tbuckley/cabot-search huggingface dataset:
Abstract 4003: Colon sessile serrated polyps associate with endometrial polyps
Authors: Hassan Brim, Taraneh Tarjoman, Shirin Ganjali, Saman Azam, Negin Farsi, Edward Lee, Babak Shokrani, Farshad Aduli, Carla Williams, Adeyinka Laiyemo, Akbar Soleimani, Zaki Sherif, Mehdi syed Nouraie, Hassan Ashktorab
Journal: Cancer Research (2019)

Abstract Background: Colon and endometrial polyps are current health issues and their incidences are on the rise. Due to conflicting reports of higher colon polyps in patients with endometrial polyps, we aimed to evaluate if there is such an association in African Americans, a population at high risk for colorectal cancer. Method: We retrospectively reviewed all female patients who had endometrial (EN) presentations (n=3,600) and colonoscopy (n=14,888) at Howard University Hospital from January 2004 to December 2015. We selected cases with endometrial poly and control without this diagnosis who underwent colonoscopy. Clinical [Body Mass Index (BMI), diabetes (DM), hypertension (HTN), Tamoxifen intake, age] and pathological (histology, location, type of lesions) features of Cases and Controls were collected. Association between EN and colon polyp was tested using multivariable logistic regression analysis. We excluded the patients with endometrial cancer. Results: We recruited 664 cases and 118 controls. Cases were statistically significant older (median age of 60 vs. 57 in controls) and had higher rates of smoking and DM than controls. However, the overall colon polyp prevalence in the two groups was not statistically different (54% vs 52% in controls and cases, respectively). In subgroups of subject with colon polyp, sigmoid and rectal polyps were more prevalent in controls than cases. Sessile serrated polyps/adenomas (SSPs) were more frequent in cases (8% vs. 2%, p=0.03) while benign mucosa was more so in controls. Whether considering the overall study population or just those with colon polyps, SSPs lesions associated with an Odds Ratio of 4.6 (p=0.02) for EN polyp occurrence, after adjusting for confounder. Conclusion: Our study shows that the overall colon polyp’s prevalence was similar in endometrial polyp patients compared to endometrial-polyp free controls. However, a significant association between SSP with endometrial polyps was noted. Females with colon lesions of the SSP type might benefit from a screening for endometrial polyp in an age-independent manner. Note: This abstract was not presented at the meeting. Citation Format: Hassan Brim, Taraneh Tarjoman, Shirin Ganjali, Saman Azam, Negin Farsi, Edward Lee, Babak Shokrani, Farshad Aduli, Carla Williams, Adeyinka Laiyemo, Akbar Soleimani, Zaki Sherif, Mehdi syed Nouraie, Hassan Ashktorab. Colon sessile serrated polyps associate with endometrial polyps [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4003.
Abstract 5110: An online tool for summarizing and searching human cancer-genomic publications
Authors: Kevin Williams, Myron Zhang, Anayancy Ramos, Andrew Johnson, Stefanos Stravoravdis, Megan Heenehan, Garrett M. Dancik
Journal: Cancer Research (2019)

Abstract PubMed catalogs over 33,000 articles published with the keywords “cancer” and “gene” in the past year alone. The large volume of cancer genomic publications necessitates the development of text-mining tools to help cancer researchers navigate and summarize articles efficiently. Here we present a Cancer Publication Portal (CPP) that allows a researcher to search and summarize cancer genomic literature based on a gene of interest. CPP integrates data from several sources, including PubTator, which uses robust text-mining tools to identify associations between articles and biological concepts; the Medical Subject Headings (MeSH) database; the HUGO Gene Nomenclature Committee human gene name database; PubMed, a database of biomedical literature citations; and the National Cancer Institute (NCI) Thesaurus. To begin a search, a user selects a gene of interest. CPP then summarizes the relevant cancer-related publications mentioning this gene through tabular and graphical summaries showing the frequency of articles stratified by references to any (1) cancer type, (2) pharmacological agent, (3) genomic mutation, and (4) additional human gene. Additionally, CPP catalogs and summarizes articles based on mentions of &amp;gt;30 additional cancer-related terms, based on an analysis of terms that are significantly more likely to occur in cancer-related abstracts. CPP allows users to quickly obtain statistics, e.g., to find the frequency of articles mentioning EGFR and Erlotinib across cancer types. Interactive summaries allow users to narrow in on a topic of interest by applying additional filters, in which case the summaries are updated and the process can be repeated. At any point, the user can browse through the current set of article abstracts and citation information to get more information about an article. Finally, we introduce a Citation Analysis module for helping users identify “important” articles. This module identifies articles which cite articles in a provided list. The module then generates an edge list that can be imported into network analysis tools such as Gephi for visualization and analysis. CPP currently includes information for ~1.1 million cancer-related publications associated with &amp;gt;19,000 human genes. The underlying data is stored in an MySQL database while R/Shiny is used to implement the web interface. CPP is available from the following link: https://gdancik.github.io/bioinformatics/CPP/ Citation Format: Kevin Williams, Myron Zhang, Anayancy Ramos, Andrew Johnson, Stefanos Stravoravdis, Megan Heenehan, Garrett M. Dancik. An online tool for summarizing and searching human cancer-genomic publications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5110.
Abstract 912: Macrophage inhibitory factor (MIF), osteopontin (OPN) and anti-interleukin-8 (IL-8) autoantibodies (AAb) complement CA125 for detection of early-stage ovarian cancer
Authors: Jing Guo, Wei-lei Yang, Joseph Celestino, Karen Lu, Anna E. Lokshin, Zhen Lu, Robert C. Bast
Journal: Cancer Research (2019)

Abstract Background: Early detection of ovarian cancer promises to reduce mortality. At present, only 20 percent of ovarian cancer is found in early stage (I-II). CA125 is found in sera from approximately 60% of patients with early stage disease. Greater sensitivity could be observed with a panel of blood tests. Methods: A panel of 10 antigen biomarkers (MIF, Leptin, IL-6, IL-8, TNFa, OPN, FGF2, HE4, TGFa and a panel of autoantibodies (AAbs) against 12 antigens (IL-8, MDM2, c-myc, PLAT, EpCAM, HOXA7, ENO1, PDI, HSPA5, HSPA8, ANXA2, Cathepsin D) were analyzed in sera of 77 ovarian cancer patients with early stage (I-II), 50 patients with late stage (III-IV), and 216 healthy women from the Normal Risk Ovarian Cancer Screening Study (NROSS) using Luminex-based immunoassays. Serum levels of serum tumor marker CA-125 were routinely measured in all patients using a Roche assay. The most promising markers (CA125, MIF, OPN, and anti-IL-8 autoantibodies were validated using an independent panel with sera from 69 early stage and 50 late ovarian cancer patients and 200 healthy controls. Result: Serum level of CA125, MIF, OPN and IL-8 AAb were elevated in early stage (I-II) and late stage (III-IV) ovarian cancer patients compared with healthy controls. Analyzing the positive biomarkers in combination with CA125 increased detection of early stage disease from 62% with CA125 alone to 92% a panel of CA125, MIF, OPN and IL-8 AAb at 98% specificity. For patients with late stage disease sensitivity increased from 90% to 98% with the panel. Complementarity of CA125 with MIF, OPN and IL-8 AAb was confirmed with an independent validation set, where sensitivity for early stage disease was improved from 84% to 91% at 98% specificity. Conclusion: MIF, OPN and IL8 AAb could be used in combination with CA125 to distinguish ovarian cancer patients from health controls with high sensitivity. Citation Format: Jing Guo, Wei-lei Yang, Joseph Celestino, Karen Lu, Anna E. Lokshin, Zhen Lu, Robert C. Bast. Macrophage inhibitory factor (MIF), osteopontin (OPN) and anti-interleukin-8 (IL-8) autoantibodies (AAb) complement CA125 for detection of early-stage ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 912.
Abstract 16908: Will Alternating Between Fast and Slow Chest Compressions Improve Resuscitation Outcomes?
Authors: Tyson G Taylor, Alexander Esibov, Sharon B Melnick, Fred W Chapman, Gregory P Walcott
Journal: Circulation (2017)

Mechanical chest compression devices could be designed to deliver compression patterns impractical for manual CPR. Different compression patterns may increase or change the distribution of blood fl...
Hepatocellular carcinomas: evolution to sorafenib resistance through hepatic leukaemia factor
Authors: Orlando Musso, Naiara Beraza
Journal: Gut (2019)

Hepatocellular carcinoma (HCC) is the second cause of cancer-related death and it represents the leading cause of death in patients with cirrhosis.1 The vast majority of HCCs develop in a background of severe liver fibrosis, commonly caused by HBV or HCV infection, exposure to aflatoxin B, alcoholic and non-alcoholic steatohepatitis (NASH), as well as genetic diseases.1 Despite recent advances in the treatment of viral hepatitis, modelling of the dramatic rise in the incidence of NASH predicts a substantial increase in the global burden of HCC.1 

HCC allocation to treatment options is based on tumour number, size and vascular invasion, as well as on the functional liver reserve. Although HCC aggressiveness can be inferred from these clinical parameters, screening programmes in patients at risk increasingly detect early-stage HCCs that share homogeneous clinical features, but that diverge in terms of biological and molecular features.1 Therefore, a more precise prediction of HCC aggressiveness is expected from a better insight on HCC heterogeneity.

Liver transplantation is the most effective curative option for HCC though it suffers from obvious limitations such as donor (organ) shortage. Alternative treatments include hepatic resection and tumour ablation, chemoembolisation and systemic therapy, which is limited to sorafenib and lenvatinib as first-line treatment, and second-line options like regorafenib among others.1 Sorafenib, a multikinase inhibitor with antiproliferative and antiangiogenic properties, is the gold-standard systemic treatment option improving patient survival.1 Still, some tumours are resistant to sorafenib, underlining the urge to understand how HCC cells develop treatment resistance.

Cancer progression results from the coevolution of a heterogeneous ecosystem …
Abstract LB-203: Metformin enhances the efficacy of tumor membrane vesicle (TMV)-based vaccine immunotherapy in a murine model of breast
Authors: Luis E. Munoz, Ramireddy Bommireddy, Haley Huang, Janet Kim, Periasamy Selvaraj
Journal: Cancer Research (2019)

Abstract Breast cancer remains the most commonly diagnosed cancers among women, with over 250,000 new cases per year in the United States. Immunotherapy has emerged as a promising treatment of breast cancer, however response rates to therapy remain far from ideal. In this study, we investigated the combinatorial effect of tumor membrane vesicle (TMV)-based vaccine immunotherapy, to induce an anti-tumor immune response, with the type 2 diabetes drug metformin, which has been reported to exert anti-tumor effects by maintaining CD8 T cell activity in the tumor microenvironment. Our results show that TMV vaccination inhibits primary tumor growth in preclinical tumor models, while combination with metformin resulted in greater inhibition of primary growth. Importantly, TMV vaccination reduced the metastatic burden in the lungs while combination with metformin further abrogated metastatic spread. Interestingly, TMV vaccination alone induced a significant increase in T cell infiltration to the tumor, while combination with metformin caused a decrease in the accumulation of T cells, despite having better outcomes. Further, we show that metformin is capable of reducing PD-L1 expression within the tumor microenvironment in both tumor cells as well as myeloid-derived suppressor cells, providing insight for the improvement of TMV-based immunotherapy. Citation Format: Luis E. Munoz, Ramireddy Bommireddy, Haley Huang, Janet Kim, Periasamy Selvaraj. Metformin enhances the efficacy of tumor membrane vesicle (TMV)-based vaccine immunotherapy in a murine model of breast [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-203.
High Blood Alcohol Levels in Women
Authors: Mario Frezza, Carlo di Padova, Gabriele Pozzato, Maddalena Terpin, Enrique Baraona, Charles S. Lieber
Journal: New England Journal of Medicine (1990)

After consuming comparable amounts of ethanol, women have higher blood ethanol concentrations than men, even with allowance for differences in size, and are more susceptible to alcoholic liver disease. Recently, we documented significant "first-pass metabolism" of ethanol due to its oxidation by gastric tissue. We report a study of the possible contribution of this metabolism to the sex-related difference in blood alcohol concentrations in 20 men and 23 women. Six in each group were alcoholics.
Abstract 15127: Dobutamine Stress Testing as an Early Diagnostic Tool to Detect Radiation-Induced Heart Disease
Authors: Benjamin J Lieblong, Sabha Bhatti, Vijayalakshmi Sridharan, Robin L Mulkey, Terry W Fletcher, Marjan Boerma, Nancy J Rusch
Journal: Circulation (2016)

Introduction: Radiation-induced heart disease (RIHD) is a potentially severe side effect of radiotherapy for intrathoracic and chest wall tumors. There is no recommended approach for early detectio...
Abstract 4307: RAGE is the key receptor for LPA in lung and mammary cancer progression and metastasis
Authors: Nitish Jangde, Rashmi Ray, Vivek Rai
Journal: Cancer Research (2019)

Abstract Lung and breast cancer signaling are very complex; receptor for advanced glycation end products (RAGE) is highly expressed in various cancers and is correlated with poorer outcome in lung and other cancers. It is an immunoglobulin like membrane receptor shows binding with various ligands sharing structural likeness such as amyloid beta, advanced glycation end products (AGEs), S100B proteins, amphoterin and HMGB1 and mediates numerous inflammatory and cellular events including diseases including various cancers. LPA a RAGE ligand is a biologically active phospholipid involved in cell proliferation, migration and survival via its different G protein couple receptors (GPCRs). LPA and its signalling pathways have been implicated in different pathological conditions of lung tissue, including inflammation, fibrosis and cancer activating various signalling pathways. Here, we have identified RAGE-LPA signaling mechanisms showing AKT, STAT3 and ERK as downstream signaling pathways gets activated upon LPA treatment via RAGE receptor in both lung and breast cancer cells. RAGE knockdown with multiple independent shRNAs in lung and breast cancer cells led to decreased transwell invasion and soft agar colony formation, and proliferation upon LPA stimulation. Our RAGE silencing study in lung and breast cancer cells upon LPA treatment showed upregulation of specific oncogenes Cyclin D1, c-Myc and VEGF via RAGE receptor. RAGE association with LPA induced epithelial to mesenchymal transition (EMT) in both lung and breast cancer cells have also been observed by the RAGE attenuation studies by examining the expression of some EMT markers. The physiological significance of LPA-RAGE axis was exposed by our xenograft study by nude mice intraperitoneal injections of control and RAGE inhibited lung and mammary tumors generated by LPA doses in alternative days, results the formation of tumor foci on peritoneum wall via RAGE receptor. This study provides novel therapeutic insights as the use of RAGE blocking antibodies and antagonists or competitive inhibitors of LPA against RAGE might be useful of breast cancer treatment. This study also suggests that RAGE and LPA can be used as biomarkers for the early detection of lung and breast cancers. Citation Format: Nitish Jangde, Rashmi Ray, Vivek Rai. RAGE is the key receptor for LPA in lung and mammary cancer progression and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4307.
Abstract 1644: Pancreatic cancer survival prediction using machine learning and comparing its performance with TNM staging system and prognostic nomograms
Authors: Mohamed H. Osman
Journal: Cancer Research (2019)

Abstract Background: Pancreatic cancer is one of the deadliest cancers with a 5-year survival rate of only 6%. Patients with cancer often want to know how long they have left to live and it’s the first question patients ask after diagnosis. Reliable predictions are very important for achieving more personalized care and better management. However, the accuracy of physicians' clinical predictions of survival is poor. Predicting pancreatic cancer survival is challenging due to different tumor characteristics, treatments and patient populations. In this study, we evaluate the performance of Machine Learning (ML) in survival prediction compared to TNM system and published nomograms. Methods: Pancreatic cancer patients were identified through the Surveillance, Epidemiology and End Results database (SEER). Clinical data of the patients were extracted including: age, sex, race, marital status, tumor site, tumor histology, grade, tumor size, extension, Lymph Node (L.N) involvement, metastasis, cancer sequence, TNM stage, surgery, radiotherapy, chemotherapy, examined (L.N), positive (L.N) and survival months. Patients’ records were randomly divided into a training set (80%) and a validation set (20%). ML algorithms were tested to predict survival at 6, 12 and 24 months as well as TNM staging system and two nomograms. Results: A total number of 22,700 patients were identified through SEER from 2004 – 2013 with median survival of 12 months. The most common primary sites were head of pancreas (62.8%), tail (13.2%), and body (10.7%). Random Forests algorithm achieved better results compared to other models. The trained model yielded Area under the Receiver Operating Characteristic Curve (AUCs) of 86.6% at 6 months, 83.4% at 12 months and 82.2% at 24 months. Compared to TNM staging system which achieved AUCs of 66.6% at 6 months, 65.5% at 12 months and 57% at 24 months. The nomograms achieved AUCs of 71.1% and 55.2% in predicting 1-year-survival. Sensitivity of the trained model were 80%, 75% and 79% at 6, 12 and 24 months, respectively. The most important characteristics which influenced the model prediction performance were: age at diagnosis, surgery and tumor size. Conclusion: Machine learning achieved a much better performance compared to TNM staging system and prognostic nomograms. Improved survival prediction can help in in making better treatment decisions and planning social and care needs. Citation Format: Mohamed H. Osman. Pancreatic cancer survival prediction using machine learning and comparing its performance with TNM staging system and prognostic nomograms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1644.
Abstract 4135: Novel dual A2A A2B adenosine receptor antagonists for cancer immunotherapy: in vitro and in vivo characterization
Authors: Michal Galezowski, Paulina Węgrzyn, Aneta Bobowska, Katarzyna Dziedzic, Joanna Szeremeta-Spisak, Marcin Nowogrodzki, Grzegorz Satala, Alicja Obara, Iwona Lozinska-Raj, Marcelina Dudek, Anita Janiga, Jacek Reus, Marek Wronowski, Magdalena Zastawna, Grzegorz Statkiewicz, Maciej Rogacki, Magdalena Ziembik, Karolina Grycuk, Foteini Soukou, Kinga Michalik, Agnieszka Adamus, Karolina Wiatrowska, Natalia Lewandowska, Aniela Golas, Olga Haberkiewicz, Rod Porter, Krzysztof Brzozka, Mateusz Nowak
Journal: Cancer Research (2019)

Abstract Adenosine is important messenger molecule that is involved in signal transmission in central nervous, cardiovascular and immunological systems. The immunosuppressive role of adenosine attract attention of many researchers recently and reversal of that effect is addressed by several different approaches i.e.: inhibition of enzymes that are producing the adenosine in tumor microenvironment like CD39 and CD73 but also the antagonization of adenosine receptors mainly A2A and A2B subtypes. Here we present a novel series of unsurmountable, dual A2A/A2B antagonists that retain its nanomolar potency in tumor-like adenosine-rich environment. This advantageous profile comes mainly from long residence time in adenosine receptors which transfers into high receptor occupancy even after full clearance of the compound from plasma. We are demonstrating how our inhibitors restore adenosine depleted immune functionality in the series of functional in vitro assays in primary cells. This includes the cytokine release by activated CD4+ and CD8+ human T-lymphocytes (driven by A2A) and dendritic cells (driven by A2B). Most importantly presented compounds show improved in vivo pharmacological profile in comparison to adenosine inhibitors currently tested in clinical trials manifested by high inhibition of CREB phosphorylation in mouse model. Citation Format: Michal Galezowski, Paulina Węgrzyn, Aneta Bobowska, Katarzyna Dziedzic, Joanna Szeremeta-Spisak, Marcin Nowogrodzki, Grzegorz Satala, Alicja Obara, Iwona Lozinska-Raj, Marcelina Dudek, Anita Janiga, Jacek Reus, Marek Wronowski, Magdalena Zastawna, Grzegorz Statkiewicz, Maciej Rogacki, Magdalena Ziembik, Karolina Grycuk, Foteini Soukou, Kinga Michalik, Agnieszka Adamus, Karolina Wiatrowska, Natalia Lewandowska, Aniela Golas, Olga Haberkiewicz, Rod Porter, Krzysztof Brzozka, Mateusz Nowak. Novel dual A2A A2B adenosine receptor antagonists for cancer immunotherapy: in vitro and in vivo characterization [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4135.