PPP1R3C Mediates Metformin-Inhibited Hepatic Gluconeogenesis
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Downloaded on November Tured Output Support Vector Machine (SVM) Approach 6, 2013
Funk et al. Journal of Biomedical Semantics (2015) 6:9 DOI 10.1186/s13326-015-0006-4 JOURNAL OF BIOMEDICAL SEMANTICS RESEARCH Open Access Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct Christopher S Funk1*, Indika Kahanda2, Asa Ben-Hur2 and Karin M Verspoor3,4 Abstract Most computational methods that predict protein function do not take advantage of the large amount of information contained in the biomedical literature. In this work we evaluate both ontology term co-mention and bag-of-words features mined from the biomedical literature and analyze their impact in the context of a structured output support vector machine model, GOstruct. We find that even simple literature based features are useful for predicting human protein function (F-max: Molecular Function = 0.408, Biological Process = 0.461, Cellular Component = 0.608). One advantage of using literature features is their ability to offer easy verification of automated predictions. We find through manual inspection of misclassifications that some false positive predictions could be biologically valid predictions based upon support extracted from the literature. Additionally, we present a “medium-throughput” pipeline that was used to annotate a large subset of co-mentions; we suggest that this strategy could help to speed up the rate at which proteins are curated. Keywords: Text mining, Protein function prediction, Biomedical concept recognition Introduction Background Characterizing the functions of proteins is an important Literature mining has been shown to have substantial task in bioinformatics today. In recent years, many com- promise in the context of automated function prediction, putational methods to predict protein function have been although there has been limited exploration to date [2]. -
Resveratrol Improves Glycemic Control in Insulin-Treated Diabetic Rats
Yonamine et al. Nutrition & Metabolism (2016) 13:44 DOI 10.1186/s12986-016-0103-0 RESEARCH Open Access Resveratrol improves glycemic control in insulin-treated diabetic rats: participation of the hepatic territory Caio Yogi Yonamine1†, Erika Pinheiro-Machado1†, Maria Luiza Michalani1, Helayne Soares Freitas1, Maristela Mitiko Okamoto1, Maria Lucia Corrêa-Giannella2 and Ubiratan Fabres Machado1* Abstract Background: Resveratrol is a natural polyphenol that has been proposed to improve glycemic control in diabetes, by mechanisms that involve improvement in insulin secretion and activity. In type 1 diabetes (T1D), in which insulin therapy is obligatory, resveratrol treatment has never been investigated. The present study aimed to evaluate resveratrol as an adjunctive agent to insulin therapy in a T1D-like experimental model. Methods: Rats were rendered diabetic by streptozotocin (STZ) treatment. Twenty days later, four groups of animals were studied: non-diabetic (ND); diabetic treated with placebo (DP); diabetic treated with insulin (DI) and diabetic treated with insulin plus resveratrol (DIR). After 30 days of treatment, 24-hour urine was collected; then, blood, soleus muscle, proximal small intestine, renal cortex and liver were sampled. Specific glucose transporter proteins were analyzed (Western blotting) in each territory of interest. Solute carrier family 2 member 2 (Slc2a2), phosphoenolpyruvate carboxykinase (Pck1) and glucose-6-phosphatase catalytic subunit (G6pc) mRNAs (qPCR), glycogen storage and sirtuin 1 (SIRT1) activity were analyzed in liver. Results: Diabetes induction increased blood glucose, plasma fructosamine concentrations, and glycosuria. Insulin therapy partially recovered the glycemic control; however, resveratrol as adjunctive therapy additionally improved glycemic control and restored plasma fructosamine concentration to values of non-diabetic rats. -
Protein Interactions in the Cancer Proteome† Cite This: Mol
Molecular BioSystems View Article Online PAPER View Journal | View Issue Small-molecule binding sites to explore protein– protein interactions in the cancer proteome† Cite this: Mol. BioSyst., 2016, 12,3067 David Xu,ab Shadia I. Jalal,c George W. Sledge Jr.d and Samy O. Meroueh*aef The Cancer Genome Atlas (TCGA) offers an unprecedented opportunity to identify small-molecule binding sites on proteins with overexpressed mRNA levels that correlate with poor survival. Here, we analyze RNA-seq and clinical data for 10 tumor types to identify genes that are both overexpressed and correlate with patient survival. Protein products of these genes were scanned for binding sites that possess shape and physicochemical properties that can accommodate small-molecule probes or therapeutic agents (druggable). These binding sites were classified as enzyme active sites (ENZ), protein–protein interaction sites (PPI), or other sites whose function is unknown (OTH). Interestingly, the overwhelming majority of binding sites were classified as OTH. We find that ENZ, PPI, and OTH binding sites often occurred on the same structure suggesting that many of these OTH cavities can be used for allosteric modulation of Creative Commons Attribution 3.0 Unported Licence. enzyme activity or protein–protein interactions with small molecules. We discovered several ENZ (PYCR1, QPRT,andHSPA6)andPPI(CASC5, ZBTB32,andCSAD) binding sites on proteins that have been seldom explored in cancer. We also found proteins that have been extensively studied in cancer that have not been previously explored with small molecules that harbor ENZ (PKMYT1, STEAP3,andNNMT) and PPI (HNF4A, MEF2B,andCBX2) binding sites. All binding sites were classified by the signaling pathways to Received 29th March 2016, which the protein that harbors them belongs using KEGG. -
Role of PCK1 Gene on Oil Tea-Induced Glucose Homeostasis and Type 2
Hu et al. Nutrition & Metabolism (2019) 16:12 https://doi.org/10.1186/s12986-019-0337-8 RESEARCH Open Access Role of PCK1 gene on oil tea-induced glucose homeostasis and type 2 diabetes: an animal experiment and a case-control study Qiantu Hu1†, Huafeng Chen2†, Yanli Zuo3†, Qin He2, Xuan He2, Steve Simpson Jr4,5, Wei Huang2, Hui Yang2, Haiying Zhang1,6* and Rui Lin1,2,6* Abstract Background: Oil tea is a type of traditional tea beverage used for treating various ailments in minority population in Guangxi, China. Our previous study showed oil tea improved glucose and lipid levels in type 2 diabetic mice. Yet, the underling molecular mechanisms are still not understood. This study aimed at assessing the effect of oil tea on glucose homeostasis and elucidating the molecular mechanisms underlying the oil tea-induced antidiabetic effects. Methods: Twenty seven db/db mice were gavaged with saline, metformin and oil tea for 8 weeks with measurement of biochemical profiles. A real-time2 (RT2) profiler polymerase chain reaction (PCR) array comprising 84 genes involved in glucose metabolism was measured and validated by quantitative PCR (qPCR). The association between the candidate genes and type 2 diabetes were further analyzed in a case-control study in the Chinese minority population. Results: Oil tea treatment facilitated glucose homeostasis by decreasing fasting blood glucose and total cholesterol, and improving glucose tolerance. Suppressing phosphoenolpyruvate carboxykinase 1 (PCK1) expression was observed in the oil tea treatment group and the expression was significantly correlated with fasting blood glucose levels. Target prediction and functional annotation by WEB-based GEne SeT AnaLysis Toolkit (WebGestalt) revealed that PCK1 mainly involved in the glycolysis/gluconeogenesis pathway among the top Kyoto Encyclopedia of Genes and Genomes (KEGG) database pathways. -
B-Cell Translocation Gene 2 Regulates Hepatic Glucose Homeostasis Via Induction of Orphan Nuclear Receptor Nur77 in Diabetic Mouse Model
1870 Diabetes Volume 63, June 2014 Yong Deuk Kim,1 Sun-Gyun Kim,2 Seung-Lark Hwang,3 Hueng-Sik Choi,4 Jae-Hoon Bae,1 Dae-Kyu Song,1 and Seung-Soon Im1 B-Cell Translocation Gene 2 Regulates Hepatic Glucose Homeostasis via Induction of Orphan Nuclear Receptor Nur77 in Diabetic Mouse Model Diabetes 2014;63:1870–1880 | DOI: 10.2337/db13-1368 B-cell translocation gene 2 (BTG2) is a member of an might serve as a potential therapeutic target for com- emerging gene family that is involved in cellular func- bating metabolic dysfunction. tions. In this study, we demonstrate that BTG2 regu- lates glucose homeostasis via upregulation of Nur77 in diabetic mice. Hepatic BTG2 gene expression was The liver plays a crucial role in glucose homeostasis by elevated by fasting and forskolin. Overexpression of maintaining a balance between uptake and storage of Btg2 increased the expression of hepatic gluconeogenic glucose via glycogenesis and in the release of glucose by genes and blood glucose output and subsequently im- both glycogenolysis and gluconeogenesis (1,2). Gluconeo- paired glucose and insulin tolerance. Upregulation METABOLISM genesis is commonly triggered by key hormones including of the transcriptional activity of Nur77, gluconeogenic insulin, glucagon, and glucocorticoid, which contribute to genes, and glucose production by forskolin was ob- the expression of key metabolic enzymes, such as phospho- served by Btg2 transduction, but not in Btg2 knockdown. enolpyruvate carboxykinase (Pck1), fructose biphosphatase BTG2-stimulated glucose production and glucose-6- (Fbp) 1, and glucose-6-phosphatase (G6pc) (3). A variety phosphatase promoter activity were attenuated by of transcriptional factors and cofactors regulated by dominant-negative Nur77. -
Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol . -
PEPCK): a Target of the P53-SIRT6-Foxo1 Axis
LETTER LETTER Reply to Leithner et al.: Focus on phopshoenolpyruvate carboxykinase (PEPCK): A target of the p53-SIRT6-FoxO1 axis Cancer metabolism has drawn widespread attention has been paid to PCK2 because it in-depth discussion and further study. The attention since the unique metabolic proper- has proved to be less enzymatically active discrepancy between normal and tumor ties of cancer cells were characterized. We than PCK1, nevertheless, based on previous cells in PEPCK may provide a window found that p53, a potent tumor suppressor, studies of PCK2, we may make a bold spec- to understand cancer metabolism and the down-regulates the expression of phopshoe- ulation that PCK2 might be responsible for Warburg effect. nolpyruvate carboxykinase (PEPCK, PCK1) basal level gluconeogenesis and PCK1 for in coordination with histone deacetylase hormone and nutrient stimulation, with Zhiming Li a and Wei-Guo Zhua,b,1 sirtuin 6 (SIRT6) to inhibit tumor cell more flexible regulation. Given the facts that aKey Laboratory of Carcinogenesis and gluconeogenesis (1). Because p53 is malfunc- cancer cells have faster metabolism rates and Translational Research (Ministry of Education), tioning in numerous types of cancer, the PCK1 is absent or expressed in low levels in Department of Biochemistry and Molecular p53-SIRT6-forkhead box protein O1 (FoxO1) manyotherorgans,theseeminglymorefun- Biology, Peking University Health Science axis may shed light on the “Warburg effect,” damental PCK2 may be motivated in tumor Center, Beijing 100191, China Beijing 100191, a phenomenon in cancer metabolism that cells under glucose starvation. In addition, b has harassed scientists for decades. PCK1 is the general expression of PCK2 in most China; and Center for Life Sciences, Peking- mainly expressed in liver and kidney, with an organs other than liver, such as islets, and its Tsinghua University, Beijing 100871, China increasing expression and maturation after mitochondrial location, may endow it with birth. -
Omics Knowledgebase for Mammalian Cellular Signaling Pathways
bioRxiv preprint doi: https://doi.org/10.1101/401729; this version posted August 27, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The Signaling Pathways Project: an integrated ‘omics knowledgebase for mammalian cellular signaling pathways Scott Ochsner, David Abraham*, Kirt Martin*, Wei Ding, Apollo McOwiti, Zichen Wang, Kaitlyn Andreano, Ross A. Hamilton, Yue Chen, Angelica Hamilton, Marin L. Gantner, Michael Dehart, Shijing Qu, Susan G. Hilsenbeck, Lauren B. Becnel, Dave Bridges, Avi Ma’ayan, Janice M. Huss, Fabio Stossi, Charles E. Foulds, Anastasia Kralli, Donald P. McDonnell and Neil J. McKenna Address Correspondence To: Neil J. McKenna Department of Molecular and Cellular Biology Baylor College of Medicine Houston, TX 77030 USA e: [email protected] t: 713-798-8568 *These authors contributed equally to this study 1 bioRxiv preprint doi: https://doi.org/10.1101/401729; this version posted August 27, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Summary Public transcriptomic and ChIP-Seq datasets have the potential to illuminate facets of transcriptional regulation by mammalian cellular signaling pathways not yet explored in the research literature. Unfortunately, a variety of obstacles prevent routine re-use of these datasets by bench biologists for hypothesis generation and data validation. Here, we designed a web knowledgebase, the Signaling Pathways Project (SPP), which incorporates stable community classifications of three major categories of cellular signaling pathway node (receptors, enzymes and transcription factors) and the bioactive small molecules (BSMs) known to modulate their functions. -
Omics Knowledgebase for Mammalian Cellular Signaling Pathways Scott A
www.nature.com/scientificdata OPEN The Signaling Pathways Project, an ARTICLE integrated ‘omics knowledgebase for mammalian cellular signaling pathways Scott A. Ochsner1, David Abraham1,8, Kirt Martin1,8, Wei Ding2, Apollo McOwiti2, Wasula Kankanamge2, Zichen Wang 3, Kaitlyn Andreano4, Ross A. Hamilton1, Yue Chen1, Angelica Hamilton5, Marin L. Gantner6, Michael Dehart2, Shijing Qu2, Susan G. Hilsenbeck2, Lauren B. Becnel2, Dave Bridges7, Avi Ma’ayan 3, Janice M. Huss5, Fabio Stossi1, Charles E. Foulds1, Anastasia Kralli6, Donald P. McDonnell4 & Neil J. McKenna 1* Mining of integrated public transcriptomic and ChIP-Seq (cistromic) datasets can illuminate functions of mammalian cellular signaling pathways not yet explored in the research literature. Here, we designed a web knowledgebase, the Signaling Pathways Project (SPP), which incorporates community classifcations of signaling pathway nodes (receptors, enzymes, transcription factors and co-nodes) and their cognate bioactive small molecules. We then mapped over 10,000 public transcriptomic or cistromic experiments to their pathway node or biosample of study. To enable prediction of pathway node-gene target transcriptional regulatory relationships through SPP, we generated consensus ‘omics signatures, or consensomes, which ranked genes based on measures of their signifcant diferential expression or promoter occupancy across transcriptomic or cistromic experiments mapped to a specifc node family. Consensomes were validated using alignment with canonical literature knowledge, gene target-level integration of transcriptomic and cistromic data points, and in bench experiments confrming previously uncharacterized node-gene target regulatory relationships. To expose the SPP knowledgebase to researchers, a web browser interface was designed that accommodates numerous routine data mining strategies. SPP is freely accessible at https://www.signalingpathways.org. -
Identification of Common Gene Networks Responsive To
Cancer Gene Therapy (2014) 21, 542–548 © 2014 Nature America, Inc. All rights reserved 0929-1903/14 www.nature.com/cgt ORIGINAL ARTICLE Identification of common gene networks responsive to radiotherapy in human cancer cells D-L Hou1, L Chen2, B Liu1, L-N Song1 and T Fang1 Identification of the genes that are differentially expressed between radiosensitive and radioresistant cancers by global gene analysis may help to elucidate the mechanisms underlying tumor radioresistance and improve the efficacy of radiotherapy. An integrated analysis was conducted using publicly available GEO datasets to detect differentially expressed genes (DEGs) between cancer cells exhibiting radioresistance and cancer cells exhibiting radiosensitivity. Gene Ontology (GO) enrichment analyses, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and protein–protein interaction (PPI) networks analysis were also performed. Five GEO datasets including 16 samples of radiosensitive cancers and radioresistant cancers were obtained. A total of 688 DEGs across these studies were identified, of which 374 were upregulated and 314 were downregulated in radioresistant cancer cell. The most significantly enriched GO terms were regulation of transcription, DNA-dependent (GO: 0006355, P = 7.00E-09) for biological processes, while those for molecular functions was protein binding (GO: 0005515, P = 1.01E-28), and those for cellular component was cytoplasm (GO: 0005737, P = 2.81E-26). The most significantly enriched pathway in our KEGG analysis was Pathways in cancer (P = 4.20E-07). PPI network analysis showed that IFIH1 (Degree = 33) was selected as the most significant hub protein. This integrated analysis may help to predict responses to radiotherapy and may also provide insights into the development of individualized therapies and novel therapeutic targets. -
Genomic and Transcriptome Analysis Revealing an Oncogenic Functional Module in Meningiomas
Neurosurg Focus 35 (6):E3, 2013 ©AANS, 2013 Genomic and transcriptome analysis revealing an oncogenic functional module in meningiomas XIAO CHANG, PH.D.,1 LINGLING SHI, PH.D.,2 FAN GAO, PH.D.,1 JONATHAN RUssIN, M.D.,3 LIYUN ZENG, PH.D.,1 SHUHAN HE, B.S.,3 THOMAS C. CHEN, M.D.,3 STEVEN L. GIANNOTTA, M.D.,3 DANIEL J. WEISENBERGER, PH.D.,4 GAbrIEL ZADA, M.D.,3 KAI WANG, PH.D.,1,5,6 AND WIllIAM J. MAck, M.D.1,3 1Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California; 2GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China; 3Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, California; 4USC Epigenome Center, Keck School of Medicine, University of Southern California, Los Angeles, California; 5Department of Psychiatry, Keck School of Medicine, University of Southern California, Los Angeles, California; and 6Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California Object. Meningiomas are among the most common primary adult brain tumors. Although typically benign, roughly 2%–5% display malignant pathological features. The key molecular pathways involved in malignant trans- formation remain to be determined. Methods. Illumina expression microarrays were used to assess gene expression levels, and Illumina single- nucleotide polymorphism arrays were used to identify copy number variants in benign, atypical, and malignant me- ningiomas (19 tumors, including 4 malignant ones). The authors also reanalyzed 2 expression data sets generated on Affymetrix microarrays (n = 68, including 6 malignant ones; n = 56, including 3 malignant ones). -
Mitochondrial PCK2 Missense Variant in Shetland Sheepdogs with Paroxysmal Exercise-Induced Dyskinesia (PED)
G C A T T A C G G C A T genes Article Mitochondrial PCK2 Missense Variant in Shetland Sheepdogs with Paroxysmal Exercise-Induced Dyskinesia (PED) 1, 2, 3 3 Jasmin Nessler y, Petra Hug y, Paul J. J. Mandigers , Peter A. J. Leegwater , Vidhya Jagannathan 2 , Anibh M. Das 4, Marco Rosati 5, Kaspar Matiasek 5, Adrian C. Sewell 6, Marion Kornberg 7, Marina Hoffmann 8 , Petra Wolf 9 , Andrea Fischer 10 , Andrea Tipold 1 and Tosso Leeb 2,* 1 Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hannover Foundation, 30559 Hannover, Germany; [email protected] (J.N.); [email protected] (A.T.) 2 Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; [email protected] (P.H.); [email protected] (V.J.) 3 Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; [email protected] (P.J.J.M.); [email protected] (P.A.J.L.) 4 Department of Pediatrics, Hannover Medical School, 30625 Hannover, Germany; [email protected] 5 Section of Clinical and Comparative Neuropathology, Institute of Veterinary Pathology at the Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany; [email protected] (M.R.); [email protected] (K.M.) 6 Biocontrol, Labor für Veterinärmedizinische Diagnostik, 55218 Ingelheim, Germany; [email protected] 7 AniCura Tierklinik Trier GbR, 54294 Trier, Germany; [email protected] 8 Tierklinik Stommeln, 50259 Puhlheim, Germany; dr.marinahoff[email protected] 9 Nutritional Physiology and Animal Nutrition, University of Rostock, 18059 Rostock, Germany; [email protected] 10 Section of Neurology, Clinic of Small Animal Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany; [email protected] * Correspondence: [email protected]; Tel.: +41-316-312-326 These authors contributed equally to this work.