D ex-vivo organoid-fibroblast coculture system using primary organoid and fibroblast cultures successfully derived from Gift of Life pancreata or PDAC patients undergoing surgical resection. Our coculture system retains histological features of heterogeneity observed in vivo. Using single cell RNA-sequencing analysis of matched fibroblast-organoid cocultures we identified factors that were highly expressed in fibroblasts in tumor cocultures, but not in normal cocultures. We are currently interrogating candidate ligand/receptor interactions in our cocultures to determine the mediators of this epithelial-mediated fibroblast polarization. This model will allow us to gain an understanding about how components of the microenvironment restrain or promote malignant transformation and serve as a great tool to study therapies targeting tumor and stromal cells in a patient specific manner. Citation Format: Padma Kadiyala, Ahmed Elhossiny, Jianhua Liu, Alexander Bray, Katelyn Donahue, Arvind Rao, Jiaqi Shi, Yaqing Zhang, Filip Bednar, Timothy Frankel, Eileen Carpenter, Marina Pasca Di Magliano. Investigating Fibroblast-Epithelial crosstalk in pre-malignant and cancerous microenvironment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A057.
Abstract IA-03: Functional heterogeneity of fibroblast populations in pancreatic cancer
Authors: Giulia Biffi
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is especially lethal among cancers because current treatments are few and ineffective. One key stromal factor thought to contribute to the dismal prognosis of PDAC is the presence of cancer-associated fibroblasts (CAFs). However, CAF-targeting therapeutic strategies have so far failed. Recently, providing an explanation for this apparent contrasting observations, phenotypically distinct PDAC CAF subtypes have been discovered. We previously described two main PDAC CAF populations that are defined by distinct targetable molecular mechanisms: TGF-beta-dependent myofibroblastic CAFs (myCAFs) and IL-1-dependent inflammatory CAFs (iCAFs) (J Exp Med 2017). We also demonstrated how the activation of one pathway (i.e., TGF-beta signaling) blocks the activation of another (i.e., IL-1 signaling), leading to this CAF heterogeneity (Cancer Discovery 2019). Despite our progress, the roles of distinct PDAC CAF subtypes remain to be largely elucidated. Indeed, the ability of myCAFs and iCAFs to at least partially interconvert and the lack of genetically engineered mouse models (GEMMs) for their in vivo manipulation have so far hindered careful investigation of their functions in PDAC progression. To overcome these challenges, we have engineered new mouse models and ‘CAF-locked’ fibroblast lines that enable to alter CAF composition in vitro and in vivo. Leveraging these new models, we are starting to understand the respective crosstalk of iCAFs and myCAFs with each other, with PDAC malignant cells, with immune cells and with other stromal cells. Improving PDAC survival for all patients will likely require a better understanding of the complex nature of the tumor microenvironment in these heterogeneous cancers. While further genetic manipulation of myCAF (e.g., EGFR-activated myCAFs – Cancer Cell 2024) and iCAF subsets will be required to achieve that, our studies are crucial to begin to decipher this complexity. Citation Format: Giulia Biffi. Functional heterogeneity of fibroblast populations in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr IA-03.