tbuckley/cabot-search huggingface dataset:
Abstract C044: Macropinocytic stress reprograms cancer-associated fibroblasts and enhances therapeutic responses in pancreatic cancer
Authors: Yijuan Zhang, Swetha Maganti, Jennifer Hope, Li Ling, Cheska Marie Galapate, Florent Carrette, Linda Bradley, Cosimo Commisso
Journal: Cancer Research (2024)

Abstract Macropinocytosis is a fundamental metabolic pathway that has been demonstrated to support the survival and function of tumor cells and cancer-associated fibroblasts (CAFs) in pancreatic ductal adenocarcinoma (PDAC) through in vitro studies and xenograft mouse models. However, the impact of macropinocytosis on the PDAC tumor microenvironment in an immune-competent setting remains poorly understood. In this study, we utilized the selective inhibitor 5-(N-ethyl-N-isopropyl)-amiloride (EIPA) to block macropinocytosis in both tumor cells and CAFs in syngeneic PDAC mouse models. We observed that EIPA treatment inhibited PDAC tumor growth, which was accompanied by reduced tumor proliferation and increased cell apoptosis. Moreover, EIPA treatment decreased the presence of myofibroblastic CAFs and collagen deposition within PDAC tumors, while also promoting the expansion of tumor vasculature. By modifying the tumor stroma, EIPA priming enhanced drug delivery and improved the effectiveness of PDAC chemotherapy. Interestingly, immune profiling of PDAC tumors revealed that EIPA administration specifically increased the infiltration of CD8+ and CD4+ T cells. We discovered that EIPA induced changes in the cytokine/chemokine landscape within tumors by triggering an inflammatory CAF (iCAF)-like phenotype. Mechanistically, we discerned that inhibition of macropinocytosis triggers metabolic stress that in turn activates stress-responsive transcription factors and promotes the expression of early-phase proinflammatory cytokines and chemokines in mouse CAFs. Notably, combination treatment with EIPA and immune checkpoint blockade (ICB) reduced PDAC tumor burden and significantly inhibited tumor metastasis. Overall, our findings establish that macropinocytosis functions to support the barrier function of the stroma by maintaining fibroblastic identity and provide further evidence that inhibition of macropinocytosis represents a promising therapeutic modality in PDAC. Citation Format: Yijuan Zhang, Swetha Maganti, Jennifer Hope, Li Ling, Cheska Marie Galapate, Florent Carrette, Linda Bradley, Cosimo Commisso. Macropinocytic stress reprograms cancer-associated fibroblasts and enhances therapeutic responses 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 C044.
Abstract C065: Base excision repair pathway regulates transcription-replication conflicts in pancreatic ductal adenocarcinoma
Authors: Fan Meng, Anup K. Singh, Tiane Li, Marc Attiyeh, Fatemeh Kohram, Terence Williams, Yilun Liu, Mustafa Raoof
Journal: Cancer Research (2024)

Abstract Oncogenic mutations (such as in KRAS) can dysregulate transcription and replication leading to transcription conflicts (TRCs). Unresolved TRCs can cause lethal DNA damage. Here, we sought to investigate the causal role of oncogenic mutations in regulating TRCs in pancreatic ductal adenocarcinoma (PDAC). Further, we characterize the adaptive pathways that mitigate TRCs for PDAC survival. Human PDAC demonstrated 30-120-fold higher levels of TRC genomic signature compared to breast, colon and lung cancer (p&amp;lt;0.001). Gene expression analysis demonstrated high levels of known TRC resolution factors in human tumors compared to normal tissues. TRCs as measured by RNAPII-PCNA proximity ligation assay were significantly enriched in human PDAC cells (Panc-1, BxPC3, MiaPaca2) compared to immortalized normal HPNE cells (p&amp;lt;0.001). Similarly transcriptomic complexes were enriched in nascent DNA immunoprecipitates from Panc1 cells but not HPNE cells. Ectopic expression of oncogenic KRAS(G12D) in human pancreatic ductal epithelial (HPNE) cells enhanced TRCs, and TRC-related DNA:RNA hybrids (R-loops). Inhibition of KRAS or downstream effectors abrogated TRCs in Panc1 and MiaPaca2 cells. An siRNA screen identified several factors in the base-excision repair (BER) pathway as regulators of TRCs. Sub-lethal exposure to hydrogen peroxide enhanced TRCs, whereas N-acetyl cysteine abrogated TRCs. These findings were validated by a pharmacologic approach using inhibitors of APE1 endonuclease in BER pathway (Methoxyamine and CRT). Mechanistic studies revealed that BER pathway inhibition severely altered RNA polymerase II dynamics at nascent DNA; causing RNAPII trapping and contributing to enhanced TRCs. The ensuing DNA damage activated Chk2-ATR pathway but not Chk1-ATM pathway. Co-treatment with ATR inhibitor (VX970, 10-80nM) and BER inhibitor (methoxyamine, 6-12mM) at clinically relevant doses, synergistically enhanced DNA damage and reduced clonogenic survival in PDAC cells. The study uncovers a novel role of BER pathway defects and oxidative DNA damage in promoting TRCs. Our studies provide mechanistic insights into the regulation of TRCs in PDAC which has implications for genome instability and therapy in PDAC. Citation Format: Fan Meng, Anup K. Singh, Tiane Li, Marc Attiyeh, Fatemeh Kohram, Terence Williams, Yilun Liu, Mustafa Raoof. Base excision repair pathway regulates transcription-replication conflicts 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 C065.
Abstract A118: Chromatin accessibility profiling of human pancreatic tumors reveals epigenetic features of malignancy and rapid recurrence
Authors: Kevin MacPherson, Jason M. Link, Patrick Worth, Brett Sheppard, Andrew Fields, Colin Daniel, Andrew Nishida, Carl Pelz, Trent Waugh, Ethan Agritelle, John Muschler, Andrew Adey, Rosalie Sears
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) disease progression involves complex cell state transitions in both malignant and non-malignant populations within the tumor microenvironment. To uncover PDAC cell states and epigenetic features associated with clinical outcome, we studied 42 PDAC samples (35 primary tumors and 7 metastases) from 41 patients with single cell ATAC-seq, along with 10 sample-matched single cell RNA-seq profiles. Our work uncovered thousands of chromatin regions with altered accessibility in malignant cells relative to normal ductal and acinar cells. Numerous epigenetic changes were universal to all PDAC clusters regardless of patient-of-origin and occurred proximal to genes involved in glycolysis, regulation of MYC, hypoxic response, extracellular matrix remodeling, and repression of transposable elements. Topic modeling of high dimensional chromatin data revealed networks of co-accessible cis-regulatory regions active in malignant cells, as well as networks specific to basal-like and classical PDAC molecular subtypes. Furthermore, our epigenomic data also suggest alternate paths of lineage infidelity across the classical-basal continuum: while basal-like PDAC cells acquire chromatin accessibility mimicking that of skin or mammary epithelial tissue, several classical subtype tumors featured a subpopulation of malignant cells with increased accessibility of neural-associated chromatin regions genome-wide. Within the immune compartment, we also identified a cis-regulatory network with increased activity in T-cells sampled from rapidly recurring PDAC tumors. Motif analysis of this network revealed enrichment for SMAD and FOXP1 motifs, suggesting widespread modification of T-cells by TGF-β. To our knowledge, our work is the largest single-cell resolution study of chromatin state in human PDAC to date, revealing key epigenetic features associated with PDAC subtype and clinical outcome. Citation Format: Kevin MacPherson, Jason M. Link, Patrick Worth, Brett Sheppard, Andrew Fields, Colin Daniel, Andrew Nishida, Carl Pelz, Trent Waugh, Ethan Agritelle, John Muschler, Andrew Adey, Rosalie Sears. Chromatin accessibility profiling of human pancreatic tumors reveals epigenetic features of malignancy and rapid recurrence [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 A118.
Abstract C041: Oncostatin-M and transforming growth factor-beta promote loss of PTEN in PDAC cancer associated fibroblasts
Authors: Ivo N. Woogeng, Lu Han, Samaneh Saberi, Cameron Bumbleburg, Joseph Beaudet, Sudarshana Sharma, Michael Ostrowski
Journal: Cancer Research (2024)

Abstract Pancreatic Ductal Adenocarcinoma (PDAC) is a deadly malignancy with poor prognosis and treatment options. Cancer associated fibroblasts (CAFs) play a complex role in the PDAC tumor microenvironment (TME), contributing significantly to the progression of the tumor and the dense desmoplastic stroma. Phosphatase and tensin homolog (PTEN) is a tumor suppressor and its loss in both the tumor and in CAFs is associated with increased tumor aggressiveness and resistance to therapy. Our group previously demonstrated PTEN loss occurs in CAFs in ~25% of PDAC patient samples, which correlated with worsened outcomes. In addition, PTEN expression was lost in 80% of SMA+ CAFs in mouse PDAC models. Genetic or pharmacologic inhibition of the hedegehog pathway leads to ubiquitin-dependent destruction of PTEN by the proteosome. However, little is known of the signals produced by tumor cells that trigger PTEN degradation in CAFs. In order to address this problem, we developed an in vitro assay system based on wild type murine PDAC-CAFs that expresses a PTEN-GFP fusion protein. Initially, we focused on IL6 and IL6 family members Leukemia Inhibitory Factor (LIF) and Oncostatin-M (OSM) and Transforming Growth Factor beta 1 (TGFb1). The SMO inhibitor GDC-0449 was used as a positive control. PTEN stability was evaluated using the LSM 880 confocal microscope and GFP+ cells were quantified with QuPath-0.4.3 and analyzed with GraphPad Prism. Among the repertoire of secreted factors, we found that only OSM and TGFb1 could destabilize PTEN after 48H of treatment. When queried against the single cell RNA sequence dataset produced by our lab, we observed that CD45+ leukocytes were the likely source of OSM whereas TGFb1 was produced by tumor cells, fibroblasts, and immune cells. In conclusion, OSM and TGFb1 can downregulate PTEN in CAFs in vitro. Current efforts are aimed at testing whether inhibition of these pathways can restore PTEN expression in mouse PDAC models, and in identifying signaling pathways and E3-ligases that mediate PTEN destruction. These pathways and interactions could be further exploited for selective inhibition aimed at therapeutic benefits in curbing PDAC progression. Citation Format: Ivo N. Woogeng, Lu Han, Samaneh Saberi, Cameron Bumbleburg, Joseph Beaudet, Sudarshana Sharma, Michael Ostrowski. Oncostatin-M and transforming growth factor-beta promote loss of PTEN in PDAC 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 C041.
Abstract B101: Tumor-selective inhibition of active RAS in pancreatic ductal adenocarcinoma
Authors: Urszula N. Wasko, Jingjing Jiang, Lorenzo Tomassoni, Yingyun Wang, Bianca Lee, Margo Orlen, Kristina Drizyte-Miller, Marie Menard, Julien Dilly, Steven A. Sastra, Carmine F. Palermo, Stephanie Chang, Andrew J. Aguirre, Channing J. Der, Robert H. Vonderheide, Ben Z. Stanger, Andrea Califano, Mallika Singh, Kenneth P. Olive
Journal: Cancer Research (2024)

Abstract RM-042 is a broad-spectrum inhibitor of the active (GTP-bound) form of KRAS, HRAS, and NRAS, with affinity for both mutant and wild type (WT) variants (RASMULTI(ON)). Given that more than 90% of human pancreatic ductal adenocarcinoma (PDAC) cases are driven by activating mutations in KRAS, we assessed the therapeutic potential of RM-042 in a comprehensive range of PDAC models, including human and murine cell lines, human patient-derived organoids, human PDAC explants, subcutaneous and orthotopic cell-line or patient derived xenografts, syngeneic allografts, and genetically engineered mouse models. We observed broad and remarkable anti-tumor activity across these models following direct RAS inhibition by RM-042 at doses and concentrations that were tolerable in vivo. Analyses of tumor and normal tissues following RM-042 treatment revealed divergent cellular responses to RAS inhibition. While we observed anti-proliferative effects in both normal and tumor tissues, RAS-dependent tumors alone exhibited a susceptibility to cell death via apoptosis within hours of dosing. Finally, using single cell regulatory network analysis, we found that different subtypes of PDAC malignant epithelial cells responded in distinct ways to RAS inhibition by RM-042, resulting in an enrichment of the more differentiated gastro-intestinal lineage state (GLS) cellular subtype. Together, these data have significant implications for the clinical development of RAS inhibitors in the setting of PDAC. A related inhibitor, RMC-6236, is currently in early clinical evaluation (NCT05379985). Citation Format: Urszula N. Wasko, Jingjing Jiang, Lorenzo Tomassoni, Yingyun Wang, Bianca Lee, Margo Orlen, Kristina Drizyte-Miller, Marie Menard, Julien Dilly, Steven A. Sastra, Carmine F. Palermo, Stephanie Chang, Andrew J. Aguirre, Channing J. Der, Robert H. Vonderheide, Ben Z. Stanger, Andrea Califano, Mallika Singh, Kenneth P. Olive. Tumor-selective inhibition of active RAS 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 B101.
Abstract B098: Oncogenic KRAS relies on β1 integrin expression to drive pancreatic neoplasia and PDAC development
Authors: John L. Muschler, Ge Huang, Alexander C. Smith, Rosalie C. Sears
Journal: Cancer Research (2024)

Abstract Oncogenic Kras drives cancer progression through cooperation with multiple cellular factors, many of which are yet to be determined. The β1 integrins, a family of extracellular matrix receptors, are strong candidates; they are implicated in many aspects of cancer progression including cell growth and survival signaling, cell migration and metastasis. Additionally, multiple studies have identified β1 integrins within the interactome of oncogenic Kras. We are investigating the potential cooperation if β1 integrins in Kras-mediated oncogenesis using genetic perturbations within the tamoxifen-inducible and conditional Ptf1a-CreERTM; LSL- KrasG12D (p48-KCER) model of pancreatic cancer. Conditional deletion of the β1 integrins from the adult pancreas produced minimal tissue abnormalities; there were no obvious tissue defects at 6 months post induction, although there was some evidence of pancreatitis at 1 year post induction. However, deletion of the β1 integrins within the KCER model of pancreatic cancer (KCER-Δβ1) resulted in a profound suppression of pancreatic disease progression. There was no detectable neoplasias at 3 months post-induction and minimally detectable neoplasias at 6 months post-induction, compared to prominent neoplasia development and stromal expansion in the control KCER mice at these time-points. Moderate stromal expansion was observed in KCER-Δβ1 mice at 6 months post-induction despite the lack of neoplasia development. To investigate the mechanisms of this integrin-KRAS cooperation, we conditionally deleted the expression of two canonical integrin signaling molecules, the integrin-linked kinase (ILK) and the focal adhesion kinase (FAK). Neither the ILK knockout (KCER-ΔILK) nor the FAK knockout (KCER-ΔFAK) phenocopied the KCER-Δβ1 mice, as both developed neoplasias and stromal expansion at 3 months post-induction and beyond. To explore the role of integrin activation, we next deleted expression of the integrin-cytoskeleton linker molecule Talin-1 in the KCER model. Surprisingly, even though Talin-1 is key to integrin activation, the KCER-ΔTalin-1 mice also failed to phenocopy the KCER-Δβ1, showing ample neoplasia development at 3 and 6 months post-induction, and trending towards faster disease progression at later stages. These combined results demonstrate crucial cooperation between oncogenic Kras and β1 integrins to drive pancreatic cancer progression, and point to non-canonical β1 integrin functions in mediating this cooperation. Citation Format: John L. Muschler, Ge Huang, Alexander C. Smith, Rosalie C. Sears. Oncogenic KRAS relies on β1 integrin expression to drive pancreatic neoplasia and PDAC development [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 B098.
Abstract C039: Disruption of ADAM17-dependent cellular crosstalk inhibits tumor progression of pancreatic ductal adenocarcinoma
Authors: Hui-Ju Wen, Howard Crawford
Journal: Cancer Research (2024)

Abstract Activation of cellular signaling pathways by crosstalk between tumor cells and their microenvironment is an essential mechanism supporting pancreatic carcinogenesis. In this study, we aim to disrupt cellular signaling pathways by targeting ADAM17 (a disintegrin and metalloprotease 17). ADAM17 is a membrane bound enzyme which cleaves cell surface proteins. Its function is closely linked with autocrine and paracrine signaling of immunomodulation as well as activation of EGFR, which is a central molecule for pancreatic tumorigenesis. To investigate whether EGFR is activated via a paracrine manner from macrophages, the most abundant immune-related stromal cells in pancreas cancers, we generated a pancreatic tumor mouse model with ADAM17 deletion in myeloid cells by using a dual recombinase strategy. We observed that lack of ADAM17 in the myeloid cells resulted in a delay of acinar cell transformation and an associated decrease in EGFR activation. To further examine the tumor supportive role of ADAM17, inhibition of ADAM17 using anti-ADAM17 antibody, MEDI3622, was tested in orthotopic tumor bearing mice. systemic inhibition of ADAM17 led to a reduction in tumor burden and a concomitant decrease in EGFR activation. These effects were observed exclusively in the immunocompetent animals, but not in the immunodeficient animals. It implicates that inhibition of tumor growth by MEDI3622 is highly dependent on the immune response. Furthermore, we found an elevated level of CCL21 in the MEDI3622-treated tumors resulting in increased tumor infiltration by dendritic cells and cytotoxic T cells for tumor killing. Altogether, ADAM17 blockade displays a pronounced anti-tumor effect, suggesting ADAM17 as a therapeutic target of pancreatic cancer. Citation Format: Hui-Ju Wen, Howard Crawford. Disruption of ADAM17-dependent cellular crosstalk inhibits tumor progression of 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 C039.
Abstract PR12: Targeting CDK7/9 in basal pancreatic cancer
Authors: Sita Kugel, Nithya Kartha, Jessica E. Gianopulos, Zach Schrank, Sarah M. Cavender, Stephanie Dobersch, Notta Faiyaz, David H. Price, Andrew C. Hsieh, Sunil R. Hingorani
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDA) is classified into two distinct subtypes, classical and basal, with the basal subtype predicting worse survival in patients. We hope that with a deeper understanding of the biology that drives these subtypes, we can identify novel subtype-specific therapies. We recently described a novel finding that basal PDAs are uniquely sensitive to transcriptional inhibition by targeting cyclin-dependent kinase 7 (CDK7) and CDK9. Additionally, we identified that Sirtuin 6 histone deacetylase (SIRT6) expression levels correlate with PDA subtype, showing that basal PDA is low in SIRT6 expression and classical PDA is high through analysis of hundreds of human PDA tumors. Furthermore, we uncovered an important mechanism by which SIRT6 regulation of the integrated stress response (ISR) can control sensitivity of PDA to CDK7/9 inhibitors. By using a variety of in vitro drug assays, genetic manipulation experiments, immunofluorescence, cycloheximide chase experiments, and in vivo drug studies in human patient-derived xenografts (PDXs) of PDA, we were able to show that SIRT6 regulates activating transcription factor 4 (ATF4) protein stability. Therefore, SIRT6 high/classical PDA has a constitutively active ISR, enabling it to recover and survive the stress of CDK7/9 transcriptional inhibition. On the other hand, basal PDA has low SIRT6 which promotes ATF4 protein instability and a nonfunctional ISR, therefore CDK7/9 transcription inhibition leads to apoptosis. Furthermore, we found that similar to intrinsic resistance, acquired resistance to CDK7/9 inhibitors occurs through the loss of basal state drivers and that restoration of these genes re-sensitizes cells to CDK7/9 inhibition. Importantly, this work highlights the role of chromatin modifiers in regulating PDA subtypes and sensitivity to CDK7/9 inhibitors. PDA subtypes have very distinct chromatin landscapes. We have found that classical PDA maintains its epithelial cell state through chromatin regulators like the SETDB1 heterochromatin complex and more specifically the KRAB-Zinc Finger protein ZNF274. Loss or gain of ZNF274 can induce a cell state change in which classical PDA loses its epithelial characteristics and becomes more mesenchymal in nature. Excitingly, this sensitizes cells to CDK7/9 inhibition. Thus, our work demonstrates the importance of cell state and subtype in therapeutic response to CDK7/9 inhibitors in pancreatic cancer. Citation Format: Sita Kugel, Nithya Kartha, Jessica E. Gianopulos, Zach Schrank, Sarah M. Cavender, Stephanie Dobersch, Notta Faiyaz, David H. Price, Andrew C. Hsieh, Sunil R. Hingorani. Targeting CDK7/9 in basal 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 PR12.