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https://www.readbyqxmd.com/read/28528511/met-overexpression-and-gene-amplification-prevalence-clinico-pathological-characteristics-and-prognostic-significance-in-a-large-cohort-of-patients-with-surgically-resected-nsclc
#1
William Sterlacci, Michael Fiegl, Mathias Gugger, Lukas Bubendorf, Spasenija Savic, Alexandar Tzankov
The prevalence of overexpression and amplification of the proto-oncogene mesenchymal epithelial transition (MET) in non-small cell lung cancer (NSCLC) varies greatly in the literature. Since MET is a potential treatment target, knowledge of its prevalence and prognostic importance is crucial. We investigated MET expression and gene status in 735 NSCLC cases using tissue microarrays. Prognostic significance as well as correlations with various clinico-pathological parameters were evaluated. The prevalence of MET overexpression was 17% and MET amplification was present in 2...
May 20, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28528450/high-expression-of-cyclin-d1-is-associated-to-high-proliferation-rate-and-increased-risk-of-mortality-in-women-with-er-positive-but-not-in-er-negative-breast-cancers
#2
Cecilia Ahlin, Claudia Lundgren, Elin Embretsén-Varro, Karin Jirström, Carl Blomqvist, M -L Fjällskog
PURPOSE: Cyclin D1 has a central role in cell cycle control and is an important component of estrogen regulation of cell cycle progression. We have previously shown that high cyclin D expression is related to aggressive features of ER-positive but not ER-negative breast cancer. The aims of the present study were to validate this differential ER-related effect and furthermore explore the relationship between cyclin D overexpression and CCND1 gene amplification status in a node-negative breast cancer case-control study...
May 20, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28528398/squamous-and-neuroendocrine-specific-immunohistochemical-markers-in-head-and-neck-squamous-cell-carcinoma-a-tissue-microarray-study
#3
J S Lewis, R D Chernock, J A Bishop
The performance characteristics of neuroendocrine-specific and squamous-specific immunohistochemical markers in head and neck squamous cell carcinomas (SCC), in particular in oropharyngeal tumors in this era of human papillomavirus (HPV)-induced cases, are not well-established. The differential diagnosis for poorly differentiated SCCs, for nonkeratinizing oropharyngeal SCCs, and for other specific SCC variants such as basaloid SCC and undifferentiated (or lymphoepithelial-like) carcinomas includes neuroendocrine carcinomas...
May 20, 2017: Head and Neck Pathology
https://www.readbyqxmd.com/read/28528256/evaluation-of-artificial-time-series-microarray-data-for-dynamic-gene-regulatory-network-inference
#4
P Xenitidis, I Seimenis, S Kakolyris, A Adamopoulos
High-throughput technology like microarrays is widely used in the inference of gene regulatory networks (GRNs). We focused on time series data since we are interested in the dynamics of GRNs and the identification of dynamic networks. We evaluated the amount of information that exists in artificial time series microarray data and the ability of an inference process to produce accurate models based on them. We used dynamic artificial gene regulatory networks in order to create artificial microarray data. Key features that characterize microarray data such as the time separation of directly triggered genes, the percentage of directly triggered genes and the triggering function type were altered in order to reveal the limits that are imposed by the nature of microarray data on the inference process...
May 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28528200/sputum-transcriptomics-reveal-up-regulation-of-il-1-receptor-family-members-in-severe-asthma
#5
Christos Rossios, Stelios Pavlidis, Uruj Hoda, Chih-Hsi Kuo, Coen Wiegman, Kirsty Russell, Kai Sun, Matthew J Loza, Frederic Baribaud, Andrew L Durham, Oluwaseun Ojo, Rene Lutter, Anthony Rowe, Aruna Bansal, Charles Auffray, Ana Sousa, Julie Corfield, Ratko Djukanovic, Yike Guo, Peter J Sterk, Kian Fan Chung, Ian M Adcock
BACKGROUND: Sputum analysis in asthma is used to define airway inflammatory processes and may guide therapy. OBJECTIVE: To determine differential gene and protein expression in sputum samples from patients with severe asthma (SA) compared to mild-moderate non-smoking asthmatics (MMA). METHODS: Induced sputum was obtained from non-smoking SA (SAn), smokers/ex-smokers with SA (SAsm), MMA and healthy non-smoking controls. Differential cell counts, microarray analysis of cell pellets and SOMAscan analysis of sputum analytes was performed...
May 17, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28527971/identification-and-comprehensive-evaluation-of-reference-genes-for-rt-qpcr-analysis-of-host-gene-expression-in-brassica-juncea-aphid-interaction-using-microarray-data
#6
Chet Ram, Murali Krishna Koramutla, Ramcharan Bhattacharya
Brassica juncea is a chief oil yielding crop in many parts of the world including India. With advancement of molecular techniques, RT-qPCR based study of gene-expression has become an integral part of experimentations in crop breeding. In RT-qPCR, use of appropriate reference gene(s) is pivotal. The virtue of the reference genes, being constant in expression throughout the experimental treatments, needs to be validated case by case. Appropriate reference gene(s) for normalization of gene-expression data in B...
May 11, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28527910/radiative-decay-engineering-8-coupled-emission-microscopy-for-lens-free-high-throughput-fluorescence-detection
#7
Liangfu Zhu, Ramachandram Badugu, Douguo Zhang, Ruxue Wang, Emiliano Descrovi, Joseph R Lakowicz
Fluorescence spectroscopy and imaging are now used throughout the biosciences. Fluorescence microscopes, spectrofluorometers, microwell plate readers and microarray imagers all use multiple optical components to collect, redirect and focus the emission onto single point or array imaging detectors. For almost all biological samples, except those with regular nanoscale features, emission occurs in all directions. With the exception of complex microscope objectives with large collection angles (NA ≤ 0.5), all these instruments collect only a small fraction of the total emission...
May 17, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28527352/a-cbr-framework-with-gradient-boosting-based-feature-selection-for-lung-cancer-subtype-classification
#8
Juan Ramos-González, Daniel López-Sánchez, Jose A Castellanos-Garzón, Juan F de Paz, Juan M Corchado
Molecular subtype classification represents a challenging field in lung cancer diagnosis. Although different methods have been proposed for biomarker selection, efficient discrimination between adenocarcinoma and squamous cell carcinoma in clinical practice presents several difficulties, especially when the latter is poorly differentiated. This is an area of growing importance, since certain treatments and other medical decisions are based on molecular and histological features. An urgent need exists for a system and a set of biomarkers that provide an accurate diagnosis...
May 13, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28526936/fingerprint-of-long-non-coding-rna-regulated-by-cyclic-mechanical-stretch-in-human-aortic-smooth-muscle-cells-implications-for-hypertension
#9
Laura-Eve Mantella, Krishna K Singh, Paul Sandhu, Crystal Kantores, Azza Ramadan, Nadiya Khyzha, Adrian Quan, Mohammed Al-Omran, Jason E Fish, Robert P Jankov, Subodh Verma
Emerging evidence suggests that long non-coding RNAs (lncRNAs) represent a cellular hub coordinating various cellular processes that are critical in health and disease. Mechanical stress triggers changes in vascular smooth muscle cells (VSMCs) that in turn contribute to pathophysiological changes within the vasculature. We sought to evaluate the role that lncRNAs play in mechanical stretch-induced alterations of human aortic smooth muscle cells (HASMCs). RNA (lncRNA and mRNA) samples isolated from HASMCs that had been subjected to 10 or 20% elongation (1 Hz) for 24 h were profiled with the Arraystar Human LncRNA Microarray V3...
May 19, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28526854/induction-of-senescence-in-primary-glioblastoma-cells-by-serum-and-tgf%C3%AE
#10
Ritesh Kumar, Alexander Gont, Theodore J Perkins, Jennifer E L Hanson, Ian A J Lorimer
Glioblastoma is the most common type of adult brain tumour and has a median survival after diagnosis of a little more than a year. Glioblastomas have a high frequency of mutations in the TERT promoter and CDKN2A locus that are expected to render them resistant to both replicative and oncogene-induced senescence. However, exposure of PriGO8A primary glioblastoma cells to media with 10% serum induced a senescence-like phenotype characterized by increased senescence-associated β galactosidase activity, PML bodies and p21 and morphological changes typical of senescence...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526277/gene-expression-patterns-in-distinct-endoscopic-findings-for-eosinophilic-gastritis-in-children
#11
Masamichi Sato, Tetsuo Shoda, Hirotaka Shimizu, Kanami Orihara, Kyoko Futamura, Akio Matsuda, Yoshiyuki Yamada, Rie Irie, Takako Yoshioka, Toshiaki Shimizu, Yukihiro Ohya, Ichiro Nomura, Kenji Matsumoto, Katsuhiro Arai
BACKGROUND: Eosinophilic gastritis (EG) is clinicopathologically characterized by both marked gastric eosinophilia and clinical symptoms. The endoscopic findings in EG vary among patients, leading to clinical confusion. However, little is known about the relationship between precise endoscopic findings and the pathophysiological process responsible for EG. OBJECTIVE: We aimed to elucidate whether the gross endoscopic findings of EG can be classified into distinct gene expression profiles...
May 16, 2017: Journal of Allergy and Clinical Immunology in Practice
https://www.readbyqxmd.com/read/28524267/synaptic-activity-suppresses-expression-of-neurogenic-differentiation-factor-2-in-an-nmda-receptor-dependent-manner
#12
Fading Chen, Benjamin J Hall
Neurogenic differentiation factor 2 (NeuroD2) is a highly expressed transcription factor in the developing central nervous system. In newborn neurons, NeuroD2-mediated gene expression promotes differentiation, maturation, and survival. In addition to these early, cell-intrinsic developmental processes, NeuroD2 in post-mitotic neurons also regulates synapse growth and ion channel expression to control excitability. While NeuroD2 transactivation can be induced in an activity-dependent manner, little is known about how expression of NeuroD2 itself is regulated...
May 19, 2017: Synapse
https://www.readbyqxmd.com/read/28524155/statin-use-candidate-mevalonate-pathway-biomarkers-and-colon-cancer-survival-in-a-population-based-cohort-study
#13
Ronan T Gray, Maurice B Loughrey, Peter Bankhead, Chris R Cardwell, Stephen McQuaid, Roisin F O'Neill, Kenneth Arthur, Victoria Bingham, Claire McGready, Anna T Gavin, Jacqueline A James, Peter W Hamilton, Manuel Salto-Tellez, Liam J Murray, Helen G Coleman
BACKGROUND: Statin use after colorectal cancer diagnosis may improve survival but evidence from observational studies is conflicting. The anti-cancer effect of statins may be restricted to certain molecular subgroups. In this population-based cohort study, the interaction between p53 and 3-hydroxy-3-methylglutaryl coenzyme-A reductase (HMGCR) expression, KRAS mutations, and the association between statin use and colon cancer survival was assessed. METHODS: The cohort consisted of 740 stage II and III colon cancer patients diagnosed between 2004 and 2008...
May 18, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28524153/transcriptome-analysis-of-mirna-lncrna-mrna-interactions-in-the-malignant-transformation-process-of-gastric-cancer-initiation
#14
Y Mao, R Liu, H Zhou, S Yin, Q Zhao, X Ding, H Wang
Gastric cancer is a common heterogeneous malignancy that is pathologically characterized by the development of chronic atrophic gastritis and dysplasia of the epithelium. The pathogenic mechanisms at the molecular level are completely unclear. In the present study, we first address the expression network and miRNA-lncRNA-mRNA interaction in the malignant transformation process from normal mucosa and atrophic gastritis to a tumor. First, the long non-coding RNA (lncRNA), micro RNA (miRNA) and messenger RNA (mRNA) expression profiles of normal gastric mucosa, atrophic gastritis, gastric cancer and the peri-tumor tissues were analyzed using microarrays...
May 19, 2017: Cancer Gene Therapy
https://www.readbyqxmd.com/read/28524003/targeting-the-programmed-cell-death-1-pathway-in-genitourinary-tumors-current-progress-and-future-perspectives
#15
Rodolfo Montironi, Liang Cheng, Holger Moch, Antonio Lopez-Beltran, Marina Scarpelli, Francesco Massari, Michelangelo Fiorentino, Chiara Ciccarese, Michael Koch, Hristos Z Kaimakliotis, Lisha Wang, Roberto Pili, Steven A Mann
Immune checkpoint inhibitors have revolutionized the treatment many malignancies with over a dozen new United States Food and Drug Administration (FDA) approvals in the past six years. Due to the combination of potent treatment success and potentially deadly adverse effects from immune checkpoint inhibitors, gathering prognostic and predictive information about FDA-indicated tumors is prudent. PD-L1 expression is a poor prognostic factor and predictive of better responses from both PD-1 and PD-L1 inhibitors in a variety of tumor types including RCC and urothelial carcinoma...
May 18, 2017: Current Drug Metabolism
https://www.readbyqxmd.com/read/28523980/diverse-endometrial-mrna-signatures-during-the-window-of-implantation-in-patients-with-repeated-implantation-failure
#16
Cheng Shi, Hong Jing Han, Li Juan Fan, Jing Guan, Xing Bang Zheng, Xi Chen, Rong Liang, Xiao Wei Zhang, Kun Kun Sun, Qing Hua Cui, Huan Shen
High endometrial receptivity in the window of implantation (WOI) is essential for successful implantation. However, a diagnostic tool with high specificity for impaired endometrial receptivity remains to be developed. We collected endometrium specimens during the WOI from patients with RIF and women who conceived after one IVF/ICSI attempt. We conducted mRNA microarray on the samples followed by relevant comparative and functional analysis. Microarray analysis revealed 357 dysregulated mRNAs between the two groups...
May 19, 2017: Human Fertility: Journal of the British Fertility Society
https://www.readbyqxmd.com/read/28523851/identification-of-multiple-druggable-secondary-sites-by-fragment-screening-against-dc-sign
#17
Jonas Aretz, Hannes Baukmann, Elena Shanina, Jonas Hanske, Robert Wawrzinek, Viktor A Zapol'skii, Peter H Seeberger, Dieter E Kaufmann, Christoph Rademacher
DC-SIGN is a cell-surface receptor for several pathogenic threats, such as HIV, Ebola virus, or Mycobacterium tuberculosis. Multiple attempts to develop inhibitors of the underlying carbohydrate-protein interactions have been undertaken in the past fifteen years. Still, drug-like DC-SIGN ligands are sparse, which is most likely due to its hydrophilic, solvent-exposed carbohydrate-binding site. Herein, we report on a parallel fragment screening against DC-SIGN applying SPR and a reporter displacement assay, which complements previous screenings using (19) F NMR spectroscopy and chemical fragment microarrays...
May 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28523561/technologies-for-deciphering-epigenomic-dna-patterns
#18
Sebastian Moran
DNA methylation, consisting on the covalent addition of a methyl group in cytosines, plays a vital role for the development and correct functioning of cells. It constitutes a mechanism by which cell genome is regulated, allowing from a common genome of an individual to obtain all the different cell types that constitute the individual. Nowadays, we understand how the epigenetic machinery works; however, this critical mechanism might promote the appearance of certain diseases if dysregulated, thus the importance of studying the epigenetic patterns on both normal and disease tissues...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28523553/dna-modifications-and-alzheimer-s-disease
#19
Rebecca G Smith, Katie Lunnon
Alzheimer's disease (AD) is a complex neurodegenerative disease, affecting millions of people worldwide. While a number of studies have focused on identifying genetic variants that contribute to the development and progression of late-onset AD, the majority of these only have a relatively small effect size. There are also a number of other risk factors, for example, age, gender, and other comorbidities; however, how these influence disease risk is not known. Therefore, in recent years, research has begun to investigate epigenetic mechanisms for a potential role in disease etiology...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28523289/core-canonical-pathways-involved-in-developing-human-glioblastoma-multiforme-gbm
#20
Somiranjan Ghosh, Sisir Dutta, Gabriel Thorne, Ava Boston, Alexis Barfield, Narendra Banerjee, Rayshawn Walker, Hirendra Nath Banerjee
Glioblastoma multiforme (GBM) is the most common and aggressive type of the primary brain tumors with pathologic hallmarks of necrosis and vascular proliferation. The diagnosis of GBM is currently mostly based on histological examination of brain tumor tissues, after radiological characterization and surgical biopsy. The ability to characterize tumors comprehensively at the molecular level raises the possibility that diagnosis can be made based on molecular profiling with or without histological examination, rather than solely on histological phenotype...
February 2017: Int J Sci Res Sci Eng Technol
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