tbuckley/cabot-search huggingface dataset:
Abstract C089: A novel role of p53 in pancreatic acinar cell identity
Authors: Jennifer J. Twardowski, Stephano S. Mello, Thomas I. Heist
Journal: Cancer Research (2024)

Abstract Pancreatitis is an inflammatory disease that affects acinar cells in the exocrine pancreas, and can be triggered by several factors, such as alcohol abuse, smoking and familial genetic alterations. Pancreatic injury associated with pancreatitis is characterized by inflammation, acinar cell death, and acinar-to-ductal metaplasia (ADM), a regenerative process in which metaplastic cells proliferate and re-differentiate into acinar cells. Recurrent pancreatitis can cause persistent ADM, impairing exocrine function and causing precancerous lesions known as pancreatic intraepithelial neoplasia (PanIN) that can initiate pancreatic ductal adenocarcinoma (PDAC), a nearly always fatal disease. Importantly, the lack of treatment options for pancreatitis patients reinforces the need for strategies that could resolve pancreatic damage and stop disease progression. We have recently shown that pancreatic cells harboring a hyperactive variant of p53 display increased resistance to developing acute pancreatitis induced by cerulein (a secretagogue which mimics cholecystokinin). Here, we show that p53 activation using the drug Nutlin-3a can repair the damage caused by cerulein-induced pancreatitis, and reduce the formation of PanIN lesions. This repair is achieved exclusively at low doses of Nutlin-3a, which cause a mild p53 activation, and is entirely dependent on the presence of the p53 gene. We have also identified novel p53 target genes relevant to acinar identity from ChIP-seq and RNA-seq data, and validated their dependence on p53 in mouse embryonic fibroblasts and in pancreatic precancerous lesions. Lastly, we have observed expression of p53 in the developing pancreas at embryonic day 15.5, indicating a potential function of p53 in pancreatic development. Our findings suggest a novel role of p53 in rescuing acinar cells from damage, and that p53 activation may be used as a treatment for pancreatitis and pancreatic cancer prevention. Citation Format: Jennifer J. Twardowski, Stephano S. Mello, Thomas I. Heist. A novel role of p53 in pancreatic acinar cell identity [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C089.
Abstract B109: Reinforcing risk prediction for intraductal papillary mucinous neoplasms of the pancreas with AI-optimized nucleotide-to-amino acid analyses
Authors: Nam Nguyen, Jamie K. Teer, Margaret A. Park, Patricia McDonald, Jason B. Fleming, Jennifer B. Permuth, Kwang-Cheng Chen, Aleksandra Karolak
Journal: Cancer Research (2024)

Abstract Intraductal papillary mucinous neoplasms (IPMNs) often precede invasive pancreatic ductal adenocarcinoma, with each IPMN tumor carrying a 10-25% risk of progressing to cancer within 10 years of detection. The objective of this work is to employ AI-augmented analyses of single mutations occurring at specific tri-nucleotide sequences or codons and identify markers associated with the progression of cysts to pancreatic cancer. Despite being precursors of pancreatic cancer there is a lack of validated intervention targets for precision prevention for IPMNs. Currently cancer prevention for patients with IPMN is centered on surgery using a risk-tailored approach; the clinical ability to stratify risk of cancer progression of individual IPMN tumors is poor and essentially no effective non-surgical interventions exist. To advance the precision cancer prevention for IPMNs we develop an intelligent, machine learning (ML) derived framework addressing the challenge of IPMN stratification from samples with limited data space, e.g., somatic mutations. Our study incorporates the text-based statistical and ML analyses of the mutational profiles of patients’ genomes followed by an integration of codon sequence derived mutational features for biomarkers validation. Given the potential of genome spatial organization to understand mutagenesis and genomic instability, we also map the DNA sequence information onto the local spatial genome organization to elucidate intrinsic features and molecular mechanisms that potentially lead to mutations. Results of this study show that information extracted from mutational profiles with the proposed methods significantly improves performance of the ML models in stratification of IPMNs and biomarker identification. We also present how utilization of these ML tools for mutational data, spatial genome organization, and functional analyses from tumor samples, can aid understanding of the underlying mechanisms of mutations in IPMNs and pancreatic cancer. Citation Format: Nam Nguyen, Jamie K. Teer, Margaret A. Park, Patricia McDonald, Jason B. Fleming, Jennifer B. Permuth, Kwang-Cheng Chen, Aleksandra Karolak. Reinforcing risk prediction for intraductal papillary mucinous neoplasms of the pancreas with AI-optimized nucleotide-to-amino acid analyses [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B109.
Abstract B069: Double-stranded RNA derived from tandem repeat sequences induces mesenchymal transition in pancreatic cancer cells by regulating alternative splicing
Authors: Takahiro Kishikawa, Takuma Iwata, Motoyuki Otsuka, Mitsuhiro Fujishiro
Journal: Cancer Research (2024)

Abstract Human satellite II (HSATII) composed of tandem repeats in pericentromeric regions in the human genome is aberrantly transcribed in epithelial cancers, particularly pancreatic cancer. Dysregulation of the repetitive elements in cancer tissues can facilitate incidental double-stranded RNA formation. However, it remains controversial whether double-stranded RNAs play tumor-promoting or tumor-suppressing roles during cancer progression. Therefore, we focused on the formation of double-stranded HSATII (dsHSATII) RNA and explored its molecular functions. The overexpression of dsHSATII RNA promoted mesenchymal-like morphological changes and enhanced the invasiveness of pancreatic cancer cells. We identified an RNA-binding protein, STRBP, which preferentially binds to dsHSATII RNA rather than single-stranded HSATII RNA. Depletion of STRBP induced the mesenchymal transition and enhanced the invasiveness. Conversely, the epithelial–mesenchymal transition (EMT) of dsHSATII-expressing cells was rescued by STRBP overexpression. Mechanistically, STRBP is involved in the alternative splicing of genes associated with the EMT events, which was interfered by the overexpression of dsHSATII RNA. Finally, we confirmed that isoform switching of CLSTN1, one of the target genes of STRBP-associated alternative splicing, induced EMT-like morphological changes. These findings reveal a novel cell-autonomous function of dsHSATII RNA in enhancing malignant potential, providing a better understanding of the biological significance of aberrant expression of satellite arrays in malignant tumors. Citation Format: Takahiro Kishikawa, Takuma Iwata, Motoyuki Otsuka, Mitsuhiro Fujishiro. Double-stranded RNA derived from tandem repeat sequences induces mesenchymal transition in pancreatic cancer cells by regulating alternative splicing [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B069.
Abstract A018: Exercise stimulates anti-tumoral immunity in metastatic PDAC
Authors: Mansour E. Riachi, Carolina G. Alcantara Hirsch, Erica Ma, Beny Shapiro, Ammar Javed, Christopher L. Wolfgang, Dafna Bar-Sagi
Journal: Cancer Research (2024)

Abstract The majority of pancreatic ductal adenocarcinoma (PDAC) patients are metastatic at presentation with limited treatment options and a poor overall 5-year survival of 3%. The liver is the predominant site of distant metastasis in PDAC. Our group has previously shown that aerobic exercise can inhibit tumorigenesis in a primary PDAC mouse model by promoting anti-tumor immunity, however, the effects of exercise in the metastatic setting have not been explored. As such, we developed a model of PDAC liver metastasis by isolating primary pancreatic and liver metastatic cell lines from 18–20-week-old LSL-KRasG12D/+; LSL-Trp53R172H/+; p48Cre; Rosa26LSL-tdTomato/+ (KPCTpancreas or KPCTliver, respectively) mice. KPCTpancreas cells were surgically implanted into the pancreata of syngeneic wild-type mice. One week after pancreatic implantation, KPCTliver cells were implanted into the liver either by direct injection into the parenchyma or via the portal vein. The portal vein method enables us to account for the extravasation step of the metastatic cascade, while the direct parenchymal injection offers a less invasive surgery. Both models preserve the spleen, which is the largest secondary lymphoid organ and essential to the immune response. Treadmill running was initiated in the aerobic exercise cohort 5 days per week for 2 weeks or mice were allowed to rest. Endpoint analysis revealed that aerobic exercise treatment decreased tumor burden in both primary tumors and liver metastasis as measured by tumor weights and tdTomato fluorescence imaging when compared to the rested controls. Immune profiling of the liver metastases revealed elevated IL-15Rɑ+ CD8+ T cells as well as CD19+ B cells in the exercise cohort. While identification of IL-15Rɑ+ CD8+ T cells is consistent with the immune changes we have previously reported in the primary pancreatic tumor of exercised mice, the latter changes reveal organ specific immune cell recruitment not observed in the primary pancreatic tumor of exercised mice. The combined immune profiling and phenotypic changes suggest that aerobic exercise reduces PDAC metastatic growth by modulating systemic and intra-tumoral immunity. The induction of an anti-tumorigenic immune response by aerobic exercise could open avenues for potential pharmacological intervention in downstream pathways to aid in the treatment of metastatic PDAC. Citation Format: Mansour E. Riachi, Carolina G. Alcantara Hirsch, Erica Ma, Beny Shapiro, Ammar Javed, Christopher L. Wolfgang, Dafna Bar-Sagi. Exercise stimulates anti-tumoral immunity in metastatic PDAC [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A018.
Abstract A024: B cells facilitate lymph node colonization in pancreatic ductal adenocarcinoma
Authors: Alice Bertocchi, Megan T. Hoffman, Li Qiang, Lauren Hsu, Michael Dougan, Judith Agudo, Stephanie K. Dougan
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) has 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 in PDAC, allowing their dissemination to other organs early in disease progression. Lymphatic colonization is linked to worse prognosis. Therefore, 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 consists of subcutaneous injection of highly metastatic pancreatic cancer cells, followed by surgical resection of the primary tumor. Following resection, mice spontaneously develop lymph nodes metastasis at a comparable frequency to human PDAC post-surgical recurrence, on a similar time scale relative to the lifespans of mice and humans. Expression of nuclear tdTomato allows detection of single cancer cells seeding the draining lymph nodes early in disease progression, even before metastases are histological detectable. Using this model, we are gaining insights into the first steps of metastatic seeding of lymph nodes, and have identified a pro-metastatic role for B cells. These findings will enhance our understanding of lymphatic colonization in PDAC and potentially inform immunotherapeutic interventions to disrupt the metastatic cascade. Citation Format: Alice Bertocchi, Megan T. Hoffman, Li Qiang, Lauren Hsu, Michael 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: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A024.
Abstract A060: Metabolic patterns in pancreatic cancer cachexia
Authors: Deepti Mathur, Blanca Majem, Nada Kalaany
Journal: Cancer Research (2024)

Abstract Cachexia is a multi-organ pathological state characterized by physical wasting and tissue catabolism. It occurs in 80% of pancreatic cancer patients, and to date there are no preventative or early detection methods. Cachexia leads to limited tolerance to anti-cancer therapy and is a lethal disease. Here, we have characterized a mouse model of cachexia in pancreatic ductal adenocarcinoma (PDAC) in order to better understand disease progression: the physiology across stages of cachexia in the model recaptures well the progressive disease in humans. We present the first-of-its-kind systemic metabolomic analysis across cachectic stages in the tumor, interstitial fluid, liver, fats, muscles, and blood plasma. The primary source of variation in the data is the tissue type, indicating that each tissue has a unique metabolome and trajectory across cachexia stages. We use mathematical modeling to identify metabolites that may be participating in cross-tissue networks in pre-, early-, and late-stage cachexia. Pathway analysis shows a particular emphasis on lipid alterations. Strikingly, we find systemic metabolic changes prior to weight loss or other disease symptoms, and use feature selection algorithms to identify potential predictive markers of cachexia progression. Overall, we hope our work is a valuable resource for the field and will lay the foundation for metabolic insights into pancreatic cancer cachexia and its prevention and treatment. Citation Format: Deepti Mathur, Blanca Majem, Nada Kalaany. Metabolic patterns in pancreatic cancer cachexia [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A060.
Abstract IA14: Forecasting pancreatic carcinogenesis through spatial multi-omics
Authors: Elana J. Fertig
Journal: Cancer Research (2024)

Abstract Combining genomics with mathematical modeling provides a forecast system that can yield computational predictions to anticipate cancer progression and therapeutic response. High-throughput profiling technologies can indicate the molecular and cellular pathways of malignancies, but not the effect of targeting those pathways with therapy. Precision interception requires relating therapies to the cellular phenotypes underlying pancreatic carcinogenesis. This talk presents a hybrid computational and experimental strategy to uncover interactions between neoplastic cells and the microenvironment during pancreatic carcinogenesis. As pancreatic cancer develops, it forms a complex microenvironment of multiple interacting cells. The microenvironment of advanced pancreatic cancer includes a heterogeneous and dense population of cells, such as macrophages and fibroblasts, that are associated with immunosuppression. New single-cell and spatial molecular profiling technologies enable unprecedented characterization of the cellular and molecular composition of the microenvironment. These technologies provide the potential to identify candidate therapeutics to intercept immunosuppression in pancreatic cancer. State-of-the-art mathematical approaches in computational biology are essential to uncover mechanistic insights for high-throughput data for these precision interception strategies. We have recently applied new machine learning techniques to integrate imaging and spatial transcriptomics to enable comprehensive characterization of the pancreatic precancer microenvironment. Developing targets for interception requires determining which of these cellular and molecular pathways drive subsequent development of cancer. Relating the transcriptional programs in premalignant lesions to carcinogenesis requires mapping their temporal changes across disease stages. To integrate the spatial molecular data from premalignancies and single-cell RNA-seq reference atlases, we developed a transfer learning approach. This integrated analysis identified a switch between fibroblast-induced inflammatory signaling and cellular proliferation in pancreatic cancer cells. We confirmed these transitions also occur in pancreatic cancer patient derived organoids co cultured with fibroblasts using transfer learning from the reference scRNA-seq atlases of pancreatic tumors. This approach demonstrates the potential of computational analysis of multi-omics data in human tissue with organoid models for bidirectional bench to bedside research. Citation Format: Elana J. Fertig. Forecasting pancreatic carcinogenesis through spatial multi-omics [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr IA14.
Abstract B037: Anti-fibrotic FAK ‘priming’ to improve contemporary chemotherapy in pancreatic cancer
Authors: Kendelle J. Murphy, Daniel A. Reed, Cecilia R. Chambers, Lily M. Channon, Marina Pajic, David Herrmann, Paul Timpson
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a highly metastatic, chemo-resistant malignancy and is characterized by a dense, desmoplastic stroma that increases the biomechanical force load on cancer cells and is thought to both promote and restrict disease advancement. Using the p53 mutant KPC mouse model of PDAC, we visualized transient manipulation of focal adhesion kinase (FAK), which integrates bidirectional cell-environment signalling. The fluorescent ubiquitination-based cell cycle indicator (FUCCI) cell cycle reporter was used during intravital (in vivo) imaging to monitor dynamic changes in FAK activity, stromal biomechanics and gemcitabine/Abraxane-induced effects. Critically, micropatterned pillar plates and stiffness-tuneable matrices were used to pinpoint the contribution of mechanical environmental cues to chemo-sensitization, while fluid flow– induced shear stress assessment, patient-derived matrices, and personalized in vivo models allowed us to deconstruct how FAK inhibition can reduce PDAC spread. In a precision medicine approach, stratification of PDAC patient samples via Merlin status revealed a subset of patients that are likely to respond to FAK priming before chemotherapy. This dataset has led to the establishment of a Phase II clinical trial of first- line FAK inhibition in combination with Gemcitabine/Abraxane in PDAC Patients (NCT05355298). Citation Format: Kendelle J. Murphy, Daniel A. Reed, Cecilia R. Chambers, Lily M. Channon, Marina Pajic, David Herrmann, Paul Timpson. Anti-fibrotic FAK ‘priming’ to improve contemporary chemotherapy in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B037.
Abstract A022: Novel nanoparticle delivery of toll like receptor agonists alters the tumor immune landscape and improves response to standard of care therapy in preclinical PDAC models
Authors: Nathan Beals, Anthony Sorrentino, Dafna Bar-Sagi
Journal: Cancer Research (2024)

Abstract The tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) is becoming an increasingly complex system, driven by the interactions between multiple different cell types. These drivers of cancer progression can suppress local immune responses, promote resistance to therapies, and reinforce a pro-tumorigenic TME. Despite advances in other tumor types with immune checkpoint blockade, minimal progress has been made in the treatment of PDAC with immunotherapies targeted at adaptive responses. As such, with a majority of the TME being made up of innate immune cells being skewed towards immunosuppressive phenotypes, there remains an underutilized immunologic target. Of the potential subset of targets, toll like receptors (TLR) have garnered significant interest given the key role they have in controlling the innate immune response in a number of different immune cells. On their own, agonists of these family of receptors lack efficacy, either through poor tumor penetration, lack of target specificity or toxicity. To address this unmet need, we have developed a nano-delivery approach for TLR agonists for target immune cell uptake. Thus far, we have established two conjugates, a protein-based nanoparticle termed FN-TLR7 for the delivery of a CL307-based conjugate and a DNA nanoparticle termed CAGE-TLR9 for the delivery of a CpG-based agonist. We have found that these conjugates can activate target immune cells within the TME via an advantageous pharmacokinetic profile which significantly reduces nonspecific toxicities compared to free agonists. When paired with the current standard of care options in PDAC, we see significant improvements in tumor control. The implications of nano-delivery of TLR agonists for treating PDAC tumors will be discussed. Citation Format: Nathan Beals, Anthony Sorrentino, Dafna Bar-Sagi. Novel nanoparticle delivery of toll like receptor agonists alters the tumor immune landscape and improves response to standard of care therapy in preclinical PDAC models [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A022.