bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A106: Single cell RNA sequencing of EPCAM+ cells reveals unique malignant biology
Authors: Arbe-Barnes Edward H. , Jainarayanan Ashwin , Abu-Shah Enas , Bashford-Rogers Rachael J.M. , Sivakumar Shivan 
Published: January 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is notable due to its complex and dense stroma which comprises a high proportion of non-malignant cells. Studying PDAC epithelial cells at the single cell level may yield insights which have not been appreciated through bulk tissue analysis. We analysed a novel single cell RNA sequencing (scRNA seq) dataset of 11000 epithelial (EPCAM+) cells from 7 resected PDAC samples and used a validation cohort of 43 samples from two published scRNA seq datasets. Malignant epithelial cells were identified by: gene expression, changes in copy number, and by the presence of known PDAC single nucleotide variants. This confirmed that sorting for EPCAM+ cells prior to scRNA seq resulted in an enriched proportion of malignant vs non-malignant tumor epithelial cells. This dataset of enriched single cell dataset was therefore useful for studying the influence of intrinsic malignant cell factors on PDAC biology. We observed that malignant cells do not segregate into classical or basal-like signatures, despite these being clinically validated bulk transcriptomic tumor subtypes. Indeed, classical and basal-like signatures module scores in PDAC in individual malignant cells were positively correlated, suggesting they are not divergent programs in malignant cells. Bulk transcriptomic signature subtypes are therefore most likely to reflect differences in PDAC tissue stroma, rather than in intrinsic malignant cell factors. Moreover, we sort to investigate intra- and inter- sample heterogeneity to understand the intrinsic malignant cell factors which may influence the biology of PDAC. We analysed single cell velocity to understand the dynamics of malignant cell states. This showed heterogeneity in expression of known pan-cancer malignant cell meta-programs which identified a population of cells with high expression of cell cycle genes, suggesting greater proliferation. We then explored expression of immune modulating genes to determine how malignant cells influence the immunosuppressive microenvironment. For example, we identified heterogeneity in HLA class 1 and antigen presentation gene expression which may be a mechanism of immune suppression in PDAC. Together these data demonstrate how studying scRNA seq of EPCAM+ cells reveals intrinsic malignant cell factors which cannot be appreciated through bulk RNA seq.
Citation Format: Edward H. Arbe-Barnes, Ashwin Jainarayanan, Enas Abu-Shah, Rachael J.M. Bashford-Rogers, Shivan Sivakumar. Single cell RNA sequencing of EPCAM+ cells reveals unique malignant biology [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 A106.
Abstract B006: Exosomal protein Eps8 as a new biomarker for pancreatic cancer
Authors: Hayashi Kazunao , Tsuchiya Atsunori , Terai Shuji 
Published: January 2024

Abstract
Exosomes are extracellular vesicles containing nucleic acids, proteins, and lipids of approximately 100 nm, which are released from cancer cells to create a microenvironment favorable for their survival. Epidermal growth factor receptor pathway substrate 8 (Eps8), an exosomal protein, is reportedly associated with metastasis. We investigated the relationship between Eps8 in the serum exosomes of patients with pancreatic cancer and clinicopathological factors and examined the usefulness of exosomal Eps8 as a biomarker for pancreatic cancer. Methods: Serum exosomes of 93 patients with pancreatic disease (64 cases of pancreatic cancer, 12 cases of chronic pancreatitis, and 17 cases of IPMN) were extracted via ultracentrifugation, and Eps8 in exosomes were evaluated by western blotting. We analyzed 1) the clinicopathological factors of patients with pancreatic cancer, 2) the Eps8 positive rate in each disease, 3) the sensitivity, specificity, and positive predictive value of Eps8 for the diagnosis of pancreatic cancer, 4) the relationship between Eps8 and clinicopathological factors, and 5) compared and discussed between exosomal Eps8 and serum CA19-9. Results: The median patient age was 72 years (47–85), with 35 male and 29 female patients included in the study. The median body mass index was 20.8 kg/m2 (12–26.7 kg/m2). 1) Site Ph33/Pbt31, cStageIV/III/II/I: 28/11/14/11; 2) pancreatic cancer 59.4%, chronic pancreatitis 33%, IPMN 12%; 3) sensitivity 59.4. 4) In patients with pancreatic cancer, Eps8-positive patients had significantly higher ALT (p = 0.03), significantly less cancer (p = 0.04), lower IPMN complication rates, and more chronic pancreatitis and autoimmune diseases than the exosomal Eps8-negative patients. Stage I 64% (7/11), Stage II 36% (5/14), Stage III 64% (7/11) Stage IV 68% (19/28) 5) Exosomal Eps8 positivity (64%) was higher than serum CA19-9 positivity (45%) in Stage I. We also found some patients were negative for serum CA19-9 but positive for exosomal Eps8. Conclusion: Exosomal Eps8 has a higher positive rate in Stage I than serum CA19-9. Diagnosis with exosomal Eps8 may improve diagnostic performance for pancreatic cancer.
Citation Format: Kazunao Hayashi, Atsunori Tsuchiya, Shuji Terai. Exosomal protein Eps8 as a new biomarker for 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 B006.
Abstract B016: Eosinophils alter metastatic spread in pancreatic cancer
Authors: Hoffman Megan T. , Lenehan Patrick J. , Wang Jen , Ali Lestat , Uchida Amiko , Vayrynen Sara , Costa Andressa Dias , Dougan Michael , Heckler Max , Nowak Jonathan , Wolpin Brian W. , Dougan Stephanie K. 
Published: January 2024

Abstract
Pancreatic ductal adenocarcinoma (PDA) is the third most common cause of cancer death in the US with a 11% 5-year survival rate. A key contributor of this dismal prognosis is early and frequent metastatic spread with limited treatment options for patients. Metastasis in PDA is facilitated by a robust fibroinflammatory response in the primary tumor site, a large portion of which is composed of infiltrating immune cells, and survival during transit to establish in the secondary site. In the primary tumor reactive stroma, we found increased eosinophils in both human and mouse PDA compared to the normal pancreas. Eosinophils are an innate immune cell best known for their ability to control parasite responses and have been implicated in either pro- or anti-cancer roles in various solid tumors. We used the ΔdblGata mice, which lack eosinophils, to study the role of eosinophils during metastatic spread using a resectable model of PDA metastasis. This model of metastasis was developed to facilitate consistent seeding of lung metastasis in approximately 50 percent of mice from a transient subcutaneous tumor which undergoes subsequent surgical removal and harvest to evaluate metastasis at 4 weeks. We found that mice lacking eosinophils have increased metastasis to the lung in our resectable model of PDA metastasis but no difference in establishment of IV injected PDA tumor cells, suggesting eosinophil control at the primary tumor site. Single cell sequencing of the subcutaneous tumors finds differences in the angiogenic subtypes, tip and stalk cells, in mice lacking eosinophils. Sequencing of eosinophil populations in humans and mice find an increase in angiogenic signaling suggesting a regulatory role in tumor cell access to the circulation. We conclude that eosinophils in PDA inhibit the metastatic process through control of angiogenic signaling.
Citation Format: Megan T. Hoffman, Patrick J. Lenehan, Jen Wang, Lestat Ali, Amiko Uchida, Sara Vayrynen, Andressa Dias Costa, Michael Dougan, Max Heckler, Jonathan Nowak, Brian W. Wolpin, Stephanie K. Dougan. Eosinophils alter metastatic spread 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 B016.
Abstract B020: Charting the cellular heterogeneity of primary and metastatic PDAC microenvironment
Authors: Blanco-Gomez Adrian , Felton Catherine , Banyard Antonia , Jorgensen Claus 
Published: January 2024

Abstract
Cancer-associated fibroblasts (CAFs) are important regulators of tumor progression and therapeutic response in PDAC, with several functionally diverse populations now identified. However, while CAF populations with similar transcriptional characteristics have been identified across different tissues, emerging data suggests that these populations may diverge functionally. For example, whereas antigen presenting CAFs (apCAFs) have been suggested to promote immune evasion in PDAC, apCAFs have been associated with anti-tumor immunity in lung cancer. Thus, high resolution mapping of the microenvironment in both primary and metastatic tumors is required to define tissue specific and conserved subsets for functional interrogation. We deployed cytometry by time of flight (CyTOF) to annotate stromal and immune subsets in healthy and tumor bearing murine pancreas, liver and lung. Spatial proximity of tumor and host cells was further annotated using sLP-mCherry, a secreted lipo-permeable form of mCherry. In total, we annotated 50.3 million cells across normal and tumor bearing tissues. Stromal fibroblast populations were highly divergent across both healthy and tumor bearing tissues. Commonly used markers were expressed in a manner dominated by tissue of origin, with less than 10% of fibroblasts and CAFs displaying common phenotypes across tissues. For example, aSMApos/PDGFRalow myCAFs were abundant in lung and liver, Ly6cpos/PDGFRapos/aSMAlow iCAFs were more abundant in the pancreas and MHCIIpos/CD74pos apCAFs were more dominant in lung. In contrast, most immune subsets, with exception of alveolar macrophages and Kupfer cells, were consistently observed across all tissues analysed albeit at different abundances. Tumors arising from epithelial and mesenchymal PDAC cells induce unique changes in CAF subset abundances where epithelial tumors are enriched for myCAFs and mesenchymal tumors induce more apCAFs. These observations were consistent across tumor bearing liver and lung. MyCAFs and PD-L1 or PDL-2 expressing macrophages were generally more proximal to epithelial tumor cells, whereas tumors originating from mesenchymal PDAC cells were enriched for antigen-experienced T cells. Taken together these analyses reveal tissue specific effects on the emerging microenvironment, with shared properties emerging from immune and mesenchymal niche composition.
Citation Format: Adrian Blanco-Gomez, Catherine Felton, Antonia Banyard, Claus Jorgensen. Charting the cellular heterogeneity of primary and metastatic PDAC 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 B020.
Abstract B031: Targeting epigenetic machinery to revoke stromal pro-tumorigenicity and enhance efficacy in pancreatic cancer therapy
Authors: Liang Gaoyang , Johnson Jeremiah A. , Evans Ronald M. 
Published: January 2024

Abstract
Oncogenic lesions in pancreatic ductal adenocarcinoma (PDAC) induce prominent desmoplasia in part by activating fibroblasts or their progenitors in the stroma. The resultant cancer-associated fibroblasts (CAFs) often switch on the pro-desmoplastic, pro-inflammatory and/or pro-tumorigenic transcriptional programs, contributing to tumor progression and therapeutic resistance. Identifying and targeting epigenetic machinery essential for stromal fibroblast activation provides potential strategies to revoke stromal pro-tumorigenicity and overcome therapeutic resistance in PDAC. Here we identify Class I histone deacetylases (HDACs) as key epigenetic regulators facilitating the induction of pro-desmoplastic and pro-tumorigenic transcriptional programs in stromal fibroblasts. Mechanistically, HDACs coordinate the establishment of chromatin architecture that enables the activation of pro-desmoplastic programs directed by the transcriptional factor axis of serum response factor (SRF) and forkhead box M1 (FOXM1). HDACs also facilitate the induction of pro-inflammatory program in stromal fibroblasts, supporting leukemia inhibitory factor (LIF)-mediated pro-tumorigenic crosstalk. Both HDAC depletion in CAFs and treatment of the HDAC inhibitor entinostat (Ent) in PDAC mouse models reduce stromal activation and curb tumor progression. Notably, HDAC inhibition (HDACi) enriches a novel lipogenic fibroblast subpopulation in CAFs, a potential precursor population for activated myofibroblasts in vivo. Our work pinpoints a critical role of HDACs in driving stromal pro-tumorigenicity and highlights the stromal targeting capacity of HDACi therapy. Furthermore, the clinical utility of HDACi therapy is often hindered by limited potency and nonnegligible systemic toxicity of the HDAC inhibitors. To facilitate the translation of HDACi-based therapy, we develop a polymer-based bottlebrush pro-drug (BPD) nanoparticle incorporating Ent. The Ent-BPD nanoparticle overcomes the limitations of conventional HDACi therapy by sustaining long-lasting release of HDACi activity specifically at the tumor sites. Administration of Ent-BPD in PDAC mouse models achieves superior intratumoral HDACi potency and enhanced therapeutic efficacy compared to the free drug Ent treatment; meanwhile, it avoids the systemic toxicity associated with the free drug treatment. Our work further demonstrates a promising strategy for the clinical adaptation of HDACi-based therapy.
Citation Format: Gaoyang Liang, Jeremiah A. Johnson, Ronald M. Evans. Targeting epigenetic machinery to revoke stromal pro-tumorigenicity and enhance efficacy in pancreatic cancer therapy [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 B031.
Abstract B034: Antigen-presenting cancer-associated fibroblasts are found in immunotherapy-sensitive murine models of pancreatic ductal adenocarcinoma
Authors: Maru Saumya , Howe Kathryn , Andaloori Lalitya , Leatherman James , Tandurella Joseph , Pearce Edward J. , Jaffee Elizabeth M. 
Published: January 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer-related deaths. Despite the advent of immune checkpoint inhibition (ICI) that has markedly changed the treatment landscape for select tumors with respect to both outcomes and tolerability, PDAC remains unresponsive to such an approach. One feature of the PDAC tumor microenvironment (TME) that remains poorly understood is the interaction between cancer-associated fibroblasts (CAFs) and immune and tumor cells. Unique subsets of CAFs have been identified, including antigen-presenting CAFs (apCAFs) which are defined by expression of MHC-II and can activate CD4 T cells in genetically engineered mouse models of PDAC. apCAFs are rarely found in human PDAC; in a human PDAC atlas consisting of six published human single cell RNA-sequencing (scRNA-seq) datasets, we identified 370 apCAFs out of 8736 total CAFs, the majority of which were found in one dataset. Here, we have orthotopically implanted cell lines derived from the autochthonous KPC murine model of PDAC which mimics the stromal components of human disease to further study the influence of apCAFs on the anti-tumor response. We have found that although the overall CAF population is equivalent between tumors, apCAFs are present primarily in tumors derived from KPC cell lines that display ICI sensitivity. apCAFs sorted from these tumors and pulsed with OVA peptides upregulated CD25 and CD69 expression on naïve OT-II CD4 T cells, confirming that apCAFs in our system can present via MHC-II. Furthermore, these apCAFs increased CD4 activation markers upon ex-vivo coculture with dissociated KPC tumors. We therefore hypothesize that apCAFs are required for the ICI-mediated anti-tumor effect and do so via modulation of CD4 T cell responses. Although a small proportion of the total compartment, the apCAF subset may be enhanced in number and function by CAF-targeted modulators to synergize with ICI to affect the antitumor response, which could provide a solution to the currently unmet need for new and more effective treatments for PDAC patients.
Citation Format: Saumya Maru, Kathryn Howe, Lalitya Andaloori, James Leatherman, Joseph Tandurella, Edward J. Pearce, Elizabeth M. Jaffee. Antigen-presenting cancer-associated fibroblasts are found in immunotherapy-sensitive murine models of pancreatic ductal adenocarcinoma [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 B034.
Abstract B039: Hypoxia promotes an inflammatory phenotype of fibroblasts in pancreatic cancer
Authors: Ngodup Tenzin , Mello Ashley 
Published: January 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 B040: Neural control of cancer-associated fibroblasts in PDAC
Authors: Nigri Jeremy , Lan Wenjun , Chavan Sangeeta S , Park Youngkyu , Borniger Jeremy , Tracey Kevin J , Tuveson David A 
Published: January 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) poses a formidable challenge to public health, with a dismal 5-year survival rate and a projected rise as the second leading cause of cancer-related deaths by 2030. The pathogenesis of PDAC involves a robust desmoplastic reaction and a complex tumor microenvironment (TME), constituting up to 80% of the tumor volume. The TME is a heterogeneous mixture of cells, including cancer-associated fibroblasts (CAFs), immune cells, endothelial cells, and neurons, which all interact and contribute to disease progression. However, the precise interplay between the tumor-associated nerves and PDAC development remains unclear. It is known that neural remodeling within the tumor microenvironment are closely associated with intense neuropathic pain, metastasis, and shortened patient survival. The prevalence of nerve fibers present in the dense desmoplastic stroma of PDAC tumors suggest a potential interaction between neurons and stromal cells, particularly CAFs, through various paracrine signaling mechanisms, influencing CAF behavior and facilitating neural remodeling, ultimately driving PDAC progression. Our investigation revealed that the neurotransmitter noradrenaline, induces calcium signaling and prompt contraction in pancreatic stellate cells (PSCs). Preliminary in vitro findings indicate that this calcium signaling is mediated by alpha 1 adrenergic receptors. Whole-mount 3D imaging mouse PDAC tissues, indicates a spatial organization of adrenergic neurons in immediate proximity to neoplastic cells and cancer-associated fibroblasts. Moreover, our study demonstrated that noradrenaline and alpha 1 agonists modulate extracellular matrix (ECM) production and cytokine secretion in PSCs and CAFs. Finally, we discovered that chemical ablation of the sympathetic nervous system significantly suppresses tumor growth while promoting metastasis, underscoring the critical role of the noradrenergic system in tumor development. Collectively, our findings propose that noradrenergic neurons possess the capacity to influence CAF behavior, opening new avenues of investigation to unravel the intricate crosstalk between neural regulation and tumor progression in PDAC.
Citation Format: Jeremy Nigri, Wenjun Lan, Sangeeta S Chavan, Youngkyu Park, Jeremy Borniger, Kevin J Tracey, David A Tuveson. Neural control of cancer-associated fibroblasts in PDAC [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 B040.