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Ingenuity pathway analysis

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https://www.readbyqxmd.com/read/28199183/mrna-mirna-integrative-analysis-of-diabetes-induced-cardiomyopathy-in-rats
#1
Mariana B Lopes, Renata Cc Freitas, Mario H Hirata, Rosario Dc Hirata, Adriana A Rezende, Vivian N Silbiger, Raul H Bortolin, Andre D Luchessi
An integrative analysis of miRNA and mRNA expression profiles in left ventricle (LV) of diabetes-induced rats was performed to elucidate the role of miRNAs and their mRNAs target in diabetic cardiomyopathy (DCM). mRNA (GSE4745) and miRNA (GSE44179) datasets were downloaded from Gene Expression Omnibus 2R (GEO2R) and differentially expressed mRNAs and miRNAs were selected. Cardiotoxicity-related mRNAs (n=7) were analyzed by Ingenuity Pathway Analyses 6 (IPA) and regulatory miRNAs (n=639) were identified using TargetScan 7...
March 1, 2017: Frontiers in Bioscience (Scholar Edition)
https://www.readbyqxmd.com/read/28196893/phosphorylation-of-%C3%AE-b-crystallin-supports-reactive-astrogliosis-in-demyelination
#2
Hedwich F Kuipers, Jane Yoon, Jack van Horssen, May H Han, Paul L Bollyky, Theo D Palmer, Lawrence Steinman
The small heat shock protein αB-crystallin (CRYAB) has been implicated in multiple sclerosis (MS) pathogenesis. Earlier studies have indicated that CRYAB inhibits inflammation and attenuates clinical disease when administered in the experimental autoimmune encephalomyelitis model of MS. In this study, we evaluated the role of CRYAB in primary demyelinating events. Using the cuprizone model of demyelination, a noninflammatory model that allows the analysis of glial responses in MS, we show that endogenous CRYAB expression is associated with increased severity of demyelination...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28193578/a-food-based-approach-that-targets-interleukin-6-a-key-regulator-of-chronic-intestinal-inflammation-and-colon-carcinogenesis
#3
Abigail Sido, Sridhar Radhakrishnan, Sung Woo Kim, Elisabeth Eriksson, Frank Shen, Qunhua Li, Vadiraja Bhat, Lavanya Reddivari, Jairam K P Vanamala
Studies have shown a causal link between high-calorie diet (HCD) and colon cancer. However, molecular mechanisms are not fully elucidated. To understand etiology of HCD-induced colon carcinogenesis, we screened 10 pathways linked to elevated colonic cell proliferation and chronic inflammation in an HCD-consuming human-relevant pig model. We observed elevated colonic mucosal interleukin-6 (IL-6) expression in HCD-consuming pigs compared to standard diet controls (SD, P=.04), and IL-6 strongly correlated with Ki-67 proliferative index and zone, early biomarkers of colon cancer risk (r=0...
January 28, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28184177/human-basonuclin-2-up-regulates-a-cascade-set-of-interferon-stimulated-genes-with-anti-cancerous-properties-in-a-lung-cancer-model
#4
Egon Urgard, Anu Reigo, Eva Reinmaa, Ana Rebane, Andres Metspalu
BACKGROUND: Human basonuclin 2 (BNC2) acts as a tumor suppressor in multiple cancers in an as yet unidentified manner. The role and expression of the BNC2 gene in lung cancer has not yet been investigated. METHODS: BNC2 expression was studied in the A549 and BEAS-2B cell lines, as well as in lung cancer tissue. Illumina array analysis and a viability assay were used to study the effects of transient transfection of BNC2 in A549 cells. Ingenuity pathway analysis and g:Profiler were applied to identify affected pathways and networks...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/28168424/characterization-of-dysregulated-mirna-in-peripheral-blood-mononuclear-cells-from-ischemic-stroke-patients
#5
Marpe Bam, Xiaoming Yang, Souvik Sen, Elizabeth E Zumbrun, Lauren Dennis, Jiajia Zhang, Prakash S Nagarkatti, Mitzi Nagarkatti
Epigenetic modification may play an important role in pathophysiology of ischemic stroke (IS) risk. MicroRNAs (miRNAs), which constitute one of the modes of epigenetic regulation, have been shown to be associated with a number of clinical disorders including IS. The purpose of this study was to investigate the miRNA profile in the peripheral blood mononuclear cells (PBMCs) of IS patients and compare it with stroke-free controls. Blood samples were obtained from 19 healthy age-gender-race matched individuals who served as controls to 20 IS patients...
February 6, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28153533/dysregulation-of-gene-expression-in-the-striatum-of-bachd-rats-expressing-full-length-mutant-huntingtin-and-associated-abnormalities-on-molecular-and-protein-levels
#6
Libo Yu-Taeger, Michael Bonin, Janice Stricker-Shaver, Olaf Riess, Hoa Huu Phuc Nguyen
Huntington disease (HD) is an autosomal dominantly inherited neurodegenerative disorder caused by a CAG repeat expansion in the gene coding for the huntingtin protein (HTT). Mutant HTT (mHTT) has been proposed to cause neuronal dysfunction and neuronal loss through multiple mechanisms. Transcriptional changes may be a core pathogenic feature of HD. Utilizing the Affymetrix platform we performed a genome-wide RNA expression analysis in two BACHD transgenic rat lines (TG5 and TG9) at 12 months of age, both of which carry full-length human mHTT but with different expression levels...
January 30, 2017: Neuropharmacology
https://www.readbyqxmd.com/read/28140569/silac-based-quantitative-proteomic-analysis-unveiled-the-arsenite-induced-perturbation-of-multiple-pathways-in-human-skin-fibroblast-cells
#7
Fan Zhang, Yongsheng Xiao, Yinsheng Wang
Humans are exposed to arsenic species through inhalation, ingestion and dermal contact, which may lead to skin, liver, and bladder cancers as well as cardiovascular and neurological diseases. The mechanisms underlying the cytotoxic and carcinogenic effects of arsenic species, however, remain incompletely understood. To exploit the mechanisms of toxicity of As(III), we employed stable isotope labeling by amino acids in cell culture (SILAC) together with LC-MS/MS analysis to assess quantitatively the As(III)-induced perturbation of the entire proteome of cultured human skin fibroblast cells...
January 31, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28128285/differentially-expressed-genes-and-canonical-pathway-expression-in-human-atherosclerotic-plaques-tampere-vascular-study
#8
Miska Sulkava, Emma Raitoharju, Mari Levula, Ilkka Seppälä, Leo-Pekka Lyytikäinen, Ari Mennander, Otso Järvinen, Rainer Zeitlin, Juha-Pekka Salenius, Thomas Illig, Norman Klopp, Nina Mononen, Reijo Laaksonen, Mika Kähönen, Niku Oksala, Terho Lehtimäki
Cardiovascular diseases due to atherosclerosis are the leading cause of death globally. We aimed to investigate the potentially altered gene and pathway expression in advanced peripheral atherosclerotic plaques in comparison to healthy control arteries. Gene expression analysis was performed (Illumina HumanHT-12 version 3 Expression BeadChip) for 68 advanced atherosclerotic plaques (15 aortic, 29 carotid and 24 femoral plaques) and 28 controls (left internal thoracic artery (LITA)) from Tampere Vascular Study...
January 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28118819/short-bowel-syndrome-results-in-increased-gene-expression-associated-with-proliferation-inflammation-bile-acid-synthesis-and-immune-system-activation-rna-sequencing-a-zebrafish-sbs-model
#9
Kathy A Schall, Matthew E Thornton, Mubina Isani, Kathleen A Holoyda, Xiaogang Hou, Ching-Ling Lien, Brendan H Grubbs, Tracy C Grikscheit
BACKGROUND: Much of the morbidity associated with short bowel syndrome (SBS) is attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition (TPN). We hypothesized that acute SBS alone has significant effects on gene expression beyond epithelial proliferation, and tested this in a zebrafish SBS model. METHODS: In a model of SBS in zebrafish (laparotomy, proximal stoma, distal ligation, n = 29) or sham (laparotomy alone, n = 28) surgery, RNA-Seq was performed after 2 weeks...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28117370/costunolide-and-dehydrocostuslactone-combination-treatment-inhibit-breast-cancer-by-inducing-cell-cycle-arrest-and-apoptosis-through-c-myc-p53-and-akt-14-3-3-pathway
#10
Zhangxiao Peng, Yan Wang, Jianhui Fan, Xuejing Lin, Chunying Liu, Yang Xu, Weidan Ji, Chao Yan, Changqing Su
Our previous studies demonstrated that volatile oil from saussurea lappa root (VOSL), rich in two natural sesquiterpene lactones, costunolide (Cos) and dehydrocostuslactone (Dehy), exerts better anti-breast cancer efficacy and lower side effects than Cos or Dehy alone in vivo, however, their anti-cancer molecular mechanisms were still unknown. In this study, we investigated the underlying mechanisms of Cos and Dehy combination treatment (CD) on breast cancer cells through proteomics technology coupled with Western blot validation...
January 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28114888/transcriptome-profiling-of-gene-expression-during-immunisation-trial-against-fasciola-hepatica-identification-of-genes-and-pathways-involved-in-conferring-immunoprotection-in-a-murine-model
#11
Jose Rojas-Caraballo, Julio López-Abán, Darwin Andrés Moreno-Pérez, Belén Vicente, Pedro Fernández-Soto, Esther Del Olmo, Manuel Alfonso Patarroyo, Antonio Muro
BACKGROUND: Fasciolosis remains a significant food-borne trematode disease causing high morbidity around the world and affecting grazing animals and humans. A deeper understanding concerning the molecular mechanisms by which Fasciola hepatica infection occurs, as well as the molecular basis involved in acquiring protection is extremely important when designing and selecting new vaccine candidates. The present study provides a first report of microarray-based technology for describing changes in the splenic gene expression profile for mice immunised with a highly effective, protection-inducing, multi-epitope, subunit-based, chemically-synthesised vaccine candidate against F...
January 23, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28108339/transcriptome-analysis-of-the-effect-of-polyunsaturated-fatty-acids-against-vibrio-vulnificus-infection-in-oreochromis-niloticus
#12
Chieh-Yu Pan, Yu-Hao Liu, Hong-Yi Gong, Jyh-Yih Chen
Vibrio vulnificus infection causes severe economic losses in Oreochromis niloticus aquaculture by inducing pro-inflammatory cytokines, that lead to inflammation and mortality. Omega-3 fatty acids, such as Docosahexaenoic acid (DHA) and Eicosapentaenoic acid (EPA), have been reported for their anti-inflammatory and antibacterial abilities in murine and zebrafish models. However, the anti-inflammatory and antibacterial functions of DHA and EPA in commercial aquaculture organisms such as Oreochromis niloticus remain unknown...
January 17, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28105225/mir-1297-promotes-cell-proliferation-by-inhibiting-rb1-in-liver-cancer
#13
Chengyong Liu, Chunying Wang, Ji Wang, Haibin Huang
Liver cancer is the one of the most common causes of cancer-associated mortality worldwide. MicroRNAs (miRNAs or miRs) are important in various types of cancer, including liver cancer. In the present study, with miRNA expression profile data obtained from the Gene Expression Omnibus database, three independent methods were used to investigate the miRNAs that are involved in liver carcinogenesis, including Fisher's exact test, t-test and Wilcoxon test. Five differentially expressed miRNAs were identified. Among them, miR-1297 drew specific attention...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28104435/inhibition-of-nrf2-enhances-the-anticancer-effect-of-6-o-angeloylenolin-in-lung-adenocarcinoma
#14
Yang Wang, Ru-Yuan Yu, Jing Zhang, Wei-Xia Zhang, Zhi-Hao Huang, Hui-Fang Hu, Yao-Lan Li, Bin Li, Qing-Yu He
6-O-Angeloylenolin (6-OA), a sesquiterpene lactone isolated from Centipeda minima (L.) A. Br. (Compositae), has been used to treat respiratory diseases for centuries. However, whether and how 6-OA exerts anticancer effects against lung cancer remains to be elucidated. In this study, we showed that 6-OA markedly suppressed the cell viability and colony formation of lung cancer cells H1299 and A549, with no significant toxic effect on non-cancer cells HBE. Annexin V/7-AAD assay revealed that 6-OA induced cell apoptosis in dose- and time-dependent manners, which was further confirmed by the increased expression of cleaved caspase-3...
January 16, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28101231/the-biological-significance-of-methylome-differences-in-human-papilloma-virus-associated-head-and-neck-cancer
#15
Maria J Worsham, Kang Mei Chen, Indrani Datta, Josena K Stephen, Dhananjay Chitale, Alexandra Gothard, George Divine
In recent years, studies have suggested that promoter methylation in human papilloma virus (HPV) positive head and neck squamous cell carcinoma (HNSCC) has a mechanistic role and has the potential to improve patient survival. The present study aimed to replicate key molecular findings from previous analyses of the methylomes of HPV positive and HPV negative HNSCC in an independent cohort, to assess the reliability of differentially methylated markers in HPV-associated tumors. HPV was measured using real-time quantitative PCR and the biological significance of methylation differences was assessed by Ingenuity Pathway Analysis (IPA)...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28101186/comparative-analysis-of-signaling-pathways-in-peripheral-blood-from-patients-with-kashin-beck-disease-and-osteoarthritis
#16
Yujie Ning, Xi Wang, Sen Wang, Xiong Guo
The aim of the present study was to investigate the early diagnostic biomarkers of Kashin-Beck disease (KBD), and to compare the common signaling pathways of peripheral mononuclear cells between patients with KBD and those with osteoarthritis (OA). A total of 20 and 12 peripheral blood samples were separately collected from KBD patients and normal control subjects, respectively, in an endemic area according to the diagnosis criteria. Total RNAs were extracted and gene expression levels were determined using an Agilent whole genome expression microarrays...
December 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28100627/inflammatory-biomarkers-predict-heart-failure-severity-and-prognosis-in-patients-with-heart-failure-with-preserved-ejection-fraction-a-holistic-proteomic-approach
#17
Camilla Hage, Erik Michaëlsson, Cecilia Linde, Erwan Donal, Jean-Claude Daubert, Li-Ming Gan, Lars H Lund
BACKGROUND: Underlying mechanisms in heart failure (HF) with preserved ejection fraction remain unknown. We investigated cardiovascular plasma biomarkers in HF with preserved ejection fraction and their correlation to diastolic dysfunction, functional class, pathophysiological processes, and prognosis. METHODS AND RESULTS: In 86 stable patients with HF and EF ≥45% in the Karolinska Rennes (KaRen) biomarker substudy, biomarkers were quantified by a multiplex immunoassay...
February 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28099934/tolfenamic-acid-induced-alterations-in-genes-and-pathways-in-pancreatic-cancer-cells
#18
Umesh T Sankpal, Steve Goodison, Michelle Jones-Pauley, Myrna Hurtado, Fan Zhang, Riyaz Basha
Non-steroidal anti-inflammatory drugs (NSAIDs) are being tested extensively for their role in the treatment and prevention of several cancers. Typically NSAIDs exhibit anti-tumor activities via modulation of cyclooxygenase (COX)-dependent mechanisms, however, an anti-cancer NSAID tolfenamic acid (TA) is believed to work through COX-independent pathways. Results from our laboratory and others have demonstrated the anti-cancer activity of TA in various cancer models including pancreatic cancer. TA has been shown to modulate certain cellular processes including, apoptosis, reactive oxygen species and signaling...
January 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28097204/genomics-implicates-adaptive-and-innate-immunity-in-alzheimer-s-and-parkinson-s-diseases
#19
Sarah A Gagliano, Jennie G Pouget, John Hardy, Jo Knight, Michael R Barnes, Mina Ryten, Michael E Weale
OBJECTIVES: We assessed the current genetic evidence for the involvement of various cell types and tissue types in the etiology of neurodegenerative diseases, especially in relation to the neuroinflammatory hypothesis of neurodegenerative diseases. METHODS: We obtained large-scale genome-wide association study (GWAS) summary statistics from Parkinson's disease (PD), Alzheimer's disease (AD), and amyotrophic lateral sclerosis (ALS). We used multiple sclerosis (MS), an autoimmune disease of the central nervous system, as a positive control...
December 2016: Annals of Clinical and Translational Neurology
https://www.readbyqxmd.com/read/28086790/rna-sequencing-for-global-gene-expression-associated-with-muscle-growth-in-a-single-male-modern-broiler-line-compared-to-a-foundational-barred-plymouth-rock-chicken-line
#20
Byung-Whi Kong, Nicholas Hudson, Dongwon Seo, Seok Lee, Bhuwan Khatri, Kentu Lassiter, Devin Cook, Alissa Piekarski, Sami Dridi, Nicholas Anthony, Walter Bottje
BACKGROUND: Modern broiler chickens exhibit very rapid growth and high feed efficiency compared to unselected chicken breeds. The improved production efficiency in modern broiler chickens was achieved by the intensive genetic selection for meat production. This study was designed to investigate the genetic alterations accumulated in modern broiler breeder lines during selective breeding conducted over several decades. METHODS: To identify genes important in determining muscle growth and feed efficiency in broilers, RNA sequencing (RNAseq) was conducted with breast muscle in modern pedigree male (PeM) broilers (n = 6 per group), and with an unselected foundation broiler line (Barred Plymouth Rock; BPR)...
January 13, 2017: BMC Genomics
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