tbuckley/cabot-search huggingface dataset:
Abstract C010: Single-cell profiling unleashes KRAS-driven redrafting of the tumor microenvironment before cancer onset
Authors: Chantal Allgoewer, Markus Breunig, Meike Hohwieler, Medhanie Mulaw, Alexander Kleger
Journal: Cancer Research (2024)

Abstract Pancreatic cancer is a highly lethal and aggressive disease, commonly characterized by a unique tumor microenvironment, where mutant KRAS signaling plays a pivotal role in its pathophysiology. To deepen our understanding of KRAS-dependent signaling in earliest tumor development, oncogenic KRAS (KRASG12D) expression was induced in human stem cell-derived pancreatic ductal-like organoids (PDLOs), followed by time-resolved single-cell RNA and bulk ATAC sequencing. This unique precancerous state model facilitated a comprehensive characterization of early oncogenic events at cellular resolution. Furthermore, a machine learning approach was applied to accurately predict KRAS-dependent cell identities. Within seven days, mutated KRAS triggers distinct gene signature programs related to extracellular matrix remodeling and inflammation. Although derived from dysplastic yet non-cancerous states, these gene signatures negatively correlated with overall survival in PDAC (pancreatic ductal adenocarcinoma) patients. The KRAS-dependent signatures retrieved with the machine learning approach allowed the grouping of 24 published PDAC cases, showing differences in niche composition and communication patterns. Various co-culture systems demonstrated that KRASG12D-expressing PDLOs could activate pancreatic stellate cells, inducing a cancer- associated fibroblast (CAF)-like state. Simultaneously, these KRAS-activated organoids were protected from T cell infiltration in vitro. Furthermore, in silico approaches were employed to reconstruct a virtual pancreatic cancer space, demonstrating that our PDLOs transcriptionally bridge healthy and malignant ductal states. This also revealed potential KRAS-driven pathways mediating CAF activation and T cell shielding preceding cancer onset. In summary, our human PDLO model enables us to explore the transition from normal to cancerous states, addressing gaps in our understanding of tumor development and tumor niche preparation. Citation Format: Chantal Allgoewer, Markus Breunig, Meike Hohwieler, Medhanie Mulaw, Alexander Kleger. Single-cell profiling unleashes KRAS-driven redrafting of the tumor microenvironment before cancer onset [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 C010.
Abstract A037: Role of hypoxia in fibroblast reprogramming in pancreatic cancer
Authors: Tenzin Ngodup, Ashley Mello, Katelyn Donahue
Journal: Cancer Research (2024)

Abstract Pancreatic ductal adenocarcinoma (PDAC) is characterized by a dense desmoplastic stroma, comprised of extracellular matrix, cancer-associated fibroblasts (CAFs), and immune cells. Due to the rapid tumor growth and the unusually low blood vessel density of PDAC, both tumor cells and stromal cells experience hypoxia, or the low availability of oxygen. Although hypoxia is a crucial feature of the tumor milieu and predicts poor clinical outcome, the effects of hypoxia on the PDAC stromal cells, as well as the interplay between tumor and stroma, is not well understood. Cancer-associated fibroblasts (CAFs) are a predominant and heterogeneous stromal cell type in PDAC, and single-cell transcriptomics of human and mouse PDAC revealed a distinct CAF subpopulation, inflammatory CAFs (iCAFs). These inflammatory fibroblasts produce high levels of cytokines and chemokines in PDAC, potentially contributing to its immunosuppressive microenvironment and tumorigenesis. By injecting a hypoxia probe into PDAC mouse models, we previously showed that iCAFs predominantly reside in oxygen- starved regions of the tumor. Furthermore, we observed that the hypoxia-related gene signature is positively enriched in iCAFs in human PDAC tissues. By exposing three-dimensional (3D) cocultures of pancreatic tumor cells and fibroblasts to hypoxia, we found that hypoxia induces IL1ɑ from tumor cells, thereby promoting iCAF formation. Importantly, tumor cell IL1ɑ was further elevated in the presence of hypoxic fibroblasts, implicating hypoxia as a modulator of bidirectional tumor cell-CAF interactions. Efforts are ongoing to understand the mechanism by which hypoxia regulates CAF phenotype by modulating the bidirectional crosstalk between tumor cells and fibroblasts in PDAC. Together, our study identifies hypoxia as a crucial environmental factor in promoting the iCAF phenotype, thus highlighting an instructive role of hypoxia in shaping the stromal microenvironment. Citation Format: Tenzin Ngodup, Ashley Mello, Katelyn Donahue. Role of hypoxia in fibroblast reprogramming in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A037.
Abstract C061: Loss of CaMK2B accelerates tumor formation and enhances metastatic competency in genetically engineered mouse models of PDAC
Authors: Jessica Peura, Nikita Bhalerao, Calvin Johnson, Yamini Ogoti, Faith Keller, Emma Watson, Zhen Zhao, Jason Pitarresi
Journal: Cancer Research (2024)

Abstract Background Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer- related deaths in the United States and is often not diagnosed until it has already metastasized. Our prior work established that calcium signaling pathways facilitate a pro-metastatic phenotype through the induction of an epithelial-to-mesenchymal transition (EMT) program in PDAC tumor cells, but the downstream signaling molecules mediating this phenotype have remained elusive. MethodsUsing a novel genetically engineered model of pancreatic cancer, we demonstrate that loss of Calcium/calmodulin-dependent kinase-II B (CaMK2B), a downstream effector kinase activated by calcium, enhances cellular plasticity, and increases metastasis. To this end, we generated a genetically engineered mouse model where Camk2b was knocked out in tumor cells in a lineage-labeled Kras- and p53-driven PDAC mouse model (herein KPCY-Camk2bcKO). Results Genetic deletion of Camk2b in the KPCY genetically engineered model accelerated tumor formation and dramatically reduced the overall median survival of KPCY- Camk2b cKO mice (78 days) relative to KPCY controls (136 days). Pathological and immunofluorescence analysis of KPCY-Camk2b cKO animals showed an increased number of poorly differentiated tumor regions and a higher metastatic burden, with &amp;gt;85% of KPCY- Camk2b cKO animals presenting with multi-focal metastases. Further analysis of tumor cells in KPCY-Camk2b cKO mice showed enhanced expression of markers of the highly aggressive squamous PDAC subtypes. Strikingly, Camk2b deletion combined with oncogenic Kras G12D (in the absence of p53 alterations), was sufficient to form lethal metastatic PDAC tumors, while age-matched control Kras G12D tumors with intact Camk2b only progressed to the acinar-to-ductal metaplasia (ADM) or Pancreatic Intraepithelial Neoplasia (PanIN) stage. Collectively, these results establish Camk2b loss as a new oncogenic and pro-metastatic mechanism in PDAC Conclusion This work demonstrates that Camk2b loss enhances tumor cell evolution and plasticity within PDAC to promote metastasis. In this context, we speculate that loss of Camk2b rewires calcium signaling to drive an aggressive subtype of PDAC with increased metastasis. Citation Format: Jessica Peura, Nikita Bhalerao, Calvin Johnson, Yamini Ogoti, Faith Keller, Emma Watson, Zhen Zhao, Jason Pitarresi. Loss of CaMK2B accelerates tumor formation and enhances metastatic competency in genetically engineered mouse models of PDAC [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 C061.
Abstract C024: Quantitative mass spectrometry-based multi-omic profiling to overcome drug resistance in pancreatic cancer post KRAS G12D inhibition
Authors: Qijia Yu, Nicole Sindoni, Huan Zhang, Ziyue Li, Joao A. Paulo, Andrew J. Aguirre, Joseph D. Mancias
Journal: Cancer Research (2024)

Abstract Recently developed inhibitors targeting the KRASG12D oncoprotein are undergoing clinical trial evaluation including in patients with pancreatic adenocarcinoma (PDAC). However, resistance to such targeted therapies is a frequent occurrence, potentially undermining the long-term success of KRAS inhibitors (KRASi). To uncover the adaptive pathways and cell surface biomarkers to KRASi and to identify effective drug combinations that can overcome resistance, we employ a mass spectrometry-based quantitative temporal proteomics workflow. This approach allows us to map the proteomic changes in response to KRASi in both in vitro and in vivo PDAC models. We identify and quantify 10,898 proteins, creating the most extensive proteomic dataset related to KRASi to date. We identify shared mechanisms of both acute and long-term adaptation to KRASi across PDAC models. Utilizing this proteomic information, we are pinpointing drug combinations that pair KRASi with inhibitors of CDK4/6, AURKA, and mTOR to increase cytotoxicity and thereby reduce development of long-term resistance. Surfaceome analyses identifies cell surface proteins upregulated upon acute and long-term KRASi, including TACSTD2 (Trop-2). Antibody-drug conjugates targeting upregulated surface proteins may be a useful orthogonal approach towards preventing or circumventing KRASi resistance with testing of Trop-2 and other candidates ongoing. In summary, through mass spectrometry-based quantitative temporal proteomics, we identify proteomic adaptations to KRASi in PDAC and propose combination treatments with promising therapeutic potential. Citation Format: Qijia Yu, Nicole Sindoni, Huan Zhang, Ziyue Li, Joao A. Paulo, Andrew J. Aguirre, Joseph D. Mancias. Quantitative mass spectrometry-based multi-omic profiling to overcome drug resistance in pancreatic cancer post KRAS G12D inhibition [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 C024.
Abstract C058: A novel approach to understanding pancreas cancer risk through enhancer- promoter interactions
Authors: Li Wang, Songjoon Baek, Gauri Prasad, Thucnhi Truongvo, Jason Hoskins, Laufey Amundadottir, Efsun Arda
Journal: Cancer Research (2024)

Abstract Genetic or epigenetic variations in regulatory enhancer elements increase susceptibility to a range of pathologies, including pancreas cancer. Pinpointing genes affecting pancreas cancer risk holds promise for early detection, prevention, and effective therapies. Despite recent advances, linking enhancer elements to target genes and predicting the transcriptional outcome of enhancer dysfunction remain significant challenges. Using 3D chromatin assays, we generated an extensive enhancer interaction dataset for the human pancreas, spanning more than 20 donors and five major cell types, including both the exocrine and endocrine compartments. We employed a network approach to parse chromatin interactions into enhancer-promoter tree models, facilitating quantitative, genome-wide analysis of enhancer connectivity. Using the tree models, we developed a machine learning algorithm capable of estimating the impact of enhancer perturbations on cell-type specific gene expression in the human pancreas. Complementing this computational approach, we streamlined an experimental platform using CRISPR-interference and RNA-FISH coupled with high-throughput imaging to quantitatively measure the effect size of enhancer perturbations in primary human pancreas cells. Our enhancer tree models enabled functional annotation of genetic variants associated with pancreas diseases, revealing novel target genes in specific cell types. For pancreas cancer (PDAC), our data suggests a stronger association of disease susceptibility variants with acinar cells, even though ductal cells historically have been the focus of PDAC. This discovery linked three potentially functional variants associated with PDAC risk to acinar cell enhancers, revealing novel target genes to further investigation. By integrating genomics with mechanistic findings into enhancer function, our work offers a framework for understanding genetic basis of pancreas cancer disease risk. Citation Format: Li Wang, Songjoon Baek, Gauri Prasad, Thucnhi Truongvo, Jason Hoskins, Laufey Amundadottir, Efsun Arda. A novel approach to understanding pancreas cancer risk through enhancer- promoter interactions [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 C058.
Abstract B064: Antigen-presenting type-I conventional dendritic cells facilitate curative checkpoint blockade immunotherapy in pancreatic cancer
Authors: Krishnan K Mahadevan, Allison M. Dyevoich, Yang Chen, Bingrui Li, Hikaru Sugimoto, Amari Sockwell, Kathleen McAndrews, Huamin Wang, Shabnam Shalapour, Stephanie Watowich, Raghu Kalluri
Journal: Cancer Research (2024)

Abstract The link between cancers and inflammation was first made by Rudolph Virchow more than a century ago when cancers were observed at sites with chronic inflammation. The host response to cancer shares many parallels with inflammation and wound healing process.Inflammation and tissue damage associated with pancreatitis can precede or occur concurrently with pancreatic ductal adenocarcinoma (PDAC). We demonstrate that in PDAC coupled with pancreatitis (ptPDAC), antigen-presenting type-I conventional dendritic cells (cDC1s) are specifically activated. Immune checkpoint blockade therapy (iCBT) leads to cytotoxic CD8+ T cell activation and eradication of ptPDAC with restoration of lifespan even upon PDAC re-challenge. Such eradication of ptPDAC was reversed following specific depletion of dendritic cells. Employing PDAC antigen-loaded cDC1s as a vaccine, immunotherapy-resistant PDAC was rendered sensitive to iCBT with a curative outcome. Analysis of the T-cell receptor (TCR) sequences in the tumor infiltrating CD8+ T cells following cDC1 vaccination coupled with iCBT identified unique CDR3 sequences with potential therapeutic significance. Our findings identify a fundamental difference in the immune microenvironment and adaptive immune response in PDAC concurrent with, or without pancreatitis, and provides a rationale for combining cDC1 vaccination with iCBT as a potential treatment option. Citation Format: Krishnan K Mahadevan, Allison M. Dyevoich, Yang Chen, Bingrui Li, Hikaru Sugimoto, Amari Sockwell, Kathleen McAndrews, Huamin Wang, Shabnam Shalapour, Stephanie Watowich, Raghu Kalluri. Antigen-presenting type-I conventional dendritic cells facilitate curative checkpoint blockade immunotherapy 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 B064.
Abstract B037: Banana Lectin expressing CAR T cells to target Pancreatic Cancer
Authors: Katie McKenna, Ada I Ozcan, David Markovitz, Malcolm K Brenner
Journal: Cancer Research (2024)

Abstract To overcome both the heterogenous and dynamic expression of tumor antigen expression in pancreatic ductal adenocarcinoma (PDAC) and the physical barrier provided by the associated fibrotic stroma, we have developed a novel therapy that recognizes and binds to distinct patterns of aberrant glycosylation specifically expressed on tumor cells and their surrounding stroma. Aberrant glycosylation patterns are a hallmark of cancer and are widely present on tumors including PDAC. We therefore incorporated H84T BanLec as part of a chimeric antigen receptor and co-expressed the construct in T cells and showed that H84T BanLec CAR expressing T-cells can effectively target pancreatic tumors. We hypothesized that our novel lectin CAR would enhance the activity of T cells when co-expressed with conventional scFV – derived CARs targeting tumor associated antigens We compared the activity of dual-expressing H84T/HER.2 CAR-T or H84T/PSMA CAR-T cells against single- expressing CARs targeting PDAC. We determined anti-tumor cytotoxicity by measuring residual GFP+ tumor cells in a sequential killing assay using flow cytometry. We observed superior anti-tumor activity using dual expressing CAR T cells compared to T cells expressing either HER.2- or H84T- or PSMA- CAR alone. Similarly, in 3D multicellular spheroids containing tumor and cancer-supportive stromal cells, an IncuCyte live imaging assay shows dual CAR T cells have greater cytotoxicity against PDAC than single CAR expressing T cells (p= 0.02 H84T/HER.2 vs HER.2 CAR; p=0.00003 H84T/PSMA CAR vs PSMA CAR). These results also translate to improved anti- tumor function of dual CAR T cells in PDAC xenograft in vivo models where H84T/HER.2 CAR T cells significantly reduced the tumor volume burden (p=0.015; H84T/HER.2 average=57.1mm3; HER.2 average=116.1mm3; H84T average=130.3mm3). These findings suggest that H84T BanLec CAR T cells provide a tool to target the aberrant glycosylation patterns of malignant cells and their supporting stroma and may contribute to an effective treatment option for PDAC patients. We are now elucidating the underlying mechanism by which H84T BanLec CARs enhance tumor activity and promote T cell infiltration. Citation Format: Katie McKenna, Ada I Ozcan, David Markovitz, Malcolm K Brenner. Banana Lectin expressing CAR T cells to target 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 B037.
Abstract C041: Emerging role of P2X receptors as Golgi pH regulators in pancreatic cancer
Authors: Cheska Marie Galapate, Koen Galenkamp, Charles Fisher, Susanne Heynen-Genel, Cosimo Commisso
Journal: Cancer Research (2024)

Abstract Cancer cells reprogram their metabolism to meet their elevated energy demands, favoring energy production via glycolysis even with functional mitochondria. Upregulated glycolysis results in rapid production of lactate and protons in the cytoplasm. This would normally reduce the intracellular pH (pHi); however, cancer cells employ mechanisms such as ion transporters that remove excess protons from the cytoplasm to maintain an alkaline pHi, allowing for cell growth, evasion of cell death and cell proliferation. Our previous studies have shown that in pancreatic ductal adenocarcinoma (PDAC), the Golgi apparatus is among the intracellular compartments that can uptake excess protons, giving PDAC cells a cell fitness advantage. The underlying mechanisms that drive Golgi acidification in PDAC are incompletely understood. Here, we set out to comprehensively identify novel modulators that can affect this process. By using a fluorescent-protein-based ratiometric pH biosensor targeted to the Golgi membrane, we screened thousands of chemical compounds for an impairment in Golgi acidification, which would lead to pHi dysregulation and cell death. One of our hits from the screen was an inhibitor of the P2X family of receptors (P2XRs). P2XRs consist of seven subtypes (P2X1-7) and are ATP-gated ion channels that mediate the passage of non-selective cations through the plasma membrane and intracellular compartments. P2XRs have also been shown to regulate the pHi. We are elucidating the mechanism by which P2XRs may regulate pHi via the Golgi in PDAC. Our preliminary results show that concomitant with the alkalinization of the Golgi, P2XR inhibition leads to a pronounced decrease of pHi and results in cell death in PDAC while normal untransformed pancreas cells are unaffected. These data suggest that P2XRs play a role in pHi regulation and cell fitness maintenance through a function in the Golgi. Targeting this metabolic reprograming dependency may serve as a novel therapeutic tool for PDAC. Citation Format: Cheska Marie Galapate, Koen Galenkamp, Charles Fisher, Susanne Heynen-Genel, Cosimo Commisso. Emerging role of P2X receptors as Golgi pH regulators 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 C041.
Abstract IA-05: Targeting KRAS for pancreatic cancer treatment
Authors: Channing J. Der
Journal: Cancer Research (2024)

Abstract The approval of clinically effective inhibitors for KRAS G12C mutant non-small cell lung cancers in 2021 and 2022 marks a significant milestone in anti-KRAS oncogene drug discovery. This success has fueled intense efforts to develop inhibitors targeting additional KRAS mutations. However, primary and treatment-associated acquired resistance limit the depth and duration of efficacy of KRAS G12C selective and likely other KRAS inhibitors. Thus, a major challenge moving forward will be the elucidation of mechanisms of resistance to then guide development of effective combination anti-KRAS therapies. Recent studies have begun to identify mechanisms of acquired resistance, where most involve alterations in components in the RAS signaling network that then cause reactivation of KRAS effector signaling that bypass drug activity. Our studies have established the critical role of reactivation of the RAF-MEK-ERK mitogen activated protein kinase cascade, and the ERK target MYC, in driving resistance in KRAS-mutant pancreatic cancer. To fully understand how aberrant ERK and MYC activation overcomes KRAS inhibitor response, we have established a comprehensive molecular portrait of ERK- and MYC-dependent activities. We have also identified YAP/TAZ-TEAD activation as a mechanism of acquired resistance and have characterized KEAP1 loss as a mechanism of primary resistance. Together, these studies have identified drug combination strategies that enhance KRAS inhibitor activity. Progress in these and other studies will be presented. Citation Format: Channing J. Der. Targeting KRAS for pancreatic cancer treatment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr IA-05.