bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract C019: The circadian master regulator BMAL1 blocks immune cell recognition of pancreatic ductal adenocarcinomas by reducing proteasome activity and MHC1 cell surface localization
Authors: Prela Orjola , Wang Lan , Shih Ching-Hua , de Menezes Juliana Cazarin , Altman Brian , Vertino Paula M. , Harris Chris R. , Carpizo Darren R. 
Published: January 2024

Abstract
Many tumor types, including pancreatic adenocarcinomas, have dysregulated circadian rhythms. Here we show that the master regulator of circadian control, BMAL1, is overexpressed in pancreatic ductal adenocarcinoma (PDAC) relative to normal tissue and plays a role in protecting PDAC cells from recognition by the immune system. Using CRISPR-generated knockout (KO) cell lines, we evaluated the cells ability to create liver metastasis using a splenic metastasis assay and found that loss of Bmal1 KO abrograted metastasis. We hypothesized that could be through an immune mediated mechanism and evaluated the Bmal KO cells for their expression of cell surface MHCI. Remarkably loss of Bmal1 led to a significant increase in cell surface MHCI expression. This was due to a change in localization of the MHCI molecule. Proper localization of MHC1 is known to depend upon proteasome-generated peptides, and we found that loss of Bmal1 increased proteosomal activity. We used Cut and Run to demonstrate that Bmal1 binds directly to the promoters for core components of the proteosome. Taken together these studies implicate Bmal1 in regulating anti-tumor immunity in PDAC through its regulation of protesomal activity and MHC1 surface expression. This is a novel function for a circadian rhythm gene in PDAC biology.
Citation Format: Orjola Prela, Lan Wang, Ching-Hua Shih, Juliana Cazarin de Menezes, Brian Altman, Paula M. Vertino, Chris R. Harris, Darren R. Carpizo. The circadian master regulator BMAL1 blocks immune cell recognition of pancreatic ductal adenocarcinomas by reducing proteasome activity and MHC1 cell surface localization [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 C019.
Abstract C022: T cell movement through complex obstacles presented by the microenvironment of pancreatic tumor spheroids
Authors: Roy Shambojit , Chen Zhongming , Qian Guhan , Provenzano Paolo P. 
Published: January 2024

Abstract
Immunotherapy has emerged as a promising approach for treating pancreatic cancer, however its efficacy against solid tumors has been largely limited. In order to be effective, cell-based immunotherapies are required to be in close proximity with the target cancerous cells. However, owing to its dense desmoplastic stroma, many regions of a pancreatic tumor, have areas within the tumor volumes that exclude anti-tumor immune cells. Therefore, we need to define mechanisms used by therapeutic T cells to navigate effectively in some tumor regions and the barriers that limit their infiltration and distribution in other regions of the tumor microenvironment (TME). In this work, we have advanced our knowledge of T cell migration and infiltration through complex TMEs by analyzing T cell dynamics in 3D engineered in vitro environments that can replicate key TME features of pancreatic ductal adenocarcinoma (PDA). Using our state-of the-art imaging techniques with multiphoton excitation (MPE) and second harmonic generation (SHG), we have monitored the migration of engineered human mesothelin reactive CAR-T cells through fibrous microenvironments and their interactions with pancreatic tumor spheroids. Quantitative analysis of interactions between CAR-T cells and carcinoma cells, in terms of velocity, directionality and mean square displacement (MSD) were performed, with the aim of utilizing these phenotypes as “design criteria” for the development of more effective engineered T cell therapies. The therapeutic efficacy of engineered T cells was also evaluated in standard 2D killing assays and then new 3D assays of increased complexity, both of which revealed mesothelin specific cancer cell death. Overall, we are starting to define the physical and molecular mechanisms that result in resistance to immunotherapy against pancreatic cancer, and we anticipate that our work will be applicable to other solid tumors with similar challenges and address key unanswered question in cancer biology.
Citation Format: Shambojit Roy, Zhongming Chen, Guhan Qian, Paolo P. Provenzano. T cell movement through complex obstacles presented by the microenvironment of pancreatic tumor spheroids [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 C022.
Abstract C033: The circadian rhythm gene Dec2 promotes pancreatic cancer dormancy by facilitating immune evasion
Authors: Wang Lan , Prela Orjola , Shih Ching-Hua , de Menezes Juliana Cazarin , Altman Brian , Vertino Paula , Harris Chris , Carpizo Darren 
Published: January 2024

Abstract
Metastatic recurrence following curative-intent pancreatic cancer surgery is a major clinical problem as nearly all die of this at both early and latent periods following surgery. Latent recurrences are due to reactivation of dormant tumor cells that disseminate before the primary tumor has been removed. The mechanisms that drive cancer dormancy are poorly understood in part because of the lack of animal models that recapitulate the biology of the resected patient. Here we introduce a novel mouse model of pancreatic cancer dormancy in which we establish distal pancreatic tumors by orthotopic injection, resect them four weeks later and then follow the mice for recurrence. We observed recurrence patterns and survival outcomes that mimic human patients undergoing surgery for pancreatic cancer where two thirds of the mice succumb to early metastatic recurrence (median survival 26 days) and one third of the mice (called dormant mice) live substantially long (median survival 554 days) without clinical evidence of disease yet harbor disseminated tumor cells in most organs of the body. Disseminated tumor cells isolated from the livers of dormant mice were quiescent, exhibited stem cell properties and upregulated the expression of Dec2, a transcriptional repressor previously best known for its importance in maintaining circadian rhythms. Dec2 enabled the dormant tumor cells to evade the immune system by reducing the amount of MHC1 on their surfaces, and thereby lowered the number of CD8+ T cells within the tumor microenvironment. Knocking out Dec2 significantly improved the overall survival of immunocompetent mice and increased CD8+ T cell tumor infiltration. The decrease in cell surface MHCI was likely due to impaired surface localization of the protein. RNA-seq analysis demonstrated a loss of antigen presentation pathway genes in Dec2 WT cells, particularly in genes encoding subunits of the proteasome. Proper localization of MHC1 is known to depend upon proteasome-generated peptides. By cut-and-run analysis, Dec2 bound directly to the promoters of a number of proteasomal genes, lowered expression of these genes, and decreased proteasomal activity. These studies describe a new mechanism for Dec2 in regulating cancer dormancy through its downregulation of proteasomal activity which in turn converts a hot to a cold TME by decreasing cell surface MHC1.
Citation Format: Lan Wang, Orjola Prela, Ching-Hua Shih, Juliana Cazarin de Menezes, Brian Altman, Paula Vertino, Chris Harris, Darren Carpizo. The circadian rhythm gene Dec2 promotes pancreatic cancer dormancy by facilitating immune evasion [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 C033.
Abstract C040: Investigating oncogene-inflammation cooperativity in pancreatic cancer
Authors: Woess Katharina , Araguás Sandra Blázquez , Diéguez Andrea , Mateo Lidia , Curbelo Direna Alonso 
Published: January 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is generally diagnosed at advanced late stages when current treatments are usually ineffective. It is initiated from a poorly understood interplay between genetic mutations (mutant KRAS) and inflammatory insults that cooperatively remodel the pancreatic epithelium and its tissue environment. Through integrating innovative autochthonous mouse models, single-cell technologies, and genomics methods, we recently identified early, tumor-specific chromatin changes induced by cooperative effects between mutant KRAS and inflammation, and which establish functionally-relevant cell-cell communication networks that direct pancreatic tumorigenesis (Alonso-Curbelo et al. Nature 2021; Burdziak*, Alonso-Curbelo* et al. Science 2023). These findings provide a molecular and cellular framework to understand inflammation-driven tumorigenesis, and raise the possibility of harnessing epigenetically-dysregulated cell-cell communication traits of KRAS-mutant cells to detect or block PDAC development. Towards this end, we are currently combining single-cell multiomics, multiplexed tissue analyses, and functional approaches in pre-clinical models to identify how tissue signals shape the state and fate of early KRAS-mutant cells, define paracrine effects of these changes in reprogramming the immune microenvironment, and establish the functional significance of these interactions in disease progression. With the advent of inhibitors targeting mutant KRAS, we expect that the proposed dissection of the cell-cell crosstalk networks cooperating with mutant KRAS in driving tumor development will uncover tissue-level mechanisms that may be harnessed for the interception and rationale treatment of PDAC.
Citation Format: Katharina Woess, Sandra Blázquez Araguás, Andrea Diéguez, Lidia Mateo, Direna Alonso Curbelo. Investigating oncogene-inflammation cooperativity 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 C040.
Abstract C046: Enhancing T cell infiltration and migration in the pancreatic tumor microenvironment
Authors: Zhang Hongrong , Qian Guhan , Chen Zhongming , Moriarity Branden , Stromnes Ingunn , Odde David , Provenzano Paolo 
Published: January 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest cancers, with a five-year survival rate only increasing from 6% to 12% in the last decade, indicating an urgent need for new therapeutic approaches. In recent years, immunotherapies like chimeric antigen receptor (CAR)-T cell therapy, have demonstrated promising therapeutic results in treating several hematological malignancies. However, the success has been limited in treating solid tumors, especially for PDAC. Factors contributing to this poor response include poor immunogenicity, highly heterogeneous and robust fibrotic and immunosuppressive tumor microenvironments (TMEs). Here, we used state-of-the-art imaging coupled with quantitative analysis to study dynamic T cell migration behavior in organotypic pancreatic tumor slices harvested from genetically engineered KPC mice. Our data showed that T cell speed and overall motility are both significantly lower in stroma-rich region PDA regions than observations in carcinoma cell-rich regions, where collagen fibers are loosely connected. Next, we utilized stroma-targeted approaches to deplete collagen and hyaluronan, the most abundant ECM components in the TME, to remove the biophysical barriers for effective immune therapy. Indeed, preliminary data demonstrated improved T cell infiltration and migration in the tumor slices in the STT-treated groups compared to the control groups. The observation is also confirmed with a therapeutic cell line generated with mesothelin-specific T cell receptors. Furthermore, we utilized genome engineering to generate CD8+ T cells that more effectively migrate in fibrous TMEs. Time-lapse imaging of the engineered T cells shows an increased 3D migration compared to control groups. Taken together, our data suggest that engineered T cell approaches in combination with stromal targeted therapies to diminish stromal ECM content have the potential to improve immunotherapy by allowing effector T cells to sample the tumor volume more effectively.
Citation Format: Hongrong Zhang, Guhan Qian, Zhongming Chen, Branden Moriarity, Ingunn Stromnes, David Odde, Paolo Provenzano. Enhancing T cell infiltration and migration in the pancreatic 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 C046.
Abstract C058: Identifying cell-intrinsic drivers of transcriptional plasticity in pancreatic cancer
Authors: Tong Yuzhou Evelyn , Katan Walaa E. , Bott Alex , Joung Julia , Shalek Alex K. , Winter Peter S. , Raghavan Srivatsan 
Published: January 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with few effective therapies. Contributing to the complexity of this deadly cancer, PDAC tumors with similar genomic backgrounds can express divergent transcriptional programs with clinical importance. These transcriptional subtypes, termed “cell states”, have prognostic significance: PDAC tumors in the “classical state” generally have better outcomes and are thought to be more responsive to chemotherapy while those in the “basal state” are more aggressive. Currently, cell state is not used to direct therapy. Cell state is an integrative property shaped by both cell-intrinsic (e.g., mutations, epigenetics) and cell-extrinsic (e.g., growth factors, cytokines) factors. In our prior work, single-cell analysis of clinical PDAC samples demonstrated notable intra-tumoral cell state heterogeneity with evidence for cells that co-expressed both basal and classical markers, suggestive of cell state plasticity. In addition, longitudinal monitoring of patient-derived organoids has shown that cells can shift from classical to coexpressor/basal states as the environment changes, and this shift in cell states can drastically influence drug response. However, it remains unknown which signaling and transcriptional pathways induce basal or classical states, and whether these gene regulatory networks can be targeted therapeutically. Thus, there is a pressing need to devise scalable methods to determine essential drivers for prognostically-relevant cancer cell states. Here, we aim to define transcriptional drivers of basal and classical cell states in pancreatic cancer. We are currently optimizing a flow cytometry-fluorescence in situ hybridization (Flow-FISH) workflow to enable a multi-gene cell state readout. We plan to perform a transcription factor over-expression screen within a cohort of PDAC models using this Flow-FISH readout to identify those factors that can drive cells toward basal (n=3), classical (n=2), or coexpressor (n=3) states. As a proof of concept, we have confirmed that TP63A overexpression induces basal state expression, even in models that initially express a classical phenotype. Through these efforts, we aim to construct high-fidelity isogenic but state-variant PDAC models for use both in therapeutic screening and as a substrate for investigating mechanisms governing cancer cell state plasticity.
Citation Format: Yuzhou Evelyn Tong, Walaa E. Katan, Alex Bott, Julia Joung, Alex K. Shalek, Peter S. Winter, Srivatsan Raghavan. Identifying cell-intrinsic drivers of transcriptional plasticity 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 C058.
Abstract C066: Metaplastic tuft cells transdifferentiate into metaplastic neuroendocrine cells as pancreatic cancer progresses into late stage carcinoma
Authors: Salas-Escabillas Daniel J. , Moore Jacee , Long Dan , Hoffman Megan , Rempinski Don , Steele Nina , Crawford Howard 
Published: January 2024

Abstract
Progression of pancreatic disease is in part driven by the transdifferentiation of acinar cells into metaplastic ducts in the pancreas. Metaplastic tuft cells (MTCs) are a specialized subset of the metaplastic epithelium that have the potential to drive tumor progression through communication with the microenvironment and modulate PDA progression. Also known as solitary chemosensory cells, tuft cells were first discovered in rodent luminal surfaces, including the nose, stomach, intestine, and bladder, more than 60 years ago. They are characterized by the “tuft” of microvilli reaching into the lumen and, only recently, have studies started to determine the role of normal tuft cells in different organs. These studies determined that tuft cells have different roles depending on the organ in which they reside. Tuft cells are found in several different organs during normal development; however, studies have shown that tuft cells are not present in a normal pancreas. MTCs are only present in the pancreas in PanINs during PDA progression in both humans and mice. Furthermore, the population of MTCs in the pancreas disappears as PDA progresses into invasive carcinoma when using canonical markers of tuft cells. We know little about the role of MTCs in the pancreas, but prior studies have suggested their role as a progenitor cell during PDA. However, these studies do not exclusively mark MTCs during their genesis in a progressive model to of PDA due to a lack of mouse model as well as the complexity of culturing them ex vivo. We have generated a unique dual recombinase mouse model to drive lineage tracing of MTCs during PDA, and our data to suggests that MTCs are not disappearing as PDA progresses but can transdifferentiate into metaplastic neuroendocrine cells.
Citation Format: Daniel J. Salas-Escabillas, Jacee Moore, Dan Long, Megan Hoffman, Don Rempinski, Nina Steele, Howard Crawford. Metaplastic tuft cells transdifferentiate into metaplastic neuroendocrine cells as pancreatic cancer progresses into late stage carcinoma [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 C066.
Abstract C078: Inhibiting the autophagy-lysosomal pathway in pancreatic ductal adenocarcinoma using novel small molecules
Authors: Ruan Yangjingyi , Worroll Daniel W. , Nelson Grady , Li Yue-Ming 
Published: January 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers with a 5-year survival rate of 11.5% due to poor early detection and a lack of effective therapies. To meet the energetic demands, PDAC relies on autophagy to sustain growth and proliferation. Autophagy inhibitors such as hydroxychloroquine (HCQ) only showed limited autophagy inhibition in vivo and failed to provide clinical benefit to patients. However, studies have shown that the combination of HCQ and the MEK/ERK inhibitors can render better therapeutic results with stronger cytotoxicity. Our lab has designed and developed a class of small molecules (GN compounds) that target the autophagy-lysosomal pathway (ALP). Our GN compounds show autophagy inhibition and induction of extrinsic apoptosis markers by Western blot. Furthermore, GN64 affects the function of endosomes and lysosomes by immunofluorescence (IF). The combination treatment of GN79 and Binimetinib, a MEKi, inhibits the ALP and confers enhanced cytotoxicity in a panel of human PDAC cell lines. Future directions are aimed at determining the protein target and mechanism of GN compounds that leads to ALP inhibition. Completion of this project will advance the therapeutic development of novel ALP inhibitors and advance our understanding of the ALP with the possibility to imrpove the current therapeutic regimen for PDAC patients.
Citation Format: Yangjingyi Ruan, Daniel W. Worroll, Grady Nelson, Yue-Ming Li. Inhibiting the autophagy-lysosomal pathway in pancreatic ductal adenocarcinoma using novel small molecules [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 C078.
Abstract C091: Harnessing proteostatic vulnerabilities in pancreatic cancer
Authors: Vogt Sandra , Bar-Sagi Dafna 
Published: January 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) harbors mutations in KRAS in greater than 90% of cases and is characterized by a dense, fibrotic stroma that fosters the formation of a hypoxic, nutrient-poor tumor microenvironment, rendering tumor cells susceptible to proteotoxic stress. In order to prevent endoplasmic reticulum (ER) stress-induced cell death caused by accumulation of toxic protein aggregates, tumor cells must adapt proteostatic mechanisms including activation of the unfolded protein response (UPR) pathway and degradation of misfolded or aggregated proteins through proteasome-dependent or -independent mechanisms, such as ER-specific autophagy (ERphagy). Despite evidence suggesting that tumor cells may experience proteotoxic stress, little is known about the mechanisms pancreatic cancer cells employ to maintain proteostasis. We found that pancreatic cancer cells exhibit KRas-dependent constitutive UPR activation at the expense of ERphagy, suggesting that tumor cells preferentially employ UPR signaling to maintain proteostasis. Accordingly, mutant KRas pancreatic cancer cells have little to no aggregated proteins at baseline as a consequence of UPR activation. Furthermore, upon pharmacological enhancement of ER stress by 26S proteasome inhibition with bortezomib, ERphagy is engaged as a protective mechanism against UPR hyperactivation and apoptosis. In order to target protective ERphagy to promote apoptosis, we suppressed ERphagy activation through siRNA-mediated knockdown of ERphagy receptors under conditions of bortezomib-induced ER stress and found that depletion of CCPG1 but not other ERphagy receptors augmented the growth-suppressive effects of bortezomib due to greater UPR activation and accumulation of aggregated proteins. Overall, our findings implicate context-dependent reliance on both UPR signaling and ERphagy in pancreatic cancer cell survival and identify a targetable cell-intrinsic vulnerability that can leveraged for enhancing the cytotoxic effects of bortezomib, which alone is clinically ineffective in treating PDAC.
Citation Format: Sandra Vogt, Dafna Bar-Sagi. Harnessing proteostatic vulnerabilities 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 C091.