bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract C045: Targeting metabolic heterogeneity in pancreatic ductal adenocarcinoma
Authors: Morningstar Taryn , Anaraki Cecily , Scipioni Lorenzo , Tedeschi Giulia , Digman Michelle , Edinger Aimee , Jorgensen Claus , Fishel Melissa , Halbrook Christopher J
Published: September 2024

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 C047: Autophagy-mediated proline-supply is important for cell survival in pancreatic cancers
Authors: Kim Ji hyeon , Cheong Heesun
Published: September 2024

Oncogenic KRAS mutations present in 90–95% of pancreatic cancer patients. KRAS mutation in pancreatic cancer increased the dependency on glutamine and consumption of proline. Proline is a non-essential amino acid but it is important for the synthesis of proteins such as collagen, and also for precursors of antioxidant molecules. Several enzymes such as P5CS(ALDH18A1),PYCR1 and PYCR2 are involving proline synthesis. The effects of proline synthesis enzymes on pancreatic cancer cells are relatively less studied than that of enzymes catalyzing proline. Here, we examined the impact of proline synthesis enzymes on pancreatic cancer cell survival and proliferation. We first examined that exogenous proline promotes cell survival under low glutamine conditions in various pancreatic cancer cells. Exogenous proline supplementation increased some pancreatic cell survival even when glutamine was not sufficiently available, whereas proline supplement is dispensible for certain cell types of pancreatic cancer. Next, to investigate the importance of proline synthesis enzymes in cell survival, we measured the cell proliferation of pancreatic cancer with knock-down the proline synthesis enzymes. The knockdown of ALDH18A1 and PYCR1,2, which are proline biosynthesis enzyme genes, reduced cell survival in pancreatic cancer cells, suggesting that in PDAC cells, the enzymes that synthesize proline from glutamine are crucial for cancer cell survival and growth. To test the effect of proline-sysnthesis enzymes on autophagy, we measured autophagy flux in the cell harboring GFP-RFP-LC3 or GFP-LC3 as a reporter. Knockdown of proline synthesis enzymes, particularly ALDH18A1 or PYCR1 led to an increase in autophagy levels, indicating that proline-independent cells can bypass proline synthesis by autophagy induction in the absence of proline synthesis genes. Furthermore gemcitabine-resistant cells showed reduced levels of proline synthesis enzymes. In pancreatic cancer cell lines, proline promotes cancer cell survival, generated by both biosynthesis from glutamine and starvation-induced autophagy, which also critically important for supporting cellular drug resistance. Taken together, these results indicate that proline synthesis is mechanistically associated with autophagy induced by glutamine-starvation, which is pivotal for supplying proline in pancreatic cancer cells.

Citation Format: Ji hyeon Kim, Heesun Cheong. Autophagy-mediated proline-supply is important for cell survival in pancreatic cancers [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 C047.
Abstract C049: Computational Methods for Central and Lipid Metabolism Networks Analysis to Reveals Flux Change in PDAC
Authors: Cao Sha , Zhu Haiqi , Wang Yijie , Fishel Melissa , Zhang Chi
Published: September 2024

Pancreatic ductal adenocarcinoma (PDAC) is among the most challenging cancers to treat due to its aggressive nature and the difficulties in early detection. The disease progresses rapidly from stage T1 to T4, leaving a narrow window for effective intervention. This swift progression is closely tied to significant metabolic alterations, and current studies have highlighted specific metabolic changes. This includes elevated glutamine metabolism and altered aspartate and alpha-ketoglutarate production to support uncontrolled tumor growth; and elevated lysophosphatidylcholines secretion by cancer-associated fibroblasts to support tumor progression. These insights underscore the need for a holistic understanding of PDAC metabolism. Hence, there is an urgent need for a comprehensive and high-resolution analysis of PDAC's metabolic landscape remains unexplored. To computationally characterize the PDAC metabolism and fully leverage the large-scale transcriptomics with matched or unmatched metabolomics data, we developed an algorithm based on the Michaelis-Menten equation to estimate distribution-wise variations in mass-carrying metabolic networks using gene expression and metabolomics data. We start by manually curating a PDAC-specific metabolic network that focuses on central metabolism, glutamine-glutamate metabolism, and lipid metabolism. We then gathered comprehensive kinetic parameters, predicted enzyme activity from transcriptomics data, and conducted metabolomic profiling to determine metabolic compound concentrations. By applying Monte Carlo sampling methods, we achieved an overall balance of metabolic flux, enabling us to model reaction rates accurately and predict metabolic shifts. This approach holds potential to provide a comprehensive perspective on the rewired metabolism in PDAC, inspiring the development of metabolic targets or diet interventions for therapeutic treatment.

Citation Format: Sha Cao, Haiqi Zhu, Yijie Wang, Melissa Fishel, Chi Zhang. Computational Methods for Central and Lipid Metabolism Networks Analysis to Reveals Flux Change in PDAC [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 C049.
Abstract C050: Vitamin B6 restriction impairs pancreatic cancer progression
Authors: He Chunbo , Mehla Kamiya
Published: September 2024

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 C052: Repurposing Statins to Target Gemcitabine Resistance in Pancreatic Cancer
Authors: Calderon Sabrina , Beutel Alica K. , Nghiem Ethan , Singh Rima , Yousefian Natalie , Anaraki Cecily , Gulay Kevin , Juarez Dennis , Kleger Alexander , Seufferlein Thomas , Muir Alexander , Jang Cholsoon , Tiriac Herve , Fruman David , Halbrook Christopher
Published: September 2024

Pancreatic ductal adenocarcinoma (PDA) is a lethal malignancy with a devastating prognosis. Gemcitabine, a pyrimidine anti-metabolite, is a cornerstone in PDA therapy, but resistance remains a major hurdle in clinical care. Metabolic reprogramming is an important driver of chemoresistance. Accordingly, targeting these altered metabolic pathways can improve response to treatment. To investigate metabolic vulnerabilities, we generated models of acquired PDA gemcitabine resistance. Screening common metabolic inhibitors we observed that gemcitabine-resistant cells were exquisitely susceptible to statins, inhibitors of the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase. This is due to a downregulation of the mevalonate biosynthesis pathway in gemcitabine-resistant cells. Importantly, the statin sensitivity correlates with the extent of the gemcitabine resistance, suggesting this metabolic vulnerability is gradually gained during acquisition of resistance. Rescue experiments showed that statins induce apoptosis by reduced protein geranylation of small GTPases. Finally, we find that pitavastatin inhibits growth of gemcitabine resistant tumors in immune competent models. Collectively, these data suggest that targeting the HMG-CoA reductase is a metabolic vulnerability that is gained in PDA cells upon the acquisition of gemcitabine resistance. The treatment combination of gemcitabine and pitavastatin, two widely used compounds in patients, has potential to translate into an immediate clinical benefit and improve survival in this deadly disease.

Citation Format: Sabrina Calderon, Alica K. Beutel, Ethan Nghiem, Rima Singh, Natalie Yousefian, Cecily Anaraki, Kevin Gulay, Dennis Juarez, Alexander Kleger, Thomas Seufferlein, Alexander Muir, Cholsoon Jang, Herve Tiriac, David Fruman, Christopher Halbrook. Repurposing Statins to Target Gemcitabine Resistance 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 C052.
Abstract C058: A novel approach to understanding pancreas cancer risk through enhancer- promoter interactions
Authors: Wang Li , Baek Songjoon , Prasad Gauri , Truongvo Thucnhi , Hoskins Jason , Amundadottir Laufey , Arda Efsun
Published: September 2024

Genetic or epigenetic variations in regulatory enhancer elements increase susceptibility to a range of pathologies, including pancreas cancer. Pinpointing genes affecting pancreas cancer risk holds promise for early detection, prevention, and effective therapies. Despite recent advances, linking enhancer elements to target genes and predicting the transcriptional outcome of enhancer dysfunction remain significant challenges. Using 3D chromatin assays, we generated an extensive enhancer interaction dataset for the human pancreas, spanning more than 20 donors and five major cell types, including both the exocrine and endocrine compartments. We employed a network approach to parse chromatin interactions into enhancer-promoter tree models, facilitating quantitative, genome-wide analysis of enhancer connectivity. Using the tree models, we developed a machine learning algorithm capable of estimating the impact of enhancer perturbations on cell-type specific gene expression in the human pancreas. Complementing this computational approach, we streamlined an experimental platform using CRISPR-interference and RNA-FISH coupled with high-throughput imaging to quantitatively measure the effect size of enhancer perturbations in primary human pancreas cells. Our enhancer tree models enabled functional annotation of genetic variants associated with pancreas diseases, revealing novel target genes in specific cell types. For pancreas cancer (PDAC), our data suggests a stronger association of disease susceptibility variants with acinar cells, even though ductal cells historically have been the focus of PDAC. This discovery linked three potentially functional variants associated with PDAC risk to acinar cell enhancers, revealing novel target genes to further investigation. By integrating genomics with mechanistic findings into enhancer function, our work offers a framework for understanding genetic basis of pancreas cancer disease risk.

Citation Format: Li Wang, Songjoon Baek, Gauri Prasad, Thucnhi Truongvo, Jason Hoskins, Laufey Amundadottir, Efsun Arda. A novel approach to understanding pancreas cancer risk through enhancer- promoter interactions [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 C058.
Abstract C061: Loss of CaMK2B accelerates tumor formation and enhances metastatic competency in genetically engineered mouse models of PDAC
Authors: Peura Jessica , Bhalerao Nikita , Johnson Calvin , Ogoti Yamini , Keller Faith , Watson Emma , Zhao Zhen , Pitarresi Jason
Published: September 2024

Background Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer- related deaths in the United States and is often not diagnosed until it has already metastasized. Our prior work established that calcium signaling pathways facilitate a pro-metastatic phenotype through the induction of an epithelial-to-mesenchymal transition (EMT) program in PDAC tumor cells, but the downstream signaling molecules mediating this phenotype have remained elusive. MethodsUsing a novel genetically engineered model of pancreatic cancer, we demonstrate that loss of Calcium/calmodulin-dependent kinase-II B (CaMK2B), a downstream effector kinase activated by calcium, enhances cellular plasticity, and increases metastasis. To this end, we generated a genetically engineered mouse model where Camk2b was knocked out in tumor cells in a lineage-labeled Kras- and p53-driven PDAC mouse model (herein KPCY-Camk2bcKO). Results Genetic deletion of Camk2b in the KPCY genetically engineered model accelerated tumor formation and dramatically reduced the overall median survival of KPCY- Camk2b cKO mice (78 days) relative to KPCY controls (136 days). Pathological and immunofluorescence analysis of KPCY-Camk2b cKO animals showed an increased number of poorly differentiated tumor regions and a higher metastatic burden, with >85% of KPCY- Camk2b cKO animals presenting with multi-focal metastases. Further analysis of tumor cells in KPCY-Camk2b cKO mice showed enhanced expression of markers of the highly aggressive squamous PDAC subtypes. Strikingly, Camk2b deletion combined with oncogenic Kras G12D (in the absence of p53 alterations), was sufficient to form lethal metastatic PDAC tumors, while age-matched control Kras G12D tumors with intact Camk2b only progressed to the acinar-to-ductal metaplasia (ADM) or Pancreatic Intraepithelial Neoplasia (PanIN) stage. Collectively, these results establish Camk2b loss as a new oncogenic and pro-metastatic mechanism in PDAC Conclusion This work demonstrates that Camk2b loss enhances tumor cell evolution and plasticity within PDAC to promote metastasis. In this context, we speculate that loss of Camk2b rewires calcium signaling to drive an aggressive subtype of PDAC with increased metastasis.

Citation Format: Jessica Peura, Nikita Bhalerao, Calvin Johnson, Yamini Ogoti, Faith Keller, Emma Watson, Zhen Zhao, Jason Pitarresi. Loss of CaMK2B accelerates tumor formation and enhances metastatic competency in genetically engineered mouse models of PDAC [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 C061.
Abstract C063: Inhibition of PRMT5 reduces aggressiveness in basal-like pancreatic ductal adenocarcinoma
Authors: Wang Christina , Soares Zamira Guerra , Esgdaille Dakarai , Mello Stephano Spano
Published: September 2024

The basal-like pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive type of mesenchymal PDAC that resists treatment and has a poor prognosis. Understanding the mechanisms driving basal-like PDAC biology is crucial for unraveling the intricacies of PDAC plasticity and developing effective treatment strategies for this aggressive tumor. Recent studies from our laboratory have shown that protein arginine methyl transferase 5 (PRMT5) significantly contributes to PDAC plasticity and progression towards the basal-like subtype. Specifically, our data show that patients with high levels of PRMT5 expression have a worse outcome, thus arguing that PRMT5 plays a role in PDAC aggressiveness and outcome. Moreover, our experiments indicate that inhibiting PRMT5, either genetically or chemically, in basal-like PDAC cells induces the expression of epithelial markers like GATA6 and E-CADHERIN, suggesting that PRMT5 promotes mesenchymal features in PDAC. Using wound healing and transwell assays, we have demonstrated that pharmacological inhibition of PRMT5 significantly suppresses cell migration and invasion. Additionally, colony formation and cell proliferation are markedly reduced upon PRMT5 inhibition in basal-like PDAC. Collectively, these findings suggest that inhibiting PRMT5 can effectively constrain the aggressive cellular features characteristic of basal-like PDAC, such as cell proliferation, clonogenicity, and migration. Recent research indicates that PRMT5 preferentially methylates splicing factors in various cell types, implying that RNA splicing regulation is crucial to PRMT5’s role in enhancing tumor plasticity and aggressiveness. We are currently investigating whether PRMT5-mediated RNA splicing alterations contribute to the maintenance of the basal-like PDAC phenotype. These studies provide key evidence that PRMT5 is essential for maintaining the aggressive characteristics of basal-like PDAC, highlighting its potential as a therapeutic target for this challenging cancer subtype.

Citation Format: Christina Wang, Zamira Guerra Soares, Dakarai Esgdaille, Stephano Spano Mello. Inhibition of PRMT5 reduces aggressiveness in basal-like 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 C063.
Abstract C067: Tuft cells transdifferentiate to neural-like progenitor cells in the progression of pancreatic cancer
Authors: Salas-Escabillas Daniel J. , Hoffman Megan T. , Brender Sydney M. , Moore Jacee S. , Wen Hui-Ju , Benitz Simone , Davis Erick T. , Long Daniel , Wombwell Allison , Steele Nina G. , Allen-Petersen Brittany , Sears Rosalie C. , Matsumoto Ichiro , DelGiorno Kathleen E. , Crawford Howard C.
Published: September 2024

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 C069: A conserved reepithelialization program driven by FOSL1 underlies malignancy in pancreatic ductal adenocarcinoma
Authors: David Charles , Zhuo Melian , Li Yong , Zhang Yifeng , Yang Chenlu , Deng Ziqing , Zhao Yupei , Wu Wennming , Peng Junya , Chen Mo
Published: September 2024

Benign lesions named pancreatic intraepithelial neoplasia (PanIN) are frequent in the healthy population but are precursors to deadly pancreatic ductal adenocarcinoma (PDAC). Conversion of PanINs to PDAC is poorly understood. Here we harness high resolution spatial transcriptomics to identify a core transcriptional program associated with invasive growth across human PDAC and required for PanIN-to-PDAC progression in mice. The malignancy program is lineage restricted, and predominantly comprised of transcripts activated to drive reepithelialization during skin wound healing. This wound-like program appears in rare PanIN cells that also activate tumor suppressor genes (TSGs), which keep the incipient malignant cells in check. TSG KO in PanINs leads to rapid outgrowth of the wound-like population, unleashing invasive growth, driven by the wound-induced TF FOSL1. Bidirectional interactions between malignant epithelial cells and wound-like CTHRC1-expressing CAFs enforce the malignant state. Our results suggest that wound recapitulation drives the highly invasive properties of PDAC.

Citation Format: Charles David, Melian Zhuo, Yong Li, Yifeng Zhang, Chenlu Yang, Ziqing Deng, Yupei Zhao, Wennming Wu, Junya Peng, Mo Chen. A conserved reepithelialization program driven by FOSL1 underlies malignancy 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 C069.
Abstract C072: Bmi1 expression is upregulated in response to injury/stress in the pancreas
Authors: Renollet Nur Muhammad , Thompson Joyce K , Wu Emily , Alkhalili Osama , Steele Nina , Bednar Filip
Published: September 2024

Pancreatic homeostasis is regulated in part through epigenetic mechanisms that restrict or enable access of pancreatic lineage transcription factors to their target genes. These epigenetic protein cascades are also required for regeneration of the pancreas after injury. B-cell Moloney murine leukemia virus integration site 1 (Bmi1), a central protein in the Polycomb repressor complex 1 (PRC1), has been shown to be required for the regeneration of the pancreas after injury and its absence prevents pancreatic neoplasia in mice. Previous work also suggests that Bmi1 marks a subset of acinar cells contributing to pancreatic renewal and tissue maintenance. It remains unclear how Bmi1 expression levels are regulated in response to pancreatic stress and injury. Here we assess the baseline expression of Bmi1 in pancreatic tissue with a genetic reporter mouse model as well as changes in Bmi1 mRNA levels at different time points after the induction of pancreatitis in wild-type mice via RNA in situ hybridization (RNAscope). We also compare the ability of the murine pancreas to regenerate after acute pancreatitis in the presence and absence of Bmi1. Our data indicates that rather than a specific subpopulation, most, if not all, acinar cells in the pancreas express Bmi1 during their life and specific loss of Bmi1 in the pancreas impairs regeneration after acute pancreatitis. We also show an increase in Bmi1 mRNA levels within the pancreas shortly after the induction of acute pancreatitis which reduces as the pancreas resumes its normal histology. Altogether, our data indicate that Bmi1 expression is dynamic, responsive to injury and necessary for pancreatic homeostasis and regeneration.

Citation Format: Nur Muhammad Renollet, Joyce K Thompson, Emily Wu, Osama Alkhalili, Nina Steele, Filip Bednar. Bmi1 expression is upregulated in response to injury/stress in the pancreas [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 C072.
Abstract C076: Transcriptomic analyses of normal human pancreatic acinar cells reveal the presence of cancer subtypes that correlate with acinar ductal metaplasia
Authors: Perkins Corey M , Jiang Jinmai , Greenberg Zachary , Talha Siddique Md Abu , Williams Linda C , Brant Jason O , Shirlekar Kalyanne , Han Bo , Ali Jamel , Fredenburg Kristianna M , Graim Kiley , Wilkie Diana J , He Mei , Schmittgen Thomas D
Published: September 2024

Gene expression subtypes exist in pancreatic ductal adenocarcinoma (PDAC), however comparable subtypes are not known to exist in normal human pancreas. Our laboratory has collected a large (N=55) and racially diverse (14 Black, 27 White and 14 Hispanic) cohort of normal human pancreatic acinar cell specimens that were processed at islet transplantation centers. Deceased organ donors were maintained on life support until the time the pancreas was surgically removed. Samples of primary, uncultured (Day 0) or ADM transdifferentiated (Day 6) normal pancreatic acinar cells were subjected to bulk transcriptomic sequencing. UMAP analysis of the transcriptomic data from the Day 0 samples revealed the presence of two distinguishable clusters of data that we arbitrarily refer to as Group 1 (n = 31) and Group 2 (n = 24). Heatmaps of the expression of 57 genes belonging to the exocrine-like, classical and basal subtypes produced a clear separation of the data. Since the exocrine-like genes increased in Group 1 and the basal and classical genes increased in Group 2, we refer to Group 1 as the exocrine-like subtype and Group 2 as the basal/classical subtype. The basal/classical subtype samples showed greater morphological and molecular acinar ductal metaplasia compared to those in the exocrine-like subtype. When stratified by demographics and subtype, volcano plots revealed a striking trend with Blacks, women, obese and younger individuals having significantly fewer differentially expressed genes (basal/classical vs exocrine-like) compared to Hispanics, men, nonobese and older individuals. Our data demonstrate that, similar to PDAC, normal pancreatic acinar cells are distinguishable by gene subtypes. Moreover, the gene expression ratio of these subtypes varies dramatically by donor demographics.

Citation Format: Corey M Perkins, Jinmai Jiang, Zachary Greenberg, Md Abu Talha Siddique, Linda C Williams, Jason O Brant, Kalyanne Shirlekar, Bo Han, Jamel Ali, Kristianna M Fredenburg, Kiley Graim, Diana J Wilkie, Mei He, Thomas D Schmittgen. Transcriptomic analyses of normal human pancreatic acinar cells reveal the presence of cancer subtypes that correlate with acinar ductal metaplasia [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 C076.
Abstract C077: Functional Dissection of the Highly Plastic Basal Cell State in Pancreatic Cancer
Authors: Singhal Anupriya , Styers Hannah C. , Rub Jonathan , Li Zhuxuan , Tarcan Zeynep , Hallin Jill , Basturk Olca , Yaeger Rona , Christensen James G. , Betel Doron , Yan Yan , de Stanchina Elisa , Tammela Tuomas
Published: September 2024

Pancreatic ductal adenocarcinoma (PDAC) is a treatment-refractory malignancy with a dismal prognosis. Targeting cancer cell plasticity—the capacity to adapt to cell-extrinsic pressure via non-genetic mechanisms—is a promising therapeutic strategy, yet cell states within PDAC harboring high plasticity remain poorly understood. Using genetically engineered mouse models driven by oncogenic KrasG12D and loss of p53 (“KPC” model), we profiled primary PDAC tumors using single-cell RNA sequencing and single cell ATAC sequencing. We identified a cancer cell differentiation state that co-expresses both epithelial and mesenchymal programs and has a distinct epigenetic landscape with accessible chromatin across gene sets that mark cancer cell states with divergent phenotypes, suggesting that this cell state is primed for cell state switching. Notably, this high-plasticity cell state (HPCS) signature aligns with a "basal" signature in human PDAC, which associates with poor prognosis and chemoresistance. To functionally interrogate the HPCS in PDAC progression, we developed a novel lineage-tracing and ablation system. Lineage-tracing experiments revealed that the HPCS has a robust capacity for differentiation into epithelial and mesenchymal states, indicating that the HPCS is functionally plastic and acts as a source of fixed malignant states. Strikingly, targeted elimination of the HPCS over short time periods resulted in tumor collapse, underscoring a critical role in tumor maintenance. Further, we found that the HPCS is highly dependent on KRAS activity, with acute KRAS inhibitor treatment leading to a selective depletion of the HPCS. Taken together, our data indicates that PDAC harbors a striking dependency on the HPCS and encourages therapeutic approaches aimed at eradicating this critical subset of cancer cells.

Citation Format: Anupriya Singhal, Hannah C. Styers, Jonathan Rub, Zhuxuan Li, Zeynep Tarcan, Jill Hallin, Olca Basturk, Rona Yaeger, James G. Christensen, Doron Betel, Yan Yan, Elisa de Stanchina, Tuomas Tammela. Functional Dissection of the Highly Plastic Basal Cell State 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 C077.
Abstract C078: Chromatin accessibility profiling of human pancreatic tumors reveals epigenetic features of malignant and stromal cell subtypes
Authors: MacPherson-Hawthorne Kevin , Link Jason M. , Worth Patrick , Sheppard Brett , Fields Andrew , Daniel Colin , Nishida Andrew , Pelz Carl , Waugh Trent , Agritelle Ethan , Muschler John , Adey Andrew , Sears Rosalie
Published: September 2024

Pancreatic ductal adenocarcinoma (PDAC) disease progression involves complex cell state transitions in both malignant and non-malignant populations within the tumor microenvironment. To uncover PDAC cell states and epigenetic features associated with clinical outcome, we profiled 40 tumor samples (33 primary tumors and 7 metastases) from 39 patients with single cell ATAC-seq, along with 10 sample-matched single cell RNA-seq profiles. Through topic modeling of high dimensional chromatin data, we uncovered distinct cis-regulatory networks underlying the classical and basal-like molecular subtypes of PDAC, which showed differential activity in basal-classical hybrid cells. Furthermore, delineation of epigenetic alterations by basal, classical, and hybrid subtypes revealed a core set of chromatin regions opened in all PDAC subtypes relative to ductal and acinar cells. These universally open regions showed striking overlap with gastrointestinal enhancers, highlighting a common endoderm lineage infidelity process across pancreatic tumors. Within the stromal compartment, we identified novel regulators of myofibroblastic cancer-associated fibroblasts (myCAFs) and inflammatory CAFs (iCAFs) from enhancer networks active in each CAF subtype. Importantly, our data uncover a highly prognostic gene program active in only one of two distinct myCAF chromatin states found in our data, highlighting a putative tumor-promoting myCAF subpopulation. Our work provides a high-resolution description of epigenetic cell state heterogeneity in PDAC, revealing novel regulators and gene programs associated with PDAC subtypes and clinical outcome.

Citation Format: Kevin MacPherson-Hawthorne, Jason M. Link, Patrick Worth, Brett Sheppard, Andrew Fields, Colin Daniel, Andrew Nishida, Carl Pelz, Trent Waugh, Ethan Agritelle, John Muschler, Andrew Adey, Rosalie Sears. Chromatin accessibility profiling of human pancreatic tumors reveals epigenetic features of malignant and stromal cell subtypes [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 C078.
Abstract C079: Exploring acinar to ductal metaplasia in pancreatitis and precancerous contexts using FixNCut
Authors: Aney Katherine , Jeong Woo-Jeong , Koak Pal , Kim Isabel , Nissim Sahar
Published: September 2024

Acinar to ductal metaplasia (ADM) is the process by which acinar cells transition to a duct-like state acquiring ductal markers and morphology. This process can be driven by pancreas inflammation or injury, such as pancreatitis, where it is thought to be an adaptive response to help mitigate damage and facilitate repair. ADM is also observed following acinar-specific oncogenic KRAS mutations and known to precede PDAC precancerous lesions termed pancreatic intraepithelial neoplasias (PanINs). While ADM is well characterized histologically, cellular and molecular details of ADM and PanIN formation remain less well understood, in part due to high levels of digestive enzyme production in acinar cells that hamper characterization. Leveraging our recently described DSP-fixation method, FixNCut, to improve capture and transcriptome quality of acinar and ADM populations in the pancreas, we characterize ADM arising in three contexts: acute pancreatitis, recurrent acute pancreatitis, and acute pancreatitis with an oncogenic KRAS mutation known to drive the formation of PanINs. FixNCut and single-cell RNA-sequencing enabled us to elucidate the transcriptomic landscape of ADM and define changes to the microenvironment in unprecedented detail. Our findings indicate that the cellular and transcriptional landscape of recurrent acute pancreatitis closely mirrors that of acute pancreatitis for up to 6 weeks (or 6 bouts of 2-day acute pancreatitis), which was the longest timepoint tested. In contrast, acute pancreatitis in the presence of an acinar-specific oncogenic KRAS mutation results in a distinct transcriptional profile for both ADM and the surrounding microenvironment compared to pancreatitis alone. Additionally, we use FixNCut to preserve the epigenomes of acinar cells, enabling us to sort acinar cells and profile their histone modifications in various contexts of ADM. We benchmark and validate our results against existing mouse and human datasets of precancer and cancer. Through this work, we aim to enhance our understanding of ADM in various contexts, providing insights into acinar cell plasticity and early PDAC precursor formation that may inform strategies for early detection and interception.

Citation Format: Katherine Aney, Woo-Jeong Jeong, Pal Koak, Isabel Kim, Sahar Nissim. Exploring acinar to ductal metaplasia in pancreatitis and precancerous contexts using FixNCut [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 C079.
Abstract IA-02: The tumor-reactive CD8+ T-cell repertoire in pancreatic cancer as revealed by single-cell sequencing
Authors: Offringa Rienk
Published: September 2024

We recently reported on the analysis of the tumor-infiltrating T-cell repertoire in human pancreatic cancer by means of single cell RNA-sequencing (scRNA-seq), demonstrating the presence of expanded tumor-reactive CD8+ TCR clonotypes in these tumors (Sci Transl Med 2023 Nov 15;15(722):eadh9562). In view of the low numbers of somatic mutations in pancreatic cancer, we chose to perform an unbiased screening against autologous tumor cells rather than against predicted mutanome-encoded neoepitopes as performed in other recent studies. Systematical testing of tumor-reactive TCRs against predicted neoepitopes thus far did not result in hits, suggesting that linear, mutanome-encoded peptides may not represent the immunodominant T cell epitopes targeted by the natural T-cell response. In parallel, we conducted a similar analysis of the tumor-infiltrating T-cell repertoire in two distinct syngeneic mouse models for pancreatic cancer from which we isolated > 100 tumor-reactive TCRs. While some of these TCRs were exclusively reactive against the tumor of origin, we found most to react against recurrent tumor antigens. By means of immunopeptidome analyses, we identified a number of T-cell epitopes that reflect this reactivity pattern: a ‘private’ mutanome-encoded neoepitope and several epitopes derived from over-expressed tumor-associated autoantigens. In a third, complementary study, we addressed the question whether T-cell receptors (TCRs) raised through immunization with tumor-specific neoepitopes, as identified by mutanome analysis and HLA-peptide binding algorithms in human pancreatic cancer, would duly mediate T-cell reactivity against the autologous tumors in which the epitope-encoding mutations were identified. We therefore immunized humanized (human TCR-locus, HLA-transgenic) mice with synthetic peptides representing 18 carefully selected candidate neoepitopes. For 4 of these epitopes, we successfully isolated fully human TCRs that specifically recognize naturally processed neoepitopes on tumor cells. Taken together, our studies demonstrate that pancreatic cancer can be targeted by T-cells directed against neoepitopes and tumor-associated autoantigens, but also raise important questions concerning the pros and cons of these options.

Citation Format: Rienk Offringa. The tumor-reactive CD8+ T-cell repertoire in pancreatic cancer as revealed by single-cell sequencing [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-02.
Abstract IA-03: Functional heterogeneity of fibroblast populations in pancreatic cancer
Authors: Biffi Giulia
Published: September 2024

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.
Abstract IA-04: Targeting the oncogenic state of RAS with tri-complex inhibitors
Authors: Singh Mallika
Published: September 2024

KRAS oncogenic driver mutations occur in approximately 30% of all human cancers, and in particular, in over 90% of patients with pancreatic ductal adenocarcinoma (PDAC). Small molecule inhibitors that selectively target the inactive, GDP-bound state of KRAS G12C mutant proteins have demonstrated clinical efficacy in non-small cell lung cancer (NSCLC) as monotherapies, and in the small subset of PDAC patients that harbor this mutation. However, there are no currently approved RAS-targeted therapy options for the majority of patients with non-G12C RAS mutant PDAC. We have designed a series of tri-complex inhibitors that specifically target the GTP-bound, active state of RAS (RAS(ON)). These small molecule inhibitors bind non-covalently to an abundant intracellular protein, cyclophilin A (CypA). The resulting binary complex selectively engages RAS(ON), forming a tri-complex that sterically inhibits RAS interaction with downstream effectors. We have generated mutant-selective inhibitors that covalently engage RAS(ON) G12C (RMC-6291) or RAS(ON) G12D (RMC-9805). In addition, RMC-6236 is a RAS(ON) multi-selective inhibitor that non-covalently inhibits the active, GTP-bound state of mutant and wild-type variants of the canonical RAS isoforms (KRAS, NRAS, and HRAS). Here we will describe the mechanism of action of these investigational agents and the preclinical profiles that support their clinical evaluation in patients with PDAC as monotherapies and in combination therapy regimens with standard-of-care agents or as novel RAS(ON) inhibitor doublets.

Citation Format: Mallika Singh. Targeting the oncogenic state of RAS with tri-complex inhibitors [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-04.
Abstract IA-05: Targeting KRAS for pancreatic cancer treatment
Authors: Der Channing J.
Published: September 2024

The approval of clinically effective inhibitors for KRAS G12C mutant non-small cell lung cancers in 2021 and 2022 marks a significant milestone in anti-KRAS oncogene drug discovery. This success has fueled intense efforts to develop inhibitors targeting additional KRAS mutations. However, primary and treatment-associated acquired resistance limit the depth and duration of efficacy of KRAS G12C selective and likely other KRAS inhibitors. Thus, a major challenge moving forward will be the elucidation of mechanisms of resistance to then guide development of effective combination anti-KRAS therapies. Recent studies have begun to identify mechanisms of acquired resistance, where most involve alterations in components in the RAS signaling network that then cause reactivation of KRAS effector signaling that bypass drug activity. Our studies have established the critical role of reactivation of the RAF-MEK-ERK mitogen activated protein kinase cascade, and the ERK target MYC, in driving resistance in KRAS-mutant pancreatic cancer. To fully understand how aberrant ERK and MYC activation overcomes KRAS inhibitor response, we have established a comprehensive molecular portrait of ERK- and MYC-dependent activities. We have also identified YAP/TAZ-TEAD activation as a mechanism of acquired resistance and have characterized KEAP1 loss as a mechanism of primary resistance. Together, these studies have identified drug combination strategies that enhance KRAS inhibitor activity. Progress in these and other studies will be presented.

Citation Format: Channing J. Der. Targeting KRAS for pancreatic cancer treatment [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-05.