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Ingenuity pathway analysis

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https://www.readbyqxmd.com/read/28345661/stepwise-analysis-of-mir9-loci-identifies-mir-9-5p-to-be-involved-in-oestrogen-regulated-pathways-in-breast-cancer-patients
#1
Raffaela Barbano, Barbara Pasculli, Michelina Rendina, Andrea Fontana, Caterina Fusilli, Massimiliano Copetti, Stefano Castellana, Vanna Maria Valori, Maria Morritti, Paolo Graziano, Ciuffreda Luigi, Michelina Coco, Francesco Picardo, Tommaso Mazza, Ella Evron, Roberto Murgo, Evaristo Maiello, Manel Esteller, Vito Michele Fazio, Paola Parrella
miR-9 was initially identified as an epigenetically regulated miRNA in tumours, but inconsistent findings have been reported so far. We analysed the expression of miR-9-5p, miR-9-3p, pri-miRs and MIR9 promoters methylation status in 131 breast cancer cases and 12 normal breast tissues (NBTs). The expression of both mature miRs was increased in tumours as compared to NBTs (P < 0.001) and negatively correlated with ER protein expression (P = 0.005 and P = 0.003, for miR-9-3p and miR-9-5p respectively)...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28344862/expression-profiles-of-immune-related-genes-are-associated-with-neoadjuvant-ipilimumab-clinical-benefit
#2
Ahmad A Tarhini, Yan Lin, Hui-Min Lin, Priyanka Vallabhaneni, Cindy Sander, William LaFramboise, Lana Hamieh
Purpose: Patients with regionally advanced melanoma were treated with neoadjuvant ipilimumab in a previously reported study (PLOS One 2014). Gene expression profiles of tumors of treated patients were investigated for their association with immunotherapeutic benefit. Methods: Patients were treated with ipilimumab (10 mg/kg intravenously every 3 weeks × 2 doses) before and after surgery. Tumor specimens were obtained at baseline and at definitive surgery (weeks 6-8). Gene expression profiling was performed on the tumor biopsies of 27 patients...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28341621/cancer-cachexia-induced-muscle-atrophy-evidence-for-alterations-in-micrornas-important-for-muscle-size
#3
David Edward Lee, Jacob L Brown, Megan E Rosa-Caldwell, Thomas A Blackwell, Richard A Perry, Lemuel A Brown, Bhuwan Khatri, Dongwon Seo, Walter Gay Bottje, Tyrone Anthony Washington, Michael P Wiggs, Byung-Whi Kong, Nicholas Perry Greene
Muscle atrophy is a hallmark of cancer cachexia resulting in impaired function and quality of life and cachexia is the immediate cause of death for 20-40% of cancer patients. Multiple microRNAs (miRNAs) have been identified as being involved in muscle development and atrophy, however less is known specifically on miRNAs in cancer cachexia. PURPOSE: The purpose of this investigation was to examine the miRNA profile of skeletal muscle atrophy induced by cancer cachexia to uncover potential miRNAs involved with this catabolic condition...
March 24, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28341207/transcriptome-analysis-of-airborne-pm2-5-induced-detrimental-effects-on-human-keratinocytes
#4
Hyoung-June Kim, Il-Hong Bae, Eui Dong Son, Juyearl Park, Nari Cha, Hyewon Na, Changjo Jung, You-Seak Go, Dae-Yong Kim, Tae Ryong Lee, Dong Wook Shin
Ambient air pollution is becoming more severe worldwide, posing a serious threat to human health. Fine airborne particles of particulate matter (PM2.5) show higher cytotoxicity than other coarse fractions. Indeed, PM2.5 induces cardiovascular or respiratory damage; however, few studies have evaluated the detrimental effect of PM2.5 to normal human skin. We used a next-generation sequencing-based (RNA-Seq) method with transcriptome and Gene Ontology (GO) enrichment analysis to determine the harmful influences of PM2...
March 21, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/28337427/comparative-proteomics-analysis-of-human-macrophages-infected-with-virulent-mycobacterium-bovis
#5
Pei Li, Rui Wang, Wenqi Dong, Linlin Hu, Bingbing Zong, Yanyan Zhang, Xiangru Wang, Aizhen Guo, Anding Zhang, Yaozu Xiang, Huanchun Chen, Chen Tan
Mycobacterium bovis (M. bovis), the most common pathogens of tuberculosis (TB), is virulent to human and cattle, and transmission between cattle and humans warrants reconsideration concerning food safety and public health. Recently, efforts have begun to analyze cellular proteomic responses induced by Mycobacterium tuberculosis (M. tb). However, the underlying mechanisms by which virulent M. bovis affects human hosts are not fully understood. For the present study, we utilized a global and comparative labeling strategy of isobaric tag for relative and absolute quantitation (iTRAQ) to assess proteomic changes in the human monocyte cell line (THP-1) using a vaccine strain and two virulent strains H37Rv and M...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28329397/resveratrol-improves-vascular-function-and-mitochondrial-number-but-not-glucose-metabolism-in-older-adults
#6
Rena M Pollack, Nir Barzilai, Valentin Anghel, Ameya S Kulkarni, Aaron Golden, Pilib O'Broin, David A Sinclair, Michael S Bonkowski, Alexander J Coleville, Danielle Powell, Sharon Kim, Ruin Moaddel, Daniel Stein, Kehao Zhang, Meredith Hawkins, Jill P Crandall
Background: Resveratrol, a plant-derived polyphenol, has been reported to improve glucose metabolism and vascular function and to extend life span in animal models, but studies in humans have been inconclusive. Methods: In a randomized, double-blind crossover study, we treated older glucose-intolerant adults (n = 30) with resveratrol (2-3 g/daily) or placebo, each for 6 weeks. A standard mixed-meal test was used to assess insulin sensitivity (Matsuda index) and secretion (C-peptide deconvolution) and vascular function by reactive hyperemia peripheral arterial tonometry...
March 16, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28329018/a-unique-microrna-profile-in-end-stage-heart-failure-indicates-alterations-in-specific-cardiovascular-signaling-networks
#7
Sathyamangla V Naga Prasad, Manveen K Gupta, Zhong-Hui Duan, Venkata Suresh K Surampudi, Chang-Gong Liu, Ashwin Kotwal, Christine S Moravec, Randall C Starling, Dianne M Perez, Subha Sen, Qingyu Wu, Edward F Plow, Sadashiva Karnik
It is well established that the gene expression patterns are substantially altered in cardiac hypertrophy and heart failure, however, less is known about the reasons behind such global differences. MicroRNAs (miRNAs) are short non-coding RNAs that can target multiple molecules to regulate wide array of proteins in diverse pathways. The goal of the study was to profile alterations in miRNA expression using end-stage human heart failure samples with an aim to build signaling network pathways using predicted targets for the altered miRNA and to determine nodal molecules regulating individual networks...
2017: PloS One
https://www.readbyqxmd.com/read/28319593/profiles-of-long-noncoding-rnas-in-hypertensive-rats-long-noncoding-rna-xr007793-regulates-cyclic-strain-induced-proliferation-and-migration-of-vascular-smooth-muscle-cells
#8
Qing-Ping Yao, Zhi-Wei Xie, Kai-Xuan Wang, Ping Zhang, Yue Han, Ying-Xin Qi, Zong-Lai Jiang
BACKGROUND: Long noncoding RNAs (lncRNAs) are being discovered in multiple diseases at a rapid pace. However, the contribution of lncRNAs to hypertension remains largely unknown. In hypertension, the vascular walls are exposed to abnormal mechanical cyclic strain, which leads to vascular remodelling. Here, we investigated the mechanobiological role of lncRNAs in hypertension. METHODS AND RESULTS: Differences in the lncRNAs and mRNAs between spontaneously hypertensive rats and Wistar-Kyoto rats were screened using a gene microarray...
March 17, 2017: Journal of Hypertension
https://www.readbyqxmd.com/read/28317380/systems-biology-reveals-ns4b-cyclophilin-a-interaction-a-new-target-to-inhibit-yfv-replication
#9
Alessandra Vidotto, Ana T S Morais, Milene R Ribeiro, Carolina C Pacca, Ana C B Terzian, Laura H V G Gil, Ronaldo Mohana-Borges, Philippe Gallay, Mauricio L Nogueira
Yellow fever virus (YFV) replication is highly dependent on host cell factors. YFV NS4B is reported to be involved in viral replication and immune evasion. Here interactions between NS4B and human proteins were determined using a GST pull-down assay and analyzed using 1-DE and LC-MS/MS. We present a total of 207 proteins confirmed using Scaffold 3 Software. Cyclophilin A (CypA), a protein that has been shown to be necessary for the positive regulation of flavivirus replication, was identified as a possible NS4B partner...
March 27, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28315470/the-nitric-oxide-synthase-2-pathway-is-targeted-by-both-pro-and-anti-inflammatory-treatments-in-the-immature-human-intestine
#10
Emanuela Ferretti, Eric Tremblay, Marie-Pier Thibault, David Grynspan, Karolina M Burghardt, Marcos Bettolli, Corentin Babakissa, Emile Levy, Jean-François Beaulieu
BACKGROUND AND AIM: NO synthase 2 (NOS2) was recently identified as one the most overexpressed genes in intestinal samples of premature infants with necrotizing enterocolitis (NEC). NOS2 is widely implicated in the processes of epithelial cell injury/apoptosis and host immune defense but its specific role in inflammation of the immature human intestinal mucosa remains unclear. Interestingly, factors that prevent NEC such as epidermal growth factor (EGF) attenuate the inflammatory response in the mid-gestation human small intestine using serum-free organ culture while drugs that are associated with NEC occurrence such as the non-steroidal anti-inflammatory drug, indomethacin (INDO), exert multiple detrimental effects on the immature human intestine...
March 14, 2017: Nitric Oxide: Biology and Chemistry
https://www.readbyqxmd.com/read/28303893/changes-in-mirna-in-the-lung-and-whole-blood-after-whole-thorax-irradiation-in-rats
#11
Feng Gao, Pengyuan Liu, Jayashree Narayanan, Meiying Yang, Brian L Fish, Yong Liu, Mingyu Liang, Elizabeth R Jacobs, Meetha Medhora
We used a rat model of whole thorax x-ray irradiation to profile the microRNA (miRNA) in lung and blood up to 4 weeks after radiation. MiRNA from normal and irradiated Wistar rat lungs and whole blood were analyzed by next-generation sequencing and the changes by radiation were identified by differential deRNA-seq 1, 2, 3 and 4 weeks after irradiation. The average total reads/library was 2,703,137 with a mean of 88% mapping to the rat genome. Detailed profiles of 100 of the most abundant miRNA in rat blood and lung are described...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28300755/vitamin-d-impacts-the-expression-of-runx2-target-genes-and-modulates-inflammation-oxidative-stress-and-membrane-vesicle-biogenesis-gene-networks-in-143b-osteosarcoma-cells
#12
Rama Garimella, Priyanka Tadikonda, Ossama Tawfik, Sumedha Gunewardena, Peter Rowe, Peter Van Veldhuizen
Osteosarcoma (OS) is an aggressive malignancy of bone affecting children, adolescents and young adults. Understanding vitamin D metabolism and vitamin D regulated genes in OS is an important aspect of vitamin D/cancer paradigm, and in evaluating vitamin D as adjuvant therapy for human OS. Vitamin D treatment of 143B OS cells induced significant and novel changes in the expression of genes that regulate: (a) inflammation and immunity; (b) formation of reactive oxygen species, metabolism of cyclic nucleotides, sterols, vitamins and mineral (calcium), quantity of gap junctions and skeletogenesis; (c) bone mineral density; and (d) cell viability of skeletal cells, aggregation of bone cancer cells and exocytosis of secretory vesicles...
March 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28298639/benzyl-butyl-phthalate-decreases-myogenic-differentiation-of-endometrial-mesenchymal-stem-stromal-cells-through-mir-137-mediated-regulation-of-pitx2
#13
Hung-Sheng Chen, Chia-Yi Hsu, Yu-Chia Chang, Hui-Yu Chuang, Cheng-Yu Long, Tsung-Hua Hsieh, Eing-Mei Tsai
Phthalate, an environmental toxin, has been considered as an endocrine-disrupting chemical. Growing evidence has demonstrated links between endocrine-disrupting chemicals, tissue development, and reproductive physiology, but the mechanisms of gene expression regulation by environmental factors that affect cell differentiation are unclear. Herein, we investigated the effects of butyl benzyl phthalate (BBP) on human endometrial mesenchymal stem/stromal cell (EN-MSC) differentiation and identified a novel signaling pathway...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28282394/transcriptomal-profiling-of-bovine-ovarian-granulosa-and-theca-interna-cells-in-primary-culture-in-comparison-with-their-in-vivo-counterparts
#14
Nicholas Hatzirodos, Claire Glister, Katja Hummitzsch, Helen F Irving-Rodgers, Philip G Knight, Raymond J Rodgers
In vitro culture of ovarian granulosa cells and theca cells has been very important for our understanding of their function and regulation. One of the most eagerly sought attributes of cell culture is the use of chemically-defined conditions. However, even under such in vitro conditions cell behaviour could differ from the in vivo situation because of differences in oxygen tension, nutrients, adhesion matrix and other factors. To examine this further we compared the transcriptomes of both granulosa cells and cells from the theca interna that were cultured in what are arguably the best in vitro conditions for maintaining the 'follicular' phenotypes of both tissue types, as displayed by their respective freshly-isolated counterparts...
2017: PloS One
https://www.readbyqxmd.com/read/28281307/integrated-expression-analysis-identifies-transcription-networks-in-mouse-and-human-gastric-neoplasia
#15
Zheng Chen, Mohammed Soutto, Bushra Rahman, Muhammad W Fazili, DunFa Peng, Maria Blanca Piazuelo, Heidi Chen, M Kay Washington, Yu Shyr, Wael El-Rifai
Gastric cancer is a leading cause of cancer-related deaths worldwide. The Tff1 knockout (KO) mouse model develops gastric lesions that include low-grade dysplasia (LGD), high-grade dysplasia (HGD), and adenocarcinomas. In this study, we used Affymetrix microarrays gene expression platforms for analysis of molecular signatures in the mouse stomach (Tff1-KO (LGD) and Tff1 wild-type (normal)) and human gastric cancer tissues and their adjacent normal tissue samples. Combined integrated bioinformatics analysis of mouse and human datasets indicated that 172 genes were consistently deregulated in both human gastric cancer samples and Tff1-KO LGD lesions (P<0...
March 9, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28255762/semax-an-analog-of-acth-4-7-regulates-expression-of-immune-response-genes-during-ischemic-brain-injury-in-rats
#16
Ekaterina V Medvedeva, Veronika G Dmitrieva, Svetlana A Limborska, Nikolay F Myasoedov, Lyudmila V Dergunova
Brain stroke continues to claim the lives of million people every year. To build the effective strategies for stroke treatment it is necessary to understand the neuroprotective mechanisms that are able to prevent the ischemic injury. Consisting of the ACTH(4-7) fragment and the tripeptide Pro-Gly-Pro (PGP), the synthetic peptide Semax effectively protects brain against ischemic stroke. However, the molecular mechanisms underlying its neuroprotection and participation of PGP in them are still needed to be clarified...
March 2, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28253108/ischemia-induces-quiescence-and-autophagy-dependence-in-hepatocellular-carcinoma
#17
Terence P F Gade, Elizabeth Tucker, Michael S Nakazawa, Stephen J Hunt, Waihay Wong, Bryan Krock, Charles N Weber, Gregory J Nadolski, Timothy W I Clark, Michael C Soulen, Emma E Furth, Jeffrey D Winkler, Ravi K Amaravadi, M Celeste Simon
Purpose To characterize hepatocellular carcinoma (HCC) cells surviving ischemia with respect to cell cycle kinetics, chemosensitivity, and molecular dependencies that may be exploited to potentiate treatment with transarterial embolization (TAE). Materials and Methods Animal studies were performed according to institutionally approved protocols. The growth kinetics of HCC cells were studied in standard and ischemic conditions. Viability and cell cycle kinetics were measured by using flow cytometry. Cytotoxicity profiling was performed by using a colorimetric cell proliferation assay...
March 2, 2017: Radiology
https://www.readbyqxmd.com/read/28252568/time-course-of-inflammatory-gene-expression-following-crush-injury-in-murine-skeletal-muscle
#18
Joachim G Voss, Ayelet Goldshmid Shagal, Joyce M Tsuji, James W MacDonald, Theo K Bammler, Fred M Farin, Barbara St Pierre Schneider
BACKGROUND: Early inflammation and secretion of proinflammatory cytokines such as IL-1β, IL-6, and TNF-α act as the key drivers to regulate inflammation after muscle injury. However, the effects of these key proinflammatory drivers in a noninvasive crush injury model are not well known. Understanding these effects is important for treating crush injuries that occur during natural disasters and military conflicts. PURPOSE: We studied the timed mRNA expression of IL-1β, IL-6, and TNF-α in a noninvasive murine crush injury model to further understand their impact on proinflammatory cytokine pathways that are activated within the first 48 hours after a crush muscle injury...
March 2017: Nursing Research
https://www.readbyqxmd.com/read/28252104/altered-gene-expression-and-repressed-markers-of-autophagy-in-skeletal-muscle-of-insulin-resistant-patients-with-type-2-diabetes
#19
Andreas Buch Møller, Ulla Kampmann, Jakob Hedegaard, Kasper Thorsen, Iver Nordentoft, Mikkel Holm Vendelbo, Niels Møller, Niels Jessen
This case-control study was designed to investigate the gene expression profile in skeletal muscle from severely insulin resistant patients with long-standing type 2 diabetes (T2D), and to determine associated signaling pathways. Gene expression profiles were examined by whole transcriptome, strand-specific RNA-sequencing and associated signaling was determined by western blot. We identified 117 differentially expressed gene transcripts. Ingenuity Pathway Analysis related these differences to abnormal muscle morphology and mitochondrial dysfunction...
March 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28249909/morphoproteomics-identifies-sirt1-and-ezh2-pathways-as-commonalities-in-b-cell-acute-lymphoblastic-leukemia-pathogenetic-implications-and-opportunities-for-therapeutic-intervention
#20
Robert E Brown, Kristine E Konopka, Priya Weerasinghe, Vanya Jaitly, Amitava Dasgupta, Mary F McGuire, Nghia D Nguyen
B-cell acute lymphoblastic leukemia (ALL) represents a malignant process in which bone marrow-derived lymphoblasts retain their undifferentiated state. Genetic testing has revealed either no identifiable cytogenetic and genomic abnormalities in such patients or a wide range of aberrations that may or may not contribute to the block in differentiation and the associated proliferation of the malignant lymphoblasts in cases of B-cell ALL. In this study, we applied morphoproteomics to a representative spectrum of cases of newly diagnosed B-cell ALL in order to identify pathways that are known to be associated with the maintenance of the undifferentiated state while promoting proliferation...
January 2017: Annals of Clinical and Laboratory Science
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