tbuckley/cabot-search huggingface dataset:
Abstract 1400: An additive effect of ebv-miR-BART5-5p and hsa-miR18a-5p in the downregulation of CDH1 transcript in Epstein-Barr virus associated gastric cancer
Authors: Keila Torres, Natalia Landeros, Ignacio Wichmann, Allan Peñaloza-Otárola, Iva Polakovicova, Vinicius Maracaja-Coutinho, Maria Jose Maturana, Franz Villaroel-Espindola, Alejandro Corvalan
Journal: Cancer Research (2020)

Abstract Background. Nine percent of Gastric Cancer (GC) is associated with Epstein-Barr virus (EBV-associated GC), with significant variations in the global prevalence rates. Emerging evidence shows that, in addition to cellular miRNAs, viral miRNAs can also bind human mRNAs. EBV miRNAs are examples of this binding and are associated with oncogenic capacities of EBV. ebv-miR-BART5-5p shares the exact seed sequence with hsa-miR-18a-5p. However, common mRNA targets have not been fully described. The aim of this study is to determine predicted targets shared by both miRNAs in EBV-associated GC. Methodology. By in house method we identified predicted mRNA targets for ebv-miR-BART5-5p and hsa-miR-18a-5p. These targets were queried in published results from the supplementary files of the STAD TCGA study and miRwalk 2.0 software. Validation was performed in 7 EBV-associated GC (cases) and 6 EBV-negative GC (controls) samples by miQ-PCR (ebv-miR-BART5-5p and hsa-miR-18a-5p) and qRT-PCR (predicted targets). Results. We identified 25 downregulated and 11 upregulated mRNAs in EBV-associated GC cases compared with EBV-negative tumors in validated databases. Interestingly CDH1, which has been associated with diffuse and hereditary GC, was among the predicted targets by miRwalk 2.0. In clinical samples of EBV-associated GC, ebv-miR-BART5-5p and hsa-miR-18a-5p were overexpressed compared with control samples (p=0.0253 and p=0.0205, respectively). Furthermore, CDH1 was downregulated in EBV-associated tumors (p=0.0290). Conclusion: We identified a common human mRNA target, the CDH1 transcript for ebv-miR-BART5-5p and hsa-miR-18a-5p in EBV-associated GC. An additive effect can be suggested between both miRNAs, which may explain the unique downregulation of CDH1 in EBV-associated GC. This work warrants future validation in vitro, as well as in a larger cohort of EBV-associated GC. Grant support: CONICYT-FONDAP-15130011, Fondecyt Regular-1191928 and Fondecyt PostDoc-3201028 Citation Format: Keila Torres, Natalia Landeros, Ignacio Wichmann, Allan Peñaloza-Otárola, Iva Polakovicova, Vinicius Maracaja-Coutinho, Maria Jose Maturana, Franz Villaroel-Espindola, Alejandro Corvalan. An additive effect of ebv-miR-BART5-5p and hsa-miR18a-5p in the downregulation of CDH1 transcript in Epstein-Barr virus associated gastric cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1400.
A prefrontal–paraventricular thalamus circuit requires juvenile social experience to regulate adult sociability in mice
Authors: Kazuhiko Yamamuro, Lucy K. Bicks, Michael B. Leventhal, Daisuke Kato, Susanna Im, Meghan E. Flanigan, Yury Garkun, Kevin J. Norman, Keaven Caro, Masato Sadahiro, Klas Kullander, Schahram Akbarian, Scott J. Russo, Hirofumi Morishita
Journal: Nature Neuroscience (2020)
Endoscopic ultrasound-guided hepaticogastrostomy combined with gastroenterostomy in a case of complete duodenal obstruction
Authors: Shupeng Wang, Jintao Guo, Nan Ge, Sheng Wang, Wen Liu, Siyu Sun
Journal: Endoscopy (2020)

We report a successful case of hepaticogastrostomy combined with gastroenterostomy guided by endoscopic ultrasound (EUS) in a patient with unresectable carcinoma of the pancreatic head.
Abstract 4038: ABM-1310, A novel BRAF Inhibitor, combined with EGFR and MEK inhibitors, inhibits colorectal tumor growth and increases overall survival in vivo
Authors: Yong Hu, Chen Chen, Charles Huang, Min Xu, Youqin Chen, Xiyuan Zhao, Li Zhao
Journal: Cancer Research (2020)

Abstract Colorectal cancer (CRC) is a cancer that starts in the colon or the rectum, and the current treatment mainly relies on chemotherapies. For example, ERBITUX® /cetuximab is an FDA approved targetedtherapy drug to treat CRC with wild-type KRAS, the 11% low response rate limits its clinical application. BRAF inhibitors have been widely used clinically for melanoma and lung cancer, however, they have dismally low response rate at only approximately 5% of colorectal cancer patients with BRAFv600 mutation. Here, we report that ABM-1310, a novel small molecule inhibitor of BRAF (specifically inhibit BRAFv600 mutant), has shown good potency in colon cancer xenograft models, when combined with a MEK inhibitor and EGFR antibody. In the HT-29 xenograft subcutaneous model, 10 to 25mg/kg/day oral dose of ABM-1310 combined with cetuximab (0.1mg/dose, twice a week) and 3 mg/kg/day of Binimetinib (MEK inhibitor) significantly inhibited HT-29 tumor growth with TGI of 85% to 92% after 34-days treatment. As a monotherapy or combined with cetuximab alone, ABM-1310 also brought the TGI of 74% and 82% at 25mg/kg/day, which indicates ABM-1310 played a key role in tumor growth inhibition in the combinations. Beside with Binimetinib, we also tested combination of ABM-1310 with other different MEK inhibitors in this model. ABM-1310 is highly water-soluble small molecule with high cell permeability and blood brain barrier penetration. ABM-1310 shown good efficacy in melanoma A375 (luciferase labelled cells) in the subcutaneous/intracranial/intracardiac xenograft models (brain metastasis models). In the HT-29 colon intracranial model, ABM-1310 also demonstrated significant tumor inhibition effect and increased animal overall survival. Compared with vehicle or marketed BRAF inhibitor vemurafenib, the median survival time of ABM-1310 group was &amp;gt;90 days vs 51 days (vemurafenib) and 38 days (vehicle), respectively. In Summary, ABM-1310, as a novel small molecule BRAF inhibitor, combined with EGFR and MEK inhibitors, has shown strong anti-tumor effect in preclinical in vivo models of colon cancer with BRAFv600 mutation, especially with brain metastasis. Citation Format: Yong Hu, Chen Chen, Charles Huang, Min Xu, Youqin Chen, Xiyuan Zhao, Li Zhao. ABM-1310, A novel BRAF Inhibitor, combined with EGFR and MEK inhibitors, inhibits colorectal tumor growth and increases overall survival in vivo [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4038.
Overcoming resistance to rituximab in relapsed non-Hodgkin lymphomas by antibody-polymer drug conjugates actively targeted by anti-CD38 daratumumab
Authors: Ondřej Lidický, Pavel Klener, Daniela Machová, Petra Vočková, Eva Pokorná, Karel Helman, Cory Mavis, Olga Janoušková, Tomáš Etrych
Journal: Journal of Controlled Release (2020)

B-cell non-Hodgkin lymphomas (B-NHL) represent the most common type of hematologic malignancies in the Western hemisphere. The therapy of all B-NHL is based on the combination of different genotoxic cytostatics and anti-CD20 monoclonal antibody (mAb) rituximab. Unfortunately, many patients relapse after the mentioned front-line treatment approaches. The therapy of patients with relapsed/refractory (R/R) B-NHL represents an unmet medical need. We designed, developed and tested novel actively targeted hybrid mAb-polymer-drug conjugate (APDC) containing anti-CD20, anti-CD38 or anti-CD19 mAbs. Biocompatible copolymers based on N-(2-hydroxypropyl)methacrylamide (HPMA) with cytostatic agent doxorubicin attached via stimuli-sensitive hydrazone bond were employed for the mAb grafting. Anti-lymphoma efficacy of the APDC nanotherapeutics was evaluated in vivo on a panel of three patient-derived lymphoma xenografts derived from two patients with R/R B-NHL and one patient with so far untreated B-NHL. In both PDX models derived from patients with R/R B-NHL, the targeting with anti-CD38 antibody daratumumab demonstrated highly improved anti-lymphoma efficacy compared to the targeting with anti-CD20 rituximab, two experimental anti-CD19 antibodies and non-targeted controls. The results represent a proof-of-concept of a new algorithm of personalized anti-tumor therapy based on highly innovative APDC biomaterials.
3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data
Authors: Lindsey R. Fernandez, Thomas G. Gilgenast, Jennifer E. Phillips-Cremins
Journal: Genome biology (2020)

An important unanswered question in chromatin biology is the extent to which long-range looping interactions change across developmental models, genetic perturbations, drug treatments, and disease states. Computational tools for rigorous assessment of cell type-specific loops across multiple biological conditions are needed. We present 3DeFDR, a simple and effective statistical tool for classifying dynamic loops across biological conditions from Chromosome-Conformation-Capture-Carbon-Copy (5C) and Hi-C data. Our work provides a statistical framework and open-source coding libraries for sensitive detection of cell type-specific loops in high-resolution 5C and Hi-C data from multiple cellular conditions.
Targeting Rehabilitation to Improve Outcomes following total knee arthroplasty (TRIO): a randomised controlled trial of post-operative physiotherapy interventions
Authors: David Hamilton, David Beard, Karen Barker, Gary Macfarlane, Chris Tuck, Andrew Stoddart, Timothy Wilton, James Hutchinson, Gordon Murray, Hamish Simpson
Journal: BMJ (2020)

Acknowledgements We thank those that took part in the study and the investigators, physiotherapists and research teams that delivered the study at the participating centres. We thank the Edinburgh Clinical Trials Unit for coordinating the project, in particular: Chris Tuck, Elaine Kinsella and Philip Rayson (trial management team), Valentina Assi (statistics), Ronnie Harkess (programming) and Lyndsey Milne (data management). We acknowledge the support and advice at all stages of the study of the independent trial oversight and data monitoring committee: Prof. Alex MacGregor (University of East Anglia), Dr. Martin Lewis (Keele University), Prof. Michael Docherty (University of Nottingham) and Prof (emeritus) Merfyn Williams, (lay member). Funding: This study was funded by Arthritis Research UK (now Versus Arthritis), ref 20100, and sponsored by ACCORD (the University of Edinburgh and NHS Lothian). The funder had no role in study design, data collection, data analysis, data interpretation, writing of the article, or the decision to submit the paper for publication.
<i>IL2RA</i> Promotes Aggressiveness and Stem Cell–Related Properties of Acute Myeloid Leukemia
Authors: Chi Huu Nguyen, Angela Schlerka, Alexander M. Grandits, Elisabeth Koller, Emiel van der Kouwe, George S. Vassiliou, Philipp B. Staber, Gerwin Heller, Rotraud Wieser
Journal: Cancer Research (2020)

Overexpression of IL2RA, which encodes the alpha chain of the IL2 receptor, is associated with chemotherapy resistance and poor outcome in acute myeloid leukemia (AML). The clinical potential of anti-IL2RA therapy is, therefore, being explored in early-stage clinical trials. Notwithstanding, only very limited information regarding the biological function of IL2RA in AML is available. Using genetic manipulation of IL2RA expression as well as antibody-mediated inhibition of IL2RA in human cell lines, mouse models, and primary patient samples, we investigated the effects of IL2RA on AML cell proliferation and apoptosis, and on pertinent signaling pathways. The impact of IL2RA on the properties of leukemic stem cells (LSC) and on leukemogenesis were queried. IL2RA promoted proliferation and cell-cycle activity and inhibited apoptosis in human AML cell lines and primary cells. These phenotypes were accompanied by corresponding alterations in cell-cycle machinery and in pathways associated with cell survival and apoptosis. The biological roles of IL2RA were confirmed in two genetically distinct AML mouse models, revealing that IL2RA inhibits differentiation, promotes stem cell-related properties, and is required for leukemogenesis. IL2RA antibodies inhibited leukemic, but not normal, hematopoietic cells and synergized with other antileukemic agents in this regard. Collectively, these data show for the first time that IL2RA plays key biological roles in AML and underscore its value as a potential therapeutic target in this disease. SIGNIFICANCE: This study identifies IL2RA as a potential therapeutic target in AML, where it is shown to regulate proliferation, differentiation, apoptosis, stem cell-related properties, and leukemogenesis.
Abstract 1817: C/EBPβ antagonist peptide, ST101, attenuates oncogenic gene transactivation in cancer cells to drive antitumor activity
Authors: Jim A. Rotolo, Rick Ramirez, Mark Koester, Erin Gallagher, Siok Leong, Lila Ghamsari, Gene Merutka, Barry J. Kappel
Journal: Cancer Research (2020)

Abstract Transcription factor dysregulation is common in cancer, resulting in aberrant gene expression that drives oncogenesis. Antagonism of oncogenic transcription factor activity, by disrupting essential protein-protein interactions needed for activation of downstream effector molecules or association with DNA, represents a powerful approach to target this previously ‘undruggable' class of proteins. CCAAT/Enhancer Binding Protein Beta (C/EBPβ) is a transcription factor overexpressed in many cancers that regulates expression of factors that promote tumor survival, proliferation and inhibit differentiation. Here, we decribe the anti-tumor activity of ST101, a cell-penetrating peptide antagonist of C/EBPβ. To demonstrate ST101 disruption of the interaction of C/EBPβ with co-factor activating transcription factor 5 (ATF5), a competition ELISA assay was performed. Recombinant ATF5 associated with plate-bound C/EBPβ with a binding affinity of ∼1 nM. Addition of ST101 inhibited this interaction in dose-dependent manner, resulting in an IC50 of 25 nM. To demonstrate ST101 disruption of C/EBPβ phosphorylation and gene transactivation in cancer cells, western blot analysis and quantitative polymerase chain reaction (qPCR) were performed on U251 glioblastoma, MCF7 breast adenocarcinoma and A549 lung adenocarcinoma cells. Administration of ST101 resulted in a dose-dependent decrease in C/EBPβ activation, as evidenced by a decrease in Thr189 phosphorylation. Anatgonism of C/EBPβ activity resulted in a dose-dependent decrease in mRNA expression of genes involved in survival (BCL2 and the baculoviral inhibitor of apoptosis factors BIRC3, BIRC5), inhibition of differentiation (Inhibitor of DNA binding proteins ID1, ID2 and ID3) and proliferation (cyclins CCNB1 and CCNA2 and cyclin-dependent kinases CDK1 and CDK2). Finally, in a mouse xenograft model, 25mg/kg ST101 administered three times per week for three weeks resulted in significant and sustained tumor growth inhibition in U251 subcutaneous tumors, both when ST101 administration was initiated early (day 2, 200 mm3 tumors, p&amp;lt;0.05) or late (day 16, &amp;gt;500mm3 tumors, p&amp;lt;0.05). These data demonstrate the therapeutic potential of systemic administration of ST101 and support clinical development of ST101 as a potent peptide therapeutic for a variety of solid tumor malignancies. Citation Format: Jim A. Rotolo, Rick Ramirez, Mark Koester, Erin Gallagher, Siok Leong, Lila Ghamsari, Gene Merutka, Barry J. Kappel. C/EBPβ antagonist peptide, ST101, attenuates oncogenic gene transactivation in cancer cells to drive antitumor activity [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1817.
Abstract 5454: A data driven pipeline to detect somatic mutations in oncology
Authors: Katherine Shortt, Christopher Johnson, Archana Ramesh, Tom Neuwerth, Chris Giauque, Sharanya Raghunath
Journal: Cancer Research (2020)

Abstract The analysis of Next Generation Sequencing (NGS) data relies on workflows that integrate different bioinformatics tools. Designing workflows that are assay agnostic and have a robust computational framework for result generation in a timely manner is particularly important for clinical applications of NGS. These technologies play an important role in classifying a patient's tumor at a molecular level however, there is still a need to develop workflows that generate consistent mutation profiles for oncology. We developed a bioinformatics tool to analyze DNA and RNA sequencing data in a single pipeline and to specifically detect somatic mutations in oncology clinical workflows. Our automated pipeline report contains extensive quality metrics for each sample and generates a robust mutation annotation and filtration module vital for clinical use. We use data driven filters and algorithms that predict the effectiveness of mutations to filter out mutations of poor quality or mutations without clinical significance. We applied our pipeline to standard cell lines and various cancer FFPE samples acquired from the Intermountain Healthcare Biorepository. Our pipeline successfully processes different mutation classes including Single Nucleotide Variants (SNVs), small (&amp;lt;20 bp) and large (&amp;gt;21 bp) insertions and deletions (InDels), gene fusions, and exon skipping mutations. In addition, we established a reference set that allows us to call Copy Number Variants (CNVs) in a gene panel designed to detect clinically relevant mutations in lung cancers. Comparison of this pipeline to a validated external workflow yield high concordance of clinically significant mutations. We conclude that our pipeline offers a sensitive and specific methodology to analyze DNA and RNA sequencing data to clinically relevant results from low input amplicon-based assays for various solid tumor cancer types. Citation Format: Katherine Shortt, Christopher Johnson, Archana Ramesh, Tom Neuwerth, Chris Giauque, Sharanya Raghunath. A data driven pipeline to detect somatic mutations in oncology [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5454.
Abstract 1700: Excessive ROS in ovarian cancer cells impairs anti-tumor capacities of immune cells through exosomal miR-155/PD-L1 pathway
Authors: Xiang Li, Gao-chan Wang, Jun He
Journal: Cancer Research (2020)

Abstract Background and Objective: Genetic and metabolic alterations in cancer cells promote the sustained oxidative stress as reflected by excessive production of reactive oxygen species (ROS). We and other groups have identified that the ROS-sensitive microRNAs regulate the cancer cell response to ROS. However, it has yet to be determined how these miRNAs convey the ROS signal to downstream effectors and thus produce biological consequences. Accumulative evidence indicates that tumor-derived exosomes are emerging mediators of tumorigenesis. In this study, we aimed to investigate how ROS convey the oncogenic signals through cellular interactions via exosomes within the tumor microenvironment. Methods and Results: Through NanoString nCounter miRNA analysis, we identified miR-155-5p as the most abundant miRNAs enriched in the exosomes derived from epithelial ovarian cancer (EOC) cells treated with a ROS scavenger N-acetylcysteine (NAC). Mechanistically, tumor exosomal miR-155-5p was transferred to tumor-associated macrophages (TAM), directly targeting PD-L1 to inhibit the infiltration of TAM into tumor microenvironment. The role of tumor-derived exosomal miR-155-5p was determined by co-culture experiments and gain or loss of function studies in vitro, and confirmed in xenograft mouse models in nude mice and immunocompetent mice. In addition, we established a 3D-3-culture system to entail the co-culture of NAC-treated EOC cell spheroids, TAM and T cells. We found that CD8+ T-cell ratio was increased and production of IFN-γ, IL-2, and TNF-α was promoted. What's more, the immunocompetent EOC mouse model was established and treated with NAC-modified mouse ovarian cancer cell-released exosomes. The results showed that NAC-modified tumor growth was significantly reduced compared to control group. Further analysis showed that miR-155-5p increased in TAM, while PD-L1 expression levels decreased in macrophages from tumors and spleens. Moreover, the T cell function was also augmented as evaluated by the expression of Ki-67 and Granzyme B on CD8+ T cells. Conclusion: In conclusion, our study reveals a novel mechanism underlying PD-L1 expression in EOC. Ovarian cancer cells with excessive ROS levels release exosomes that mediate the interaction between cancer cells and immune cells; it is this interplay that produces an immunosuppressive tumor microenvironment by upregulation of PD-L1 in macrophages, and eventually contributes to the progress of EOC through the ROS/miR-155-5p/PD-L1 pathway. Citation Format: Xiang Li, Gao-chan Wang, Jun He. Excessive ROS in ovarian cancer cells impairs anti-tumor capacities of immune cells through exosomal miR-155/PD-L1 pathway [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1700.
Packed red cell age associated with adverse cardiovascular changes in an ovine model of septic shock resuscitation
Authors: Jonathon P. Fanning, Nchafatso G. Obonyo, John-Paul Tung, Liam Byrne, Gabriela Simonova, Sara Diab, Kimble Dunster, Margaret Passmore, Ai-Ching Boon, See Louise Hoe, Sanne Engkilde-Pedersen, Arlanna Esguerra-Lallen, Hashairi Mohd Fauzi, Pimenta Leticia Pretti, Jonathan Millar, Christopher Anstey, Frank van Haren, Louise Cullen, Jacky Suen, Kiran Shekar, Kathryn Maitland, John Fraser
Journal: Circulation (2018)

Introduction: Packed red blood cell (PRBC) transfusion in septic shock is generally reserved as a last resort hemodynamic resuscitative measure or for haemoglobin less than 7.0 g/dL. Ex-vivo preservation and storage predispose PRBCs to biochemical / mechanical changes whose impact in a septic host is unknown. This randomised pre-clinical trial specifically evaluates select markers of cardiovascular stress in an ovine model of endotoxemic shock receiving either fresh or stored blood.

Methods: Twenty six anesthetised and mechanically ventilated merino ewes were randomly divided into endotoxemic shock (n = 16) or healthy (n = 10) groups. Endotoxemic shock was induced over 4 hours by infusing an escalating dose (total 11.25 mcg / kg) of lipopolysaccharide, LPS (E.coli 055:B5). During the last hour of LPS infusion, 10 mls / kg of either fresh, ≤ 5 days (n = 8) or stored, ≥ 30 days (n = 8) ovine packed PRBCs were administered. Healthy ewes received either fresh, ≤ 5 days (n = 5) or stored, ≥ 30 days (n = 5) ovine PRBCs at corresponding time points. Invasive haemodynamic monitoring and serial echocardiographic assessments were performed in all. Blood samples were measured for cardiac troponin I (cTnI), atrial natriuretic peptide (ANP) and hyaluronan at baseline (T0), 1, 3, 4, 5, 10 and 16h after which the ewes were euthanized.

Results: Stored versus fresh PRBCs produced raised hyaluronan levels (P < 0.001) from T3 onwards in both sepsis and healthy groups and resulted in significant (P < 0.001) adverse haemodynamic changes (cardiac index, central venous pressure, pulmonary artery pressure and mixed venous oxygen saturation). Elevated ANP was observed between T3 to T10 (P < 0.001) in septic compared to healthy ewes but there was no association with age of PRBCs. No statistical differences were observed between groups for TnI.

Conclusions: Sepsis and storage duration of PRBCs are associated with increased cardiovascular stress suggesting that stored PRBCs may predispose patients with septic shock to poor clinical outcomes.