tbuckley/cabot-search huggingface dataset:
Abstract 4033: Gene expression of EdU proliferating cells made possible with improved click chemistry.
Authors: Scott T. Clarke, Angie Cheng, Aleksey Rukavishnikov, Michelle Yan, Upinder Singh, Kyle Gee, Susan Magdaleno
Journal: Cancer Research (2013)

Abstract Gene expression profiling of cancer cells has become increasingly common over the past five years. Especially important is identifying changes in gene expression caused by drug treatment leading to side populations with altered pathways. These populations can escape drug treatment and lead to recurrence. Characterizing gene expression of proliferating cells requires a method of identifying proliferation while simultaneously maintaining high quality RNA. Typically, cells are screened in a drug panel in the presence of tritiated thymidine or BrdU to identify the drug resistance in the proliferating population. Proliferation detection with these methods is neither rapid nor does it yield high quality RNA for profiling. A new proliferation method based on click chemistry using an alkyne modified thymidine analog (EdU), which can be used to rapidly identify replicating cells appears ideally suited for this application; however, copper used for the catalysis of the click reaction causes undesired degradation of RNA. Recent improvements to the copper based click reaction are presented here whereby the copper is tightly controlled, resulting in higher quality RNA useful for sequencing. In this study we demonstrate gene expression changes in the proliferating population of a drug resistant cancer cell line compared to the parental cell lines. Proliferating cells were identified using an improved click reaction comprising of a copper(I) ligand combined with a picolyl modified dye azide detection reagent. Total RNA from these cells was isolated and gene expression was assessed by targeted RNA sequencing using an RNA Apoptosis panel and an RNA Cancer panel using proton based sequencing technology. Use of an improved copper “safe” click reaction for detection of nascent DNA, allows for detection of incorporated click analog for measuring proliferation and subsequent isolation of high quality RNA for use in sequence analysis. Citation Format: Scott T. Clarke, Angie Cheng, Aleksey Rukavishnikov, Michelle Yan, Upinder Singh, Kyle Gee, Susan Magdaleno. Gene expression of EdU proliferating cells made possible with improved click chemistry. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4033. doi:10.1158/1538-7445.AM2013-4033
P17.78 * SECONDARY GLIOBLASTOMA - OUTCOME AND PROGNOSTIC FACTORS
Authors: C. Senft, J. Zappi, F. Gessler, M. Mittelbronn, K. Franz, V. Seifert
Journal: Neuro-Oncology (2014)

BACKGROUND: Prognostic factors and outcome of patients with primary glioblastoma (GBM) are well reported. In contrast, there is limited information about patients with secondary GBM (sGBM). The goal of this work was to report on the outcome of patients with sGBM and to identify prognostic factors. METHODS: We retrospectively analyzed our institutional database of brain tumor patients for clinical patient data. All patients had histological proof of WHO II-III glioma and subsequent WHO IV secondary glioblastoma. Using paraffin embedded tissue we screened for mutations of the isocitrate dehydrogenase-1 (IDH-1) using immunohistochemical staining (IHC) with an R132H (clone H09) specific antibody. We performed uni- and multivariate analyses to identify factors potentially affecting survival. RESULTS: We analyzed 45 patients with histologically proven sGBM. Median age was 41 years. 31 patients underwent radiologically complete resection of sGBM, 14 underwent subtotal resection or biopsy only. Initially, 36 patients had astrocytic tumors, the other suffered from oligodendrogliomas or mixed gliomas; at first diagnosis, there were 18 WHO II tumors, and 27 were WHO III. Median time between first glioma diagnosis and occurence of sGBM was 158.9 weeks; median overall survival (OS) following diagnosis of sGBM was 63.6 weeks. IDH-1 mutations were present in 24 patients and absent in 17; in 4 patients, IHC could not be performed. On univariate analysis, time between first diagnosis and progression to sGBM was a statistically significant factor - patients with an interval >2 years had a better OS (67.4 vs. 60.1 weeks, p = 0.027). Also, patients receiving combined adjuvant radio- and chemotherapy did better than those who only had either therapy (87.3 vs. 54.3 weeks). Following multivariate analysis, IDH-1 (R132H) mutation was associated with longer OS (p = 0.012); there was a trend for patients with initial WHO II tumors having a better prognosis (p = 0.057). Using patient specific data, we established two prognostic groups; patients in the good prognosis group appeared to benefit from complete tumor removal (p = 0.06), while resection did not play a role for the other (p = 0.97). CONCLUSION: Although of relatively young age, prognosis of patients with sGBM is dismal. IDH-1 (R132H) mutation and WHO grade of the initial tumor are associated with OS after progression to sGBM. Patients in the good prognosis group appear to benefit from complete tumor removal, while the others do not.
Abstract 5142: A naturally occurring model for gastric cancer
Authors: Manar A. AbdelMageed, Monica Betancur-Boissel, Parthena Foltopoulou, Sureshkumar Muthupalani, James G. Fox, Elizabeth A. McNiel
Journal: Cancer Research (2015)

Abstract Gastric cancer is the fourth most common cancer and the second leading cause of cancer related deaths. While there are increasing data characterizing the molecular features and defining potential targets for gastric carcinoma, preclinical animal models that recapitulate the human disease are limited. We have developed a number of resources to permit the characterization of spontaneously occurring canine gastric cancer which may provide a useful resource to understand gastric cancer carcinogenesis, its prevention and treatment. While gastric carcinoma is reportedly uncommon in dogs, certain breeds have significantly increased risk. To study this disease, we have established a database and tissue repository. Our goal has been to characterize canine gastric carcinoma clinically, histologically, and molecularly to determine its comparative value as a model for the human disease. Recently, we have performed a histologic review of 50 canine gastric carcinomas and have found that the canine disease is comprises largely of diffuse type gastric carcinoma and is enriched in the signet ring variant. We report for the first time a technique for culturing primary gastric cancer from affected dogs. Gastric cancer tissue specimens collected from spontaneously occurring tumors in dogs were disaggregated with collagenase and cells were grown in mammary epithelial growth media with or without 5% FBS. Four different cell lines were derived from tumors of a Labrador mix (GC1), a Basset hound (GC2), a Bouvier de Flandres (GC3) and a mixed breed (GC4). Early passages of all cell lines were able to form colonies when grown in soft agar. Different growth patterns were observed when cells were cultured with versus without serum. Serum treated cells tend to be fast growing, fibroblastic in appearance and senesce within 10 to 18 passages and these may represent cancer associated fibroblasts or mesenchymal differentiation of cancer cells. However, cells grown in mammary epithelial growth media without serum tend to form spheres that grow well when transferred to ultra-low attachment plate and form extensions when grown in matrigel. That semi-attached growth behavior is consistent with that reported for some human gastric cancer cell lines. Canine gastric cancer cell lines provide a new resource for the characterization of this spontaneous model that recapitulates diffuse, signet ring cell gastric carcinoma. Citation Format: Manar A. AbdelMageed, Monica Betancur-Boissel, Parthena Foltopoulou, Sureshkumar Muthupalani, James G. Fox, Elizabeth A. McNiel. A naturally occurring model for gastric cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5142. doi:10.1158/1538-7445.AM2015-5142
VISUALIZATION OF RIGHT VENTRICULAR PERFUSION DEFECTS ON RESTING THALLIUM IMAGING.
Authors: Michael B. Brachman, D. Bellil, J. Maddahi, A. Waxman, D. B. Berman
Journal: Clinical Nuclear Medicine (1988)

Brachman, Michael B.; Bellil, D.; Maddahi, J.; Waxman, A.; Berman, D. B. Author Information
Sentinel lymph node detection in breast cancer patients by real-time virtual sonography constructed with three-dimensional computed tomography-lymphography.
Authors: S Yamamoto, N Maeda, M Tamesa, Y Nagashima, M Oka
Journal: Cancer Research (2009)

Abstract Abstract #1026 Background: Ultrasonography (US) is one tool for preoperative diagnosis of lymph node metastases in breast cancer. However, US cannot detect true sentinel lymph nodes (SLNs).&amp;#x2028; Methods: We identified SLNs in 60 clinically node-negative breast cancer patients using a real-time virtual sonography (RVS) system to display in real time a virtual multi-planar reconstruction obtained from computed tomography (CT) volume data corresponding to the same cross-sectional image from US. CT volume data were obtained from our original three-dimensional CT lymphography (3DCT-LG), which accurately detects SLNs in breast cancer. SLN metastases were assessed by shape and visibility of the hilum. All patients underwent SLN biopsy and SLN metastases were examined pathologically.&amp;#x2028; Results: In all 60 patients, we were able to detect the same SLNs visualized by 3DCT-LG. Suspicious SLN metastases were identified in 7 of the 60 patients, and 4 of 7 patients were pathologically positive. Positive predictive value was 57%. The remaining 53 patients displayed non-suspect SLNs in which absence of metastasis from the SLN was confirmed histologically. Overall accuracy was 95%.&amp;#x2028; Conclusions: This is a first attempt at preoperatively identifying SLNs using US guided by the RVS system in breast cancer patients. Although evaluation of SLN metastases was unsatisfactory, this method may be useful for preoperative fine-needle aspiration cytology for diagnosis of SLN metastases. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 1026.
Abstract LB-273: Transcriptional regulation by androgen receptor in prostate cancer
Authors: Jonathan Zhao, Christine Runkle, Longtao Wu, Hong-Jian Jin, Jindan Yu
Journal: Cancer Research (2012)

Abstract Transcriptional regulation by the androgen receptor (AR) is critical to prostate cancer development and progression. Through integrative analysis of genome-wide AR occupancy and androgen-regulated gene expression, we have recently reported AR as a globally acting transcriptional repressor. This repression is mediated by androgen responsive elements (ARE) and dictated by Polycomb group protein EZH2 and repressive chromatin remodeling. In addition, AR-repressed genes are enriched for developmental regulators controlling cell differentiation. They tend to get down-regulated in advanced prostate cancer probably accountable for stem cell-like de-differentiation and thus tumor progression. However, critical AR-repressed genes of functional relevance are yet to be identified and their roles to be carefully characterized. Through meta-analysis of several expression microarray data, we nominate one top candidate AR-repressed gene. Using this gene as a model, we present further evidence that AR directly inhibits gene expression through physically binding to the enhancer, establishing promoter-enhancer DNA looping, and inducing repressive chromatin remodeling. Further, overexpression of this gene inhibits prostate cancer cell growth, migration, and invasion in vitro and xenograft tumor growth in mice, thus exhibiting a tumor suppressive role. In addition, the loss of this gene drives castration-resistant prostate cancer. Therefore, our findings support that AR-mediated inhibition of tumor suppressors plays important roles during prostate cancer progression. Our study provides an innovative mechanism for AR in castration resistance, which may eventually lead to novel therapeutic targets for treatment of advanced prostate cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-273. doi:1538-7445.AM2012-LB-273
OC-062 A comparative study of laparoscopic vs open cystgastrostomy for pancreatic pseudocysts
Authors: D J Malde, Y Khaled, T Fox, P Laftsidis, N De Liguori, R Deshpande, D O'Reilly, D Sherlock, B J Ammori
Journal: Gut (2012)

<h3>Introduction</h3> While large and persistent pancreatic pseudocysts are amenable to internal drainage by laparoscopic techniques, the benefits of this minimally invasive approach remain to be demonstrated. The aim of this study was to compare the open and laparoscopic approaches for internal drainage of large and persistent pancreatic pseudocysts. <h3>Methods</h3> Patients who underwent cystgastrostomy were selected, and the demographic features, clinical characteristics and outcomes of those who had the surgery performed laparoscopically were compared to those who had open surgery. The two approaches were compared on an intention-to-treat basis. Data shown represent medians. <h3>Results</h3> Between 1997 and 2010, 42 patients (15 female and 27 male) underwent 45 surgical internal drainage procedures for pancreatic pseudocysts (36 laparoscopic with two conversions to open surgery, and nine open). The laparoscopic and open groups were comparable for age (56 vs 53 years, p<i>=</i>0.448), sex distribution, and size of pseudocyst (12 vs 13 cm, p<i>=</i>0.305). The two approaches had comparable operating times (90 vs 75 min, p=0.630) but laparoscopic surgery carried a significantly lower risk of postoperative morbidity (5.8% vs 54.5%, p=0.001) and shorter postoperative hospital stay (2 vs 10.5 days, p&lt;0.001). Laparoscopic surgery was also associated with a more rapid resumption of dietary intake (median 4 vs 6 days, p<i>=</i>0.065). There was one death in the open group (11.1%) but none in the laparoscopic group. <h3>Conclusion</h3> The laparoscopic approach to cystgastrostomy for large and persistent retrogastric pancreatic pseudocysts is associated with a smoother and more rapid recovery and a shorter hospital stay compared with open surgery. <h3>Competing interests</h3> None declared.
LEFT VENTRICULAR MASS VERSUS PULSE WAVE VELOCITY AS PREDICTORS OF CORONARY ARTERY DISEASE IN PATIENTS WITH ESSENTIAL HYPERTENSION: DATA FROM A GREEK 6-YEAR-FOLLOW-UP STUDY
Authors: Konstantinos P. Tsioufis, Kyriakos Dimitriadis, Alexandros Kasiakogias, Theodoros Kalos, Evaggelia Koutra, Panagiotis Vasileiou, Eirini Andrikou, Anastasios Milkas, Dimitris Tousoulis
Journal: Journal of the American College of Cardiology (2016)
BRCA1 4153delA and 5382insC Mutations Confer Different Risks of Contralateral Breast and Second Primary Malignancies in Breast Cancer Patients
Authors: G. Plakhins, A. Irmejs, S. Subatniece, G. Trofimovics, G. Purkalne, J. Gardovskis, E. Miklasevics
Journal: Annals of Oncology (2013)
1109 HIGH VS STANDARD DOSE OF RIBAVIRIN PLUS PEGINTERFERON-ALFA-2A IN CHRONIC HEPATITIS C, GENOTYPE 3 AND HIGH VIRAL LOAD. FINAL RESULTS OF THE DARGEN-3 STUDY
Authors: C.M. Fernandez Rodriguez, H. Masnou, R. Morillas, J.M. Navarro, R. Barcena, J.M. Hernandez, L. Martin Martin, A. Garcia Poyato, M. Miquel Planas, F. Jorquera, T. Casanova, M. Romero-Gómez, J. Salmeron, J.L. Calleja, R. Solà
Journal: Journal of Hepatology (2012)
Abstract 1572: Characterising the tumor vasculature <i>in vivo</i> in mouse models of colorectal cancer using contrast enhanced high-frequency ultrasound
Authors: Gemma Marston, Pam F. Jones, John A. Evans, Mark A. Hull, Alex F. Markham, Patricia L. Coletta
Journal: Cancer Research (2011)

Abstract Angiogenesis is essential for tumours to grow beyond a few millimetres in size and to metastasise, making it an attractive target for both cancer imaging and therapeutic intervention. Although microvessel density (MVD) is routinely used to assess tumour vascularity in fixed tissue, few techniques are currently available for imaging and quantitating tumour vasculature parameters in vivo. High-frequency ultrasound (HFUS) allows high resolution, non-invasive longitudinal imaging of tumours in vivo. Incorporation of microbubble contrast agent into imaging protocols allows visualisation of the vasculature, determination of relative blood flow and perfusion, and the ability to directly target and quantify molecular biomarkers of disease in vivo. We have been investigating in vivo tumour blood flow and vascularity in the growth of human colorectal cancer (CRC) cell xenografts. CD1 Nu/Nu mice implanted with SW480 cell xenografts were used to investigate the relationship between tumour growth and different vascular parameters obtained by contrast enhanced (CE) HFUS. Mice were imaged at day 21 and day 27 of tumour growth using the VisualSonics Vevo 770 system. A single bolus of microbubbles was injected via a syringe driver into the tail vein during 2D CE HFUS imaging, with the wash-in data loops captured prior to 3D CE HFUS imaging, and tissue samples collected for histology and immunohistochemistry. Time intensity curves were generated post-acquisition and used to determine perfusion kinetics and vascular data. A number of strongly significant correlations were observed relating in vivo and histological tumour characteristics with relative blood flow and total vascularity. These included the size of the tumour, tumour growth and the total vascular space. This study shows that CE HFUS is a powerful qualitative and quantitative tool for the analysis of tumour angiogenesis in vivo. It provides a relatively non-invasive method to monitor tumour blood flow and vascularity in longitudinal studies thus allowing effects on angiogenesis due to therapeutic intervention to be monitored. We are currently developing this technique for use with autochthonous colorectal cancer models. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1572. doi:10.1158/1538-7445.AM2011-1572
Abstract LB-74: The estrogen receptor regulates the transcription of p53 target genes in breast cancer cells
Authors: Shannon T. Bailey, Hyunjin Shin, X. Shirley Liu, Myles Brown
Journal: Cancer Research (2012)

Abstract Breast Cancer is a disease that affects thousands of women every year. A large subset of breast cancer is attributed to estrogen receptor (ER) dysregulation. Previously, our lab and others have determined the estradiol-stimulated ER cistrome in the MCF7 mammary epithelial cell line. To determine the relationship between ER and the apoptotic response, we compared our ER cistrome to a published p53 dataset. The p53 transcription factor is a tumor suppressor protein that is responsible for cell-cycle control and apoptosis. Our lab generated a doxorubicin-stimulated p53 cistrome in MCF7 cells, and we employed an integrative analysis approach examining the p53 and ER cistromes and gene expression microarray data to determine the genes coordinately regulated by both transcription factors. We identified a number of genes that are involved in the cell cycle, apoptosis, and DNA damage repair. By treating MCF7 cells with both stimuli, we found that the ER could inhibit the expression of a p53 target gene subset, thus diminishing the efficacy of the p53 program. These genes correlate with poor breast cancer clinical outcome. Moreover, we found that treatment of breast cancer cells with a combination of the anti-estrogen fulvestrant with p53 stimuli (i.e., doxorubicin and nutlin-3) leads to the synergistic enhancement of pro-apoptotic genes. Together, these data point to a set of genes essential for breast cell survival in ER-mediated breast cancer and suggest an improved paradigm for ER-positive breast cancer treatment i.e., the addition of fulvestrant with a p53 stabilizing drug. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-74. doi:1538-7445.AM2012-LB-74
Inhibition of the Adherence of P-Fimbriated<i>Escherichia coli</i>to Uroepithelial-Cell Surfaces by Proanthocyanidin Extracts from Cranberries
Authors: Amy B. Howell, Nicholi Vorsa, Ara Der Marderosian, Lai Yeap Foo
Journal: New England Journal of Medicine (1998)

The article "Global Surveillance for Antituberculosis-Drug Resistance, 1994-1997" by Pablos-Méndez et al. (June 4 issue) 1 is a clarion call to action by governments and health officials worldwide to combat the increasing prevalence of multidrug-resistant tuberculosis.The prevalence of this disease may in fact be higher than reported, because of two limitations of the study.First, data from regions in which the disease is highly endemic, such as China and most of India, were not obtained.Second, the study included relatively few countries in Africa and none in the Middle East.Furthermore, the ongoing pandemic of human immunodeficiency virus (HIV) infection is a major factor in the projected increases in the incidence of multidrug-resistant tuberculosis. 2-4. . .