bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A021: In silico Prediction of Proteins Interacting with a Basal-like Pancreatic Cancer marker, RhoV, Using AlphaFold
Authors: Li Zebang Mark , Zhou Xiaoxu , Lu Shaolei 
Published: September 2024

Abstract
Introduction Basal-like pancreatic cancer is a subtype with a worse clinical outcome than other subtypes. Ras homolog family member V (RhoV) is one of the basal-like markers that was recently identified. RhoV is a Rho GTPase and is closely regulated by guanine exchange factors (GEFs) and GTPase activating proteins (GAPs). An in silico prediction was performed using AlphaFold to identify RhoV regulators. Methods Amino acid sequences of 120 known GEFs and GAPs were collected. AlphaFold Colab, which uses AlphaFold2 and AlphaFold2-multier, was initially used to screen GEFs and GAPs for their binding affinities to RhoV. The top hits from AlphaFold2 were further verified by AlphaFold3, the most current version of AlphaFold partially open to nonprofit users. RAC1, a well-studied Rho GTPase with known GEFs and GAPs, was used as a control for the prediction process. Results AlphaFold predicted strong interactions of RAC1 and RhoV with GTP and GDP (ipTM of 0.92 between RAC1 and GTP; 0.95 between RAC1 and GDP; 0.92 between GTP and RhoV; 0.95 between GDP and RhoV). Known RAC1 binding partners, ARHGEF5 and ARHGAP21, showed strong binding affinities with RAC1 with ipTM of 0.91 and 0.92, respectively. Out of 120 GEFs and GAPs, AlphaFold2 predicted 6 of them with high binding affinities to RhoV (ipTM greater than 0.79). They are ARHGEF5, ARHGEF3, ARHGAP21, ITSN1, and ITSN2. Their binding affinities were confirmed by AlphaFold3, showing a strong correlation with AlphaFold2 (R of 0.79). AlphaFold3 also demonstrated high binding affinities between RhoV and compounds Palmitic acid (PLM), Citric acid (CIT), and Oleic acid (OLA). Conclusion AlphaFold is a revolutionary protein structural prediction tool with the ability to predict protein-protein binding affinities with high accuracy. AlphaFold2 is open to researchers in the field and allows unlimited queries on its server. AlphaFold3 only allows 20 predictions per research account per day. AlphaFold successfully predicted known binding partners of RAC1 and that RhoV could interact with the following GEFs and GAPs, ARHGEF5, ARHGAP21, and ARHGEF3, with high affinities. AlphaFold is a reliable in silico tool to screen binding partners of any protein of interest before meaningful biochemical interaction is confirmed in vitro and in vivo.
Citation Format: Zebang Mark Li, Xiaoxu Zhou, Shaolei Lu. In silico Prediction of Proteins Interacting with a Basal-like Pancreatic Cancer marker, RhoV, Using AlphaFold [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A021.
Abstract A025: Cell of origin does not underlie transcription heterogeneity in pancreatic ductal adenocarcinoma
Authors: Chu Ken , Lee Alex , Sarai Karnjit , Dou Yan , Hunt Wesley , Croft Emma , Samani Atefeh , Taghizedeh Farnaz , Dubois Claire , Flibotte Stephane , Kopp Janel 
Published: September 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) it though to develop through induction of different precursor lesions, however, the normal cell type that gives rise to these precancerous lesions and PDAC is unclear. Recent studies using mouse models and ex vivo cultured human cells suggest that the cellular origin of PDAC may be either acinar or ductal cells. Potential transcriptional markers associated with PDAC of different cellular origins have been identified. Here, we interrogate whether these markers are predictive of cellular of origin across models using mouse models where acinar and ductal cells (Ptf1aCreER or Sox9CreER) expressing oncogenic Kras in the absence of Trp53 or Pten give rise to PDAC tumors. We found that acinar- and ductal-cell-derived PDAC exhibit transcriptional differences both in vivo and in vitro when comparing within one genotype or sample source type (e.g. bulk tumor or primary cell lines). However, previously predicted markers of cellular origin had variable expression across models and sample types suggestive of differences specific to those sample sets. Using our larger sample sets and multiple genotypes and source types, we proposed a more comprehensive set of cell of origin markers for consideration. Application of these markers to our own data sets, however, failed to properly segregate acinar- and ductal-cell-derived PDAC into separate groups. This suggests that the transcriptional heterogeneity observed in our sample set was not driven by the tumors arising from different cellular origins. We also examined the relationship between cell of origin and patient PDAC transcriptional subtypes using our mouse model datasets. Our findings support previous research indicating that mouse models of acinar-cell-derived PDAC favor those of a classical subtype. However, our mouse PDAC samples all express similar or very low levels of the genes denoting the basal subtype, suggesting that the basal subtype was not strongly present in any of the datasets we examined. In summary, our data suggest that acinar and ductal cells converge into a very similar PDAC transcriptional state and that, if differences can be identified, they will likely be identified by non-transcript based readouts.
Citation Format: Ken Chu, Alex Lee, Karnjit Sarai, Yan Dou, Wesley Hunt, Emma Croft, Atefeh Samani, Farnaz Taghizedeh, Claire Dubois, Stephane Flibotte, Janel Kopp. Cell of origin does not underlie transcription heterogeneity in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A025.
Abstract A026: Studying the synergistic potential of a p53 reactivator with ROS-mediated therapies for the treatment of pancreatic cancer
Authors: Sánchez Daniel Parra , García-Sampedro Andrés , Laughland Isabela , Peuget Sylvain , Selivanova Galina , Pereira Stephen P , Acedo Pilar 
Published: September 2024

Abstract
Introduction: Pancreatic cancer, with a dismal five-year survival rate of just 12%, demands innovative approaches due to its resistance to current therapies. TP53 mutations, present in 75% of patients, make mutant p53 an appealing target. Thus, p53 reactivation, restoring its tumour suppressor functions, represents a promising strategy to address this challenge. While the proposed reactivator has shown efficacy in other malignancies, its potential in pancreatic cancer therapy requires further exploration. Methods: In this project, we have assessed the potential of repurposing a reactivator of mutant p53 protein, to inactivate pancreatic cancer cells. We have performed RNA-sequencing analysis in patient-derived models available in the lab, to study the signalling pathways regulated by the p53 reactivator anticancer activity. We have also studied the possibility to synergistically combine this repurposing strategy with reactive oxygen species (ROS)-mediated therapeutic approaches, as we previously observed p53 reactivation inhibits the glutathione antioxidant pathway. Results: The combination treatment induced synergistic cell death (3-fold increase) compared to monotherapy as evaluated by different molecular assays (e.g. MTT and Live/Death Assay). It also increased ROS levels (Flow cytometry) and induced paraptosis and apoptosis (Western Blot, Tomography Electron Microscopy). The RNA-seq data revealed differential expression of more than 200 genes, confirming the activation of oxidative stress and a cellular response to unfolded proteins. Moreover, Sanger sequencing results demonstrated that the sensibility of each pancreatic model to treatment was dependent on the mutational status of TP53. Conclusion/discussion: The combination therapy of a TP53 reactivator and a ROS mediated therapeutic strategy works synergistically in patient derived models, inducing cell death and changes in the expression of certain RNAs directly involved in unfolded protein response. This pilot study shows that this combination is a feasible strategy to treat pancreatic cancer, setting the path for its testing on in vivo models.
Citation Format: Daniel Parra Sánchez, Andrés García-Sampedro, Isabela Laughland, Sylvain Peuget, Galina Selivanova, Stephen P Pereira, Pilar Acedo. Studying the synergistic potential of a p53 reactivator with ROS-mediated therapies for the treatment of pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A026.
Abstract A027: Enhancing pancreatic cancer chemotherapy through photochemical internalisation
Authors: Rosado Maria , Mahamed Ismahan , Garcia-Sampedro Andres , MacRoberts Sandy , Selbo Pål , Pereira Stephen , Acedo Pilar 
Published: September 2024

Abstract
Introduction Pancreatic cancer is the deadliest common cancer. Its poor prognosis is associated with its complex biology and lack of early detection strategies. Although much progress has been made in finding more effective therapeutic strategies, pancreatic tumours remain difficult to treat. A major reason why chemotherapy is relatively ineffective against this type of cancer is inefficient delivery of drugs to their target sites combined with multidrug resistance. Our aim is to use the technique called Photochemical Internalisation (PCI), a light-triggered intracellular drug delivery method which combines low dose Photodynamic Therapy (PDT) with chemotherapy, to induce efficient cytosolic delivery of therapeutic compounds to their specific subcellular targets. Methodology Treatment outcomes using saporin (a type I ribosome-inactivating protein) and gemcitabine as monotherapies, or in combination with a light-activated photosensitizer (the porphyrin TPPS2a), were thoroughly analysed in both established pancreatic cancer cell lines and patient-derived xenograft (PDX) models. The efficacy of these treatments was assessed in both 2D and 3D tumour models through various cell viability assays, including MTT, crystal violet staining, and neutral red staining. Additionally, molecular techniques such as western blotting, protein arrays, and flow cytometry were employed to determine the effects on cell viability and to elucidate changes in signalling pathways leading to the therapeutic response. Results In this study, we observed minimal cytotoxicity induced by saporin, gemcitabine or TPPS2a + light monotherapies. However, PCI synergistically enhanced saporin and gemcitabine cytotoxicity (p&lt;0.001) using very low concentrations in all tumour models. Moreover, we determined the mechanism of cell death triggered by these protocols. PCI induced endosomal disruption following light excitation and apoptosis leading to caspases 3/7 activation, in a time dependent manner. Conclusions Overall, our findings demonstrate the potential of PCI to enhance the efficacy of cancer chemotherapy for pancreatic cancer using lower doses than in monotherapy and open a new window for future translational studies. By using low doses of light therapy, we have found a promising avenue for future studies that could eventually lead to better treatments for this challenging disease.
Citation Format: Maria Rosado, Ismahan Mahamed, Andres Garcia-Sampedro, Sandy MacRoberts, Pål Selbo, Stephen Pereira, Pilar Acedo. Enhancing pancreatic cancer chemotherapy through photochemical internalisation [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A027.
Abstract A033: Mapping age-specific biomarker dynamics in pancreatic ductal adenocarcinoma
Authors: Gupta Priyanka , Duong-Polk Karen , Murad Rabi , Commisso Cosimo 
Published: September 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal age-related disease, with a median age of diagnosis over 70 years. Understanding age-dependent aberrations in the blood proteome might facilitate early detection, prognosis, and treatment personalization of PDAC. In this study, we aim to decipher novel clinically relevant biomarkers that distinguish between younger and older PDAC patients. To do this, we used a syngeneic orthotopic PDAC animal model where we implanted murine KPC cells (KRasG12D/+; Tp53R172H/+) into the pancreata of age-restricted groups of young (6-8 weeks) and old (80-84 weeks) C57BL/6 mice. Our previous findings demonstrated accelerated tumor growth and an increased metastatic burden in older mice relative to younger ones. Proteomic analysis of plasma from tumor-bearing young and old mice revealed an array of upregulated age-specific circulating proteins relative to their non-tumor, age- and sex-matched controls. Using a threshold of &gt;2-fold change and p&lt;0.05, our analysis identified 22 and 24 proteins preferentially increased in young and old mice, respectively. To ascertain the clinical relevance of our findings in humans, we analyzed expression profiles of selected proteins in human PDAC datasets from The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses have highlighted proteins involved in an array of processes as key candidates, which are consistent with our mouse proteomics findings. These candidate proteins show higher expression levels in human tumors compared to healthy controls and exhibit significant correlations with patient age and overall survival. Our ongoing validation studies have identified a protein from the immunoglobulin superfamily of cell adhesion molecules as a potential biomarker of PDAC, particularly relevant for younger patients. We are currently conducting age-dependent characterization of cell adhesion molecules to understand their role in intercellular crosstalk between cancer and stromal cells, immune surveillance, and metastasis.
Citation Format: Priyanka Gupta, Karen Duong-Polk, Rabi Murad, Cosimo Commisso. Mapping age-specific biomarker dynamics in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A033.
Abstract A034: KRAS Mutation-Specific effects on the Tumor Immune Microenvironment Drive Tumor Progression
Authors: Andrew wenger  , Baron Tal , Hissong Erika , Vega-Perez Adrian , Sisso Whitney , Zafra Maria Paz , Chandwani Rohit , Dow Lukas , Siolas Despina 
Published: September 2024

Abstract
The immune microenvironment plays a critical role in cancer development, progression and resistance to therapy. KRAS mutations are near-ubiquitous in pancreatic ductal adenocarcinoma (PDAC) and several studies have demonstrated that KRASG12D can create an immunosuppressive tumor microenvironment. However, the immune effects of other oncogenic KRAS variants, such as KRASG12R (representing 20% of PDAC cases) are unknown. Given that specific KRAS mutants display distinct molecular phenotypes, we examined the immune cell composition of KRASG12R pancreatic tumors. Orthotopically implanted mouse tumors derived from KrasG12R/+;Trp53KO pancreatic organoids have a distinct immune profile in comparison to KrasG12D/+;Trp53KO tumors, characterized by an influx of intratumoral CD4+ T cells and mature dendritic cells. RNA sequencing of KRASG12R tumor cells revealed enrichment of Type I interferon (IFN) pathways accompanied by related chemokines, CXCL9 and CXCL10 in comparison to KRASG12D tumors. Analysis of publicly available human PDAC cohorts revealed enrichment of genes in inflammatory pathways in KRASG12R tumors. Collectively, these data link KRASG12R to a unique immune landscape that is distinct from KRASG12D tumors.
Citation Format: Andrew wenger, Tal Baron, Erika Hissong, Adrian Vega-Perez, Whitney Sisso, Maria Paz Zafra, Rohit Chandwani, Lukas Dow, Despina Siolas. KRAS Mutation-Specific effects on the Tumor Immune Microenvironment Drive Tumor Progression [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A034.
Abstract A035: 3D High-Density Collagen I Improves the Modeling of Aggressive Pancreatic Cancer
Authors: Nguyen-Ta Kim , Ranamukhaarachchi Sural , Turner Jeffrey , Joshi Utsav , Sonowal Himangshu , Medina Jorge de la Torre , Tiriac Herve , Fraley Stephanie , White Rebekah 
Published: September 2024

Abstract
Background: Fibrillar collagen type I constitutes the majority of the extracellular matrix in pancreatic ductal adenocarcinoma (PDAC), yet most in vivo murine models involve the use of basement membrane extracts, which instead contain collagen type IV, as matrices to embed PDAC cells. Type I collagen in the PDAC tumor microenvironment has been associated with worse prognosis. Our hypothesis is that PDAC cells grown in 3D high-density collagen I (HDC) gels behave more aggressively compared to the same cells grown using conventional basement membrane matrix (BMM). Methods: The KPC1199 2D cell line was previously generated from a tumor-bearing male KPC mouse. KPC1199 cells were cultured in vitro in HDC or BMM for one week. Orthotopic tumors were established by embedding KPC1199 cells in HDC (N=10) or BMM (N=10) in the pancreatic tail of syngeneic C57BL/6J mice via laparotomy. Half of the tumors were collected five weeks after tumor implantation, and the other half utilized for a survival study. Collagen was imaged by second harmonic generation (SHG) microscopy. Results: In vitro imaging of single KPC1199 cells grown in HDC revealed an aggressive phenotype with clonal network-like structures compared to a spheroidal, non-aggressive phenotype for cells grown in BMM over the course of seven days. SHG imaging confirmed consistent formation and organization of collagen in HDC tumors but minimal to faint collagen formation in BMM tumors. Gross examination of HDC mice showed 60% with visible liver metastasis compared with none in the BMM mice. In the survival study, the entire HDC group died before the BMM group (p-value &lt; 0.01). Conclusions: Our pilot study is the first, to our knowledge, to successfully generate orthotopic PDAC tumors using 3D high-density collagen I in a mouse model. KPC1199 cells embedded in HDC showed an aggressive phenotype in vitro, and resultant tumors demonstrated more robust collagen organization compared to the same cells grown in the BMM substrate. This aggressive phenotype translated to visible liver metastasis within five weeks in the HDC mice and prior to death from primary tumor burden. This is not typical for most KPC-derived cell lines but is typical for human PDAC patients. Our preliminary findings support the use of HDC as an alternative substrate for better modeling of this aggressive cancer.
Citation Format: Kim Nguyen-Ta, Sural Ranamukhaarachchi, Jeffrey Turner, Utsav Joshi, Himangshu Sonowal, Jorge de la Torre Medina, Herve Tiriac, Stephanie Fraley, Rebekah White. 3D High-Density Collagen I Improves the Modeling of Aggressive Pancreatic Cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A035.
Abstract A036: The role of hypoxia in CD8+ T cell localization and function in pancreatic cancer
Authors: Mello Ashley M. , Ngodup Tenzin , Donahue Katelyn L. , Di Magliano Marina Pasca , Lee Kyoung Eun 
Published: September 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a deadly malignancy characterized by poor response to existing therapeutic options. This resistance to treatment is partly due to its extensive inflammatory, desmoplastic stromal response, along with a hypoxic microenvironment. Although tumor hypoxia induces adaptive responses in both cancer cells and the surrounding stroma, most studies on the role of hypoxia in tumorigenesis have focused on cancer cell-intrinsic properties. The impact of hypoxia on stromal cells themselves and their interactions with cancer cells has remained largely unknown. We previously showed that inflammatory cancer-associated fibroblasts (iCAFs), which express high levels of cytokines and chemokines, are preferentially located in hypoxic regions of PDAC, and that hypoxia promotes an inflammatory fibroblast phenotype. The iCAF phenotype has been correlated with highly immunosuppressive features of PDAC. These findings and our preliminary observation that CD8+ T cells are largely excluded from hypoxic PDAC regions, raise the possibility that hypoxia suppresses the infiltration and activation of CD8+ T cells by modulating their interactions with inflammatory fibroblasts. By culturing CD8+ T cells under hypoxia with conditioned media from co-cultures of pancreatic cancer cells and fibroblasts, we have found that cancer cells and fibroblasts decrease CD8+ T cell proliferation and cytotoxic activity under low oxygen conditions. We are working to elucidate the mechanism by which hypoxia regulates CD8+ T cell infiltration and activation through cancer cell-fibroblast crosstalk.
Citation Format: Ashley M. Mello, Tenzin Ngodup, Katelyn L. Donahue, Marina Pasca Di Magliano, Kyoung Eun Lee. The role of hypoxia in CD8+ T cell localization and function in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A036.