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Beaumont TL, Yao B, Shah A, Kapatos G, Loeb JA. Layer-specific CREB target gene induction in human neocortical epilepsy. J Neurosci 2012; 32:14389-401. [PMID: 23055509 PMCID: PMC3478758 DOI: 10.1523/jneurosci.3408-12.2012] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 07/17/2012] [Accepted: 08/20/2012] [Indexed: 11/21/2022] Open
Abstract
Epilepsy is a disorder of recurrent seizures that affects 1% of the population. To understand why some areas of cerebral cortex produce seizures and others do not, we identified differentially expressed genes in human epileptic neocortex compared with nearby regions that did not produce seizures. The transcriptome that emerged strongly implicates MAPK signaling and CREB-dependent transcription, with 74% of differentially expressed genes containing a cAMP response element (CRE) in their proximal promoter, more than half of which are conserved. Despite the absence of recent seizures in these patients, epileptic brain regions prone to seizures showed persistent activation of ERK and CREB. Persistent CREB activation was directly linked to CREB-dependent gene transcription by chromatin immunoprecipitation that showed phosphorylated CREB constitutively associated with the proximal promoters of many of the induced target genes involved in neuronal signaling, excitability, and synaptic plasticity. A distinct spatial pattern of ERK activation was seen in superficial axodendritic processes of epileptic neocortex that colocalized with both CREB phosphorylation and CREB target gene induction in well demarcated populations of layer 2/3 neurons. These same neuronal lamina showed a marked increase in synaptic density. The findings generated in this study generate a robust and spatially restricted pattern of epileptic biomarkers and associated synaptic changes that could lead to new mechanistic insights and potential therapeutic targets for human epilepsy.
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Affiliation(s)
- Thomas L. Beaumont
- The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201
| | | | | | - Gregory Kapatos
- The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Jeffrey A. Loeb
- Department of Neurology and
- The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201
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2
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Ansari NA, Bao R, Voichiţa C, Drăghici S. Detecting phenotype-specific interactions between biological processes from microarray data and annotations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012; 9:1399-1409. [PMID: 22547431 PMCID: PMC3748606 DOI: 10.1109/tcbb.2012.65] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
High throughput technologies enable researchers to measure expression levels on a genomic scale. However, the correct and efficient biological interpretation of such voluminous data remains a challenging problem. Many tools have been developed for the analysis of GO terms that are over- or under-represented in a list of differentially expressed genes. However, a previously unexplored aspect is the identification of changes in the way various biological processes interact in a given condition with respect to a reference. Here, we present a novel approach that aims at identifying such interactions between biological processes that are significantly different in a given phenotype with respect to normal. The proposed technique uses vector-space representation, SVD-based dimensionality reduction, differential weighting, and bootstrapping to asses the significance of the interactions under the multiple and complex dependencies expected between the biological processes. We illustrate our approach on two real data sets involving breast and lung cancer. More than 88 percent of the interactions found by our approach were deemed to be correct by an extensive manual review of literature. An interesting subset of such interactions is discussed in detail and shown to have the potential to open new avenues for research in lung and breast cancer.
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Affiliation(s)
| | - Riyue Bao
- The Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202.
| | - Călin Voichiţa
- The Department of Computer Science, Wayne State University, 5057 Woodward Ave, Detroit, MI 48202.
| | - Sorin Drăghici
- The Department of Obstetrics & Gynecology, Wayne State University, 3750 Woodward Ave., Detroit, MI 48201, the Department of Clinical and Translational Science, Wayne State University, Detroit, MI 48201, and the Department of Computer Science, Wayne State University, 5057 Woodward Ave., Detroit, MI 48202.
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3
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Song KH, Lee SH, Kim BY, Park AY, Kim JY. Extracts of Scutellaria baicalensis reduced body weight and blood triglyceride in db/db Mice. Phytother Res 2012; 27:244-50. [PMID: 22532505 DOI: 10.1002/ptr.4691] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 01/15/2012] [Accepted: 03/02/2012] [Indexed: 11/10/2022]
Abstract
Scutellaria baicalensis has been extensively employed for the clinical treatment of hyperlipidemia, atherosclerosis, hypertension, dysentery, inflammatory diseases, and the common cold. The present study was performed to investigate the anti-obesity and anti-dyslipidemia effect of Scutellaria baicalensis extracts (SBE) in type 2 diabetic db/db mice. Male db/db mice were divided into three groups (n = 5) and orally administrated vehicle (control), SBE 10, and 100 mg/kg body weight/day for 4 weeks everyday. Administration of SBE improves weight gain, hypertriglyceridemia, and hyperinsulinemia in db/db mice. In obese db/db mice, SBE treatment also reduced plasma alanine aminotransferase levels. In the livers of db/db mice, SBE promoted 5' AMP-activated protein kinase activity and restored metabolic process and insulin signaling pathways. Our data demonstrate that SBE exerts potent anti-obesity and anti-hypertriglyceride effects suggesting its useful potential function as adjuvant therapeutic agent for the treatment of weight gain and hypertriglyceridemia.
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Affiliation(s)
- Kwang Hoon Song
- Division of constitutional medicine research, Korea Institute of Oriental Medicine, Daejeon, Korea
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4
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Li R, Ackerman WE, Summerfield TL, Yu L, Gulati P, Zhang J, Huang K, Romero R, Kniss DA. Inflammatory gene regulatory networks in amnion cells following cytokine stimulation: translational systems approach to modeling human parturition. PLoS One 2011; 6:e20560. [PMID: 21655103 PMCID: PMC3107214 DOI: 10.1371/journal.pone.0020560] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 05/05/2011] [Indexed: 11/18/2022] Open
Abstract
A majority of the studies examining the molecular regulation of human labor have been conducted using single gene approaches. While the technology to produce multi-dimensional datasets is readily available, the means for facile analysis of such data are limited. The objective of this study was to develop a systems approach to infer regulatory mechanisms governing global gene expression in cytokine-challenged cells in vitro, and to apply these methods to predict gene regulatory networks (GRNs) in intrauterine tissues during term parturition. To this end, microarray analysis was applied to human amnion mesenchymal cells (AMCs) stimulated with interleukin-1β, and differentially expressed transcripts were subjected to hierarchical clustering, temporal expression profiling, and motif enrichment analysis, from which a GRN was constructed. These methods were then applied to fetal membrane specimens collected in the absence or presence of spontaneous term labor. Analysis of cytokine-responsive genes in AMCs revealed a sterile immune response signature, with promoters enriched in response elements for several inflammation-associated transcription factors. In comparison to the fetal membrane dataset, there were 34 genes commonly upregulated, many of which were part of an acute inflammation gene expression signature. Binding motifs for nuclear factor-κB were prominent in the gene interaction and regulatory networks for both datasets; however, we found little evidence to support the utilization of pathogen-associated molecular pattern (PAMP) signaling. The tissue specimens were also enriched for transcripts governed by hypoxia-inducible factor. The approach presented here provides an uncomplicated means to infer global relationships among gene clusters involved in cellular responses to labor-associated signals.
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Affiliation(s)
- Ruth Li
- Division of Maternal-Fetal Medicine and Laboratory of Perinatal Research,
Department of Obstetrics and Gynecology, The Ohio State University, Columbus,
Ohio, United States of America
| | - William E. Ackerman
- Division of Maternal-Fetal Medicine and Laboratory of Perinatal Research,
Department of Obstetrics and Gynecology, The Ohio State University, Columbus,
Ohio, United States of America
| | - Taryn L. Summerfield
- Division of Maternal-Fetal Medicine and Laboratory of Perinatal Research,
Department of Obstetrics and Gynecology, The Ohio State University, Columbus,
Ohio, United States of America
| | - Lianbo Yu
- Center for Biostatistics, The Ohio State University, Columbus, Ohio,
United States of America
| | - Parul Gulati
- Center for Biostatistics, The Ohio State University, Columbus, Ohio,
United States of America
| | - Jie Zhang
- Department of Biomedical Informatics, The Ohio State University,
Columbus, Ohio, United States of America
| | - Kun Huang
- Department of Biomedical Informatics, The Ohio State University,
Columbus, Ohio, United States of America
| | - Roberto Romero
- Perinatology Research Branch, Intramural Division, Eunice Kennedy Shriver
National Institute of Child Health and Human Development, National Institutes of
Health, Department of Health and Human Services, Bethesda, Maryland, United
States of America
- Hutzel Women's Hospital, Detroit, Michigan, United States of
America
| | - Douglas A. Kniss
- Division of Maternal-Fetal Medicine and Laboratory of Perinatal Research,
Department of Obstetrics and Gynecology, The Ohio State University, Columbus,
Ohio, United States of America
- Department of Biomedical Engineering, The Ohio State University,
Columbus, Ohio, United States of America
- * E-mail:
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5
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Lee SH, Kim BJ, Kim HJ, Lee HE, Yu US. IdBean: a Java GUI application for conversion of biological identifiers. BMB Rep 2011; 44:107-12. [DOI: 10.5483/bmbrep.2011.44.2.107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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6
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Wang H, Li ZY, Liu Y, Persson J, Beyer I, Möller T, Koyuncu D, Drescher MR, Strauss R, Zhang XB, Wahl JK, Urban N, Drescher C, Hemminki A, Fender P, Lieber A. Desmoglein 2 is a receptor for adenovirus serotypes 3, 7, 11 and 14. Nat Med 2010; 17:96-104. [PMID: 21151137 PMCID: PMC3074512 DOI: 10.1038/nm.2270] [Citation(s) in RCA: 309] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 11/08/2010] [Indexed: 11/15/2022]
Abstract
We have identified desmoglein 2 (DSG2) as the primary high-affinity receptor used by adenovirus (Ad) serotypes Ad3, Ad7, Ad11, and Ad14. These serotypes represent important human pathogens causing respiratory tract infections. In epithelial cells, adenovirus binding to DSG2 triggers events reminiscent of epithelial-to-mesenchymal transition, leading to transient opening of intercellular junctions. This improves access to receptors, e.g. CD46 and Her2/neu, that are trapped in intercellular junctions. In addition to complete virions, dodecahedral particles (PtDd), formed by viral penton and fiber in excess during viral replication, can trigger DSG2-mediated opening of intercellular junctions as shown by studies with recombinant Ad3 PtDd. Our findings shed light on adenovirus biology and pathogenesis and have implications for cancer therapy.
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Affiliation(s)
- Hongjie Wang
- University of Washington, Division of Medical Genetics, Seattle, Washington, USA
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7
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Sansanwal P, Li L, Hsieh SC, Sarwal MM. Insights into novel cellular injury mechanisms by gene expression profiling in nephropathic cystinosis. J Inherit Metab Dis 2010; 33:775-86. [PMID: 20865335 DOI: 10.1007/s10545-010-9203-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/18/2010] [Accepted: 08/24/2010] [Indexed: 01/27/2023]
Abstract
Nephropathic cystinosis is a rare, inherited metabolic disease caused by functional defects of cystinosin associated with mutations in the CTNS gene. The mechanisms underlying the phenotypic alterations associated with this disease are not well known. In this study, gene expression profiles in peripheral blood of nephropathic cystinosis patients (N = 7) were compared with controls (N = 7) using microarray technology. In unsupervised hierarchical clustering analysis, cystinosis samples co-clustered, and 1,604 genes were significantly differentially expressed between both groups. Gene ontology analysis revealed that differentially expressed genes in cystinosis were enriched in cell organelles such as mitochondria, lysosomes, and endoplasmic reticulum (p ≤ 0.030). The majority of the differentially regulated genes were involved in oxidative phosphorylation, apoptosis, mitochondrial dysfunction, endoplasmic reticulum stress, antigen processing and presentation, B-cell-receptor signaling, and oxidative stress (p ≤ 0.003). Validation of selected genes involved in apoptosis and oxidative phosphorylation was performed by quantitative real-time polymerase chain reaction (PCR). Electron microscopy and confocal imaging of cystinotic renal proximal tubular epithelial cells further confirmed anomalies in the cellular organelles and pathways identified by microarray analysis. Further analysis of these genes and pathways may offer critical insights into the clinical spectrum of cystinosis patients and ultimately lead to novel links for targeted therapy.
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Affiliation(s)
- Poonam Sansanwal
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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8
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Soh D, Dong D, Guo Y, Wong L. Consistency, comprehensiveness, and compatibility of pathway databases. BMC Bioinformatics 2010; 11:449. [PMID: 20819233 PMCID: PMC2944280 DOI: 10.1186/1471-2105-11-449] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Accepted: 09/07/2010] [Indexed: 11/16/2022] Open
Abstract
Background It is necessary to analyze microarray experiments together with biological information to make better biological inferences. We investigate the adequacy of current biological databases to address this need. Description Our results show a low level of consistency, comprehensiveness and compatibility among three popular pathway databases (KEGG, Ingenuity and Wikipathways). The level of consistency for genes in similar pathways across databases ranges from 0% to 88%. The corresponding level of consistency for interacting genes pairs is 0%-61%. These three original sources can be assumed to be reliable in the sense that the interacting gene pairs reported in them are correct because they are curated. However, the lack of concordance between these databases suggests each source has missed out many genes and interacting gene pairs. Conclusions Researchers will hence find it challenging to obtain consistent pathway information out of these diverse data sources. It is therefore critical to enable them to access these sources via a consistent, comprehensive and unified pathway API. We accumulated sufficient data to create such an aggregated resource with the convenience of an API to access its information. This unified resource can be accessed at http://www.pathwayapi.com.
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Affiliation(s)
- Donny Soh
- School of Computing, National University of Singapore, Building COM1, 117417 Singapore.
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9
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Mak S, Sun H, Acevedo F, Shimmin LC, Zhao L, Teng BB, Hixson JE. Differential expression of genes in the calcium-signaling pathway underlies lesion development in the LDb mouse model of atherosclerosis. Atherosclerosis 2010; 213:40-51. [PMID: 20667539 DOI: 10.1016/j.atherosclerosis.2010.06.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2009] [Revised: 06/16/2010] [Accepted: 06/23/2010] [Indexed: 01/30/2023]
Abstract
OBJECTIVE Atherosclerosis is influenced by the interaction of environmental and genetic susceptibility risk factors. We used global microarray expression profiling to investigate differentially regulated genes in aorta during development of atherosclerosis in a susceptible genetically modified mouse model in response to the interaction between risk factors including hyperlipidemic genotype, shear stress, diet, and age. METHODS AND RESULTS In this study we investigated transcriptional changes in lesion-prone and lesion-resistant regions of aortas in genetically modified mice lacking both genes of the LDL receptor and the apolipoprotein B mRNA editing enzyme (LDb; Ldlr(-/-)Apobec1(-/-)). Risk factors including hyperlipidemic genotype (LDb vs. C57BL/6 wildtype), shear stress (lesion-prone vs. lesion resistant aortic regions), diet (chow vs. Western high-fat), and age (2- vs. 8-months) were studied. We hybridized aortic RNA samples with microarray chips containing probes for 45,000 mouse genes and expressed sequence tags (ESTs). Overall, the differentially expressed genes were components of 20 metabolic and physiological pathways. Notably, calcium signaling is the major pathway identified with differential regulation of 30 genes within this pathway. We also found differential expression of calcium-signaling genes in cultured primary endothelial cells from lesion-prone and lesion-resistant arterial regions (LDb mice vs. C57BL/6 controls), providing further support for involvement of calcium signaling in the pathogenesis of atherosclerosis. Moreover, we demonstrated protein expression of genes in the calcium-signaling pathway using Western blot analysis and immunofluorescence. CONCLUSIONS Our results suggest that calcium signaling may play an important role in regulation of genes expressed in aorta during development of atherosclerosis. Calcium signaling may act via mechanistic responses to genetic, mechanical, and environmental insults that trigger an imbalance of intracellular calcium homeostasis, resulting in altered biological processes leading to lesion development.
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Affiliation(s)
- Solida Mak
- The University of Texas Graduate School of Biomedical Science at Houston, Houston, TX 77030, USA
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10
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Abstract
The introduction of new high-throughput methodologies such as DNA microarrays constitutes a major breakthrough in cancer research. The unprecedented amount of data produced by such technologies has opened new avenues for interrogating living systems although, at the same time, it has demanded of the development of new data analytical methods as well as new strategies for testing hypotheses. A history of early successful applications in cancer boosted the use of microarrays and fostered further applications in other fields. Keeping the pace with these technologies, bioinformatics offers new solutions for data analysis and, what is more important, permits the formulation of a new class of hypotheses inspired in systems biology, more oriented to pathways or, in general, to modules of functionally related genes. Although these analytical methodologies are new, some options are already available and are discussed in this chapter.
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Affiliation(s)
- Joaquín Dopazo
- Bioinformatics Department, Centro de Investigación Príncipe Felipe, Valencio, Spain
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11
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Lee HK, Kim HJ, Yu US. IdMapper: A Java Application for ID Mapping across Multiple Cross-referencing Providers. Genomics Inform 2009. [DOI: 10.5808/gi.2009.7.4.208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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12
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Essack M, Radovanovic A, Schaefer U, Schmeier S, Seshadri SV, Christoffels A, Kaur M, Bajic VB. DDEC: Dragon database of genes implicated in esophageal cancer. BMC Cancer 2009; 9:219. [PMID: 19580656 PMCID: PMC2711974 DOI: 10.1186/1471-2407-9-219] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 07/06/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Esophageal cancer ranks eighth in order of cancer occurrence. Its lethality primarily stems from inability to detect the disease during the early organ-confined stage and the lack of effective therapies for advanced-stage disease. Moreover, the understanding of molecular processes involved in esophageal cancer is not complete, hampering the development of efficient diagnostics and therapy. Efforts made by the scientific community to improve the survival rate of esophageal cancer have resulted in a wealth of scattered information that is difficult to find and not easily amendable to data-mining. To reduce this gap and to complement available cancer related bioinformatic resources, we have developed a comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer) with esophageal cancer related information, as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data. DESCRIPTION Manually curated 529 genes differentially expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined reports about each of these genes to allow for easy exploration of information about associations of EC-implicated genes with other human genes and proteins, metabolites and enzymes, toxins, chemicals with pharmacological effects, disease concepts and human anatomy. The resulting database, DDEC, has a useful feature to display potential associations that are rarely reported and thus difficult to identify. Moreover, DDEC enables inspection of potentially new 'association hypotheses' generated based on the precompiled reports. CONCLUSION We hope that this resource will serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in EC genetics. DDEC is freely accessible to academic and non-profit users at http://apps.sanbi.ac.za/ddec/. DDEC will be updated twice a year.
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Affiliation(s)
- Magbubah Essack
- South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
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Strauss R, Sova P, Liu Y, Li ZY, Tuve S, Pritchard D, Brinkkoetter P, Möller T, Wildner O, Pesonen S, Hemminki A, Urban N, Drescher C, Lieber A. Epithelial phenotype confers resistance of ovarian cancer cells to oncolytic adenoviruses. Cancer Res 2009; 69:5115-25. [PMID: 19491256 DOI: 10.1158/0008-5472.can-09-0645] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We studied the susceptibility of primary ovarian cancer cells to oncolytic adenoviruses. Using gene expression profiling of cancer cells either resistant or susceptible to viral oncolysis, we discovered that the epithelial phenotype of ovarian cancer represents a barrier to infection by commonly used oncolytic adenoviruses targeted to coxsackie-adenovirus receptor or CD46. Specifically, we found that these adenovirus receptors were trapped in tight junctions and not accessible for virus binding. Accessibility to viral receptors was critically linked to depolarization and the loss of tight and adherens junctions, both hallmarks of epithelial-to-mesenchymal transition (EMT). We showed that specific, thus far little-explored adenovirus serotypes (Ad3, Ad7, Ad11, and Ad14) that use receptor(s) other than coxsackie-adenovirus receptor and CD46 were able to trigger EMT in epithelial ovarian cancer cells and cause efficient oncolysis. Our studies on ovarian cancer cultures and xenografts also revealed several interesting cancer cell biology features. Tumors in situ as well as tumor xenografts in mice mostly contained epithelial cells and cells that were in a hybrid stage where they expressed both epithelial and mesenchymal markers (epithelial/mesenchymal cells). These epithelial/mesenchymal cells are the only xenograft-derived cells that can be cultured and with passaging undergo EMT and differentiate into mesenchymal cells. Our study provides a venue for improved virotherapy of cancer as well as new insights into cancer cell biology.
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Affiliation(s)
- Robert Strauss
- Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
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14
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Gene expression profiling reveals signatures characterizing histologic subtypes of hepatoblastoma and global deregulation in cell growth and survival pathways. Hum Pathol 2009; 40:843-53. [PMID: 19200578 DOI: 10.1016/j.humpath.2008.10.022] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 10/10/2008] [Accepted: 10/29/2008] [Indexed: 11/22/2022]
Abstract
Hepatoblastoma is the most common malignant tumor of the liver of children worldwide. Histologically, hepatoblastomas show marked variation in the type and proportion of epithelial (fetal, embryonal, or small cell) and mesenchymal components with differing prognosis and response to therapy. The pure fetal-type hepatoblastoma, presenting as stage 1 and resectable, has the best prognosis, whereas the small cell histology has been associated with unfavorable outcome. Using gene expression profiling, we demonstrate that in addition to Wnt pathway deregulation, cell growth and survival pathways are also globally deregulated in hepatoblastomas. Furthermore, the different histologic subtypes are characterized by specific gene expression and pathway signatures that give insight into the degree of molecular heterogeneity that is present among these tumors. Although Wnt signaling pathway upregulation is common to all histologic types of hepatoblastoma, this pathway is even more significantly deregulated in aggressive hepatoblastomas. In addition, deregulation of MAPK signaling pathway and antiapoptotic signaling is preferentially upregulated in aggressive epithelial hepatoblastomas with a small cell component. The gene expression signatures reported here provide possible prognostic and diagnostic markers as well as therapeutic targets for this disease.
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15
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Dopazo J. Formulating and testing hypotheses in functional genomics. Artif Intell Med 2008; 45:97-107. [PMID: 18789659 DOI: 10.1016/j.artmed.2008.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 08/04/2008] [Accepted: 08/04/2008] [Indexed: 01/08/2023]
Abstract
OBJECTIVE The ultimate goal of any genome-scale experiment is to provide a functional interpretation of the results, relating the available genomic information to the hypotheses that originated the experiment. METHODS AND RESULTS Initially, this interpretation has been made on a pre-selection of relevant genes, based on the experimental values, followed by the study of the enrichment in some functional properties. Nevertheless, functional enrichment methods, demonstrated to have a flaw: the first step of gene selection was too stringent given that the cooperation among genes was ignored. The assumption that modules of genes related by relevant biological properties (functionality, co-regulation, chromosomal location, etc.) are the real actors of the cell biology lead to the development of new procedures, inspired in systems biology criteria, generically known as gene-set methods. These methods have been successfully used to analyze transcriptomic and large-scale genotyping experiments as well as to test other different genome-scale hypothesis in other fields such as phylogenomics.
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Affiliation(s)
- Joaquin Dopazo
- Department of Bioinformatics, and Functional Genomics Node (INB), Valencia E-46013, Spain.
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Al-Shahrour F, Carbonell J, Minguez P, Goetz S, Conesa A, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J. Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. Nucleic Acids Res 2008; 36:W341-6. [PMID: 18515841 PMCID: PMC2447758 DOI: 10.1093/nar/gkn318] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We present a new version of Babelomics, a complete suite of web tools for the functional profiling of genome scale experiments, with new and improved methods as well as more types of functional definitions. Babelomics includes different flavours of conventional functional enrichment methods as well as more advanced gene set analysis methods that makes it a unique tool among the similar resources available. In addition to the well-known functional definitions (GO, KEGG), Babelomics includes new ones such as Biocarta pathways or text mining-derived functional terms. Regulatory modules implemented include transcriptional control (Transfac, CisRed) and other levels of regulation such as miRNA-mediated interference. Moreover, Babelomics allows for sub-selection of terms in order to test more focused hypothesis. Also gene annotation correspondence tables can be imported, which allows testing with user-defined functional modules. Finally, a tool for the ‘de novo’ functional annotation of sequences has been included in the system. This allows using yet unannotated organisms in the program. Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. Babelomics is available at http://www.babelomics.org
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Affiliation(s)
- Fátima Al-Shahrour
- Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF), Autopista del Saler 16, E46013 Valencia, Spain
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17
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Khatri P, Voichita C, Kattan K, Ansari N, Khatri A, Georgescu C, Tarca AL, Draghici S. Onto-Tools: new additions and improvements in 2006. Nucleic Acids Res 2007; 35:W206-11. [PMID: 17584796 PMCID: PMC1933142 DOI: 10.1093/nar/gkm327] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Onto-Tools is a freely available web-accessible software suite, composed of an annotation database and nine complementary data-mining tools. This article describes a new tool, Onto-Express-to-go (OE2GO), as well as some new features implemented in Pathway-Express and Onto-Miner over the past year. Pathway-Express (PE) has been enhanced to identify significantly perturbed pathways in a given condition using the differentially expressed genes in the input. OE2GO is a tool for functional profiling using custom annotations. The development of this tool was aimed at the researchers working with organisms for which annotations are not yet available in the public domain. OE2GO allows researchers to use either annotation data from the Onto-Tools database, or their own custom annotations. By removing the necessity to use any specific database, OE2GO makes the functional profiling available for all organisms, with annotations using any ontology. The Onto-Tools are freely available at http://vortex.cs.wayne.edu/projects.htm.
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Affiliation(s)
- Purvesh Khatri
- Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI, 48202 and Perinatology Research Branch-NIH/NICHD, 4 Brush, 3990 John R, Detroit, MI 48201, USA
| | - Calin Voichita
- Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI, 48202 and Perinatology Research Branch-NIH/NICHD, 4 Brush, 3990 John R, Detroit, MI 48201, USA
| | - Khalid Kattan
- Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI, 48202 and Perinatology Research Branch-NIH/NICHD, 4 Brush, 3990 John R, Detroit, MI 48201, USA
| | - Nadeem Ansari
- Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI, 48202 and Perinatology Research Branch-NIH/NICHD, 4 Brush, 3990 John R, Detroit, MI 48201, USA
| | - Avani Khatri
- Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI, 48202 and Perinatology Research Branch-NIH/NICHD, 4 Brush, 3990 John R, Detroit, MI 48201, USA
| | - Constantin Georgescu
- Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI, 48202 and Perinatology Research Branch-NIH/NICHD, 4 Brush, 3990 John R, Detroit, MI 48201, USA
| | - Adi L. Tarca
- Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI, 48202 and Perinatology Research Branch-NIH/NICHD, 4 Brush, 3990 John R, Detroit, MI 48201, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI, 48202 and Perinatology Research Branch-NIH/NICHD, 4 Brush, 3990 John R, Detroit, MI 48201, USA
- *To whom correspondence should be addressed. +1 313 577 5484+1 313 577 6868
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