tbuckley/cabot-search huggingface dataset:
Abstract C017: Targeting KRAS selectively induce metabolic reprogramming in pancreatic cancer
Authors: Laiba Shiekh, Matthew Cheung, Linyuhui Zheng, Erica Marlette, Chiamaka J. Ezeh, Don-Gerard Conde, Zeribe C. Nwosu
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease largely due to the lack of effective treatments that overcome the tumor drug resistance. Oncogenic KRAS mutation contribute to most PDAC and drive multiple metabolic pathways to promote tumor growth. Despite this overarching role of KRAS, inhibition of KRAS/MAPK pathway often lead to resistance by yet unclear mechanism. Here we find that the pharmacological inhibition of KRAS/MAPK pathway induces distinct responses in various pancreatic cancer cells. Specifically, while KRAS/MAPK inhibition suppressed growth in some cells, the same treatment induced or did not change the growth of other cell lines and also selectively impacted cell migration. In addition, metabolic activities were suppressed in cells where growth was suppressed or not changed but was accelerated where KRAS/MAPK inhibition induced growth. Analysis of gene expression profile of human PDAC and KRAS-driven mouse tumors identified nutrient transporters that are upregulated KRAS induction but also upregulated upon KRAS inhibition. Our study reveals context-dependent response to KRAS inhibition in pancreatic cancer and suggest targeting nutrient transporters to overcome therapeutic resistance. Citation Format: Laiba Shiekh, Matthew Cheung, Linyuhui Zheng, Erica Marlette, Chiamaka J. Ezeh, Don-Gerard Conde, Zeribe C. Nwosu. Targeting KRAS selectively induce metabolic reprogramming in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C017.
Abstract A081: Single-cell transcriptomic analysis of organoids derived from normal pancreata reveals epithelial cell heterogeneity and expression of PanIN-associated genes
Authors: Alexander W Bray, Eileen S Carpenter, Timothy L Frankel, Marina Pasca di Magliano
Journal: Cancer Research (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.
Abstract C047: Autophagy-mediated proline-supply is important for cell survival in pancreatic cancers
Authors: Ji hyeon Kim, Heesun Cheong
Journal: Cancer Research (2024)

Abstract 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 IA-02: The tumor-reactive CD8+ T-cell repertoire in pancreatic cancer as revealed by single-cell sequencing
Authors: Rienk Offringa
Journal: Cancer Research (2024)

Abstract 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 &amp;gt; 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 B040: B cells facilitate lymph node colonization in pancreatic ductal adenocarcinoma
Authors: Alice Bertocchi, Megan T Hoffman, Li Qiang, Massiel Morell, Lauren L Hsu, Michael L Dougan, Judith Agudo, Stephanie K Dougan
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) carries a low survival rate. Several factors contribute to its dismal prognosis, including resistance to available therapies and high invasiveness. Lymph nodes act as an early systemic source of circulating malignant cells, allowing their dissemination to other organs early in disease progression. Lymphatic colonization is linked to worse prognosis, and a better understanding of mechanisms regulating lymph node metastasis is clinically needed. To study each step in the metastatic cascade to the lymph nodes, we have developed a mouse co-clinical model of resectable pancreatic cancer. This model mimics the frequency of human PDAC metastatic recurrence, on a similar time scale relative to the lifespans of mice and humans and allows us to investigate very early events in the metastatic cascade. In contrast to the established anti-tumor role of T cells, the role of B cells in cancer immunology is more complex. B cells are a predominant immune population in lymph nodes, but their role in relation to lymph node colonization has never been fully addressed. Using our model of PDAC spontaneous metastasis and a mouse model of B cell depletion, we showed that lymph node metastasis does not form in the absence of B cells. We demonstrated that B cells, but not secreted antibodies, are required for successful lymph node colonization. We also gained evidence that B cells are orchestrating a complex interplay between disseminated cancer cells and other immune cells in the draining lymph node. Particularly, T cells seem to be involved in preventing cancer cell from growing into macro-metastasis only in the absence of B cells. We are now investigating the mechanisms employed by B cells to facilitate this cellular network to facilitate lymph node colonization in PDAC. The ultimate outcome of our work will be the design of effective immune strategies to prevent and treat lymph node dissemination of such a deadly disease. Citation Format: Alice Bertocchi, Megan T Hoffman, Li Qiang, Massiel Morell, Lauren L Hsu, Michael L Dougan, Judith Agudo, Stephanie K Dougan. B cells facilitate lymph node colonization 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 B040.
Abstract IA-04: Targeting the oncogenic state of RAS with tri-complex inhibitors
Authors: Mallika Singh
Journal: Cancer Research (2024)

Abstract 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 C038: Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment
Authors: Xu Han, Michelle Burrows, Laura C Kim, Jimmy Xu, Will Vostrejs, Tran Ngoc Van Le, Yanqing Jiang, Edna Cukierman, Reiss Binder Kim, Ben Z Stanger, Clementina Mesaros, Brian Keith, Celeste Simon
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy whose abundant cancer-associated fibroblasts (CAFs) create a hallmark “desmoplasia” that severely limits oxygen and nutrient delivery. Hypoxia inhibits oxygen-dependent metabolic processes. For example, unsaturated lipid biosynthesis relies on oxygen to maintain desaturase enzymatic activities. Here, we investigated the mechanisms by which PDAC cells maintain lipid homeostasis under these conditions. Exogenous unsaturated lipids, rather than de novo synthesis, sustain PDAC cell viability by relieving endoplasmic reticulum (ER) stress under nutrient scarcity. Furthermore, CAFs are less hypoxic than adjacent malignant cells in vivo due to proximal blood vessel accessibility, nominating them as a potential source of these obligatory species. CAF-conditioned medium promoted PDAC cell survival upon nutrient and oxygen deprivation, an effect reversed by delipidation. We determined that lysophosphatidylcholines (LPCs) are particularly enriched in CAF-conditioned medium and preferentially taken up by PDAC cells, where they are converted to phosphatidylcholines (PCs) to sustain membrane integrity. Inhibiting LPC to PC conversion reversed the ability of exogenous unsaturated LPCs to sustain cancer cell survival and restrain ER stress in vitro and in vivo. Collectively, these results reveal a critical lipid cross-feeding mechanism enabling PDAC cell survival and identify an innovative approach to targeting this metabolic dependency. Efforts to target lipid crosstalk between CAFs and PDAC cells will be discussed. Citation Format: Xu Han, Michelle Burrows, Laura C Kim, Jimmy Xu, Will Vostrejs, Tran Ngoc Van Le, Yanqing Jiang, Edna Cukierman, Reiss Binder Kim, Ben Z Stanger, Clementina Mesaros, Brian Keith, Celeste Simon. Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C038.
Abstract A068: Lfng-expressing centroacinar cell is a prime cell-of-origin for p53-deficient pancreatic cancer
Authors: Keli Xu, Wen-Cheng Chung, Shubing Zhang, Azeddine Atfi
Journal: Cancer Research (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 A033: Mapping age-specific biomarker dynamics in pancreatic ductal adenocarcinoma
Authors: Priyanka Gupta, Karen Duong-Polk, Rabi Murad, Cosimo Commisso
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a lethal age-related disease, with a median age of diagnosis over 70 years. Understanding age-dependent aberrations in the blood proteome might facilitate early detection, prognosis, and treatment personalization of PDAC. In this study, we aim to decipher novel clinically relevant biomarkers that distinguish between younger and older PDAC patients. To do this, we used a syngeneic orthotopic PDAC animal model where we implanted murine KPC cells (KRasG12D/+; Tp53R172H/+) into the pancreata of age-restricted groups of young (6-8 weeks) and old (80-84 weeks) C57BL/6 mice. Our previous findings demonstrated accelerated tumor growth and an increased metastatic burden in older mice relative to younger ones. Proteomic analysis of plasma from tumor-bearing young and old mice revealed an array of upregulated age-specific circulating proteins relative to their non-tumor, age- and sex-matched controls. Using a threshold of &amp;gt;2-fold change and p&amp;lt;0.05, our analysis identified 22 and 24 proteins preferentially increased in young and old mice, respectively. To ascertain the clinical relevance of our findings in humans, we analyzed expression profiles of selected proteins in human PDAC datasets from The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses have highlighted proteins involved in an array of processes as key candidates, which are consistent with our mouse proteomics findings. These candidate proteins show higher expression levels in human tumors compared to healthy controls and exhibit significant correlations with patient age and overall survival. Our ongoing validation studies have identified a protein from the immunoglobulin superfamily of cell adhesion molecules as a potential biomarker of PDAC, particularly relevant for younger patients. We are currently conducting age-dependent characterization of cell adhesion molecules to understand their role in intercellular crosstalk between cancer and stromal cells, immune surveillance, and metastasis. Citation Format: Priyanka Gupta, Karen Duong-Polk, Rabi Murad, Cosimo Commisso. Mapping age-specific biomarker dynamics 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 A033.