bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A037: Role of hypoxia in fibroblast reprogramming in pancreatic cancer
Authors: Ngodup Tenzin , Mello Ashley , Donahue Katelyn 
Published: September 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by a dense desmoplastic stroma, comprised of extracellular matrix, cancer-associated fibroblasts (CAFs), and immune cells. Due to the rapid tumor growth and the unusually low blood vessel density of PDAC, both tumor cells and stromal cells experience hypoxia, or the low availability of oxygen. Although hypoxia is a crucial feature of the tumor milieu and predicts poor clinical outcome, the effects of hypoxia on the PDAC stromal cells, as well as the interplay between tumor and stroma, is not well understood. Cancer-associated fibroblasts (CAFs) are a predominant and heterogeneous stromal cell type in PDAC, and single-cell transcriptomics of human and mouse PDAC revealed a distinct CAF subpopulation, inflammatory CAFs (iCAFs). These inflammatory fibroblasts produce high levels of cytokines and chemokines in PDAC, potentially contributing to its immunosuppressive microenvironment and tumorigenesis. By injecting a hypoxia probe into PDAC mouse models, we previously showed that iCAFs predominantly reside in oxygen- starved regions of the tumor. Furthermore, we observed that the hypoxia-related gene signature is positively enriched in iCAFs in human PDAC tissues. By exposing three-dimensional (3D) cocultures of pancreatic tumor cells and fibroblasts to hypoxia, we found that hypoxia induces IL1ɑ from tumor cells, thereby promoting iCAF formation. Importantly, tumor cell IL1ɑ was further elevated in the presence of hypoxic fibroblasts, implicating hypoxia as a modulator of bidirectional tumor cell-CAF interactions. Efforts are ongoing to understand the mechanism by which hypoxia regulates CAF phenotype by modulating the bidirectional crosstalk between tumor cells and fibroblasts in PDAC. Together, our study identifies hypoxia as a crucial environmental factor in promoting the iCAF phenotype, thus highlighting an instructive role of hypoxia in shaping the stromal microenvironment.
Citation Format: Tenzin Ngodup, Ashley Mello, Katelyn Donahue. Role of hypoxia in fibroblast reprogramming 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 A037.
Abstract A038: The hypoxic regulation of macrophage function in pancreatic cancer
Authors: Hannifin Sean , Mello Ashley M , Ngodup Tenzin , Donahue Katelyn L , Pasca di Magliano Marina , Lee Kyoung Eun 
Published: September 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is marked by an extensive fibroinflammatory stroma and a low-oxygen (hypoxic) microenvironment, which contribute to disease progression and therapeutic resistance. Within the PDAC stroma, macrophages and cancer-associated fibroblasts (CAFs) are the predominant cell types. Macrophages are a major immunosuppressive population in PDAC. These cells are highly plastic and, as a result, their environment plays an important role in regulating their function. Macrophages adapt to hypoxia primarily by stabilizing hypoxia-inducible factors (HIFs), which are oxygen-labile transcription factors. Although PDAC is profoundly hypoxic and both the tumor cells and stromal cells experience hypoxia, the effects of hypoxia and HIFs on macrophages and their interactions with other stromal cells in PDAC are not yet fully understood. We found that hypoxia promotes the acquisition of inflammatory cancer-associated fibroblasts (inflammatory CAFs), a fibroblast subtype that produces high levels of cytokines and chemokines. Utilizing a hypoxia marker in mouse models of PDAC, we have observed that inflammatory CAFs and macrophages are predominantly situated in hypoxic tumor regions compared with normoxic regions, while T cells are largely absent from these oxygen-poor regions. These preliminary data raise the possibility that inflammatory fibroblasts induced by hypoxia promote macrophage infiltration into hypoxic tumor regions and facilitate an immunosuppressive macrophage phenotype. We have also found that when macrophages are exposed to conditioned media derived from fibroblast cultures under either hypoxic or normoxic conditions, factors secreted from the hypoxia-exposed fibroblasts promote an immunosuppressive macrophage phenotype. We are currently identifying the factors released from hypoxic fibroblasts that drive the immunosuppressive macrophage phenotype. Future work will focus on evaluating the effects of macrophage-intrinsic responses to hypoxia through HIFs on pancreatic tumorigenesis in vivo.
Citation Format: Sean Hannifin, Ashley M Mello, Tenzin Ngodup, Katelyn L Donahue, Marina Pasca di Magliano, Kyoung Eun Lee. The hypoxic regulation of macrophage function 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 A038.
Abstract A039: Repeat RNA mediated disruption of cellular plasticity in pancreatic cancer
Authors: You Eunae , Danaher Patrick , Lu Chenyue , Sun Siyu , Zou Luli , Phillips Ildiko , Rojas Alexandra , Ho Natalie , Song Yuhui , Raabe Michael , Xu Katherine , Richieri Peter , Li Hao , Aston Natalie , Porter Rebecca , Patel Bidish , Nieman Linda , Schurman Nathan , Hudson Briana , North Khrystyna , Church Sarah , Deshpande Vikram , Liss Andrew , Kim Tae , Cui Yi , Kim Youngmi , Greenbaum Benjamin , Aryee Martin , Ting David 
Published: September 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 A041: Deciphering the bidirectional influences of sympathetic neurons and cancer associated fibroblasts and the resulting contributions to PDAC progression
Authors: Sattler Ariana , Diba Parham , Korzun Tetiana , Kuykendall Marigold , MacPherson-Hawthorne Kevin , Sherman Mara , Zimmers Teresa , Eksi Sebnem E 
Published: September 2024

Abstract
The pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment (TME) is innervated by a variety of peripheral nerves that are emerging as facilitators of tumor initiation, progression and metastasis. However, the influences of sympathetic nerves on the TME and how these bi-directional interactions can exacerbate PDAC progression remains unclear. Sympathetic nerves innervate both human and murine PDAC tumors and are frequently surrounded by abundant and heterogeneous cancer-associated fibroblasts (CAFs), which are known to play various crucial roles in PDAC progression. In our studies, we aim to elucidate the bidirectional CAF and sympathetic-neuron crosstalk that may promote tumor growth using a variety of in vitro coculture systems to model sympathetic-CAF interactions, as well as in vivo modeling of nerves in murine PDAC tumors. Our nerve-CAF cocultures reveal that CAFs closely and frequently interact with sympathetic nerves, and also enhance sympathetic nerve outgrowth. We further sequenced these cocultured conditions to evaluate intrinsic transcriptional changes that may be contributing to the enhanced nerve outgrowth. We identified several genes that may contribute to upregulated CAF adhesion, ECM deposition and neuroactive ligand-receptor interactions, which may also be supportive of the axon outgrowth and tumor cell growth. We are also currently characterizing human and murine PDAC samples that contain and lack sympathetic innervation to evaluate spatial phenotypic shifts within the TME. Collectively, our results suggest that this crosstalk between sympathetic neurons and CAFs may both enhance tumor innervation and tumor-promoting phenotypes in the TME, such as axonogenesis and fibrosis in PDAC.
Citation Format: Ariana Sattler, Parham Diba, Tetiana Korzun, Marigold Kuykendall, Kevin MacPherson-Hawthorne, Mara Sherman, Teresa Zimmers, Sebnem E Eksi. Deciphering the bidirectional influences of sympathetic neurons and cancer associated fibroblasts and the resulting contributions to PDAC 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 A041.
Abstract A044: Persistence of fetal splanchnic gene signature defines a tumor-restraining fibroblast subtype in pancreatic cancer
Authors: Han Lu , Walter Tom , Beaudet Joseph , Everett Caroline , Leone Gustavo , Ostrowski Michael 
Published: September 2024

Abstract
The pancreas is composed of the epithelial and mesenchymal cells. While mesenchymal fibroblasts are a minor component of the normal pancreas, fibroblast population expands drastically during tumorigenesis. In pancreatic ductal adenocarcinoma (PDAC), cancer associated fibroblasts (CAFs) play critical and complex roles in the tumor microenvironment. This study sought to define the origin, heterogeneity and function of pancreatic cancer associated fibroblasts. Recently we performed a series of lineage tracing studies in genetically engineered mouse models. This identified the splanchnic mesenchyme (a tissue layer adjacent to the developing fetal pancreatic epithelium) as the fetal origin of the adult pancreatic resident fibroblasts and pancreatic CAFs. Single cell transcriptomic analysis indicated persistent and dynamic gene expressions along the pancreatic mesenchymal trajectory during development, homeostasis, precancer and cancer. Intriguingly, we found that two splanchnic transcription factors, GATA6 and FOXF1, are expressed in only subsets of adult pancreatic fibroblasts in temporally and spatially distinct patterns. Similar patterns were observed in both mouse models and human patient samples. To determine the role of GATA6 in fibroblasts during tumorigenesis, we constructed a dual DNA recombinase mouse genetic model. DNA recombinase FlpO directs expression of an oncogene Kras (G12D mutation) and loss of a tumor suppressor p53 in pancreatic epithelial cells to induce spontaneous tumor formation in the pancreas, and DNA recombinase Cre deletes Gata6 specifically in fibroblasts. This fibroblast specific Gata6 deletion resulted in altered number and gene expression of CAFs as well as increased tumor burden in the pancreas. This suggests a non-cell autonomous function of GATA6 within CAFs to restrain pancreatic cancer progression. In summary, this study delineated a continuous cell trajectory of the mesenchymal lineage in the pancreas across different life stages. Additionally, this study provides evidence that persistent and selective gene expressions along the mesenchymal trajectory contributes to pancreatic CAF heterogeneity and such persistence may constitute an inherent host defense mechanism to restrain pancreatic cancer. The enhancement of this mechanism could be explored further for therapeutic benefits.
Citation Format: Lu Han, Tom Walter, Joseph Beaudet, Caroline Everett, Gustavo Leone, Michael Ostrowski. Persistence of fetal splanchnic gene signature defines a tumor-restraining fibroblast subtype 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 A044.
Abstract A053: Interrogating the spatial biology of pancreatic cancer-associated fibroblasts in resected human pancreatic cancer
Authors: Bryce Adam , Dreyer Stephan , Froeling Fieke , Martinelli Silvia , Pennie Rachel , Officer-Jones Leah , Le Quesne John , Chang David 
Published: September 2024

Abstract
Introduction Cancer-associated fibroblasts (CAFs) are key players in the fibrotic tumour microenvironment (TME) of pancreatic cancer. Recent evidence has demonstrated the existence of multiple CAF subtypes, however there is relatively little evidence validating and corroborating these CAF subtypes in resected human pancreatic cancer. Furthermore, the spatial interactions between CAF subtypes and the epithelial and immune compartments of the pancreatic cancer TME is not well understood. Methods We designed and optimised a bespoke 8-plex immunofluorescence panel for the purposes of CAF subtype profiling and elucidation of CAF spatial biology: panCK, FAP, SMA, CTGF, S100A4, IL6, LIF, PDGFR. This was applied to a cohort of n=215 resected pancreatic cancer, well characterised with highly granular clinico-pathological and transcriptomic data through the Australian Pancreatic Cancer Genome Initiative. Spatial analysis was performed with novel computational biology techniques. Results We demonstrate seven CAF subtypes which cluster to form distinct, highly prognostic “enrichment profiles” (EPs). The cold EP represents quiescent CAFs in close proximity to immune cells (multivariate HR 0.45, 95% CI 0.30-0.68, p&lt;0.001), and the fibrotic EP represents activated CAFs in close proximity to epithelial cells (multivariate HR 2.22, 95% CI 1.48-3.35, p&lt;0.001). We also demonstrate the prognostic power of high spatial entropy (loss of tissue architecture, correlating with the fibrotic EP) vs low spatial entropy (preservation of tissue architecture, correlating with the cold EP) (HR 2.22, 95% CI 1.47-3.35, p&lt;0.001). Conclusion We begin to unravel the elusive spatial biology of pancreatic CAFs in a large resected human cohort. We see changes in immune cell infiltrate, modulation of cellular relationships, and greater tissue disorganisation as a result of CAF activation. These features are highly prognostic and we hypothesise they are driven by changes in crosstalk between TME compartments. Current work focuses on application of these techniques to a large resected neoadjuvantly-treated cohort, allowing further interrogation of the notorious fibrotic post-neoadjuvant pancreatic cancer TME. If accepted for presentation we look forward to presenting both cohorts simultaneously.
Citation Format: Adam Bryce, Stephan Dreyer, Fieke Froeling, Silvia Martinelli, Rachel Pennie, Leah Officer-Jones, John Le Quesne, David Chang. Interrogating the spatial biology of pancreatic cancer-associated fibroblasts in resected human 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 A053.
Abstract A057: Investigating Fibroblast-Epithelial crosstalk in pre-malignant and cancerous microenvironment
Authors: Kadiyala Padma , Elhossiny Ahmed , Liu Jianhua , Bray Alexander , Donahue Katelyn , Rao Arvind , Shi Jiaqi , Zhang Yaqing , Bednar Filip , Frankel Timothy , Carpenter Eileen , Di Magliano Marina Pasca 
Published: September 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 A066: nSMase2-mediated exosome secretion shapes the tumor microenvironment to immunologically support pancreatic cancer
Authors: Hendley Audrey M , Ashe Sudipta , Urano Atsushi , Ng Martin , Phu Tuan A , Peng Xianlu Laura , Luan Changfei , Finger Anna-Marie , Jang Gun Ho , Kerper Natanya R , Berrios David I , Jin David , Lee Jonghyun , Riahi Irene R , Gbenedio Oghenekevwe M , Chung Christina , Roose Jeroen P , Yeh Jen Jen , Gallinger Steven , Biankin Andrew V , O’Kane Grainne M , Ntranos Vasilis , Chang David K , Dawson David W , Kim Grace E , Weaver Valerie M , Raffai Robert L , Hebrok Matthias 
Published: September 2024

Abstract
The pleiotropic roles of nSMase2-generated ceramide include regulation of intracellular ceramide signaling and exosome biogenesis. We investigated the effects of eliminating nSMase2 on early and advanced PDA, including its influence on the microenvironment. Employing the KPC mouse model of pancreatic cancer, we demonstrate that pancreatic epithelial nSMase2 ablation reduces neoplasia and promotes a PDA subtype switch from aggressive basal-like to classical. nSMase2 elimination prolongs survival of KPC mice, hinders vasculature development, and fosters a robust immune response. nSMase2 loss leads to recruitment of cytotoxic T cells, N1-like neutrophils, and abundant infiltration of anti-tumorigenic macrophages in the pancreatic preneoplastic microenvironment. Mechanistically, we demonstrate that nSMase2-expressing PDA cell small extracellular vesicles (sEVs) reduce survival of KPC mice; PDA cell sEVs generated independently of nSMase2 prolong survival of KPC mice and reprogram macrophages to a proinflammatory phenotype. Collectively, our study highlights previously unappreciated opposing roles for exosomes, based on biogenesis pathway, during PDA progression.
Citation Format: Audrey M Hendley, Sudipta Ashe, Atsushi Urano, Martin Ng, Tuan A Phu, Xianlu Laura Peng, Changfei Luan, Anna-Marie Finger, Gun Ho Jang, Natanya R Kerper, David I Berrios, David Jin, Jonghyun Lee, Irene R Riahi, Oghenekevwe M Gbenedio, Christina Chung, Jeroen P Roose, Jen Jen Yeh, Steven Gallinger, Andrew V Biankin, Grainne M O’Kane, Vasilis Ntranos, David K Chang, David W Dawson, Grace E Kim, Valerie M Weaver, Robert L Raffai, Matthias Hebrok. nSMase2-mediated exosome secretion shapes the tumor microenvironment to immunologically support 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 A066.