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https://www.readbyqxmd.com/read/28531945/spp1-analyzed-by-bioinformatics-methods-promotes-the-metastasis-in-colorectal-cancer-by-activating-emt-pathway
#1
Chunjie Xu, Longci Sun, Chunhui Jiang, Hong Zhou, Lei Gu, Ye Liu, Qing Xu
OBJECTIVE: Tumor metastasis is still a great challenge for the prognosis of colorectal cancer (CRC). Although secreted phosphoprotein 1 (SPP1) over-expression is confirmed to associate with invasion, metastasis of CRC, the underlying mechanism by which modulates the CRC metastasis is still not fully explained. METHOD: GDS4382 was obtained from GEO database and differentially expressed genes (DEGs) were analyzed by bioinformatics methods 55 paired samples of CRC and adjacent non-cancerous tissues were collected to detect the expression of SPP1 by q-PCR and western blot...
May 17, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28531277/genome-wide-discovery-of-viral-micrornas-based-on-phylogenetic-analysis-and-structural-evolution-of-various-human-papillomavirus-subtypes
#2
Shun-Long Weng, Kai-Yao Huang, Julia Tzu-Ya Weng, Fang-Yu Hung, Tzu-Hao Chang, Tzong-Yi Lee
In mammals, microRNAs (miRNAs) play key roles in controlling posttranscriptional regulation through binding to the mRNAs of target genes. Recently, it was discovered that viral miRNAs may be involved in human cancers and diseases. It is likely that viral miRNAs help viruses enter the latent phase of their life cycle and become undetected by the host's immune system, while increasing the host's risk for cancer development. Cervical cancer is typically related to the infection of human papillomavirus (HPV) through sexual transmission...
May 20, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28530238/micrornas-146a-b-5-and-425-3p-and-24-3p-are-markers-of-antidepressant-response-and-regulate-mapk-wnt-system-genes
#3
Juan Pablo Lopez, Laura M Fiori, Cristiana Cruceanu, Rixing Lin, Benoit Labonte, Hannah M Cates, Elizabeth A Heller, Vincent Vialou, Stacy M Ku, Christophe Gerald, Ming-Hu Han, Jane Foster, Benicio N Frey, Claudio N Soares, Daniel J Müller, Faranak Farzan, Francesco Leri, Glenda M MacQueen, Harriet Feilotter, Kathrin Tyryshkin, Kenneth R Evans, Peter Giacobbe, Pierre Blier, Raymond W Lam, Roumen Milev, Sagar V Parikh, Susan Rotzinger, Steven C Strother, Cathryn M Lewis, Katherine J Aitchison, Gayle M Wittenberg, Naguib Mechawar, Eric J Nestler, Rudolf Uher, Sidney H Kennedy, Gustavo Turecki
Antidepressants (ADs) are the most common treatment for major depressive disorder (MDD). However, only ∼30% of patients experience adequate response after a single AD trial, and this variability remains poorly understood. Here, we investigated microRNAs (miRNAs) as biomarkers of AD response using small RNA-sequencing in paired samples from MDD patients enrolled in a large, randomized placebo-controlled trial of duloxetine collected before and 8 weeks after treatment. Our results revealed differential expression of miR-146a-5p, miR-146b-5p, miR-425-3p and miR-24-3p according to treatment response...
May 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28529706/expresso-a-database-and-web-server-for-exploring-the-interaction-of-transcription-factors-and-their-target-genes-in-arabidopsis-thaliana-using-chip-seq-peak-data
#4
Delasa Aghamirzaie, Karthik Raja Velmurugan, Shuchi Wu, Doaa Altarawy, Lenwood S Heath, Ruth Grene
Motivation: The increasing availability of chromatin immunoprecipitation sequencing (ChIP-Seq) data enables us to learn more about the action of transcription factors in the regulation of gene expression. Even though in vivo transcriptional regulation often involves the concerted action of more than one transcription factor, the format of each individual ChIP-Seq dataset usually represents the action of a single transcription factor. Therefore, a relational database in which available ChIP-Seq datasets are curated is essential...
2017: F1000Research
https://www.readbyqxmd.com/read/28529696/in-silico-gene-expression-profiling-in-cannabis-sativa
#5
Luca Massimino
The cannabis plant and its active ingredients (i.e., cannabinoids and terpenoids) have been socially stigmatized for half a century. Luckily, with more than 430,000 published scientific papers and about 600 ongoing and completed clinical trials, nowadays cannabis is employed for the treatment of many different medical conditions. Nevertheless, even if a large amount of high-throughput functional genomic data exists, most researchers feature a strong background in molecular biology but lack advanced bioinformatics skills...
2017: F1000Research
https://www.readbyqxmd.com/read/28529580/microrna-592-targets-igf-1r-to-suppress-cellular-proliferation-migration-and-invasion-in-hepatocellular-carcinoma
#6
Wenyao Wang, Hongfei Zhang, Mao Tang, Longlong Liu, Zhengfang Zhou, Shaojun Zhang, Lichao Wang
MicroRNAs (miRs) can function as tumor suppressors or oncogenes in different types of human malignancy, and may provide an effective therapy for cancer. The expression and functions of miR-592 have previously been studied in relation to cancer. However, the expression and potential functions of miR-592 in hepatocellular carcinoma (HCC) are still unknown. Using quantitative polymerase chain reaction, MTT assays, cellular migration and invasion assays, bioinformatics software, western blot analysis and dual-luciferase report assays, the present study explored the expression and roles of miR-592 in HCC...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28529556/microrna-326-suppresses-the-proliferation-migration-and-invasion-of-cervical-cancer-cells-by-targeting-elk1
#7
Ping Zhang, Feng Kong, Xinchao Deng, Yunhai Yu, Congzhe Hou, Tingting Liang, Lin Zhu
Although microRNAs (miRNAs or miRs) are able to function as oncogenes or tumor suppressors, the role of miR-326 in regulating human cervical cancer cells remains unclear. In the present study, the expression of miR-326 was identified to be downregulated in cervical cancer cell lines and primary tumor samples, and the overexpression of miR-326 decreased cell proliferation, migration and invasion in cervical cell lines. Bioinformatics prediction and experimental validation results revealed that the function of miR-326 was achieved by targeting and repressing ETS domain-containing protein Elk-1 (ELK1) expression...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28529482/mode-of-action-analyses-of-neferine-a-bisbenzylisoquinoline-alkaloid-of-lotus-nelumbo-nucifera-against-multidrug-resistant-tumor-cells
#8
Onat Kadioglu, Betty Y K Law, Simon W F Mok, Su-Wei Xu, Thomas Efferth, Vincent K W Wong
Neferine, a bisbenzylisoquinoline alkaloid isolated from the green seed embryos of Lotus (Nelumbo nucifera Gaertn), has been previously shown to have various anti-cancer effects. In the present study, we evaluated the effect of neferine in terms of P-glycoprotein (P-gp) inhibition via in vitro cytotoxicity assays, R123 uptake assays in drug-resistant cancer cells, in silico molecular docking analysis on human P-gp and in silico absorption, distribution, metabolism, and excretion (ADME), quantitative structure activity relationships (QSAR) and toxicity analyses...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28529006/validation-of-a-next-generation-sequencing-pipeline-for-the-molecular-diagnosis-of-multiple-inherited-cancer-predisposing-syndromes
#9
Paula Paulo, Pedro Pinto, Ana Peixoto, Catarina Santos, Carla Pinto, Patrícia Rocha, Isabel Veiga, Gabriela Soares, Catarina Machado, Fabiana Ramos, Manuel R Teixeira
Despite the growing knowledge of the genetic background behind the cancers that occur in a context of hereditary predisposition, personal or family cancer history may not be clear enough to support directional gene testing. Defined targeted next-generation sequencing gene panels allow identification of the causative disease mutations of multigene syndromes and differential diagnosis for syndromes with phenotypically overlapping characteristics. Herein, we established a next-generation sequencing analysis pipeline for the molecular diagnosis of multiple inherited cancer predisposing syndromes using the commercially available target sequencing panel TruSight Cancer...
May 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28528975/autophagy-related-gene-microarray-and-bioinformatics-analysis-for-ischemic-stroke-detection
#10
Yinsheng Guo, Yue Ma, Yanwei Zhang, Li Zhou, Suli Huang, Ying Wen, Fei Zou, Jinquan Cheng
Ischemic stroke (IS) is characterized by high morbidity and poor prognosis. However, the mechanisms of IS induced injury are still poorly understood. The main aim of this study is to explore the role of autophagy in IS. Ten pairs of whole blood samples of IS patients and matched controls were included to select differential expressed genes (DE genes) by autophagy-related functional gene microarray analysis. And then, one hundred and fifty pairs of whole blood samples of IS patients and matched controls were included to validate the DE genes...
May 18, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28528876/modeling-covalent-modifier-drugs
#11
REVIEW
Ernest Awoonor-Williams, Andrew G Walsh, Christopher N Rowley
In this review, we present a summary of how computer modeling has been used in the development of covalent modifier drugs. Covalent modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly...
May 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28528497/microrna-30a-5p-mir-30a-regulates-cell-motility-and-emt-by-directly-targeting-oncogenic-tm4sf1-in-colorectal-cancer
#12
Y R Park, S L Kim, M R Lee, S Y Seo, J H Lee, S H Kim, I H Kim, S O Lee, S T Lee, Sang Wook Kim
PURPOSE: Colorectal cancer (CRC) is one of the leading causes of cancer death worldwide, and many oncogenes and tumor suppressor genes are involved in CRC. MicroRNAs (miRNAs) are small non-coding RNAs that can negatively regulate gene expression. Previous studies have revealed that miRNAs regulate the development and progression of many cancers. In this study, we investigated the role of microRNA-30a-5p (miR-30a) in CRC and its unknown mechanisms. METHODS: qRT-PCR was used to detect miR-30a and TM4SF1 mRNA expression in CRC specimens and cell lines...
May 20, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28528324/new-role-for-interleukin-13-receptor-%C3%AE-1-in-myocardial-homeostasis-and-heart-failure
#13
Uri Amit, David Kain, Allon Wagner, Avinash Sahu, Yael Nevo-Caspi, Nir Gonen, Natali Molotski, Tal Konfino, Natalie Landa, Nili Naftali-Shani, Galia Blum, Emmanuelle Merquiol, Danielle Karo-Atar, Yariv Kanfi, Gidi Paret, Ariel Munitz, Haim Y Cohen, Eytan Ruppin, Sridhar Hannenhalli, Jonathan Leor
BACKGROUND: The immune system plays a pivotal role in myocardial homeostasis and response to injury. Interleukins-4 and -13 are anti-inflammatory type-2 cytokines, signaling via the common interleukin-13 receptor α1 chain and the type-2 interleukin-4 receptor. The role of interleukin-13 receptor α1 in the heart is unknown. METHODS AND RESULTS: We analyzed myocardial samples from human donors (n=136) and patients with end-stage heart failure (n=177). We found that the interleukin-13 receptor α1 is present in the myocardium and, together with the complementary type-2 interleukin-4 receptor chain Il4ra, is significantly downregulated in the hearts of patients with heart failure...
May 20, 2017: Journal of the American Heart Association
https://www.readbyqxmd.com/read/28528185/simvastatin-ameliorate-memory-deficits-and-inflammation-in-clinical-and-mouse-model-of-alzheimer-s-disease-via-modulating-the-expression-of-mir-106b
#14
Wenzhong Huang, Zhenyu Li, Liandong Zhao, Wei Zhao
BACKGROUND: Alzheimer's disease (AD) as a neurodegenerative brain disorder is a devastating pathology leading to disastrous cognitive impairments and dementia, and several studies have shown that AD is closely related to the inflammation, so anti-inflammatory treatment may provide therapeutic benefits. In this study, the effect of simvastatin on inflammation was investigated and the underlying mechanisms were explored. METHODS: First, we tested the effect of simvastatin on AD in clinical research...
May 18, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28527409/molecular-characterization-of-pigeon-torque-teno-virus-pttv-in-jiangsu-province
#15
Zhicheng Zhang, Wei Dai, Dingzhen Dai
The torque teno virus (TTV) is a recently discovered DNA virus that has been detected in many different hosts, including humans, livestock and poultry. To date, there is no report of pigeon TTV (PTTV) from anywhere in the world. To investigate the distribution of PTTV in pigeons from the eastern Chinese province of Jiangsu and characterize their genomes, we employed PCR to detect PTTV in 144 samples collected from 6 pigeon plants in Jiangsu province, amplify complete genomes from representative samples and analyze genetic characteristics using bioinformatics...
May 6, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28527113/mutant-p53-promotes-cell-spreading-and-migration-via-arhgap44
#16
Jinjin Xu, Jian Jiao, Wei Xu, Lei Ji, Dongjie Jiang, Shaofang Xie, Syeda Kubra, Xiaotao Li, Junjiang Fu, Jianru Xiao, Bianhong Zhang
The tumor suppressor p53 protein is either lost or mutated in about half of all human cancers. Loss of p53 function is well known to influence cell spreading, migration and invasion. While expression of mutant p53 is not equivalent to p53 loss, mutant p53 can acquire new functions to drive cell spreading and migration via different mechanisms. In our study, we found that mutant p53 significantly increased cell spreading and migration when comparing with p53-null cells. RNA-Seq analysis suggested that Rho GTPase activating protein 44 (ARHGAP44) is a new target of mutant p53, which suppressed ARHGAP44 transcription...
May 16, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28526933/protection-of-tubular-epithelial-cells-during-renal-injury-via-post-transcriptional-control-of-bmp7
#17
Jiping Sun, Aiping Yin, Fei Zhao, Wenjing Zhang, Jia Lv, Jing Lv
Severe injury of renal tubular epithelial cells may cause acute renal failure, the progression of which results in renal fibrosis, and obstructive nephropathy. Transforming growth factor β 1 and bone morphogenic protein 7 (BMP7) play contradicting roles in and coordinate the process of epithelial-to-mesenchymal transition of renal tubular epithelial cells, but the molecular regulation of BMP7 remains ill-defined. Here, we addressed this question. We found that after induction of unilateral ureteral obstruction (UUO) in mice, the increases in BMP7 mRNA were much more pronounced than BMP7 protein in kidney, suggesting the presence of post-transcriptional control of BMP7...
May 19, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28526858/expression-and-activity-of-the-bioh-esterase-of-biotin-synthesis-is-independent-of-genome-context
#18
Xinyun Cao, Lei Zhu, Zhe Hu, John E Cronan
BioH is an α/β-hydrolase required for synthesis of the pimelate moiety of biotin in diverse bacteria. The bioH gene is found in different genomic contexts. In some cases (e.g., Escherichia coli) the gene is not located within a biotin synthetic operon and its transcription is not coregulated with the other biotin synthesis genes. In other genomes such as Pseudomonas aeruginosa the bioH gene is within a biotin synthesis operon and its transcription is coregulated with the other biotin operon genes. The esterases of pimelate moiety synthesis show remarkable genomic plasticity in that in some biotin operons bioH is replaced by other α/ß hydrolases of diverse sequence...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526816/delineation-of-b-cell-epitopes-of-salmonella-enterica-serovar-typhi-hemolysin-e-potential-antibody-therapeutic-target
#19
Chai Fung Chin, Jing Yi Lai, Yee Siew Choong, Amy Amilda Anthony, Asma Ismail, Theam Soon Lim
Hemolysin E (HlyE) is an immunogenic novel pore-forming toxin involved in the pathogenesis of typhoid fever. Thus, mapping of B-cell epitopes of Salmonella enterica serovar Typhi (S. Typhi) is critical to identify key immunogenic regions of HlyE. A random 20-mer peptide library was used for biopanning with enriched anti-HlyE polyclonal antibodies from typhoid patient sera. Bioinformatic tools were used to refine, analyze and map the enriched peptide sequences against the protein to identify the epitopes. The analysis identified both linear and conformational epitopes on the HlyE protein...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526810/bioinformatics-and-in-vitro-experimental-analyses-identify-the-selective-therapeutic-potential-of-interferon-gamma-and-apigenin-against-cervical-squamous-cell-carcinoma-and-adenocarcinoma
#20
Pei-Ming Yang, Chia-Jung Chou, Ssu-Hsueh Tseng, Chien-Fu Hung
The clinical management and treatment of cervical cancer, one of the most commonly diagnosed cancers and a leading cause of cancer-related female death, remains a huge challenge for researchers and health professionals. Cervical cancer can be categorized into two major subtypes: common squamous cell carcinoma (SCC) and adenocarcinoma (AC). Although it is a relatively rare histological subtype of cervical cancer, there has been a steady increase in the incidences of AC. Therefore, new strategies to treat cervical cancer are urgently needed...
May 2, 2017: Oncotarget
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