bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract A066: A novel approach for exocrine pancreas transcriptomics reveals the cellular landscape of the pancreas
Authors: Aney Katherine J. , Jeong Woo-Jeong , Vallejo Andres F. , Chen Ethan , Wang Austin , Dougan Stephanie K. , Wise Kellie , Jensen Kirk , Martelotto Luciano , Nissim Sahar
Published: January 2024

Pancreatic acinar cells are responsible for producing large amounts of digestive enzymes, which are essential for nutrient breakdown but make it difficult to capture the transcriptome of individual cells. To address this challenge, we use a reversible fixative that is compatible with 10X Genomics, thereby preserving the acinar transcriptome and capturing cell composition more faithful to histology. Using this method, we transcriptionally characterize all cell types in the healthy mouse pancreas, and track how these populations change during acute pancreatitis and subsequent recovery. We identify immune cells in the healthy and inflamed pancreas at a level of detail previously unappreciated, characterizing T cell subsets including Th2, γδT, and regulatory T cells. Pancreatitis elicits an influx of neutrophils along with activation and proliferation of macrophages and dendritic cells. Observing significant transcriptional changes in acinar cells after pancreatitis, we define an Acinar to Ductal Metaplasia Index (ADMI), a gene signature that can be used to measure deviation from normal acinar identity in bulk or single cell RNA datasets. We corroborate ADMI using orthogonal GeoMx data, and validate its utility in independent published datasets. We are now expanding our study to perform transcriptomics using our fixation method on pancreatic cancer precursor lesions. Together, we aim to characterize cell types in the mouse pancreas under healthy, inflamed, and precursor conditions to establish a reference atlas for future research on the exocrine pancreas in healthy and diseased states.

Citation Format: Katherine J. Aney, Woo-Jeong Jeong, Andres F. Vallejo, Ethan Chen, Austin Wang, Stephanie K. Dougan, Kellie Wise, Kirk Jensen, Luciano Martelotto, Sahar Nissim. A novel approach for exocrine pancreas transcriptomics reveals the cellular landscape of the pancreas [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 A066.
Abstract A067: A single sample classifier of Bailey's molecular subtype of PDAC
Authors: Baba Taisuke , Sunagawa Masaki , Yamaguchi Junpei , Kokuryo Toshio , Ebata Tomoki
Published: January 2024

 Transcriptomic molecular subtype of pancreatic cancer (PDAC) is expected to be an important part of future personalized medicine. However, most classifier methods are based on the relative expression patterns in the dataset. Batch correction methods are still under development, thus no one can know if the subtyping of their own dataset is accurate, which has made many researchers hesitant to perform studies involving molecular subtyping. PurIST is a robust classifier of Moffitt tumor subtype invented by Rashid et al. It calculates a score based on the expression pattern within a sample and predicts a specific subtype. Unlike traditional cluster-based subtyping, the predicted subtype never changes. Because these types of methods are independent of the cohort composition and the prediction can be made for even a single sample, these methods are called single sample classifiers (SSCs). The approaches of most SSCs to absorb the batch differences are to make the information fuzzy, thus sacrificing the predictive ability. In this study, we invented a single sample classifier called inverse pair boosting (IPB). Our approach does not lose information, instead, magnifies the differences between subtypes and relatively reduces the differences between batches to a negligible level.  Considering Moffitt's tumor classification, classical tumors have high classical gene expressions and low basal-like gene expressions, whereas, the gene expression patterns of basal-like tumors are the other way around. This kind of one side up and the other side down relationship is widely observed in the gene expression pattern. We used this to enhance the subtyping difference and overcome the batch differences. We developed a machine learning model with IPB method based on the Bailey's original RNA-seq data (PACA-AU RNA-seq), and tested its robustness with PACA-AU microarray data. Although there is a huge gap between RNA-seq data and microarray data due to their different modalities, the accuracy of the Bailey's subtype prediction on microarray data was 0.86, which was much higher than other SSCs (accuracy = 0.60 - 0.67).  We developed a single sample classifier of Bailey's molecular subtype of PDAC using novel approach called IPB. Our AI model can make a significant contribution to the development of research on molecular subtypes of PDAC.

Citation Format: Taisuke Baba, Masaki Sunagawa, Junpei Yamaguchi, Toshio Kokuryo, Tomoki Ebata. A single sample classifier of Bailey's molecular subtype of 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 A067.
Abstract A076: Spatial genomic expression profiling reveals metastatic gene markers in mucinous cystic carcinoma of the pancreas and regional lymph nodes
Authors: Gopinath Chirag S. , Ghodrati Arshia , Demirkhanyan Lusine , Gnanamony Manu , Norton Joseph A. , Orcutt Sonia T. , Gondi Christopher S.
Published: January 2024

Pancreatic cancer is a highly lethal disease characterized by low detectability in its early stages, leading to limited treatment options in advanced stages. Mucinous cystic carcinoma (MCC) is a rare subtype of pancreatic cancer that produces mucin. In this study, we investigated the genetic characteristics of MCC and its metastatic potential. Using spatial genomic analysis, we observed the upregulation of several genes in MCC, including CPA1 and CPB1, which encode carboxypeptidases produced by the pancreas. These genes were highly expressed in both the pancreatic tumor and regional lymph nodes, suggesting their potential as gene markers for the metastatic potential of MCC. Moreover, we observed co-localization and upregulation of genes encoding chymotrypsin-like-elastase in both the pancreatic tissue and lymph nodes, indicating their potential involvement in metastasis. Furthermore, we observed significant elevation in the expression of pancreatic enzymes encoded by PRSS1, PRSSA, CLPS, and PLAG2GA in both the pancreatic tissue and lymph nodes. The presence of PRSS1 and PRSSA in the lymph node suggests the presence of cancer cells in the lymphatic system, which in turn promotes tumor growth, invasion, and metastasis. Additionally, elevated expression of CLPS in the lymph nodes may be associated with altered lipid metabolism and the breakdown of fat molecules in the tumor microenvironment. This upregulation was accompanied by increased levels of SPARC, an extracellular matrix protein, in both tissues, emphasizing the correlation between metastatic potential and tumorigenesis. Notably, commonly observed tumor markers for pancreatic cancer, such as SMAD4, did not exhibit upregulation in our MCC case, indicating alternative mechanisms of tumor development in this particular subtype. Additionally, we noted heightened expression of the CA 19-9 antigen, a valuable marker for monitoring the progression of pancreatic cancer. In conclusion, our findings reveal the upregulation of several gene markers in this rare subtype of pancreatic cancer and regional lymph nodes. Understanding the expression patterns of these markers can aid in identifying potential therapeutic targets and detecting metastatic potential at an early stage for MCC.

Citation Format: Chirag S. Gopinath, Arshia Ghodrati, Lusine Demirkhanyan, Manu Gnanamony, Joseph A. Norton, Sonia T. Orcutt, Christopher S. Gondi. Spatial genomic expression profiling reveals metastatic gene markers in mucinous cystic carcinoma of the pancreas and regional lymph nodes [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 A076.
Abstract A077: The EZH2 epigenetic factor orchestrates oncogenic properties in ATM-deficient pancreatic cancer
Authors: Roger Elodie , Härle Anna , Gout Johann , Perkhofer Lukas , Hessmann Elisabeth , Kleger Alexander
Published: January 2024

Despite decades of extensive basic and translational research improving our understanding of pancreatic ductal adenocarcinoma (PDAC), its complex biology remains a significant challenge and limits overcoming its dismal prognosis. Due to its resistance to conventional therapies and heterogeneous mutational landscape, molecular stratification and the development of targeted therapeutic options are essential for improving survival of PDAC patients. Previous work from our group investigated loss-of-function mouse models for the serine/threonine kinase ATM causing homologous recombination deficiency (HRD) in PDAC. Specifically, ATM loss caused certain oncogenic features in the arising tumors, including the acquisition of an invasive phenotype along with the emergence of a prominent desmoplastic reaction, but also sensitizes toward platinum-based therapies and PARP1 inhibition (Russell, Nat Commun; Perkhofer, Cancer Res; Gout, Gut). However, the mechanisms orchestrating these oncogenic features remain unclear. Here, we identified the histone-methyltransferase EZH2 as a direct ATM substrate to operate as an epithelial-mesenchymal gatekeeper. In detail, ATM-deficient tumors accumulated EZH2, suggesting that ATM status contributes to rewiring the epigenetic landscape of pancreatic tumors, subsequently supporting oncogenic features. To investigate whether and how EZH2 impacts ATM-deficient PDAC pathogenesis, we generated conditional double ATM and EZH2-knockout in the KrasG12D/+; Ptf1aCre/+ mice. Double-null mice showed extended mouse survival, reduced metastasis burden, and decreased undifferentiated malignant cell features. Interestingly, both in vivo and in vitro investigations revealed that ATM status significantly impacts EZH2 activity via a post-translational regulation axis. Specifically, the ATM kinase activity was critical to promote Culin1 E3-ubiquitin ligase recruitment and subsequent EZH2 ubiquitination and degradation. Finally, we demonstrated that a combinatorial therapy involving a potent EZH2 inhibitor promotes genomic instability and exacerbates the cytotoxic effects of PARP interference in ATM-deficient HRD PDAC. Overall, our study demonstrates that ATM deficiency significantly impacts EZH2 epigenetic functions and pinpoints the molecular stratification according to ATM status prior to pharmacological EZH2 interference in PDAC therapies as a valuable approach to target ATM-deficient HRD tumors.

Citation Format: Elodie Roger, Anna Härle, Johann Gout, Lukas Perkhofer, Elisabeth Hessmann, Alexander Kleger. The EZH2 epigenetic factor orchestrates oncogenic properties in ATM-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 A077.
Abstract A086: TFEB protects pancreatic cancer cells against nucleolar stress
Authors: Duff Florence Mc , Bessy Laure , Marchand Benoit , Boucher Marie-Josee
Published: January 2024

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 A105: Wild-type IDH1 inhibition enhances chemotherapy response in pancreatic cancer
Authors: Zarei Mehrdad , Hajihassani Omid , Hue Jonathan J. , Graor Hallie J. , Loftus Alexander W. , Rothermel Luke D. , Winter Jordan M.
Published: January 2024

Background and Aims: Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive forms of cancer, with a five-year overall survival rate of 12% among all-comers. Current systemic therapeutic options are limited to cytotoxic chemotherapies which have limited clinical efficacy and are often associated with the rapid development of drug resistance. We examined mechanistic and therapeutic implications of combining anti-wild-type IDH1 therapy with conventional chemotherapeutics to treat PDAC. Methods: Therapeutic responses were tested in vivo and in vitro through survival studies, testing for the effects of ivosidenib (an allosteric IDH1 inhibitor) and PDAC chemotherapeutics. Usage of ivosidenib is based on pre-clinical work showing anti-wild-type IDH1 activity under tumor associated conditions. Results: Chemotherapy treatment of PDAC cells induced the production of reactive oxygen species and increased TCA cycle activity. Treatment also resulted in the rapid induction of wild-type IDH1 expression, which served as a key resistance factor. The enzyme is protective under chemotherapy-associated stress by supporting antioxidant defense and mitochondrial function, through the generation of NADPH and alpha-ketoglutarate, respectively. Pharmacologic suppression of wild-type IDH1 was synergistic with conventional chemotherapeutics in vitro, and potentiated sub-therapeutic doses of these drugs in murine PDAC models. Conclusions: Pharmacologic wild-type IDH1 inhibition with ivosidenib proved to be cooperative with conventional PDAC chemotherapeutics in diverse models. This promising new treatment approach is easily translatable, and provides the basis of an ongoing clinical trial (NCT05209074).

Citation Format: Mehrdad Zarei, Omid Hajihassani, Jonathan J. Hue, Hallie J. Graor, Alexander W. Loftus, Luke D. Rothermel, Jordan M. Winter. Wild-type IDH1 inhibition enhances chemotherapy response 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 A105.
Abstract B060: Enhancing models of pancreatic cancer: Integrating patient-derived models with tissue engineering to investigate clinical responses to therapy
Authors: Smith Alexander C. , Muschler John , Munks Mike , Sears Rosalie C. , Brody Jonathan
Published: January 2024

Cancer modeling systems can be advantageous in enabling personalized medicine through rapid testing of therapeutic responsiveness. However, modeling systems often fail in these efforts due to 1) inadequately replicating unique patient genetics, 2) inadequately modeling the patient tumor microenvironment (TME), and 3) lack of internal validation references when isolated from clinical drug response data. We have developed a patient-derived models of cancer (PDMC) program for pancreatic cancer that addresses these challenges. By integrating patient cancer modeling and tissue engineering efforts with clinical trial protocols that perform serial tissue biopsies and analyses during treatment, we can make direct assessments of how different modeling systems replicate actual patient outcomes. Clinical trial protocols include tissue biopsies pre- and post- treatment using targeted therapeutics including MEK and PARP inhibitors. The modeling program, meanwhile, includes collecting metadata from pre- and post- treatment biopsies, the banking of patient tissues, cell line and xenograft generation from each biopsy, multiomic comparisons of models to patient tissue, comparisons of therapeutic responsiveness in models, and ultimately tissue re-engineering through bioprinting of tumor cells along with TME components. Whole exome sequencing is used to confirm that genetic alterations are preserved in each model, and we have established models representing a range of human PDAC genomic profiles. This includes common KRAS and TP53 mutations, as well as rare BRCA mutations and KRAS-wild-type tumors with BRAF mutations. Many cancer-associated fibroblast (CAF) lines have also been established through this program. Including patient derived cell lines, CAD lines, endothelial cells, and PBMCs into 3D bioprinted tumors allows us to better model the TME. Assays performed upon bioprinted tissues can then be directly compared to the same assays performed on the patient tumor to assess similarities as well as further obstacles. Ongoing efforts include building a resource of precise and validated PDMCs for diverse pancreatic cancers, and establishing a path forward for improved cancer modeling for the actualization of personalized medicine in PDAC treatment.

Citation Format: Alexander C. Smith, John Muschler, Mike Munks, Rosalie C. Sears, Jonathan Brody. Enhancing models of pancreatic cancer: Integrating patient-derived models with tissue engineering to investigate clinical responses to therapy [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 B060.
Abstract B070: Histone deacetylation inhibition promotes bi-directional subtype switch in pancreatic cancer
Authors: Klein Lukas , Tu Mengyu , Schmitt Eva K. , Penz Frederike , Mizi Athanasia , Küffer Stefan , Hessmann Elisabeth , Papantonis Argyris , Ellenrieder Volker , Singh Shiv K.
Published: January 2024

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 B071: Tumor Treating Fields (TTFields) together with PARP inhibitors for treatment of pancreatic cancer cells
Authors: Martinez-Conde Antonia , Ene Hila , Ben-Meir Kerem , Dor-On Eyal , Lamichhane Puru , Haber Adi , Giladi Moshe , Palti Yoram
Published: January 2024

Purpose/Objectives: Pancreatic cancer remains a leading cause of cancer-related death, with limited treatment options available for the advanced stage. PARP inhibitors (PARPi) are effective treatment options in patients with germline BRCA mutations. Recently, TTFields – electric fields that disrupt cellular processes critical for cancer cell viability – have been shown to induce a state of BRCAness in various cancer types. The objective of this study was to examine possible sensitization of BRCA wild type pancreatic cancer cell lines to PARP inhibition by the application of TTFields. Materials/Methods: BxPC3 and AsPC1 BRCA wild type, human pancreatic cancer cells were treated for 48 and 72 h, respectively, with TTFields (intensity of 1 and 0.7 V/cm RMS, respectively) at a frequency of 150 kHz using the inovitro device. TTFields were applied to the cells alone or together with various concentrations of the PARP inhibitors niraparib or olaparib. Cell count, colony formation, and apoptosis were measured at treatment end. Results: Applying TTFields to pancreatic cell lines resulted in cytotoxicity, anti-clonogenic effect, and induction of apoptosis. PARP inhibitors also demonstrated such effects, in a dose-dependent fashion. Co-application of TTFields enhanced the effects of PARP inhibitors. Conclusions: The results show a benefit for concomitant application of TTFields and PARPi in pancreatic cancer, potentially due to the BRCAness state induced by TTFields. The data suggest TTFields may enhance PARP inhibition efficacy in the absence of background BRCA mutations.

Citation Format: Antonia Martinez-Conde, Hila Ene, Kerem Ben-Meir, Eyal Dor-On, Puru Lamichhane, Adi Haber, Moshe Giladi, Yoram Palti. Tumor Treating Fields (TTFields) together with PARP inhibitors for treatment of pancreatic cancer 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 B071.
Abstract B088: The macropinosome: Uncovering the molecular anatomy of an oncogene-driven organelle
Authors: Manceau Ambroise , Galenkamp Koen M.O. , Galapate Cheska M. , Commisso Cosimo
Published: January 2024

As an integral aspect of the metabolic reprogramming that occurs in cancer, oncogenic KRAS mutations drive the stimulation of macropinocytosis, a type of endocytosis that mediates nonselective fluid-phase uptake. Using KRAS-driven models of pancreatic ductal adenocarcinoma (PDAC), we were the first to demonstrate that macropinocytosis functions in tumor cells as a nutrient acquisition pathway. Macropinocytosis triggers the internalization of extracellular proteins via discrete endocytic vesicles called macropinosomes. The incoming protein cargo is targeted for lysosome-dependent degradation, causing the intracellular release of amino acids. These protein-derived amino acids support metabolic fitness by contributing to the intracellular amino acid pools, as well as to the biosynthesis of central carbon metabolites. In this way, macropinocytosis represents a novel amino acid supply route that tumor cells use to survive the nutrient-poor conditions of the tumor microenvironment. While the tenets of the signal transduction events that drive macropinocytosis in cancer have emerged, a detailed picture of the macropinosome itself is not yet available. With the aid of nanotechnology, we have developed a methodology to isolate a pure fraction of macropinosomes from PDAC cells. Using a large-scale proteomic approach, we have been able to generate a list of proteins that reside in macropinosomes. The specificity of this approach was confirmed through the identification and validation of proteins known to specifically localize to these organelles in different contexts, such as Rab5 or SDC1. Thanks to this innovative method, we have demonstrated the involvement of two calcium channels, ATP2B1 and ATP2B4, in the formation of macropinosomes. By elucidating the molecular anatomy of KRAS-driven macropinosomes, we will gain further insight into the regulation and function of macropinocytosis in cancer. Moreover, having a clearer picture of the macropinosome will make us better positioned to exploit this pathway therapeutically and deliver breakthroughs to patients.

Citation Format: Ambroise Manceau, Koen M.O. Galenkamp, Cheska M. Galapate, Cosimo Commisso. The macropinosome: Uncovering the molecular anatomy of an oncogene-driven organelle [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 B088.
Abstract B094: The role of paraspeckles and splicing regulation in driving basal-like pancreatic cancer
Authors: Soares Zamira G. , Berry Emily , Esgdaille Dakarai , Twardowski Jennifer , Mello Stephano S.
Published: January 2024

The basal-like pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive type of mesenchymal PDAC that resists treatment and has a poor prognosis. Understanding the mechanisms driving basal-like PDAC biology will be essential for development of treatment strategies for this aggressive tumor. We have previously shown that loss of the tumor-suppressive non-coding RNA Neat1 recapitulate the phenotype of Arid1a-deficient mice (a component of the SWI/SNF chromatin remodeling complex) in a mouse model for PDAC, with loss of exocrine pancreatic identity and development of acinar- and ductal-derived lesions (Mello et al., 2017), suggesting that Neat1 and Arid1a may share a common molecular mechanism. We now demonstrate that the loss of these two divergent genes induce the emergence of basal-like PDAC. This provides an opportunity to probe for shared features specific to Neat1- and Arid1a-deficient PDAC, as compared to PDAC in which both genes are functional. Notably, our data indicate that both Neat1- and Arid1a-deficient pancreatic cells fail to form nuclear paraspeckles, i.e. structures implicated in the retention of RNA splicing factors. Consistent with this idea, we also find significantly increased exon-skipping, including a sub-set of such events shared between Neat1- and Arid1a-deficient PDAC. In addition, nucleotide sequence motifs associated with exon-skipping locations suggest involvement of RNA splicing factors known to accumulate in paraspeckles, such as Srsf1, Srsf2, Srsf10, Rbm38, Dazap1 and others. We also show that, upon genetic or pharmacological attenuation of splicing regulator function, basal-like PDAC develop epithelial features, reminiscent of mesenchymal-epithelial transition, reduce both their proliferation and migration potential and undergo cell death. Our findings provide an important opportunity to elucidate the molecular pathways that link aberrant RNA splicing and paraspeckle deficiency to basal-like PDAC, providing new insight for the development of mechanism-based novel PDAC treatment strategies to improve patient outcome.

Citation Format: Zamira G. Soares, Emily Berry, Dakarai Esgdaille, Jennifer Twardowski, Stephano S. Mello. The role of paraspeckles and splicing regulation in driving basal-like 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 B094.
Abstract B095: Leukemia inhibitory factor fosters tumor growth in KRAS-driven pancreatic ductal adenocarcinoma
Authors: Miller-Phillips Lisa , Hanafi Imene Boukhalfa , Umetsu Sarah , Olshen Adam , Roy Ritu , Kiemen Ashley , Wang Man-Tzu , Collisson Eric
Published: January 2024

While inflammation is a known and well-validated risk factor for developing pancreatic ductal adenocarcinoma (PDA), it remains unclear how Leukemia inhibitory factor (LIF), a cytokine of the IL-6 class family, influences tumor initiation and progression in PDA. LIF is highly upregulated in PDA when compared to the normal healthy pancreas. Using a human single-cell RNAseq PDA data set, we identified pancreatic cancer cells as the main source of LIF, followed by fibroblasts and stellate cells. After confirming that Pdx1-expressing cells represent the majority of Lif-expressing cells in the pancreas, we crossed our newly developed Lif flox/flox allele into the well-established KrasLSL-G12D/+, Trp53flox/flox, Pdx1-Cre (KPC) mouse model. Lif flox/flox, Pdx1-Cre (LC) mice present with normal pancreas histology, mouse weight, and mouse size at 12 months, indicating that Lif is dispensable for mouse pancreas development and function. Lif flox/flox, Trp53flox/flox, Pdx1-Cre (LPC) mice also showed no differences in pancreas histology when compared to normal Lif-expressing PC mice. Lif flox/floxKPC (LKPC) mice develop PDA tumors. Cell lines from LKPC tumors (n=4) presented with undetectable Lif expression and no LIF protein secretion. Control KPC tumor cell lines (n=4) showed Lif expression and LIF secretion, confirming the successful deletion of Lif in our newly developed mouse model. LKPC mice (n=21) showed a significant increase in disease-specific overall survival at 72 days when compared to control KPC mice (n=26) at 62 days (p<0.05). When mice reached endpoint, LKPC mice presented with significantly smaller tumors with an average tumor weight of 0.7g compared to KPC control animals with an average tumor weight of 1.3g (p<0.05). In summary, we find that cancer-cell expressed LIF augments tumor growth and shortens disease-specific overall survival, nominating leukemia inhibitory factor depletion as a promising therapeutic target in KRAS-driven pancreatic cancer.

Citation Format: Lisa Miller-Phillips, Imene Boukhalfa Hanafi, Sarah Umetsu, Adam Olshen, Ritu Roy, Ashley Kiemen, Man-Tzu Wang, Eric Collisson. Leukemia inhibitory factor fosters tumor growth in KRAS-driven 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 B095.
Abstract B098: Oncogenic KRAS relies on β1 integrin expression to drive pancreatic neoplasia and PDAC development
Authors: Muschler John L. , Huang Ge , Smith Alexander C. , Sears Rosalie C.
Published: January 2024

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 B101: Tumor-selective inhibition of active RAS in pancreatic ductal adenocarcinoma
Authors: Wasko Urszula N. , Jiang Jingjing , Tomassoni Lorenzo , Wang Yingyun , Lee Bianca , Orlen Margo , Drizyte-Miller Kristina , Menard Marie , Dilly Julien , Sastra Steven A. , Palermo Carmine F. , Chang Stephanie , Aguirre Andrew J. , Der Channing J. , Vonderheide Robert H. , Stanger Ben Z. , Califano Andrea , Singh Mallika , Olive Kenneth P.
Published: January 2024

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 B103: Development and characterisation of KRASmulti inhibitors for the treatment of KRAS mutant pancreatic ductal adenocarcinoma
Authors: Tedeschi Antonio , Schaaf Otmar , Gmachl Michael , Herdeis Lorenz , Rocchetti Francesca , Popow Johannes , Schischlik Fiorella , Gerlach Daniel , Lipp Jesse , Bröker Joachim , Mantoulidis Andreas , Smethurst Chris , Kessler Dirk , Boettcher Jark , Wunberg Tobias , Santoro Valeria , Waterson Alex , Phan Jason , Little Andrew , Abbott Jason , Sun Qi , Fesik Stephen , Mcconnell Darryl , Pearson Mark A. , Kraut Norbert , Rudolph Dorothea
Published: January 2024

Pancreatic ductal adenocarcinoma (PDAC) is predicted to become the second most common cause of cancer related death within the next decade. Late detection and limited therapeutic options drive the dismal prognosis for PDAC patients. Activating mutations within the KRAS gene occur within the vast majority (>85%) of PDAC tumors. KRAS mutations occur at an early stage within PDAC development but remain necessary for continued tumor growth. Clinical responses observed in patients with KRASG12C mutant PDAC treated with selective KRASG12C inhibitors have driven drug development programmes that can address other, more frequently occurring KRAS alleles. Here we report the characterization of a KRASmulti inhibitor, BI-2493, that potently inhibits the proliferation of mutant KRAS PDAC cancer cell lines in vitro. The DMPK properties of the compound have been optimized so that oral administration resulted in regression of KRAS mutant PDAC xenograft models. These data support the continued development of compounds capable of addressing the most prevalent KRAS mutant alleles in PDAC with the potential to provide a therapeutic option to patients in an indication with a high unmet medical need.

Citation Format: Antonio Tedeschi, Otmar Schaaf, Michael Gmachl, Lorenz Herdeis, Francesca Rocchetti, Johannes Popow, Fiorella Schischlik, Daniel Gerlach, Jesse Lipp, Joachim Bröker, Andreas Mantoulidis, Chris Smethurst, Dirk Kessler, Jark Boettcher, Tobias Wunberg, Valeria Santoro, Alex Waterson, Jason Phan, Andrew Little, Jason Abbott, Qi Sun, Stephen Fesik, Darryl Mcconnell, Mark A. Pearson, Norbert Kraut, Dorothea Rudolph. Development and characterisation of KRASmulti inhibitors for the treatment of KRAS mutant 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 B103.
Abstract B108: Integrated in vivo dissection of metastatic phenotypes and molecular programs in pancreatic ductal adenocarcinoma
Authors: Karmakar Saswati , Lyulina Anastasia , Xiong Xiaochen , Tang Yuning J. , Lopez Steven , Hughes Nicolas William , Attardi Laura , Petrov Dmitri A. , Winslow Monte M.
Published: January 2024

The ability of pancreatic ductal adenocarcinoma (PDAC) cells to form tissue destructive metastases remains a critical impediment to therapy. Metastasis is a complex multistep process that is poorly understood and the molecular events and cellular states that enable cancer cells to overcome each step of the metastatic cascade remain elusive. To investigate the regulators of PDAC metastasis, we accrued and characterized a panel of 31 cell lines generated from mouse models of PDAC. Initial experiments indicated that these cell lines have an ~40-fold difference in their ability to form lung metastases after transplantation into immunocompetent recipient mice. To more accurately quantify the relationship between metastatic seeding, growth, organ tropism, and immune evasion across all cell lines in parallel, we tagged each cell line with a barcode that provides both cell line-level and subclonal-level resolution. We pooled all 31 barcoded cell lines, transplanted them to seed metastases in different organs, and performed barcode sequencing on DNA from the metastasis-bearing tissues after short (seeding) and long (expansion) time periods. Neither seeding nor metastatic outgrowth correlated with growth in culture. Metastatic seeding did not directly correlate with overall metastatic burden, indicating that these processes depend on distinct biological processes. Transplantation into syngeneic immune-competent and immune-deficient recipient mice quantified the impact of immune responses towards each cell line. Bulk and single cell RNA-sequencing uncovered unexpected intra- and inter-cell line heterogeneity. Future experiments will integrate the data on metastatic phenotypes with molecular information to uncover drivers and inhibitors of each step of the metastatic cascade. Broad-scale molecular profiling coupled with quantitative in vivo analysis of metastatic phenotypes will uncover the relationships between metastatic phenotypes, create a resource for the community, and reveal novel pathways that govern PDAC metastasis, which could have implications for developing novel therapeutic strategies.

Citation Format: Saswati Karmakar, Anastasia Lyulina, Xiaochen Xiong, Yuning J. Tang, Steven Lopez, Nicolas William Hughes, Laura Attardi, Dmitri A. Petrov, Monte M. Winslow. Integrated in vivo dissection of metastatic phenotypes and molecular programs 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 B108.
Abstract C020: Unconvering the hidden immunosuppressive landscape in pancreatic ductal adenocarcinoma
Authors: Qian Guhan , Zhang Hongrong , Knott Aine , Zettervall Jon , Stromnes Ingunn , Provenzano Paolo
Published: January 2024

Pancreatic ductal adenocarcinoma (PDA) is one of the deadliest forms of cancer with an extremely low survival rate. Despite the success of therapeutic T cells in hematologic cancers, many solid tumors, including PDA, remain unresponsive with such therapies, partly due to its mechanically complex, dense, and immunosuppressive stroma. Therefore, understanding the dynamic interplay between therapeutic T cells and the tumor microenvironment (TME) is crucial for revealing engineering targets for next-generation immunotherapies. We approach this problem with genetically engineered KPC (KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx-1-Cre) mouse models that recapitulates PDA disease progression and stromal dynamics. Within live tumor slices from primary tumors, we are defining how stromal components such as dense collagen fiber networks and tumor-associated macrophages (TAMs) orchestrate an immunosuppressive landscape. We employ multiphoton laser scanning microscopy (MPLSM) to generate multiphoton excitation of fluorescence (cell dyes and immunofluorescence) and second harmonic generation (SHG) for collagen fibers to acquire multidimensional data (x, y, z, c, t) of T cell migration and interaction within the TME. We subsequently reveal T cell migration and interaction as a function of its physical and biological ECM components using advanced computer vision and machine learning algorithms based on the Clustered Random Convolutional Kernel Transform (cROCKET), revealing a hidden landscape in the feature space. Perturbations to the TME in KPC mice with CCR2 inhibitor CCX598 (in vivo) and clodronate liposomes (ex vivo) deplete CD11b+ myeloid cells, resulting in altered behaviors of the infiltrating T cells. Anti-PD-1 monoclonal antibody neutralizes the PD-1/PD-L1 axis in T cells, resulting in enhanced migration and infiltration in tumor slices.

Citation Format: Guhan Qian, Hongrong Zhang, Aine Knott, Jon Zettervall, Ingunn Stromnes, Paolo Provenzano. Unconvering the hidden immunosuppressive landscape 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 C020.