bluuebunny/crossref_metadata_2025 huggingface dataset:
A Phase I/II Trial of Oral SRA737 (a Chk1 Inhibitor) Given in Combination with Low-Dose Gemcitabine in Patients with Advanced Cancer
Authors: Jones Robert , Plummer Ruth , Moreno Victor , Carter Louise , Roda Desamparados , Garralda Elena , Kristeleit Rebecca , Sarker Debashis , Arkenau Tobias , Roxburgh Patricia , Walter Harriet S. , Blagden Sarah , Anthoney Alan , Klencke Barbara J. , Kowalski Mark M. , Banerji Udai
Published: November 2022

Purpose:

This was a Phase I/II trial of the novel checkpoint kinase 1 (Chk1) inhibitor SRA737 given in combination with gemcitabine. Its objectives were to establish the safety profile, recommended Phase 2 dose (RP2D), pharmacokinetics profile, and clinical activity of SRA737.

Patients and Methods:

Patients with advanced solid tumors were enrolled into dose-escalation cohorts and treated in 28-day cycles with oral SRA737 on days 2, 3, 9, 10, 16, and 17, and intravenous gemcitabine on days 1, 8, and 15. Treatment was continued until progression. Each expansion cohort included up to 20 patients with specific genetically defined tumors.

Results:

The RP2D was determined to be 500 mg SRA737 combined with low-dose (250 mg/m2) gemcitabine. Of 143 enrolled patients, 77 were treated at doses of at least 500 mg SRA737 combined with 250 mg/m2 gemcitabine. Common toxicities of nausea, vomiting, fatigue, and diarrhea were primarily mild to moderate, and rarely led to treatment discontinuation. Anemia, neutropenia, and thrombocytopenia were grade ≥3 in 11.7%, 16.7%, and 10% of patients treated at the RP2D, respectively. The objective response rate (ORR) was 10.8% overall and notably the ORR in anogenital cancer was 25%. Partial tumor responses were observed in anogenital cancer, cervical cancer, high-grade serous ovarian cancer, rectal cancer, and small cell lung cancer.

Conclusions:

SRA737 in combination with low-dose gemcitabine was well tolerated with lower myelotoxicity than has been seen at standard doses of gemcitabine or with other combinations of Chk1 inhibitors with gemcitabine. Tumor responses were observed in anogenital and other solid tumors.
Targeting MDSC Differentiation Using ATRA: A Phase I/II Clinical Trial Combining Pembrolizumab and All-Trans Retinoic Acid for Metastatic Melanoma
Authors: Tobin Richard P. , Cogswell Dasha T. , Cates Victoria M. , Davis Dana M. , Borgers Jessica S.W. , Van Gulick Robert J. , Katsnelson Elizabeth , Couts Kasey L. , Jordan Kimberly R. , Gao Dexiang , Davila Eduardo , Medina Theresa M. , Lewis Karl D. , Gonzalez Rene , McFarland Ross W. , Robinson William A. , McCarter Martin D.
Published: November 2022

Purpose:

A phase Ib/II clinical trial was conducted to evaluate the safety and efficacy of the combination of all-trans retinoic acid (ATRA) with pembrolizumab in patients with stage IV melanoma.

Patients and Methods:

Anti–PD-1 naïve patients with stage IV melanoma were treated with pembrolizumab plus supplemental ATRA for three days surrounding each of the first four pembrolizumab infusions. The primary objective was to establish the MTD and recommended phase II dose (RP2D) of the combination. The secondary objectives were to describe the safety and toxicity of the combined treatment and to assess antitumor activity in terms of (i) the reduction in circulating myeloid-derived suppressor cell (MDSC) frequency and (ii) progression-free survival (PFS).

Results:

Twenty-four patients were enrolled, 46% diagnosed with M1a and 29% with M1c stage disease at enrollment. All patients had an ECOG status ≤1, and 75% had received no prior therapies. The combination was well tolerated, with the most common ATRA-related adverse events being headache, fatigue, and nausea. The RP2D was established at 150 mg/m2 ATRA + 200 mg Q3W pembrolizumab. Median PFS was 20.3 months, and the overall response rate was 71%, with 50% of patients experiencing a complete response, and the 1-year overall survival was 80%. The combination effectively lowered the frequency of circulating MDSCs.

Conclusions:

With a favorable tolerability and high response rate, this combination is a promising frontline treatment strategy for advanced melanoma. Targeting MDSCs remains an attractive mechanism to enhance the efficacy of immunotherapies, and this combination merits further investigation.

See related commentary by Olson and Luke, p. 1167
Abstract A006: Integrating single cell and spatial transcriptomics define gene signature for pancreatic ductal adenocarcinoma pre-neoplastic lesion
Authors: Elhossiny Ahmed M. , Carpenter Eileen , Kadiyala Padma , Zhang Yaqing , Bednar Filip , Rao Arvind , Frankel Timothy , Di Magliano Marina Pasca
Published: November 2022

Pancreatic Cancer Ductal Adenocarcinoma (PDAC) is one of the deadliest cancers with 5-year survival of 11%. Understanding the intratumor heterogeneity is a pivotal piece to unravel the complexity of PDAC. While single cell RNASeq identifies the heterogeneous cell populations within the tumor tissue, spatially characterizing the transcriptomic profile of neoplastic and pre-neoplastic populations within the tissue remains a challenge, as the spatial dimension is usually lost upon tissue dissociation. We identified an approach to integrate spatial transcriptomics data with single cell RNASeq data. To characterize the cell populations within the tissue we performed single cell RNASeq on disease pathology-free pancreas tissue and primary PDAC samples. We profiled the transcriptomic profile of Acinar, Ductal, Acinar-to-Ductal (ADM), and Pancreatic Intraepithelial Neoplasia (PanINs) regions of interest (ROIs) across the tissue using the Nanostring GeoMx platform. Differential gene expression analysis using linear mixed-effect models of the cell-type specific ROIs defined pan-marker gene sets for each cell type, which were mapped to UMAP projections of single cell RNA sequencing data using AUCell scoring. As expected, the acinar pan-markers gene set derived from the spatial transcriptomics mapped to the manually annotated acinar population in the single cell data. On the other hand, Ductal, ADM, and PanIN pan-marker gene sets were mapped to distinct clusters that previously were not well-defined by single cell sequencing. The analysis coupled with orthogonal validation using RNAScope revealed gene signatures uniquely specific to ADM lesions and PanINs, respectively. Interestingly, our list included known markers as well as novel findings, supporting the validity of the findings. Furthermore, RNA velocity analysis using scVelo revealed a trajectory of cell evolution originating from acinar cells passing through the newly-defined ADM population and ending towards the ductal population derived from tumor samples. Overall, this integration approach of spatial and single cell transcriptomics can further define the characteristics that differentiate neoplastic and pre-neoplastic populations, as well as the potential drivers for tumorigenesis that could be therapeutically targeted.

Citation Format: Ahmed M. Elhossiny, Eileen Carpenter, Padma Kadiyala, Yaqing Zhang, Filip Bednar, Arvind Rao, Timothy Frankel, Marina Pasca Di Magliano. Integrating single cell and spatial transcriptomics define gene signature for pancreatic ductal adenocarcinoma pre-neoplastic lesion [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A006.
Abstract A008: PanCAN SPARK: A cloud-based health data integration platform for pancreatic cancer data
Authors: Abdilleh Kawther , Khalid Omar , Ladnier Dennis , Wan Wenshuai , Seepo Sara , Rupp Garrett , Corelj Valentin , Worman Zelia F. , Press Bruce , DiGiovanna Jack , Chandrashekhar Satty , Collisson Eric , Cui Karen , Maitra Anirban , Rejto Paul A. , White Kevin , Matrisian Lynn , Doss Sudheer
Published: November 2022

The Pancreatic Cancer Action Network (PanCAN) is leading large-scale research initiatives that will help transform the way pancreatic cancer is detected and treated including the Know Your Tumor precision medicine service, the Precision Promise adaptive clinical trial platform, the Early Detection Initiative, and the Patient Registry. Combined, these initiatives will generate a wide range of patient health data including molecular, multi-omic, clinical, patient-reported, treatment, outcomes, and imaging data. Here we introduce SPARK, a cloud-based data and analytics platform powered by Seven Bridges. SPARK integrates patient health data from PanCAN’s research initiatives and serves to accelerate research by making pancreatic cancer data easier to access and use. The platform supports the full spectrum of clinical data analysis with PanCAN patient health data as well as bioinformatics and analytical tools designed to leverage clinico-genomic data in a centralized location. SPARK fills an unmet need in pancreatic cancer research by providing researchers rapid and secure access to a wide range of pancreatic cancer patient health data on a platform backed by a robust cloud-based analytical infrastructure. The pilot release of the PanCAN SPARK platform brings qualified researchers closer to identifying novel treatments and ultimately improving patient outcomes.

Citation Format: Kawther Abdilleh, Omar Khalid, Dennis Ladnier, Wenshuai Wan, Sara Seepo, Garrett Rupp, Valentin Corelj, Zelia F. Worman, Bruce Press, Jack DiGiovanna, Satty Chandrashekhar, Eric Collisson, Karen Cui, Anirban Maitra, Paul A. Rejto, Kevin White, Lynn Matrisian, Sudheer Doss. PanCAN SPARK: A cloud-based health data integration platform for pancreatic cancer data [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A008.
Abstract A056: Epithelial hyaluronan synthase 2 expression promotes pancreas cancer metastasis
Authors: Tu Bo , Wright Heather Wright T. , Dufort Christopher C. , Whittle Martin C. , Feng Libing , Thorsen Shelley M. , Hingorani Sunil R.
Published: November 2022

A defining characteristic of pancreatic ductal adenocarcinoma (PDA) is its robust desmoplastic reaction that promotes tumor progression and protects PDA from treatment. As a major component of the extreme microenvironment, hyaluronan (HA) is synthesized by the hyaluronan synthase (Has) family of enzymes and secreted in excess by both epithelial cells and cancer-associated fibroblasts (CAFs). We have previously described the role of HA in binding water and swelling to create vessel-crushing interstitial gel-fluid pressures and its function as a biophysical barrier. However, HA also acts by signaling through a wide range of specific receptors that can drive proliferation, migration and invasion. In an effort to understand the role of HA in PDA development and pathogenesis, we developed a KPC mouse model of autochthonous pancreas cancer in which Has2 is conditionally deleted in tumor epithelial cells (TECs). We demonstrate that Has2-deficient epithelial cells produce little to no HA and altered the dense microenvironment. We also found that deletion of Has2 leads to an increase in overall survival and a striking reduction in metastasis. We have further investigated the cell autonomous functions of Has2, associated with 3D invasion and activation of oncogenic signaling pathways in TECs. These data implicate a potential Achilles’ heel in PDA, whereby HAS2 is required to maintain a highly metastatic phenotype involving both non-cell and cell autonomous mechanisms.

Citation Format: Bo Tu, Heather Wright T. Wright, Christopher C. Dufort, Martin C. Whittle, Libing Feng, Shelley M. Thorsen, Sunil R. Hingorani. Epithelial hyaluronan synthase 2 expression promotes pancreas cancer metastasis [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A056.
Abstract A057: Therapeutic efficacy of selective CDK7 inhibition in pancreatic cancer mediated by induction of R-loop formation, DNA replication stress and genomic instability
Authors: Yang Annan , Jiang Jie , Li Ziyue , Kapner Kevin S. , Feng Hanrong , Lowder Kristen E. , Kuljanin Miljan , Johnson Whiteny , Uribe Giselle , Neggers Jasper E. , Liu Shengwu , Zhang Tinghu , Decaprio James , Sicinska Ewa , Wolpin Brian M. , Kwiatkowski Nicholas P. , Dougan Stephanie K. , Mancias Joseph D. , Gray Nathanael S. , Aguirre Andrew J.
Published: November 2022

Pancreatic ductal adenocarcinoma (PDAC) is a devastating cancer with 5-year overall survival of less than 10% and few effective therapies. Here, we demonstrate that cyclin dependent kinase 7 (CDK7) is essential for the proliferation and viability of PDAC cells by showing potent anti-tumor efficacy for the CDK7-specific inhibitor YKL-5-124 in preclinical PDAC models. Selective CDK7 inhibition leads to G2/M cell cycle arrest and apoptosis in PDAC, while mediating a more modest transcriptional response compared with multi-targeted CDK7 inhibitors. YKL-5-124 treatment impairs DNA damage repair pathways in PDAC cells and evokes genomic instability by inducing R-loop formation and DNA replication stress in telomeric regions leading to chromosomal bridging and micronuclei formation. Furthermore, we demonstrate that selective CDK7 inhibition has in vitro and in vivo combinatorial efficacy with gemcitabine chemotherapy through pronounced induction of replication stress and apoptosis. Collectively, these findings support selective CDK7 inhibition as a promising therapeutic strategy for PDAC.

Citation Format: Annan Yang, Jie Jiang, Ziyue Li, Kevin S. Kapner, Hanrong Feng, Kristen E. Lowder, Miljan Kuljanin, Whiteny Johnson, Giselle Uribe, Jasper E. Neggers, Shengwu Liu, Tinghu Zhang, James Decaprio, Ewa Sicinska, Brian M. Wolpin, Nicholas P. Kwiatkowski, Stephanie K. Dougan, Joseph D. Mancias, Nathanael S. Gray, Andrew J. Aguirre. Therapeutic efficacy of selective CDK7 inhibition in pancreatic cancer mediated by induction of R-loop formation, DNA replication stress and genomic instability [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A057.
Abstract A066: 5z-7-oxozeaenol as an epithelial mesenchymal transition plasticity inhibitor in PDAC
Authors: You Eunae , Phillips Ildiko Phillips E. , Ebright Richard Y. , Desai Niyati , Raabe Michael J. , Lang Evan R. , Nieman Linda T. , Hajizadeh Soroush , Kreuzer Johannes , Haas Wilhelm , Ting David T.
Published: November 2022

Transcriptional profiling has defined PDAC into distinct classical epithelial (E) or quasi-mesenchymal (QM) subtypes, and these subtypes exist on a continuum of interconverting cell states. This epithelial to mesenchymal transition (EMT) plasticity is thought to be important for the metastatic dissemination and intrinsic resistance to chemotherapy. Our prior work identified TAK1 as an important driver of EMT in mouse circulating tumor cells, and we had identified a compound (5z)-7-oxozeaenol (Oxo) as a small molecule inhibitor of TAK1. Here, we have expanded upon this prior work by evaluating Oxo in 3 human patient derived PDAC cell lines as an EMT plasticity inhibitor. Treatment with Oxo induced a shift of all PDAC cell lines towards an E phenotype in both E and QM PDAC cell lines using RNA-seq and quantitative RNA in situ hybridization. This was associated with increased FFX sensitivity, loss of migratory abilities of all cell lines by Boyden chamber, and decreased invasion in matrigel. Interestingly, genetic TAK1 knockout via CRISPR/Cas9 in these PDAC cell lines showed different effects from Oxo. We found that TAK1 knockout decreased E PDAC cell line migratory behavior and increased FFX sensitivity, but QM PDAC cell lines were not affected by TAK1 knockout. This suggests that QM PDAC cell lines have additional signaling cascades that compensate for TAK1 loss and that Oxo effects across PDAC cell lines are not solely TAK1 dependent. Using phospho-proteomics, in FFX treated PDAC cell lines, we have identified potential candidate pathways in RNA splicing and viral processes that may be additional processes affected by Oxo that merits further investigation. Altogether, we have identified Oxo as a potential broad EMT plasticity inhibitor across PDAC subtypes, and there is a potential role of selective TAK1 inhibitors for E PDAC tumors.

Citation Format: Eunae You, Ildiko Phillips E. Phillips, Richard Y. Ebright, Niyati Desai, Michael J. Raabe, Evan R. Lang, Linda T. Nieman, Soroush Hajizadeh, Johannes Kreuzer, Wilhelm Haas, David T. Ting. 5z-7-oxozeaenol as an epithelial mesenchymal transition plasticity inhibitor in PDAC [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A066.
Abstract A068: Investigation of changes in epithelial cell states in pancreatic cancer using human organoids
Authors: Huang Ling , Muthuswamy Senthil
Published: November 2022

Pancreatic cancer is among the deadliest cancers in the US. The low survival rates of pancreatic cancer are mainly due to late diagnosis and a lack of effective treatments. To improve the clinical management of pancreatic cancer, we need better understand the biological mechanisms underlying the initiation and progression of this disease. With a focus on elucidating pancreatic cancer biology in human patients, we have developed organoid models for pancreatic normal physiology and malignancy using pluripotent stem cells or patient tumor tissues. Using stem cell-derived organoids, we investigated the interactions between pancreatic epithelial cell states, oncogenic signaling pathways, and cytokines. In this study, we discovered that human acinar organoids, compared to ductal organoids, were more sensitive to KRasG12D oncogenic signaling in vitro and in vivo, which supported acinar cells as the main cell of origin for pancreatic cancer in human patients. We have also developed working pipelines using organoid models to identify biomarkers and predict patient drug responses. Based on those successful studies, we now focus on investigating biological principles underlying racial disparities in pancreatic cancer using human cell models.

Citation Format: Ling Huang, Senthil Muthuswamy. Investigation of changes in epithelial cell states in pancreatic cancer using human organoids [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A068.
Abstract A079: The quadruplex-binding compound QN-302 in the MIA-PaCa2 pancreatic adenocarcinoma model shows no evidence of cardiac or neurological liabilities at therapeutic doses
Authors: Ahmed Ahmed , Arshad Tariq , Neidle Stephen
Published: November 2022

The human genome contains multiple sites of quadruplex (G4) arrangements, with over-representation in promoter regions of many oncogenes. Small molecule G4 stabilization down-regulates the transcription of these genes, leading to selective inhibition of cancer cell growth and anti-tumor activity. We have developed a number of novel G4-binding small molecules. QN-302, the most potent, has significant in vivo activity in animal models for pancreatic cancer and is currently in pre-clinical development with Qualigen Therapeutics. The effects of QN-302 have been examined on (1) a panel of cardiac function receptors, (2) heart rate in vivo, and (3) on the histopathology of organs from treated animals. QN-302 was initially screened in a series of in vitro industry-standard CEREP receptor binding assays. The few apparent indications of significant receptor binding were examined in vivo by means of ELISA assays. Cardiac function was examined using a cardiac heart-beat monitor attached to animals treated with QN-302 and compared to animals dosed with a vehicle control. QN-302 gave negative results in CEREP assays, apart from micromolar inhibition of acetylcholinesterase (ACE) and muscarinic (MUSC) receptors. There was no significant hERG receptor inhibition. There was no significant inhibition of ACE and MUSC receptors in vivo. Heart rate experiments, run at both the proposed therapeutic dose of 1mg/kg and at elevated levels, did not show significant deviations from values for the vehicle control arm. Histopathology of heart, liver and brain tissues from QN-302 treated animals, did not show any deleterious effects from the drug. The lack of effects on ACE and MUSC receptors in vivo, together with the absence of effects on heart, liver and brain tissue from treated animals and the normality of heart rate during treatment, demonstrate that treatment of MIA-Paca2 tumor-bearing mice with QN-302 does not have a cardio-, nephro- or neurotoxic burden at therapeutic doses. QN-302 is bio-available at therapeutic doses and is currently in pre-clinical development with Qualigen Therapeutics Inc

Citation Format: Ahmed Ahmed, Tariq Arshad, Stephen Neidle. The quadruplex-binding compound QN-302 in the MIA-PaCa2 pancreatic adenocarcinoma model shows no evidence of cardiac or neurological liabilities at therapeutic doses [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A079.
Abstract B003: Pancreatic cancer cells activate arginine biosynthesis to adapt to myeloid-driven amino acid stress in the tumor microenvironment
Authors: Saab Juan J. Apiz , Dzierozynski Lindsey N. , Jonker Patrick B. , Zhu Zhou , Chen Riona N. , Oh Moses , Sheehan Colin , Macleod Kay F. , Weber Christopher R. , Muir Alexander
Published: November 2022

Nutrient stress in the tumor microenvironment requires cancer cells to adopt adaptive metabolic programs to maintain survival and proliferation. Therefore, knowledge of microenvironmental nutrient levels and how cancer cells cope with such nutrition is critical to understand the metabolism underpinning cancer cell biology. Previously, we performed quantitative metabolomics of the interstitial fluid (the local perfusate) of pancreatic ductal adenocarcinoma (PDAC) tumors to comprehensively characterize nutrient availability in the microenvironment of these tumors. We have used this information to develop Tumor Interstitial Fluid Medium (TIFM), a cell culture medium that contains nutrient levels representative of the PDAC microenvironment, enabling study of PDAC metabolism under physiological nutrition. By transcriptomic analysis, we show that PDAC cells cultured in TIFM, compared to standard culture models, adopt a cellular state more similar to PDAC cells in tumors. Using the TIFM model, we then identified arginine biosynthesis as a critical metabolic adaptation PDAC cells engage to cope with microenvironmental nutrition. We further find that arginine biosynthesis enables PDAC cells to cope with microenvironmental arginine starvation, which we show is driven by myeloid cells in PDAC tumors. Altogether, these data show that nutrient availability in the microenvironment is an important determinant of PDAC metabolism and behavior, and models incorporating tumor nutrition enable detailed and mechanistic study of microenvironmentally-programmed PDAC cell states and phenotypes. Further, through use of the TIFM model, we identified both myeloid-driven arginine starvation as a major metabolic stress prevalent in the PDAC microenvironment, and the metabolic adaptations PDAC cells use to counter this nutritional challenge.

Citation Format: Juan J. Apiz Saab, Lindsey N. Dzierozynski, Patrick B. Jonker, Zhou Zhu, Riona N. Chen, Moses Oh, Colin Sheehan, Kay F. Macleod, Christopher R. Weber, Alexander Muir. Pancreatic cancer cells activate arginine biosynthesis to adapt to myeloid-driven amino acid stress in the tumor microenvironment [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B003.
Abstract B007: Enhancing autophagy inhibition as a therapeutic strategy for pancreatic cancer
Authors: DeLiberty Jonathan M. , Robb Ryan , Gates Claire E. , Pieper Noah L. , Yang Runying , Stalnecker Clint A. , Bryant Kirsten L.
Published: November 2022

Pancreatic ductal adenocarcinoma (PDAC) is characterized by KRAS- and autophagy-dependent tumorigenic growth. We determined the role of mutationally activated KRAS, found in ~95% of PDAC, in supporting autophagy. Surprisingly, acute KRAS suppression was associated with increased autophagic flux. Pharmacologic inhibition of ERK MAPK phenocopied the genetic silencing of KRAS and increased autophagic flux. We speculated that the loss of ERK-driven metabolic processes may induce compensatory mechanisms to increase autophagy. We then addressed whether ERK inhibition increased PDAC dependence on autophagy. Supporting this possibility, we found that cotreatment with the autophagy inhibitor chloroquine (CQ) synergistically enhanced ERK inhibitor-mediated anti-proliferative activity. Our findings, together with similar observations by others, provided the rationale for our initiation of Phase I/II clinical trials evaluating the combination of MEKi (binimetinib; NCT04132505) or ERKi (LY3214996; NCT04386057) with hydroxychloroquine (HCQ) in PDAC. Our ongoing studies are centered on developing additional combinations for targeting autophagy. First, we performed a CRISPR/Cas-9 mediated genetic loss-of-function screen in the presence of CQ to determine additional sensitizers as well as mediators of resistance to autophagy inhibition. Top sensitizers included multiple facilitators of the DNA damage response, mTOR pathway components, and genes involved in the upstream regulation of the autophagy pathway. Second, we determined that autophagic signaling is temporally regulated following RAS pathway inhibition and hypothesize that further dissection of this regulation will improve current anti-nutrient scavenging treatment strategies. We conclude that concurrent suppression of multiple metabolic processes, to block compensatory rebound activities, will be needed for effective PDAC treatment.

Citation Format: Jonathan M. DeLiberty, Ryan Robb, Claire E. Gates, Noah L. Pieper, Runying Yang, Clint A. Stalnecker, Kirsten L. Bryant. Enhancing autophagy inhibition as a therapeutic strategy for pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B007.
Abstract B019: Inflammatory response to dietary carbohydrates contributes to the formation of hepatic metastatic niche
Authors: Surumbayeva Aizhan , Williams Riley , Kotliar Michael , Taylor Maryclare , Costa Débora B. Vendramini , Ogier Charline , Restifo Diana , Cai Kathy Q. , He Xueyang , Boutz Paul , Balachandran Siddharth , Astsaturov Igor
Published: November 2022

Mortality from colon and pancreatic cancers arises from cancer metastatic dissemination to the liver. The glycemic load from carbohydrates (carbs) has been specifically linked to the risk of metastatic recurrence of stage 3 colorectal cancer, but the mechanism of how dietary carbs contribute to the formation of liver metastases remains poorly understood. Our analyses now demonstrate that feeding mice a high carb diet (HCD) promotes liver colonization by tumor cells, and supports the survival of these cells, once in the liver. HCD also induces expression of a Type I interferon (IFN) inflammatory gene signatures which may contribute to its ability to promote metastatic seeding of the liver. Notably, this inflammatory phenotype in hepatocytes was completely abolished if animals are fed a diet enriched in fats (75% of calories), indicating a direct link between liver inflammation and consumption of carbohydrates. Specifically, we have discovered that: 1) dietary carbohydrates, but not a high-fat ketogenic diet, activate multiple independent inflammatory cascades in hepatocytes, including Type-I IFN/STAT1, NFkB, and IL6-STAT3 pathways; 2) the inflammatory signaling in hepatocytes is retained in Scid and NSG mice, indicating that it occurs in the absence of adaptive immunity; 3) HCD, but not fasting or ketogenic diet, markedly increases abundance of retained intronic sequences and formation of double-stranded RNA (dsRNAs). We nominate these yet uncharacterized dsRNAs as potential viral mimics which may trigger the Type I IFN signature observed in HCD-fed livers; and (4) a ketogenic diet showed a trend to reduce liver metastatic colonization, but was associated with mild hepatic steatosis. Overall, this study establishes a new paradigm in nutrient sensing by normal hepatocytes and nominates alternative RNA splicing as the potential trigger of inflammatory responses to HCDs via accumulation of dsRNAs. We suggest that a reduction of dietary carbohydrates, by suppressing the diet-induced hepatic inflammation, will improve the survival of cancer patients, and reduce the risk of liver metastases.

Citation Format: Aizhan Surumbayeva, Riley Williams, Michael Kotliar, Maryclare Taylor, Débora B. Vendramini Costa, Charline Ogier, Diana Restifo, Kathy Q. Cai, Xueyang He, Paul Boutz, Siddharth Balachandran, Igor Astsaturov. Inflammatory response to dietary carbohydrates contributes to the formation of hepatic metastatic niche [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B019.
Abstract B045: Evaluating the role of altered RNA metabolism in pancreatic cancer therapy resistance
Authors: Siraj Md Afjalus , Shan Xinning , Tseng Robert , Escobar-Hoyos Luisa
Published: November 2022

Pancreatic ductal adenocarcinomas (PDACs) are highly lethal, mostly because they quickly develop resistance to current chemotherapies: Gemcitabine (GEM)/paclitaxel or cocktail FOLFIRINOX. Both chemotherapies rely on nucleoside analogues (GEM and 5-fluorouracil [5-FU], and resistance is developed without acquiring mutations, suggesting the role of non-mutational mechanisms for therapy resistance. Our recent findings demonstrated that PDACs depend on RNA splicing proteins to maintain tumors and are exquisitely susceptible to a range of therapies directed at RNA splicing, supporting the role of aberrant RNA splicing in PDAC therapy resistance. Here we evaluated the role of altered RNA splicing in PDAC therapy resistance. Three murine and human isogenic lines with either sensitivity or resistance to GEM were developed. We performed deep RNA sequencing (RNASeq, 80-100 million reads, traditional is 20-40 million reads), differential gene expression, and splicing analyses. GEM resistant PDAC cells demonstrated >40% of non-canonical RNA splice variants and altered expression of 30% of RNA-binding proteins encoded in the human/murine genome, compared to GEM sensitive ones. Specific alternatively spliced exons with common cis-elements were identified in therapy resistant cells, suggesting that these splicing changes are guided by a splicing factor or other RNA-binding protein(s) (RBPs). Top splicing changes were associated to mRNAs encoding ether lipid and pyruvate metabolism. This finding is important as previous studies have linked these metabolic pathways to therapy resistance, however, they have overlooked if protein isoforms, resulting from aberrant splicing, have different impacts in therapy resistance. In addition, GEM and H3B-8800, a novel spliceosome inhibitor showed higher synergistic activity in GEM resistant PDAC cells compared to GEM sensitive cells, suggesting that the development of resistance in PDAC is highly dependent on RNA splicing. Combinedly, these data strongly suggest that resistance to chemotherapeutic agents in PDAC cells requires altered RNA splicing and aberrant expression of associated proteins. Further investigation is ongoing to identify the splicing events and RBPs related to chemotherapy resistance, which will uncover novel mechanisms of therapy resistance and therapeutic modalities by targeting RNA splicing in pancreatic cancer.

Citation Format: Md Afjalus Siraj, Xinning Shan, Robert Tseng, Luisa Escobar-Hoyos. Evaluating the role of altered RNA metabolism in pancreatic cancer therapy resistance [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B045.
Abstract B046: Restricted cellular plasticity of human pancreatic ductal cells into a pluripotent state
Authors: Grygoryev Dmytro , Ekstrom Taelor , Link Jason M. , Sears Rosalie C. , Kim Jungsun
Published: November 2022

Cancer cells undergo plasticity against stress for the survival of the fittest. Pancreatic ductal adenocarcinoma (PDAC) also shows intratumoral transcriptional heterogeneity with cell plasticity, which correlates with phenotypical aggressiveness and therapeutic resistance. Cell fates are determined by master transcription factors (TFs, also called “pioneer factors”) and their co-factors by opening up chromatin and establishing competence for gene expression specific to each cell type during normal development. Force expression of various combinations of pioneer factors can switch cell fate into other lineages, including induced pluripotent stem cells (“iPSC”). Since pluripotent stem cells do not have the cancer hallmarks of uncontrolled cell growth and migration, hypothetically, a fully reprogrammed cancer iPSC should regain gene programs to control these hallmarks of cancer. Thus, we and others have reprogrammed cancer cells into pluripotent stem cell-like cells by introducing pluripotent pioneer factors. However, intriguingly, despite the nature of the high plasticity of cancer, complete reprogramming of cancers to a pluripotent state is impeded in most cases, enabling us to study and model cancer progression. Our further studies confirm that, upon reprogramming, most PDAC cells lose the original PDAC phenotypes to some extent but remain in plasticity states during reprogramming. Herein, we further update on our efforts to optimize the reprogramming of normal pancreatic ductal epithelial cell line (PDEC) and PDAC derived from patients through the Sendai virus, which can most robustly transfer genes regardless of cell types. While control cells (e.g., acinar cells and fibroblast) were fully reprogrammed into iPSC cells, both PDEC and PDAC were impeded from being fully reprogrammed into pluripotency. Intriguingly, a subset of normal PDEC cells as well as some PDAC cell acquired a “partial reprogramming marker” upon reprogramming, suggesting that PDEC cells are stalled in early developmental states. Therefore, we now conclude that normal and cancerous pancreatic ductal cell states have an intrinsic mechanism that blocks complete reprogramming into a pluripotent state, and the oncogenic pathway is poised for activation, despite the nature of the high plasticity of PDAC. Identifying the factors responsible for maintaining this impenetrable cancer chromatin landscape is ideal for nominating therapeutic targets for intercepting PDAC plasticity. This work is supported by OHSU/CEDAR project award 68182-939-000.

Citation Format: Dmytro Grygoryev, Taelor Ekstrom, Jason M. Link, Rosalie C. Sears, Jungsun Kim. Restricted cellular plasticity of human pancreatic ductal cells into a pluripotent state [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B046.
Abstract B060: Investigating the role of ERphagy in pancreatic cancer
Authors: Vogt Sandra L. , Bar-Sagi Dafna
Published: November 2022

Pancreatic ductal adenocarcinoma (PDAC) harbors mutations in KRAS in greater than 90% of cases and is characterized by a dense, fibrotic stroma that fosters the formation of a hypoxic, nutrient-poor tumor microenvironment. Tumor cells counteract these stresses through the hyperactivation of multiple nutrient scavenging pathways, including macropinoytosis and macroautophagy. Whereas the role of the latter in the regulation of PDAC growth has been extensively studied, much less is known about the role of endoplasmic reticulum (ER)-specific autophagy (ERphagy), a homeostatic mechanism involving ER membrane remodeling which promotes the clearance of misfolded protein aggregates, thereby supporting proteostasis. Using an ERphagy reporter system, we found that pancreatic cancer cells display mutant KRas-dependent suppression of ERphagy both at baseline and in the context of nutrient deprivation, which was partially dependent on the ER-resident receptor CCPG1. Furthermore, direct perturbation of the 26S proteasome with bortezomib enhanced ERphagy, suggesting that the attenuated ERphagy capacity in pancreatic cancer cells may reflect a greater dependence on proteasomal activity for the maintenance of proteostasis. Significantly, the knockdown of CCPG1 but not other ERphagy receptors augmented the growth-suppressive effects of bortezomib in vitro, an effect likely caused by unresolved proteotoxic stress. Overall, our findings implicate CCPG1-mediated ERphagy in pancreatic cancer cell survival and identify a targetable cell-intrinsic vulnerability that can potentiate the cytotoxic effects of bortezomib, which alone is clinically ineffective in treating PDAC.

Citation Format: Sandra L. Vogt, Dafna Bar-Sagi. Investigating the role of ERphagy in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B060.
Abstract B079: Unfolding the role of cell state on stress granule heterogeneity and function in pancreatic cancer
Authors: Redding Alexandra , Fonteneau Guillaume , Grabocka Elda
Published: November 2022

Phenotypic and functional heterogeneity is a common feature of cancer cells that poses as a major therapeutic challenge. Previous work has implicated the phase-separation organelles, stress granules (SGs), as important mediators of tumorigenesis that function as a mutant KRAS-driven stress-adaptive mechanism to enhance cellular fitness. We have found that mutant KRAS pancreatic cancer cells show a high degree of intra-cellular heterogeneity in SG formation, ranging from no SGs to markedly high levels. Given the function of SGs in cancer cell fitness and the role of cancer cell heterogeneity in tumor progression and therapeutic response, we sought to understand the determinants of SG heterogeneity and its role in KRAS-driven tumorigenesis. Here, we show that the capability of KRAS mutant pancreatic cancer cells to form SGs is dependent on the cell cycle state, with cells in G2 phase showing markedly enhanced SG formation. We demonstrate that this heterogeneity in SG formation is determined by a cell cycle specific interplay between the activator of cell death, Caspase 3, and the SG regulator molecule 15-deoxy-delta-12,14-prostaglandin J2 (15-d-PGJ2). We show that 15-d-PGJ2 production in G2 is driven by calcium-dependent phospholipase A2 (cPLA2) activity and is subject to regulation by Caspase 3. Our results show that the capacity of Caspase 3 to cleave and inactivate the cPLA2 protein is specifically suppressed in G2, thus leading to upregulation of cPLA2 activity and 15-d-PGJ2 levels. As such, we find that 15d-PGJ2 levels are highest in G2 and that the inhibition of cPLA2 blocks SG formation in G2 specifically. Accordingly, exogenous 15d-PGJ2 rescues SG formation in cPLA2-inhibited G2 cells. In addition, we demonstrate that Caspase 3 inhibition increases 15-d-PGJ2 levels and stimulates SG formation in asynchronous cells, mirroring the natural suppression of Caspase 3 seen in G2. Importantly, we show that heterogeneity in SG levels translates into a functional heterogeneity whereby SG inhibition preferentially sensitizes cells in G2 to stress stimuli. Altogether these data support a model whereby SG formation integrates cues from cell death and proliferative signals and indicate that SG levels may be critical to achieve a clear signal for cell cycle progression at the G2/M border. Furthermore, our findings suggest that cancer cells may show differential sensitivity to anti-SG therapy as they progress through the cell cycle, and pairing such therapy with G2-synchronizing chemotherapeutics may increase susceptibility and thus treatment efficacy.

Citation Format: Alexandra Redding, Guillaume Fonteneau, Elda Grabocka. Unfolding the role of cell state on stress granule heterogeneity and function in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B079.
Abstract C006: Loss of the MGAT5 glycosyltransferase sensitizes pancreatic tumor cells to immune clearance
Authors: Hollander Erin , Stanger Ben
Published: November 2022

Pancreatic ductal adenocarcinoma (PDAC) is currently the third leading cause of cancer-related death in the United States. The five-year survival rate of less than nine percent is attributed mainly to a difficulty in early detection and a lack of effective treatments. Tumor-associated glycans represent a potential anti-tumor target for two reasons: (i) protein glycosylation is known to play a role in tumor progression, and (ii) alternatively glycosylated proteins may function as tumor neoantigens. The glycosyltransferase MGAT5 catalyzes the formation of beta-1,6-N-acetylglucosamine branched glycans, and overexpression has been implicated in tumor growth and metastasis in multiple cancers. Using a panel of clonal cell lines that recapitulate the immune heterogeneity of PDAC, we found that knockout of MGAT5 in some clones (“T cell-inflamed" tumors) allows for complete clearance of tumors while in other clones (“non-T cell-inflamed”) MGAT5 deficiency led to a marked decrease in tumor growth. This phenotype was confirmed in orthotopic injection as well as subcutaneous injection into syngeneic mice. By contrast, MGAT5 loss had no impact on tumor cell growth in vitro. To probe immune system involvement in this robust rejection of tumor growth, the MGAT5 KO cells were injected into Nod/Scid mice, resulting in full rescue of the phenotype. Tumor eradication or growth inhibition in vivo was found to be dependent specifically on the presence of CD4/CD8 T cells and dendritic cells. Tumor challenge experiments, in which mice were immunized with MGAT5 KO cells and challenged with wild-type tumors four weeks later, revealed that tumor rejection was associated with a durable immunologic memory. Finally, therapeutic vaccination with the knockout line concomitantly with wild-type tumor cell injection led to decreased tumor growth. These results are consistent with a model in which MGAT5 loss results in the formation of new tumor antigens and/or enhances the immunogenicity of pre-existing antigens. Ongoing work seeks to determine the identity of the responsible antigens and further investigate the relationship between altered glycosylation and anti-tumor immunity.

Citation Format: Erin Hollander, Ben Stanger. Loss of the MGAT5 glycosyltransferase sensitizes pancreatic tumor cells to immune clearance [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C006.
Abstract C010: Polymerase theta inhibition synergizes with anti-PD-1 immunotherapy in BRCA2-deficient pancreatic ductal adenocarcinoma
Authors: Patterson-Fortin Jeffrey , Jadhav Heta , Pantelidou Constantia , Phan Tin , Grochala Carter , Hao Jie , Wang Junning , Andrews Elizabeth A. , Guerriero Jennifer L. , Wolpin Brian M. , Stanger Ben Z. , Aguirre Andrew A. , Cleary James M. , D'Andrea Alan A. , Shapiro Geoffrey I.
Published: November 2022

Recently developed inhibitors of polymerase theta (POLQ) have demonstrated synthetic lethality in pre-clinical tumor models of BRCA1 and BRCA2-deficient cancers. Since other DNA repair inhibitors, including PARP inhibitors, induce changes in the tumor immune microenvironment (Pantelidou et al., Cancer Discovery, 2019), we asked whether POLQ inhibition would cause similar alterations in preclinical models of pancreatic ductal adenocarcinoma (PDAC). Initially, we generated BRCA2-deficient cells by CRISPR-mediated deletion of the BRCA2 gene in a murine KrasLSL-G12D/+;Trp53LSL-R172H/+;Pdx1-Cre;Rosa26YFP/YFP (KPCY) PDAC cell line (Li et al., Immunity, 2018). Injection of these cells into syngeneic mice generated an aggressive immunocompetent BRCA2-deficient tumor model. We next demonstrated that novobiocin (NVB), a first-in-class inhibitor of the POLQ ATPase domain (Zhou et al., Nature Cancer, 2021), induces both innate and adaptive immune responses in this model through activation of the cGAS/STING pathway. NVB exposure resulted in upregulation of micronuclei, increased cGAS/STING pathway activation, increased type I interferon expression, increased CD8+ T-cell infiltration, and local paracrine activation of dendritic cells. NVB-mediated POLQ inhibition also upregulated PD-L1 expression, correlating with increased cGAS/STING pathway activation. These NVB-induced changes were associated with antitumor activity. Whereas depletion of CD8+ T-cells compromised the efficacy of NVB, the antitumor effects of POLQ inhibition were augmented when combined with anti-PD-1 immunotherapy. Taken together, our findings demonstrate that NVB-mediated POLQ inhibition induces immune responses in a cGAS/STING-dependent manner and provides a rationale for combining POLQ inhibition with immune checkpoint blockade for the treatment of BRCA2-deficient pancreatic cancers.

Citation Format: Jeffrey Patterson-Fortin, Heta Jadhav, Constantia Pantelidou, Tin Phan, Carter Grochala, Jie Hao, Junning Wang, Elizabeth A. Andrews, Jennifer L. Guerriero, Brian M. Wolpin, Ben Z. Stanger, Andrew A. Aguirre, James M. Cleary, Alan A. D'Andrea, Geoffrey I. Shapiro. Polymerase theta inhibition synergizes with anti-PD-1 immunotherapy in BRCA2-deficient pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C010.