tbuckley/cabot-search huggingface dataset:
Abstract A079: A new vulnerability to BET inhibition due to enhanced autophagy in <i>BRCA2</i>-deficient pancreatic cancer
Authors: Suyakarn Archasappawat, EunJung Lee, Keely Ji, Jocelyn Pena, Virneliz Fernandez-Vega, Ritika Gangaraju, Nitin Sai Beesabathuni, Martin Jean Kim, Qi Tian, Priya Shah, Louis Scampavia, Timothy Spicer, Chang-Il Hwang
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer-related deaths in the United States, with the lowest five-year survival rate of all cancers. Around 10% of pancreatic cancer diagnoses are thought to be familial pancreatic cancer (FPC). BRCA2 pathogenic variants have been identified to be closely associated with FPC. Personalized medicine approaches that are tailored to FPC patients based on their mutation profiles could improve patient outcomes and minimize adverse effects. This study aims to identify novel potential drug candidates for BRCA2-deficient PDAC and dissect its underlying molecular mechanisms. To discover new vulnerabilities for BRCA2-deficient pancreatic cancer, we performed high-throughput drug screening (HTS) using isogenic murine Brca2 knockout (KO) and control PDAC cells. The HTS assay revealed that JQ1, a small molecule inhibitor of the bromodomain and extra-terminal domain protein (BET) family, selectively induced cytotoxicity in Brca2 KO cells. JQ1 significantly decreased the cell viability of Brca2 KO cells in vitro and suppressed the growth of Brca2 KO tumors in vivo compared to the controls. The transcriptomic analyses showed that JQ1 treatment resulted in upregulation of the gene sets associated with macroautophagy. Multi-orthogonal autophagy assays, including live cell imaging of fluorescence-based autophagy reporter, also supported that Brca2 KO cells had a constitutively higher basal level of autophagic activities compared to the controls, and JQ1 further induced autophagic flux in Brca2 KO cells. Moreover, blocking the autophagy process by pharmacological inhibition or knocking down essential autophagy genes rescued JQ1-induced cell death in Brca2 KO cells, indicating that the increased autophagy is responsible for JQ1-mediated cell death in Brca2 KO cells. In conclusion, we found that BRCA2 deficiency elevated autophagic flux, and extensive autophagy was further activated by BET inhibition, culminating in autophagy-dependent cell death in Brca2-deficient pancreatic cancer cells. Our findings suggest that BET inhibition could be a promising therapeutic strategy for treating BRCA2-deficient pancreatic cancer. Citation Format: Suyakarn Archasappawat, EunJung Lee, Keely Ji, Jocelyn Pena, Virneliz Fernandez-Vega, Ritika Gangaraju, Nitin Sai Beesabathuni, Martin Jean Kim, Qi Tian, Priya Shah, Louis Scampavia, Timothy Spicer, Chang-Il Hwang. A new vulnerability to BET inhibition due to enhanced autophagy in BRCA2-deficient 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 A079.
Abstract A100: KRAS inhibition targets and depends on pro-oncogenic HuR in PDAC cells
Authors: Hen Halamish, Michaela Bush, Alexander Smith, Rosalie Sears, Jonathan Brody
Journal: Cancer Research (2024)

Abstract The Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation is found in more than 90% of patients with pancreatic ductal adenocarcinomas (PDACs), making it a prime target for therapeutic drug development. HuR (ELAVL1) has been extensively studied in the context of PDAC and also plays a key role in PDAC progression and chemoresistance. In recent years, researchers have shed light on the specific role of the HuR protein in PDAC and its relationship with KRAS signaling. Using in KRASG12D – mutant patient derived models, cell lines derived from GEMM models, and conventional cell lines, we found that HuR CRISPR knock out lines showed more than 80-fold resistance to MRTX1133 (a KRAS inhibitor targeted against G12D mutation) compared to wild type cells. Furthermore, western blot and immunofluorescence studies demonstrated that therapeutic inhibition of KRAS, inhibited HuR protein expression and subcellular localization in as early as 3 hours post-treatment. Furthermore, HuR protein levels decreased post-treatment even under nutrient starvation. Herein, we show that the presence of HuR is necessary for the efficacy of KRAS targeting and Kras inhibition can rapidly degrade HuR protein levels and its active subcellular localization. Mechanistic studies determining the molecular interaction between HuR and KRAS and KRAS related proteins and mRNAs are underway. Taken together with ongoing studies, we are exploring the importance of HuR as a key downstream target of KRAS’ oncogenic activity and if the loss of HuR may be a potent, PDAC therapeutic resistance mechanism. Understanding the interplay between KRAS and HuR could offer a novel strategy to disrupt the oncogenic KRAS signaling cascade and overcome the potential inherent resistance of KRAS-mutant PDACs to promising, KRAS-targeted therapies. Citation Format: Hen Halamish, Michaela Bush, Alexander Smith, Rosalie Sears, Jonathan Brody. KRAS inhibition targets and depends on pro-oncogenic HuR in PDAC cells [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 A100.
Abstract A027: Aberrant glycosylation in mPDAC cells is associated with increased recruitment of immunosuppressive cells
Authors: Shawna Brookens, David Degaramo, Kiesha Wilson, Wilder Condori Obregon, Mitzi Nagarkatti, Avery Posey
Journal: Cancer Research (2024)

Abstract Tumor associated-glycan Tn antigen (aGalNAc-a-O-Ser/Thr) is associated with poor prognosis in various solid tumors. However, the mechanisms that Tn antigen promotes tumorigenesis is incompletely understood. Here, we generated Tn antigen-expressing murine pancreatic ductal adenocarcinoma (mPDAC) tumor cell lines through CRISPR/Cas9-mediated knockout of the C1galt1c1 gene. Tn antigen expressing mPDAC cell lines exhibited increased in vitro proliferation and migration compared to parental controls. RNA sequencing revealed that loss of C1galt1c1 in mPDAC cells correlated with increased expression of myeloid recruitment and differentiation genes, IL34 and Lif. Additionally, C1galt1c1 knockout mPDAC cells implanted into mice led to accelerated tumor growth and increased tumor infiltration of myeloid-derived suppressor cells and neutrophils as determined by flow cytometry and scRNAseq. Interestingly, surface expression of a binding partner of Tn antigen, macrophage galactose N-acetyl galactosamine specific lectin 2 (Mgl2), was decreased in the infiltrate of C1galt1c1 knockout tumors suggesting a role for the Mgl2-Tn interaction in tumor progression. Together, our data indicate that expression of Tn antigen on tumor cells promotes an immunosuppressive microenvironment in mPDAC. Citation Format: Shawna Brookens, David Degaramo, Kiesha Wilson, Wilder Condori Obregon, Mitzi Nagarkatti, Avery Posey Jr.. Aberrant glycosylation in mPDAC cells is associated with increased recruitment of immunosuppressive cells [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 A027.
Abstract C099: Mutant-selective, covalent inhibitors of K-Ras(G12D)
Authors: Qinheng Zheng, Ziyang Zhang, Keelan Guiley, Kevan Shokat
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is the most lethal common cancer. A high percentage (&amp;gt;90%) of PDAC patients harbor KRAS mutations, with the majority expressing the K-Ras(G12D) missense mutation protein. Despite extensive drug discovery efforts across academia and industry, there are no approved drugs directly targeting oncogenic K-Ras(G12D) in a mutant-selective manner. We have developed a series of small molecules that form covalent bonds with the mutant protein at its missense site. The lead molecule inhibits the interaction of K-Ras with effector proteins, and therefore inhibits growth of KRASG12D-driven cancer cell lines but not non-G12D cells. Citation Format: Qinheng Zheng, Ziyang Zhang, Keelan Guiley, Kevan Shokat. Mutant-selective, covalent inhibitors of K-Ras(G12D) [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 C099.
Abstract C032: The involvement of the splanchnic program at the cellular and molecular levels in pancreatic cancer associated fibroblasts
Authors: Tom Walter, Lu Han, Michael Ostrowski
Journal: Cancer Research (2024)

Abstract Pancreatic Ductal Adenocarcinoma (PDAC) is characterized by a dense stroma primarily composed of cancer associated fibroblasts (CAFs). Our group recently performed a lineage tracing study using genetically engineered mouse models. This study demonstrated that CAFs and pancreatic tissue resident fibroblasts (TRFs) are both derived from the fetal splanchnic mesenchyme, an area of mesoderm next to the foregut endoderm. To determine whether two major subtypes of CAFs are derived from the splanchnic mesenchyme, I analyzed co-expression of the lineage tracing marker Tomato and CAF subtype marker a smooth muscle actin (aSMA). This suggests that both myofibroblasts (aSMA high) and inflammatory fibroblasts (aSMA low) are derived from the splanchnic mesenchyme. Furthermore, we found that transcription factor Gata6 is expressed in the splanchnic mesenchyme and in some CAFs. We constructed mouse genetic models where Gata6 is specifically deleted in fibroblasts. These Gata6 conditional knock out mice had increased tumor burden, suggesting that stromally-expressed Gata6 has a tumor restraining role. We derived CAF and TRF cell lines from these genetic mouse models and their littermate normal mice. My preliminary data suggest that several important fibroblast factors, including type I collagen, aSMA, and Interleukin 6, are upregulated in the Gata6 KO CAFs and TRFs relative to normal CAFs and TRFs. In summary, our study showed that two major subtypes of pancreatic CAFs are derived from the splanchnic mesenchyme, and splanchnic factors may play a role in adult pancreatic fibroblasts to regulate the expression of critical fibroblast genes. Citation Format: Tom Walter, Lu Han, Michael Ostrowski. The involvement of the splanchnic program at the cellular and molecular levels in pancreatic cancer associated fibroblasts [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 C032.
Abstract C056: The initiation and progression of pancreatic ductal adenocarcinoma through a p53 lens
Authors: Kathryn J. Hanson, Allegra C. Minor, Brittany M. Flowers, Alyssa M. Kaiser, Nicholas Hughes, Hannes Vogel, Le Cong, Laura D. Attardi
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a 5-year survival rate of only 11%. Slated to be the 2nd most deadly cancer by 2026, pancreatic cancer survival rates have not improved substantially over the years. With a lack of early detection methods and a highly immunosuppressive tumor microenvironment (TME), PDAC tumors are highly resistant to treatment. Oncogenic mutations in KRAS are present in &amp;gt;90% of cases and mutations in the tumor suppressor gene TP53 are present in ~72% of cases. However, why p53 mutations are so prevalent and how they enhance PDAC development is not well understood. To elucidate how exactly p53 loss promotes PDAC, we are using genetically engineered mouse models combined with single-cell and spatial transcriptomic technologies. In this mouse model, PDAC is driven from adult acinar cells with a tamoxifen-inducible Ptf1aCreER allele by oncogenic Kras (KrasG12D) along with either p53 wild type (p53wt) or p53 deficiency (p53flox). In this model, acinar cells can give rise to PDAC likely through a transdifferentiation process called acinar-to-ductal metaplasia (ADM), which leads to pancreatic intraepithelial neoplasias (PanINs) and then PDAC. The initial cell fate transition, ADM, can be activated by growth factors, inflammation, and injury. We have conducted single-cell and spatial transcriptomics to compare early stages of tumor development in the presence and absence of p53, and we will present our latest analyses. Providing insight into the early events of PDAC will lead to new approaches for improving clinical intervention in human PDAC. Citation Format: Kathryn J. Hanson, Allegra C. Minor, Brittany M. Flowers, Alyssa M. Kaiser, Nicholas Hughes, Hannes Vogel, Le Cong, Laura D. Attardi. The initiation and progression of pancreatic ductal adenocarcinoma through a p53 lens [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 C056.
Abstract C114: <i>Engrailed-1</i> promotes pancreatic cancer metastasis
Authors: Jihao Xu, Jae-Seok Roe, EunJung Lee, Claudia Tonelli, Tim Somervile, Melissa Yao, Joseph Milazzo, Herve Tiriac, Anna Kolarzyk, Esak Lee, Jeam Grem, Audrey Lazenby, James Grunkemeyer, Michael Hollingsworth, Paul Grandgenett, Alexander Borowsky, Youngkyu Park, Christopher Vakoc, David Tuveson, Chang-il Hwang
Journal: Cancer Research (2024)

Abstract Engrailed-1 (EN1) is a critical homeodomain transcription factor (TF) required for neuronal survival, and EN1 expression has been shown to promote aggressive forms of triple negative breast cancer. Here, we report that EN1 is aberrantly expressed in a subset of pancreatic ductal adenocarcinoma (PDA) patients with poor outcomes. EN1 predominantly repressed its target genes through direct binding to gene enhancers and promoters, implicating a role in the acquisition of mesenchymal cell properties. Gain- and loss-of-function experiments demonstrated that EN1 promoted PDA transformation and metastasis in vitro and in vivo. Our findings nominate the targeting of EN1 and downstream pathways in aggressive PDA. Citation Format: Jihao Xu, Jae-Seok Roe, EunJung Lee, Claudia Tonelli, Tim Somervile, Melissa Yao, Joseph Milazzo, Herve Tiriac, Anna Kolarzyk, Esak Lee, Jeam Grem, Audrey Lazenby, James Grunkemeyer, Michael Hollingsworth, Paul Grandgenett, Alexander Borowsky, Youngkyu Park, Christopher Vakoc, David Tuveson, Chang-il Hwang. Engrailed-1 promotes pancreatic cancer metastasis [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 C114.
Abstract B070: Histone deacetylation inhibition promotes bi-directional subtype switch in pancreatic cancer
Authors: Lukas Klein, Mengyu Tu, Eva K. Schmitt, Frederike Penz, Athanasia Mizi, Stefan Küffer, Elisabeth Hessmann, Argyris Papantonis, Volker Ellenrieder, Shiv K. Singh
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a dismal disease with 5-year survival of just 11%. Recent large-scale transcriptomic studies have identified two prognostically relevant neoplastic tumor subtypes, i.e. the well-differentiated classical (CLA) subtype with better prognosis, characterized by epithelial gene expression, as well as the dedifferentiated, invasive basal-like (BL) subtype, which displays mesenchymal stemness-related gene signatures. These subtypes have shown to be highly plastic and responsive to extrinsic signals, e.g. from the microenvironment or treatment-induced. Here, we investigate master transcription factor networks governing lineage determination in the different subtypes and the role of histone deacetylation (HDAC) co-regulators in their maintenance. We utilized established, subtype-defined PDAC cell lines in vitro and in orthotopic transplantation models to determine subtype plasticity in response to HDAC inhibition by the pan-HDAC inhibitor suberoylanilide hydroxamic acid (SAHA). By integration of RNA-seq, ATAC-seq as well as HiChIP for the activating mark histone 3 lysine 27 acetylation (H3K27ac), we show that the subtype-dependent chromatin organization and regulatory networks can be influenced by pharmacological inhibition of chromatin remodelers, in turn promoting changes in transcription of lineage-determining factors. Targeting these transcription factor networks by HDAC inhibition can lead both to a favorable switch from BL to CLA identity, as well as a detrimental CLA to BL switch. Functional assay such as trans-well invasion further supported the changes in subtype identity following SAHA treatment. This bi-directional subtype switch was additionally validated in patient-derived xenograft cell lines. Together, our findings highlight the importance of understanding the underlying transcriptional and epigenetic mechanisms of the pancreatic cancer subtypes, as they may exhibit opposing responses to targeted therapies. Citation Format: Lukas Klein, Mengyu Tu, Eva K. Schmitt, Frederike Penz, Athanasia Mizi, Stefan Küffer, Elisabeth Hessmann, Argyris Papantonis, Volker Ellenrieder, Shiv K. Singh. Histone deacetylation inhibition promotes bi-directional subtype switch 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 B070.
Abstract A086: TFEB protects pancreatic cancer cells against nucleolar stress
Authors: Florence Mc Duff, Laure Bessy, Benoit Marchand, Marie-Josee Boucher
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) has the lowest survival rate among cancers. Despite its limited efficacy, gemcitabine is widely used in PDAC regimens. Chemoresistance to gemcitabine is likely a contributor to its poor effectiveness. Our previous research has shown that gemcitabine induces a cytoprotective autophagy and lysosomal response in pancreatic cancer cells. Further understanding of the mechanisms behind this autophagy and lysosomal response could lead to new therapeutic opportunities. It is known that gemcitabine can cause DNA replication arrest, double-strand breaks, and possibly nucleolar stress. Herein, we aim to specifically determine whether gemcitabine induces nucleolar stress and if this nucleolar stress triggers a cytoprotective response. Indicative of nucleolar stress, we demonstrate nucleoplasmic localization of nucleolin and nucleolar morphological changes upon gemcitabine treatment. Treatment of cells with the nucleolar stress inducer CX-5461 leads to an autophagy and lysosomal response as monitored by increased LC3 and LAMP1 puncta, and mature cathepsin B levels. Furthermore, enriched nuclear localization of the master regulator of autophagy and lysosomal function, TFEB, is observed in CX5461-treated cells (as detected by immunofluorescence and subcellular fractionation). This nuclear enrichment of TFEB correlates with the enrichment of faster migrating forms of TFEB (indicative of post-translational modification changes) as detected by immunoblotting. Through clonogenic assays, PDAC cells with reduced TFEB function (PDAC-shTFEB) demonstrate higher sensitivity than control cells to CX-5461. Furthermore, PDAC-shTFEB cells express higher levels of apoptotic markers upon CX-5461 treatment. Overall, our data provide the first evidence that nucleolar stress induces a TFEB-dependent protective response. Given that our work was performed in cells without functional wild-type p53 signaling, TFEB could act as a sensor of nucleolar stress relaying a protective response and assisting cells to engage in timely and coordinated action to cope with stress. Therefore, our results provide further support for the involvement of TFEB in the chemoresistance of PDAC cells. Citation Format: Florence Mc Duff, Laure Bessy, Benoit Marchand, Marie-Josee Boucher. TFEB protects pancreatic cancer cells against nucleolar stress [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 A086.
Abstract B008: Secretome labeling identifies gelsolin as a potential pro-tumorigenic PDAC biomarker
Authors: Jonathan P. Kastan, Oliver Standring, Paolo Cifani, Victoria Gaeth, Amanda Jensen, Youngkyu Park, David Tuveson
Journal: Cancer Research (2024)

Abstract Pancreatic Ductal Adenocarcinoma (PDAC) is a highly lethal malignancy with a 5-year survival rate around 10% due to late detection and therapeutic resistance. Thus, new methods to detect PDAC earlier in high-risk and general populations are greatly needed. Early detection tests have historically relied on circulating nucleic acids or proteins that have been identified as enriched in patients with PDAC by large-scale studies, but they often lack a firm basic biological context that would bolster the sensitivity and specificity of these tests. To this end, we have introduced a construct into PDAC organoid and 2D lines that enables the labeling of PDAC-secreted proteins with biotin (Sec61-BioID) in vitro and in vivo. With this system, we can specifically isolate the PDAC secretome and identify the proteins via mass spectrometry. From this approach, we have identified Gelsolin (GSN), an enzyme that regulates actin dynamics, as a highly secreted protein by a panel of PDAC cell lines in vitro and in vivo. We have explored the biological role of secreted GSN in PDAC tumorigenesis via CRISPR knockout. GSN knockout abrogated the growth of PDAC tumors in NSG mice, and we are delineating the potential mechanisms that explain this defect via histological analysis and in vitro cell proliferation and invasion assays. Additionally, we have analyzed purified secreted GSN from PDAC lines by mass spectrometry to identify potential post-translational modifications that may differentiate PDAC-derived GSN from other GSN molecules, secreted by healthy tissue, in circulation. We are currently utilizing biochemical approaches to validate these putative modifications and define their specificity in PDAC patient blood as compared to healthy age-matched controls. Citation Format: Jonathan P. Kastan, Oliver Standring, Paolo Cifani, Victoria Gaeth, Amanda Jensen, Youngkyu Park, David Tuveson. Secretome labeling identifies gelsolin as a potential pro-tumorigenic PDAC biomarker [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 B008.