tbuckley/cabot-search huggingface dataset:
Abstract B092: PP2A activation alters macropinosome processing in pancreatic cancer cells leading to metabolic stress and cancer cell death
Authors: Garima Baral, Claire M Pfeffer, Indiraa Doraivel, Sara N Filippelli, Brittany N Heil, Brittany L Allen-Petersen
Journal: Cancer Research (2024)

Abstract The majority of pancreatic ductal adenocarcinoma (PDAC) patients present with late-stage, metastatic disease that is often resistant to therapeutics, resulting in the lowest survival rate of all major cancers. Metabolic rewiring in response to oncogenic signals plays a critical role in PDAC cell survival, tumor growth, and metastasis. In contrast to normal epithelial cells, these metabolic alterations make PDAC tumors dependent on glutamine and glucose for survival, highlighting a unique metabolic vulnerability that can be therapeutically exploited. However, during times of nutrient stress, PDAC cells can circumvent this vulnerability by engulfing extracellular fluids to replenish amino acids, including glutamine, in a process called, macropinocytosis. Macropinocytosis occurs downstream of oncogenic KRAS, a small GTPase that is almost universally mutated in PDAC patients. The inhibition of macropinocytosis in vivo reduces PDAC tumor growth, underscoring the importance of this pathway to cancer cell survival. However, the signaling mechanisms that regulate this process and the contribution of macropinocytic signaling to aggressive cancer phenotypes remains poorly understood. Protein phosphatase 2A (PP2A) is a heterotrimeric complex that reguates a wide variety of cell signaling pathways, inlcuding KRAS, and is commonly deregulated in human PDAC tumors. Recently, PP2A has been implicated as an important regulator of macropinocytosis, but the mechanism by which this occurs is unknown. We demosntrate that suppression of PP2A accelerates the formation of KRAS-driven precursor lesions in an in vivo mouse model of PDAC, implicating PP2A as a critical regulator of mutant KRAS phenotypes. Here, we show that acute PP2A activation prevents the fusion of macropinosomes with the lysosome, robbing PDAC cells of critical metabolic nutrients and driving cell death. Furthermore, we find PP2A associates with the lipid kinase, PIKfyve, a key regulator of macropinosome-lysosome fusion. Finally, we determined that PP2A activating compounds can function synergistically with metabolic inhibitors, support a new therapeutic strategy in this aggressive and deadly cancer. Together, our results implicate PP2A as a critical suppressor of PDAC metabolic plasticity and highlight the use of PP2A activating compounds to prevent PDAC nutrient scavenging. Citation Format: Garima Baral, Claire M Pfeffer, Indiraa Doraivel, Sara N Filippelli, Brittany N Heil, Brittany L Allen-Petersen. PP2A activation alters macropinosome processing in pancreatic cancer cells leading to metabolic stress and cancer 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 B092.
Abstract B015: Duodenal aspiration biopsy in diagnosis of pancreatic neoplasms
Authors: Aleksei Kashintsev, Vitali Proutski
Journal: Cancer Research (2024)

Abstract Introduction Intraductal papillary mucinous neoplasms (IPMNs) are a subset of lesions with elevated malignant potential, warranting their inclusion in screening standards. Despite endoscopic ultrasound (EUS) with fine-needle aspiration biopsy (FNAB) serving as the standard for verification, the occurrence of erroneous conclusions remains significant. Consequently, analysis of pancreatic juice is considered as a potential adjunctive diagnostic method. However, the absence of methods for obtaining pancreatic juice in adequate volume and quality poses a barrier to the widespread adoption of this approach.Materials and MethodsA method of duodenal aspiration biopsy (DAB) was developed involving active aspiration from the lumen of duodenum, yielding large volume of the mix of pancreatic juice and bile uncontaminated by gastric juice. Patients diagnosed with pancreatic neoplasms utilizing EUS with FNAB, were enrolled and ALB was implemented as an adjunctive diagnostic procedure. Cytological analysis of the material obtained was performed along with measuring the level of carcinoembryonic antigen (CEA). The level &amp;gt;192 ng/mL was considered significant, according to the Fukuoka 2017 guidelines.ResultsIn patients with cystic neoplasms of the pancreas undergoing DAB, results of cytological examination were non-informative in certain cases. However, analysis of CEA levels in the pancreatic juice and bile mixture always demonstrated strong concordance with the degree of dysplasia. In some instances, elevated CEA values facilitated the adoption of a more aggressive treatment strategy, leading to the detection of carcinoma. Conversely, low CEA levels prompted the decision to opt for observation rather than radical surgery in other cases.ConclusionDiagnosing precancerous transformations of the pancreas remains a challenging task, characterized by a notable rate of false-positive or false-negative conclusions. The DAB method offers a promising solution, seamlessly integrating into routine clinical practice and offering supplementary data to enhance the verification of pancreatic cancer. Citation Format: Aleksei Kashintsev, Vitali Proutski. Duodenal aspiration biopsy in diagnosis of pancreatic neoplasms [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 B015.
Abstract C052: Repurposing Statins to Target Gemcitabine Resistance in Pancreatic Cancer
Authors: 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
Journal: Cancer Research (2024)

Abstract 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 A076: LINE-1 ORF1p mimics viral innate immune evasion mechanisms in pancreatic cancer
Authors: Eunae You, Bidish Patel, Alexandra Rojas, Siyu Sun, Natalie Ho, Ildiko Phillips, Michael Raabe, Yuhui Song, Katherine Xu, Joshua Kocher, Peter Richieri, Martin Taylor, Linda Nieman, Benjamin Greenbaum, David Ting
Journal: Cancer Research (2024)

Abstract Aberrant expression of repeat elements displaying viral mimicry is a common feature found in both mouse models and human pancreatic ductal adenocarcinoma (PDAC). However, cancer cells must employ mechanisms to manage this "viral" repeat element load to avoid triggering innate immune responses. Here, we demonstrate that the long interspersed nuclear element 1 (LINE-1) ORF1 protein (ORF1p) in PDAC cells plays a role in shielding repeat RNAs from activating pathogen recognition receptor (PRR)-mediated antiviral responses, independent of retrotransposition. Suppression of ORF1p using lentiviral shRNA induces innate immune responses through the PRRs, RIG-I and MAVS (double-stranded RNA sensors). Interestingly, PDAC cell lines with low ORF1p lack these two receptors, suggesting convergent mechanisms to suppress PRR signaling. Furthermore, RNA immunoprecipitation sequencing (RIP-seq) demonstrates ORF1p association with repeat RNA, including LINE and SINE elements that typically trigger antiviral responses. Subcellular localization of ORF1p in processing bodies (p-bodies) reveals specific interaction with MOV10, a dsRNA helicase crucial for antiviral responses. Loss of ORF1p results in significant growth reduction in vitro and in vivo, which supports ORF1p as a potential immune oncology therapeutic target. Altogether, our results demonstrate a novel function of ORF1p in shielding cytoplasmic repeat RNA from PRR sensing, shedding light on how PDAC cells evade host immune responses triggered by viral-like repeat RNA. Citation Format: Eunae You, Bidish Patel, Alexandra Rojas, Siyu Sun, Natalie Ho, Ildiko Phillips, Michael Raabe, Yuhui Song, Katherine Xu, Joshua Kocher, Peter Richieri, Martin Taylor, Linda Nieman, Benjamin Greenbaum, David Ting. LINE-1 ORF1p mimics viral innate immune evasion mechanisms 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 A076.
Abstract B065: Eosinophils alter metastatic spread in pancreatic cancer
Authors: Megan T Hoffman, Patrick J Lenehan, Alice Bertocchi, Jen Wang, Lestat Ali, Li Qiang, Amiko Uchida, Sara Vayrynen, Andressa Dias Costa, Michael Dougan, Max Heckler, Jonathan Nowak, Brian W Wolpin, Stephanie K Dougan
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDA) is the third most common cause of cancer death in the US with a 11% 5-year survival rate. A key contributor of this dismal prognosis is early and frequent metastatic spread with limited treatment options for patients. Metastasis in PDA is facilitated by a robust fibroinflammatory response in the primary tumor site, a large portion of which is composed of infiltrating immune cells, and survival during transit to establish in the secondary site. In the primary tumor reactive stroma, we found increased eosinophils in both human and mouse PDA compared to the normal pancreas. Eosinophils are an innate immune cell best known for their ability to control parasite responses and have been implicated in either pro- or anti-cancer roles in various solid tumors. We used the ΔdblGata mice, which lack eosinophils, to study the role of eosinophils during metastatic spread using a resectable model of PDA metastasis. This model of metastasis was developed to facilitate consistent seeding of lung metastasis in approximately 50 percent of mice from a transient subcutaneous tumor which undergoes subsequent surgical removal and harvest to evaluate metastasis at 4 weeks. We found that mice lacking eosinophils have increased metastasis to the lung in our resectable model of PDA metastasis but no difference in establishment of IV injected PDA tumor cells, suggesting eosinophil control at the primary tumor site. Single cell sequencing of the subcutaneous tumors finds no difference in the immune cell compartment but alterations in the EMT states of the tumor cells. Staining confirms a decreased level of E-cadherin with unchanged vimentin and zeb1 suggesting a partial EMT state in eosinophil knockout mice. We conclude that eosinophils in PDA inhibit the metastatic process, in part, through control of tumor cell state. Citation Format: Megan T Hoffman, Patrick J Lenehan, Alice Bertocchi, Jen Wang, Lestat Ali, Li Qiang, Amiko Uchida, Sara Vayrynen, Andressa Dias Costa, Michael Dougan, Max Heckler, Jonathan Nowak, Brian W Wolpin, Stephanie K Dougan. Eosinophils alter metastatic spread in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B065.
Abstract A072: Decoding human kinome specificities through a computational data-driven approach and unveiling kinase activity in pancreatic ductal adenocarcinoma
Authors: Li Cai, Jared L Johnson, Chen Peng, Tomer M Yaron, Lewis C Cantley, Ronald A DePinho
Journal: Cancer Research (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 B008: Twist1 drives pancreatic ductal adenocarcinoma-mediated muscle cachexia
Authors: Parash Parajuli, Azeddine Atfi
Journal: Cancer Research (2024)

Abstract Cancer cachexia is a debilitating syndrome that affects the survival and quality of life of cancer patients. Up to 95% of pancreatic ductal adenocarcinoma (PDAC) patients experience muscle cachexia, yet the underlying mechanisms remain poorly understood. The transcription factor Twist1 plays essential roles in mesenchymal stem cell fate determination, and its deregulation contributes to cancer progression and metastasis. In this study, we report on the serendipitous finding that Twist1 functions in PDAC to drive muscle cachexia. We found that conditional overexpression of Twist1 in the pancreatic epithelium (pTwist1) during early development resulted in severe growth retardation, which was mainly characterized by muscle hypotrophy. This intriguing observation prompted us to inquire whether pTwist1 could function in the pancreatic epithelium to regulate muscle mass, and if so, whether this has any implication as it relates to PDAC-mediated muscle cachexia. We found that enforced expression of pTwist1 in healthy adult animals was sufficient to elicit the cardinal features of muscle cachexia, including progressive decline in body weight, physical activity, muscle force, and muscle mass. In the context of PDAC, enforced expression of pTwist1 in a KrasG12D background led to a dramatic acceleration of tumor progression, and this was associated with severe muscle cachexia. To the best of our knowledge, these findings provide the first evidence that the pro-malignant transcription factor Twist1 functions in PDAC to drive muscle cachexia, thus revealing new insights into the underlying mechanisms of muscle that could be harnessed to curb this debilitating syndrome. Citation Format: Parash Parajuli, Azeddine Atfi. Twist1 drives pancreatic ductal adenocarcinoma-mediated muscle cachexia [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 B008.
Abstract B076: Morphological diversity predicts functional traits in pancreatic cancer
Authors: Dennis Gong, William L Hwang
Journal: Cancer Research (2024)

Abstract Cell morphologies represent a phenotypic integration of intrinsic cellular processes, changes in cell state, and interactions with neighboring cells. While analyses of large cell line collections such as the Cancer Dependency Map (DepMap) have greatly enhanced discovery of novel molecular biomarkers and therapeutic targets, morphological analysis of these models has not yet been performed. Hence, there is a rich opportunity to discover novel regulators and functional properties of cell morphologies by linking image-based profiling to -omics based assays. Here, we studied the transcriptional and functional properties of 16 human pancreatic cancer cell lines, associations with distinct cell morphologies, and treatment-induced remodeling. At baseline, we observed extensive morphological heterogeneity across and within cell lines, as well as differences in multicellular organization. We categorized cell line morphologies into epithelial, mesenchymal, and spheroid, and organizational patterns into tightly aggregated, multilayered, and dispersed. We performed differential expression analysis across morphological subtypes utilizing DepMap transcriptomics data and queried functional correlates including CRISPR dependency, drug sensitivity, and proclivity for metastasis. For example, we discovered that the mesenchymal morphology and multilayered organizational pattern [WH3] were associated with metastatic potential, while expressing reduced levels of tight junction and cell adhesion genes. We then explored treatment associated morphological changes and their potential as cost-effective biomarkers for cell-intrinsic resistance to chemotherapy (e.g., 5-FU and gemcitabine) and KRAS inhibitors (e.g., MRTX1133 and RMC- 6236). Cells were treated continuously and monitored with live cell imaging (Incucyte SX5) followed by Cell Painting at the three-day endpoint. We observed conserved morphological responses to therapy across cell lines including a shift towards spindle-like cell shapes with neurite-like projections in chemotherapy-treated conditions, and a cell bloating phenomena characterized by an increase in cell area in KRAS inhibitor treated conditions. To directly link transcriptional state to morphology, we performed 1000-plex spatial molecular imaging (Nanostring CosMx) at subcellular resolution to pools of cell lines, demonstrating that morphological diversity within cell lines corresponded to distinct transcriptional states. In conclusion, this study highlights the potential of harnessing cell morphological information in a rapid, cost-effective phenotyping assay to aid precision oncology efforts leveraging patient- derived in vitro models. Citation Format: Dennis Gong, William L Hwang. Morphological diversity predicts functional traits 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 B076.
Abstract C032: De novo pyrimidine biosynthesis inhibition synergizes with BCL-XL targeting in pancreatic cancer
Authors: None huan zhang, None Qijia yu, Naiara Santana-Codina, Clara Poupault, Claudia Campos, Xingping Qin, Aparna Padhye, Nicole Sindoni, Miljan Kuljanin, Junning Wang, Matthew J. Dorman, Andrew J. Aguirre, Stephanie K. Dougan, Kristopher A. Sarosiek, Joseph D. Mancias
Journal: Cancer Research (2024)

Abstract Oncogenic KRAS, the genetic driver of 90% of PDAC, induces a metabolic rewiring characterized, in part, by dependency on de novo pyrimidine biosynthesis. Dihydroorotate dehydrogenase (DHODH) is the enzymatic ‘chokepoint’ of the de novo pyrimidine biosynthesis pathway and an in vivo metabolic liability in pancreatic ductal adenocarcinoma (PDAC). Targeting enzymes in the de novo pyrimidine synthesis pathway such as dihydroorotate dehydrogenase (DHODH) with clinically available inhibitor brequinar (BQ) starved the tumor of nucleotide synthesis and restrained growth of PDAC cells in vitro. However, therapeutic resistance limited BQ long-term effects in PDAC xenografts, which suggests compensatory pathways and that combinatorial strategies are required for enhanced efficacy. Here, we integrated a mass spectrometry (MS)-based quantitative temporal proteomics workflow, LC/MS- based metabolomics and in vitro and in vivo drug-anchored CRISPR/Cas9 genetic screens to identify compensatory pathways to DHODH inhibition (DHODHi) and targets for combination strategies. We demonstrate that DHODHi alters the apoptotic regulatory proteome thereby enhancing sensitivity to inhibitors of the anti-apoptotic BCL2L1 (BCL-XL) protein. Combinatorial regimens with DHODH and BCL-XL inhibition synergistically induce apoptosis in PDAC cell lines and patient-derived PDAC organoids. In vivo DHODH inhibition with Brequinar and BCL-XL degradation with DT2216, a proteolysis targeting chimera (PROTAC), significantly inhibits the growth of PDAC tumors. Our data defines mechanisms of adaptation to DHODH inhibition and identifies a combination therapy strategy in PDAC. Citation Format: huan zhang, Qijia yu, Naiara Santana-Codina, Clara Poupault, Claudia Campos, Xingping Qin, Aparna Padhye, Nicole Sindoni, Miljan Kuljanin, Junning Wang, Matthew J. Dorman, Andrew J. Aguirre, Stephanie K. Dougan, Kristopher A. Sarosiek, Joseph D. Mancias. De novo pyrimidine biosynthesis inhibition synergizes with BCL-XL targeting 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 C032.