bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A068: Lfng-expressing centroacinar cell is a prime cell-of-origin for p53-deficient pancreatic cancer
Authors: Xu Keli , Chung Wen-Cheng , Zhang Shubing , Atfi Azeddine 
Published: September 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies with poor understanding of etiology. Studies using mouse models showed that both acinar and ductal cells of the pancreas can be transformed by combination of oncogenic Kras and p53 mutations to form PDAC. How the transforming capacities of pancreatic cells are constrained, or whether a unique subset of cells serve as a prime target for oncogenic transformation, remains obscure. We found that expression of a Notch modulator, Lunatic Fringe (Lfng), is confined to a limited number of cells with centroacinar location and morphology in the adult mouse pancreas. These cells are selectively targeted by KrasG12D coupled with p53 loss-of-function (but not gain-of-function) mutations, leading to rapid pancreatic tumor formation, whereas the elimination of Lfng completely blocks the initiation of these tumors. We showed that p53 constrains the progenitor-like property of Lfng-expressing cells and that Lfng is required for hyperproliferation of these cells when p53 is inactivated. We identified Notch3 as a functional Notch receptor for PDAC initiation and progression in this context. Lfng expression is undetectable in normal acinar and ductal cells but upregulated in acinar- as well as ductal-derived precursor lesions, and its deletion hinders both the initiation and progression of these lesions. Collectively, Lfng marks a centroacinar subpopulation that is restrained by p53 and is uniquely susceptible to oncogenic transformation with p53 loss. Furthermore, Lfng functions as an oncogene in all three exocrine lineages in the adult pancreas. Genetic alterations of LFNG, predominantly in the forms of mRNA upregulation and gene amplification, were detected in 9% of PDAC patients and were associated with shortened overall survival. Consistent with its expression in mouse pancreas, LFNG immunostaining was noted in a subset of centroacinar cells in normal adjacent pancreatic tissues from human patients, and its expression in the adenocarcinoma specimens was positively correlated to tumor grade. Thus, LFNG may play an important role in human PDAC, in parallel with the one shown in the murine models. This study offers new insights into the pancreatic cancer cell-of-origin, initiation, and progression, which may lead to the identification of a therapeutic target for the disease.
Citation Format: Keli Xu, Wen-Cheng Chung, Shubing Zhang, Azeddine Atfi. Lfng-expressing centroacinar cell is a prime cell-of-origin for p53-deficient 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 A068.
Abstract A070: Time-Dependent Oxidation and Aggregation of Vimentin upon Binding by β-lap Induced Immunogenic Cell Death
Authors: Qian Feng , Dou Lei , Wang Kaixin , Xia Yi , Chen Zhidong , Zu Yumeng , Xi Shuang 
Published: September 2024

Abstract
β-lapachone (β-lap) has been demonstrated as an NAD(P)H:quinone oxidoreductase1 (NQO1) bioactivatable compound. It initiated a futile redox cycle catalyzed by NQO1, resulting in reactive oxygen species (ROS) generation, with consumption of the reductive NAD(P)H. After a 4-h pulse of sufficiently lethal dose of β-lap, high levels of ROS diffused into nuclei to induce tumor-selective DNA damage and programmed necrosis in cancers overexpressing NQO1. Recently, our experiments showed that prolonged low dose β-lap administration exerted significant and NQO1 independent antitumor efficacy in mouse models with no overt signs of toxicity. Thus, we synthesized a photoactive β-lap probe to identify the molecular target of β-lap. Vimentin, a major constituent of the intermediate filament family of proteins, was identified as the direct binding target of β-lap. Vimentin was highly upregulated in multiple cancers including PDAC, and was a binding partner of β-lap with a dissociation constant at micromolar levels. Ligand binding assays in Panc1 cells employing β-lap as a specific competitor showed that vimentin was bound by β-lap-probe in a β-lap-competitive manner, and further confirmed that the in vivobinding target of β-lap was vimentin. Moreover, it was manifested that endogenous vimentin mRNA levels directly correlated with sensitivity to prolonged exposure of β-lap in a panel of pancreatic cancer cell lines, and knockout of vimentin in Panc1 cells markedly decreased lethality after prolonged exposure of β-lap. Mechanistically, we revealed that β-lap bound to vimentin and induced disulfide bonds that participated in disulfide cross-linking between a pair of vimentin dimers in a concentration and time dependent manner, forming vimentin oligomers of approximately 150 kDa. Prolonged exposure of β-lap promoted the disruption of filament architecture and vimentin degradation, ultimately resulting in cell death. In addition, the cell death by targeting vimentin exhibited a more inflammatory condition and enhanced DC activation. Together, our findings unveiled an unknown molecular target for β-lap and provided valuable insights into its mechanism of action. Targeting vimentin also presented a new strategy that inhibited the tumor growth and synergized with immunotherapy to disrupt immune evasion and reduce immune suppression against pancreatic cancers.
Citation Format: Feng Qian, Lei Dou, Kaixin Wang, Yi Xia, Zhidong Chen, Yumeng Zu, Shuang Xi. Time-Dependent Oxidation and Aggregation of Vimentin upon Binding by β-lap Induced Immunogenic Cell Death [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 A070.
Abstract A072: Decoding human kinome specificities through a computational data-driven approach and unveiling kinase activity in pancreatic ductal adenocarcinoma
Authors: Cai Li , Johnson Jared L , Peng Chen , Yaron Tomer M , Cantley Lewis C , DePinho Ronald A 
Published: September 2024

Abstract
Phosphorylation is a crucial post-translational modification involved in virtually all biological processes; its dysregulation is a critical factor in the development and progression of pancreatic ductal adenocarcinoma (PDAC). A large family of kinases drives the phosphorylation of specific substrates, and understanding kinase substrate specificities is central to deciphering kinase activities in PDAC. Recent experimental approaches using positional scanning peptide arrays (PSPA) have determined position-specific scoring matrices (PSSMs) for many human kinases. Inherent limitations and the resource-intensive nature of this empirical method prompted development of a bottom-up computational data-driven method (CDDM) to generate PSSMs of 289 human kinases from large kinase-substrate datasets. Our results align with previous experimental findings and proved effective in identifying kinase-substrate interactions and predicting kinase functions. Moreover, we applied the data-driven PSSMs in analyzing the phosphoproteomics data of PDAC from Clinical Proteomic Tumor Analysis Consortium (CPTAC). We generated kinase activity profiles for each patient and identified subtypes of PDAC with different kinase activities. These clusters were further correlated with key genomic alterations and hallmark cancer processes. Together, we anticipate that such comprehensive knowledge of the kinome specificities will enhance our interpretation of phosphoproteomics data from clinical samples, elucidate signaling pathways under various conditions, and identify key kinases implicated in PDAC.
Citation Format: Li Cai, Jared L Johnson, Chen Peng, Tomer M Yaron, Lewis C Cantley, Ronald A DePinho. Decoding human kinome specificities through a computational data-driven approach and unveiling kinase activity 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 A072.
Abstract A074: Integrated clinical and single-cell profiling analysis reveals cellular states associated with metastatic organotropism and survival in patients with pancreatic ductal adenocarcinoma
Authors: Hajkarim Morteza Chalabi , May Michael , Amin Amit Dipak , Jamison Jacob , Tagore Somnath , Caprio Lindsay , Walsh Zachary , Shah Parin , Abuzaid Sinan , Michel Alissa , Dajiang Sun , Wong Winston , Shaikh Neha , Ramaradj Priyanka , Bakir Basil , Kluger Michael D , Chabot John , Hibshoosh Hanina , Rustgi Anil K , Raufi Alexander , Manji Gulam A , Izar Benjamin 
Published: September 2024

Abstract
Some patients with localized pancreatic ductal adenocarcinoma (PDAC) undergo resection with curative intent, but most experience disease recurrence and succumb to their disease. Through examination of 743 PDAC patients in a single center we found that the site of first recurrence is a major predictor for survival. Patients with liver-metastatic recurrence (LIV-MR) had significantly shorter disease free and overall survival compared to those with recurrence to the lung (LUN-MR). We performed single-nucleus RNA-seq (snRNA-seq) and whole-genome sequencing (WGS) of primary PDAC with either LIV-MR or LUN-MR and found that malignant cells adopt transcriptional programs that mimicked that of their ultimate metastatic target organ. We validated this observation in independent data sets of human adult and fetal liver and lung tissues, and two additional patient cohorts who underwent molecular profiling of their actual PDAC liver and lung metastatic lesions. We reconstructed two different trajectories of malignant transformation in PDAC and found that the LIV-MR and LUN-MR are associated with these, suggesting that subsequent metastatic organotropism may be imprinted early in tumorigenesis. Furthermore, primary PDAC tumors recurring with LIV-MR compared to LUN-MR were depleted of infiltrating T cells and enriched with M2-like macrophages, highlighting potential contributions to subsequent outcomes. Taken together, this work provides evidence for pre-existing cellular adaptations that may determine metastatic organotropism in the context of cancer recurrence. These insights may be useful for prognostication and development of therapeutic strategies at the time of diagnosis of resectable PDAC.
Citation Format: Morteza Chalabi Hajkarim, Michael May, Amit Dipak Amin, Jacob Jamison, Somnath Tagore, Lindsay Caprio, Zachary Walsh, Parin Shah, Sinan Abuzaid, Alissa Michel, Sun Dajiang, Winston Wong, Neha Shaikh, Priyanka Ramaradj, Basil Bakir, Michael D Kluger, John Chabot, Hanina Hibshoosh, Anil K Rustgi, Alexander Raufi, Gulam A Manji, Benjamin Izar. Integrated clinical and single-cell profiling analysis reveals cellular states associated with metastatic organotropism and survival in patients with 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 A074.
Abstract A075: Establishing the interaction mechanism of oncoprotein, Mucin1, and extracellular vesicle marker protein, Alix, in pancreatic cancer
Authors: Hoagstrom Kristine V , Huang Ying , Borgstahl Gloria E , Hollingsworth Michael A 
Published: September 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains an aggressive disease with devastating mortality rates largely due to a poor understanding of its progression mechanism. Small extracellular vesicles (sEVs) are used by cancer cells to aid in their progression, and tumor-derived EVs (TEVs) show a distinct protein cargo composition potentially contributing to this rapid progression and metastasis of PDAC. To investigate this phenomenon, we isolated sEVs from conditioned media of pancreatic cancer cell lines using ultracentrifugation and characterized them by transmission electron microscopy (TEM), nanoparticle tracking analysis, and immunoblotting. These sEVs were then used in several studies to investigate critical TEV cargo sorting machinery. For instance, PDAC-derived sEVs have selective enrichment of the oncogenic transmembrane protein Mucin1 (MUC1). Preliminary MUC1KO studies from our lab revealed that MUC1 potentially regulates sEV formation, where we saw a clear impact on sEV cargo in the absence of MUC1. Additional studies found that the cytoplasmic adaptor protein ALG-2-Interacting Protein X (Alix), a protein known to play a critical role during TEV formation, regulates MUC1’s presence in sEVs. From this discovery, we then identified a novel MUC1-Alix interaction, which was confirmed using several techniques, including co-immunoprecipitation (CoIP). To define the Alix-interacting domain of MUC1, we utilized in silico modeling and localized surface plasmon resonance (LSPR) of MUC1.CT and Alix to quantify the interaction. This revealed the cytoplasmic tail of MUC1 (MUC1.CT) as the Alix-interacting domain. Moving forward, our central hypothesis for this study is that this MUC1.CT-Alix interaction utilizes a conserved binding motif that targets Alix to the endosomal membrane and contributes to the formation of MUC1+ sEVs. While a distinct sEV biogenesis pathway employed by cancer cells has not yet been defined, our studies will provide insight into the potential sEV sorting mechanism of MUC1 and other cancer biomarkers and advance the understanding of PDAC progression.
Citation Format: Kristine V Hoagstrom, Ying Huang, Gloria E Borgstahl, Michael A Hollingsworth. Establishing the interaction mechanism of oncoprotein, Mucin1, and extracellular vesicle marker protein, Alix, 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 A075.
Abstract A077: The role of RhoV in basal-like pancreatic cancer
Authors: Wu Shang , Feng Jia , Gao Selina , Wang Ting , Li Zebang , Liu Yifei , Huang Chiung-Kuei , Lu Shaolei 
Published: September 2024

Abstract
Background Pancreatic ductal adenocarcinoma is a devastating disease lacking targeted therapy. Basal-like pancreatic cancer is a tumor subtype with a worse clinical outcome than other subtypes. These cancers are characterized by the expression of basal keratins and mesenchymal markers. However, the genes that drive the basal-like phenotype are poorly understood. Ras homolog family member V (RhoV) is one of the Rho GTPases, and it has been demonstrated to drive the progression of lung and breast cancers. The current study aims to reveal the role of RhoV in basal-like pancreatic cancer. Design RhoV, p63, and CK5/6 were stained in sequential sections by immunohistochemistry. Expression of RhoV in pancreatic cancer and cell lines was reanalyzed based on the data from ProteinAtlas and Broad Insitute DepMap Portal. Basal cell line, BxPC3, and non-basal cell line, Panc1 were selected for functional evaluation based on their differentiated RhoV expression. RhoV gene was overexpressed and knocked down using the CRISPR/gRNA-based Lentiviral system, followed by sphere formation, colony formation, migration, and invasion assays. Results RhoV, p63, and CK5/6 were expressed in the same histologic location of basal pancreatic cancer. The gene expression level of RhoV was co-expressed with p63 (a classic basal marker) in four pancreatic cancer cell lines (broadinstitute.org). Knockout of RhoV by three runs of gRNAs in BxPC3 cells all significantly attenuated tumor sphere formation with less colony formation as compared to mock knockout. Overexpression of RhoV in non-basal-like cells, Panc 1, significantly increased the size of sphere formation, numbers of colony formation, and p38 activation compared to EV control. Cell migration and invasion assays showed the same RhoV-dependent migration and invasion in corresponding cells. Panc1 cells with RhoV knockout significantly generated smaller tumor xenografts in immunodeficient mice and RhoV overexpression led to larger tumor sizes. Conclusion Finding the driver of the basal-like phenotype helps to reveal the pathophysiology of the basal-like subtype of pancreatic cancer and facilitates the identification of new targets for therapeutic purposes. Our preliminary results indicated that RhoV, a small G protein from the Rho family of GTPases, played essential roles in tumor proliferation and progression, by activating the p38 signaling pathway. Further study will be focused on revealing Rhov's downstream pathways and exploring the role of RhoV in apoptosis/cell cycle, cell metabolism, autophagy, etc. in basel-like pancreatic cancer.
Citation Format: Shang Wu, Jia Feng, Selina Gao, Ting Wang, Zebang Li, Yifei Liu, Chiung-Kuei Huang, Shaolei Lu. The role of RhoV in basal-like 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 A077.
Abstract A078: Functional screen for mediators of onco-mRNA translation specificity in pancreatic cancer
Authors: Kovalski Joanna R , Sarioglu Goksu , Subramanyam Vishvak , Hernandez Grace , Rademaker Gilles , Oses-Prieto Juan A , Slota Macey , Wen Kwun Wah , Kim Grace E , Burlingame Alma L , Goodarzi Hani , Perera Rushika M , Ruggero Davide 
Published: September 2024

Abstract
Oncogenic protein dosage is tightly regulated to enable cancer cells to adapt and survive. In healthy cells, translation initiation of onco-mRNA transcripts encoding oncogenes and growth factors is tightly regulated to maintain accurate protein expression levels. However, this process is broken in cancer cells, which rely on the maintenance of high dosage of oncogenic proteins for their survival and to drive cancer development. Whether this is regulated at the level of translational control and the key factors in cis and trans remain unknown. The Myc oncogene is a central paradigm of an exquisitely regulated oncogene and a major driver of pancreatic ductal adenocarcinoma (PDAC). While there has been a tremendous effort to target Myc in cancer, clinically relevant Myc inhibition remains a challenge. Therefore, identifying selective promoters of MYC translation may present a novel therapeutic opportunity. Employing a genome-wide CRISPRi screen for modulators of MYC mRNA translation initiation in PDAC cells, we identified regulators of selective MYC translation and validated four RNA binding proteins (RBPs), including epitranscriptome modifiers. We focused on a top hit, a little studied RBP, RBM42, which is highly expressed in PDAC and predicts poor patient survival. We found that RBM42 binds and selectively regulates the translation of MYC and a precise, yet vital suite of pro-oncogenic transcripts, including JUN and EGFR. Mechanistically, employing immunoprecipitation-mass spectrometry analysis, we found that RMB42 is a novel ribosome-associated protein (RAP). Through RNA structure determination and mutagenesis analysis, we showed that RBM42 directly binds and remodels the MYC 5’UTR RNA structure, facilitating the formation of the translation pre-initiation complex and increasing MYC translation. Importantly, we demonstrated that RBM42 is necessary for human PDAC cell growth and fitness and PDAC tumorigenesis in xenograft mouse models in a Myc-dependent manner in vivo. In PDAC patient samples, RBM42 expression is correlated with Myc protein levels and transcriptional activity. This work transforms our understanding of the translational code in cancer and offers a new therapeutic opening to target the expression of oncogenes.
Citation Format: Joanna R Kovalski, Goksu Sarioglu, Vishvak Subramanyam, Grace Hernandez, Gilles Rademaker, Juan A Oses-Prieto, Macey Slota, Kwun Wah Wen, Grace E Kim, Alma L Burlingame, Hani Goodarzi, Rushika M Perera, Davide Ruggero. Functional screen for mediators of onco-mRNA translation specificity 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 A078.
Abstract A081: Single-cell transcriptomic analysis of organoids derived from normal pancreata reveals epithelial cell heterogeneity and expression of PanIN-associated genes
Authors: Bray Alexander W , Carpenter Eileen S , Frankel Timothy L , Pasca di Magliano Marina 
Published: September 2024

Abstract
Pancreatic intraepithelial neoplasia (PanIN) lesions are the microscopic pre-malignant precursor to pancreatic ductal adenocarcinoma (PDAC). Animal models have demonstrated that PanINs arise from acinar cells which have undergone acinar-to-ductal metaplasia (ADM), but the exact molecular mechanisms which govern this transformation remain poorly understood. Novel in vitro models of PanIN genesis are necessary to better characterize pancreatic carcinogenesis and identify clinically actionable biomarkers of early disease. Organoids cultured from normal human pancreata have generated promise in this regard, but the cellular identity and malignant potential of their component cells have not been comprehensively characterized. We performed single-cell RNA sequencing (10X Genomics) on 6 normal pancreatic organoid lines maintained in culture for 3 weeks as well as their parent pancreata obtained from donors with no history of PDAC or other exocrine pancreatic pathology. Integration of whole pancreatic and organoid data using the R package Seurat generated a UMAP with clearly defined “ductal” and “acinar” clusters based on marker gene expression. The majority of organoid cells (47.3-81.5%) colocalized to the “ductal” cluster, and expressed SOX9, KRT19, and PDX1. However, a subset of cells (1.0-33.3%) present in each organoid sample aligned with the “acinar” cluster and expressed PRSS1, PRSS3, REG3A, MUC1, and SPINK1. In accordance with prior reports, organoid cells did not meaningfully express the acinar/endocrine markers PTF1A, CPA1, CHGA, or INS. Further examination of the “acinar” organoid cells revealed heightened expression of CLDN18, TFF1, TFF2, CTSE, CA2, and LYZ, genes associated with PanIN in prior spatial RNA sequencing studies. Other genes significantly enriched in this “acinar” organoid cluster include MUC5AC, a known PanIN marker, OLFM4, a tumor suppressor implicated in intestinal carcinogenesis, and the chemokine CXCL17, which is expressed in cells undergoing ADM. Overall, this data suggests that organoids derived from normal pancreata represent a heterogeneous population of epithelial cells with both acinar and ductal features. Furthermore, these organoids may represent an in vitro model of ADM and/or early PanIN formation, though additional functional mechanistic studies are required for confirmation.
Citation Format: Alexander W Bray, Eileen S Carpenter, Timothy L Frankel, Marina Pasca di Magliano. Single-cell transcriptomic analysis of organoids derived from normal pancreata reveals epithelial cell heterogeneity and expression of PanIN-associated genes [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 A081.