title: Differentially expressed genes after treatment with adriamycin in DMBA-induced rat breast tumors

summary: The aim of this study was to compare the gene expression profile changes of DMBA-induced rat breast tumors after treatment with adriamycin. To this end, a cDNA microarray was performed (Affymetrix’s Rat Genome 230 2.0 array). This gene expression study was carried out on the tumor biopsy samples prior to adriamycin treatment, and compared with matched tumor biopsy samples after completion of the adriamycin treatment schedule.

overall_design: Breast tumors were induced with a single oral dosage of 7,12-dimethylbenz(alpha)anthracene (100 mg/kg body weight) in female Sprague-Dawley rats and subsequently treated with adriamycin (1 mg/kg body weight/week for 6 weeks) intravenously through lateral tail vein. Gene expression analysis was performed in paired samples as follows: ADR final trucut tumor vs initial trucut tumor (ADR final vs basal). For this assay, 5 samples were chosen according to histopathologic criteria (Bloom-Richardson grade II). Gene expression profiling was carried out using Affymetrix’s GeneChip technology, using the Rat Genome 230 2.0 array from this provider. All the protocols and apparatus were recommended by Affymetrix. Total RNA from frozen mammary tumors was extracted by RNeasy Mini kit and homogenized by QIAshredder columns according to manufacturer’s instructions. The quality and quantity of the obtained RNA was checked out through agarose electrophoresis and later spectrophotometry at 260/280 nm. Biotinylated cRNA was synthesized following the IVT labeling kit from Affymetrix and purified by the GeneChip Sample Cleanup Module from Affymetrix. The quality and quantity of the obtained cRNA was again checked out through agarose electrophoresis and posterior spectrophotometry at 260/280 nm. After hybridization, slides were washed and scanned following the manufacturer’s standard protocol. Intensity values were normalized by Robust Multichip Average method and subsequently these were filtered to remove the control sequences and those with a hybridization signal close to background. The spike controls were: BioB, BioC, BioD and Cre; because BioB was the least abundant in the samples, it was used to estimate the sensitivity of the experiment. The housekeeping control was GAPDH. After non-supervised clustering using Pearson correlation coefficient, statistical significance of gene expression was estimated by Student’s T test for paired samples, using GeneSpring GX 7.3 software (Agilent).


title: Effect of the Methoxychlor Metabolite HPTE on the Rat Ovarian Granulosa Cell Transcriptome in Vitro

status: Public on Jun 10 2009

city: New Brunswick

first: Mehmet

last: Uzumcu

state: NJ

address: 84 Lipman Drive Bartlett 119

department: Department of Animal ScienceS

country: USA

institute: Rutgers University

summary: Ovarian granulosa cells play a central role in steroidogenesis, which is critical for female reproduction. Follicle-stimulating hormone (FSH) promotes cAMP–mediated signaling to regulate granulosa cell steroidogenesis. We have shown previously that 2, 2-bis-(p-hydroxyphenyl)-1, 1, 1-trichloroethane (HPTE) inhibits FSH- and dibutyryl cAMP-stimulated steroidogenesis, and affects the mRNA levels of steroidogenic pathway enzymes in rat granulosa cells. However, HPTE showed a differential effect in FSH- and cAMP-stimulated cells in that HPTE more completely blocked FSH- when compared to cAMP-driven steroidogenesis. The objective of this study was to analyze the effects of HPTE on global gene expression profiles in untreated granulosa cells and those challenged with FSH or cAMP. Granulosa cells from immature rats were cultured with 0, 1, 5, or 10 µM HPTE in the presence and absence of either 3 ng FSH/ml or 1 mM cAMP for 48 h. Total RNA was isolated for microarray analysis using the GeneChip Rat Genome 230 2.0 and ArrayAssist Microarray Suite. An investigation of changes in gene expression across all HPTE treatments showed that HPTE altered more genes in FSH- (~670 genes) than in cAMP-stimulated cells (~366 genes). Analysis confirmed that HPTE more effectively inhibited FSH- than cAMP-induced steroid pathway gene expression and steroidogenesis. Furthermore, expression patterns of novel genes regulating signal transduction, transport, cell cycle, adhesion, differentiation, motility and growth, apoptosis, development, and metabolism were all altered by HPTE. This study further established that HPTE exerts differential effects within the granulosa cell steroidogenic pathway, and revealed that these effects include broader changes in gene expression.

overall_design:
Ovaries were dissected from immature (21-27 days old), Sprague-Dawley rats and were placed into ice cold Ham’s F12 medium. Granulosa cells were isolated from ovaries free of fat pads and surrounding connective tissue by performing non-enzymatic needle puncture method . Following two washes by centrifugation at 1400rpm/250xg for 5 min at 4 C˚, the cells were plated and cultured at approximately 3-4x105 viable cells/mL/well in DMEM/F-12 medium containing 5% FCS at 37 C˚ in 5% CO2 in a 24-well culture plate for 24 hours. The cells were then cultured in serum-free DMEM/F12  containing 0.1 μM androstenedione as a substrate for aromatization into E2.

Cells were treated in triplicate with increasing doses of HPTE (0, 1, 5, and 10 µM) in the absence (basal) or presence of 3 ng FSH/ml or 1 mM cAMP for 48 h. The doses of FSH and cAMP were selected based on a dose-response curve that provided a maximum level of stimulation for E2 production (data not shown). Similar doses of HPTE were previously used (Zachow and Uzumcu, 2006). Cultures were terminated at 48 h following the addition of treatments.

Cell lysate was collected for total RNA isolation for DNA microarray analysis. Total RNA were extracted using the RNeasy Mini Kit (Qiagen, Cat # 74106) followed by DNase I treatment. RNA qualities were assessed by electrophoresis using the Agilent Bioanalyzer 2100 and spectrophotometric analysis prior to cDNA synthesis. Forty nanograms of total RNA from each sample was used to generate a high fidelity cDNA for array hybridization using NuGen Ovation Biotin RNA Amplification and Labeling system (NuGen, Cat#2300-60). After fragmentation and biotin labeling, the samples were hybridized to Affymetrix Rat Genome 230 2.0 arrays. Washing and staining of all arrays were carried out in the Affymetrix fluidics module as per the manufacturer’s protocol. The detection and quantization of target hybridization was performed with an Affymetrix GeneChip Scanner. Data were assessed for array performance prior to analysis and analyzed using ArrayAssist (Stratagene).

first: Craig

middle: N

last: Harvey

first: Mahmoud

last: Esmail

first: Rob

last: Zachow


title: Differentially expressed genes after treatment with hydroxytyrosol in DMBA-induced rat breast tumors

status: Public on Jun 01 2009

city: Granada

first: Sergio

last: Granados

address: Avenida del Conocimiento

country: Spain

institute: University of Granada

summary: The aim of this study was to compare the gene expression profile changes of DMBA-induced rat breast tumors after treatment with hydroxytyrosol (a natural compound from virgin olive oil). To this end, a cDNA microarray experiment was performed (Affymetrix’s Rat Genome 230 2.0 array). This gene expression study was carried out on the tumor biopsy samples prior to hydroxytyrosol treatment, and compared with matched tumor biopsy samples after completion of the hydroxytyrosol treatment schedule. The result of this study was the identification of several genes related to apoptosis, cell cycle arrest, proliferation, differentiation, survival and transformation-related genes.

overall_design: Breast tumors were induced with a single oral dose of 7,12-dimethylbenz(alpha)anthracene (100 mg/kg body weight) in female Sprague-Dawley rats to test the antitumor power of orally administrated hydroxytyrosol (0.5 mg/kg body weight 5 days/week for 6 weeks). Gene expression analysis was performed in paired samples as follows: HT final trucut tumor vs initial trucut tumor (HT final vs basal). For this assay, 5 samples were chosen according to histopathologic criteria (Bloom-Richardson grade II). Gene expression profiling was carried out using Affymetrix’s GeneChip technology, using the Rat Genome 230 v2.0 array from this provider. All the protocols and apparatus were recommended by Affymetrix. Total RNA from frozen mammary tumors was extracted by RNeasy Mini kit and homogenized by QIAshredder columns according to manufacturer’s instructions. The quality and quantity of the obtained RNA was checked out through agarose electrophoresis and later spectrophotometry at 260/280 nm. Biotinylated cRNA was synthesized following the IVT labeling kit from Affymetrix and purified by the GeneChip Sample Cleanup Module from Affymetrix. The quality and quantity of the obtained cRNA was again checked out through agarose electrophoresis and posterior spectrophotometry at 260/280 nm. After hybridization, slides were washed and scanned following the manufacturer’s standard protocol. Intensity values were normalized by Robust Multichip Average method and subsequently these were filtered to remove the control sequences and those with a hybridization signal close to background. The spike controls were: BioB, BioC, BioD and Cre; because BioB was the least abundant in the samples, it was used to estimate the sensitivity of the experiment. The housekeeping control was GAPDH. After non-supervised clustering using Pearson correlation coefficient, statistical significance of gene expression was estimated by Student’s T test for paired samples using GeneSpring GX 7.3 software (Agilent).

last: Granados Principal

first: María

middle: C

last: Ramírez Tortosa

first: Jose

middle: L

last: Quiles

first: Cesar

first: Pedro

last: Sanchez Rovira

last: Camacho Corencia


title: Modulation of gene expression by rapamycin in hepatic cell lines

status: Public on Sep 20 2009

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Albumin, TGF-Beta1 and Blood-Brain Barrier opening induce cortical epileptogenesis.

status: Public on Jul 15 2009

city: Berkeley

first: Luisa

last: Cacheaux

state: CA

address: 5155 Valley Life Sciences Building

institute: UC Berkeley

summary: Insults to the cerebral cortex, such as trauma, ischemia or infections, may result in the development of epilepsy, one of the most common neurological disorders. Previous studies have suggested that perturbations in neurovascular integrity and breakdown of the blood-brain barrier (BBB) lead to neuronal hypersynchronization and epileptiform activity, but the underlying mechanisms are unknown. As with BBB opening, treatment with albumin or with TGF-β1 results in the development of hypersynchronized epileptiform activity. Given the latent period before the appearance of epileptiform activity, we hypothesized the underlying mechanism is a transcriptional response which would be similar for BBB breakdown and exposure to albumin or TGF-β1. In search of a common pathway and transcriptional activation pattern we performed a genome wide analysis. Genomic expression analyses demonstrated similar expression patterns for BBB opening, albumin and TGF-β1 exposure. Most importantly, TGF-β pathway blockers suppressed most albumin-induced transcriptional changes.

overall_design: RNA was extracted from cortical regions of rats treated with sodium deoxycholate (DOC, to induce BBB opening), albumin or TGF-β1 for various durations (7/8, 24, 48hr). Control RNA was extracted from a sham-operated animal and one array was run for each treatment and time point A second set of animals (labeled as Set 2) was treated with either albumin (n=3) or albumin in the presence of TGF-β receptor blockers (n=4; TGF-βR1 kinase activity inhibitor SB431542 and TGF-βR2 antibody) and sacrificed 24 hr following treatment. Sham-operated animals served as controls (n=2).

middle: P

first: Sebastian

last: Ivens

first: Yaron

last: David

first: Alexander

middle: J

last: Lakhter

first: Guy

last: Bar-Klein

first: Michael

last: Shapira

first: Uwe

last: Heinemann

first: Alon

last: Friedman

first: Daniela

last: Kaufer


title: Gene expression profiles of European wild boar naturally infected with Anaplasma phagocytophilum.

status: Public on May 12 2009

city: Ciudad Real

first: Ruth

middle: Cecilia

last: Galindo

state: Ciudad Real

address: Ronda de Toledo s/n

department: Animal Health

institute: Instituto de Investigacion en Recursos Cinegéticos

summary: Anaplasma phagocytophilum infects a wide variety of host species and causes the diseases granulocytic anaplasmosis in humans, horses and dogs and tick-borne fever in ruminants. The objective of this research was to characterize differential gene expression in wild boar naturally infected with A. phagocytophilum by microarray hybridization using the GeneChip® Porcine Genome Array

overall_design: Differential gene expression in wild boar naturally infected with A. phagocytophilum was chacarterized by microarray hybridization using the GeneChip® Porcine Genome Array and real-time RT-PCR.

first: Tatjana

last: Avsic-Zupanc

first: Katherine

middle: M

last: Kocan

first: Christian

last: Gortazar

last: de la Fuente


title: GDNF-Regulated Gene Expression in Cultures of Rat Spermatogonial Stem Cells

status: Public on Apr 14 2009

city: Philadelphia

first: Jonathan

middle: A

last: Schmidt

state: PA

address: 3850 Baltimore Avenue

institute: University of Pennsylvania

summary:
Expression of GDNF-regulated genes was studied in cultures of self-renewing rat spermatogonial stem cells established from 8-10 day old rat pups maintained in a defined serum free medium.  GDNF is the primary regulator of spermatogonial stem cell self renewal in the rat.
GDNF regulated genes were identified using microarray profiling rat spermatogonial stem cells in the presence and absence of GDNF.

overall_design: Highly enriched population of rat spermatogonial stem cells were maintained in defined serum free media which allowed for their continued self-renewal in the presence of GDNF.  GDNF was withdrawn from cultures for 18 hours followed by replacement for 2, 4, and 8 hours.  Gene expression was studied using microarray profiling prior to GDNF withdrawal, after GDNF withdrawal, and after 2, 4, and 8 hours of GDNF replacement.  3 replicate samples from each timepoint were analyzed.

first: Maray

middle: R

last: Avarbock

first: John

middle: W

last: Tobias

first: Ralph

last: Brinster


title: Gene expression data from corticosteroid-treated neonatal rat cardiomyocytes

status: Public on May 01 2009

city: Minatoku, Tokyo

first: NORITADA

last: YOSHIKAWA

address: Shirokanedai 4-6-1

department: Advanced Clinical Research Center

country: Japan

institute: Institute of Medical Science, University of Tokyo

summary:
Recent studies have highlighted the role of adrenal corticosteroid signaling in cardiac physiology and pathophysiology. It is known that glucocorticoids and aldosterone are able to bind glucocorticoid receptor (GR) and mineralocorticoid receptor (MR), and these ligand-receptor interactions are redundant. Therefore, it has been impossible to delineate how these nuclear receptors couple with corticosteroid ligands and differentially regulate gene expression for operation of their distinct functions in the heart.
Here, to particularly define the role of GR, we applied ligand-based approach involving GR-specific agonist cortivazol (CVZ) and GR antagonist RU486, and performed microarray analysis using rat neonatal cardiomyocytes. We indicated that glucocorticoids appear to be a major determinant of GR-mediated gene expression when compared with aldosterone. Moreover, expression profiles of these genes highlighted numerous roles of glucocorticoids in various aspects of cardiac physiology.

Keywords: comparison of the effect of steroidal ligands

overall_design: We analyzed gene expression changes after exposure of cells to corticosterone (COR), aldosterone (ALD), and cortivazol (CVZ) in the absence or presence of GR antagonist RU486. Since our preliminary experiments using several cell lines showed that expression of many GR target genes was induced by glucocorticoids in 3 h and to avoid secondary effects of the products of GR-regulated genes, we in the present study set the time periods of exposure to these ligands as 3 h. DNA microarray experiments were performed twice with the same protocol except for RU486 treatment.

first: Noritada

last: Yoshikawa

first: Masao

last: Nagasaki

first: Seiya

last: Imoto

first: Satoru

last: Miyano

first: Satori

last: Tokudome

first: Motoaki

last: Sano

first: Keiichi

last: Fukuda

first: Noriaki

last: Shimizu

first: Chikao

last: Morimoto

first: Hirotoshi

last: Tanaka


title: Modifications of the Rat Airway Explant Transcriptome by Cigarette Smoke

city: Stevenage

first: Darren

last: Gormley

address: Gunnelswood Road

country: United Kingdom

institute: GlaxoSmithKline

summary: Although a number of animal model studies have addressed changes in gene expression in the parenchyma and their relationship to emphysema, much less is known about the pathogenesis of cigarette smoke-induced small airway remodeling. In this study, we exposed rat tracheal explants to whole smoke for 15 minutes, and then cultured the explants in air. The airway transcriptome was evaluated using RAE 230_2 GeneChips. By 2 hours after starting smoke exposure, expression levels of 502 genes were changed up or down by more than 1.5 times (p values <0.01 or less), and by 24 hours, 1870 genes were significantly changed up or down. These included genes involved in anti-oxidant protection, epithelial defense and remodeling, inflammatory mediators and transcription factors, and a number of unexpected genes including the MMP-12 inducer, tachykinin-1 (substance P). Pre-treatment of the explants with 1 x 10-7 M dexamethasone reduced the number of significantly changed genes by approximately 47% at 2 hr and 68% at 24 hours, and in almost all instances, reduced the magnitude of the smoke-induced changes. We conclude that even a very brief exposure to cigarette smoke can lead to rapid changes in the expression of a large number of genes in rat tracheal explants, and that these effects are directly mediated by smoke, without a need for exogenous inflammatory cells.  Steroids, contrary to the usual belief, are able to ameliorate many of these changes, at least in this very acute model.

overall_design: 4x tracheal explants (approx 2-3ug) from each rat (n=6 rats) exposed to control (air), smoke (10 puffs of cigarette smoke, delivered during 15 mins), dexamethasone and dexamethasone + cigarette smoke were used for RNA extraction and hybridization on Rat230_2 Affymetrix microarrays. 1 rat, 4 explants and 4 conditions. n=6 rats per group/condition at 2hrs, n=6 rats per group/condition at 24hrs. 12 animals = 48 samples total (47 went into analysis because 1 sample failed QC metrics).

first: Yolanda

middle: S

last: López-Boado

first: Jun

middle: U

last: Li

first: Chris

last: Clayton

first: Rona

middle: D

last: Wang

first: Joanne

last: Wright

first: Andrew

last: Churg


title: FSH and FOXO1 Regulate Genes in the Sterol/Steroid and Lipid Biosynthetic Pathways in Granulosa Cells

status: Public on Apr 17 2009

city: Houston

first: JoAnne

last: Richards

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: The forkhead box transcription factor FOXO1 is highly expressed in granulosa cells of growing follicles but is down-regulated by FSH in culture or by LH-induced luteinization in vivo. To analyze the function of FOXO1, we infected rat and mouse granulosa cells with adenoviral vectors expressing two FOXO1 mutants: a gain-of-function mutant FOXOA3 that has two serine residues and one threonine residue mutated to alanines rendering this protein constitutively active and nuclear, and a FOXOA3-mutant DNA-binding domain (mDBD) in which the DBD is mutated. The infected cells were then treated with vehicle or FSH for specific time intervals. Infection of the granulosa cells was highly efficient, caused only minimal apoptosis, and maintained FOXO1 protein at levels of the endogenous protein observed in cells before exposure to FSH. RNA was prepared from control and adenoviral infected cells exposed to vehicle or FSH for 12 and 24 h. Affymetrix microarray and database analyses identified, and real time RT-PCR verified, that genes within the lipid, sterol, and steroidogenic biosynthetic pathways (Hmgcs1, Hmgcr, Mvk, Sqle, Lss, Cyp51, Tm7sf2, Dhcr24 and Star, Cyp11a1, and Cyp19), including two key transcriptional regulators Srebf1 and Srebf2 of cholesterol biosynthesis and steroidogenesis (Nr5a1, Nr5a2), were major targets induced by FSH and suppressed by FOXOA3 and FOXOA3-mDBD in the cultured granulosa cells. By contrast, FOXOA3 and FOXOA3- mDBD induced expression of Cyp27a1 mRNA that encodes an enzyme involved in cholesterol catabolism to oxysterols. The genes up-regulated by FSH in cultured granulosa cells were also induced in granulosa cells of preovulatory follicles and corpora lutea collected from immature mice primed with FSH (equine choriogonadotropin) and LH (human choriogonadotropin), respectively. Conversely, Foxo1 and Cyp27a1 mRNAs were reduced by these same treatments. Collectively, these data provide novel evidence that FOXO1 may play a key role in granulosa cells to modulate lipid and sterol biosynthesis, thereby preventing elevated steroidogenesis during early stages of follicle development.

overall_design: Immature rat granulosa cells were affected with either control (GFP) or FOXO1 mutant adenovirus (FOXOA3 and FOXOA3-mDBD) for 4 hours. Then the cells were treated with either FSH or vehicle for 24 hours. The gene expression profiles for the four treatment samples  (control, control +FSH, FOXOA3 + FSH, FOXOA3-mDBD + FSH) were compared using Rat Genome 230.2 Arrays with one array per sample.

first: Zhilin

last: Liu

first: Michael

last: Rudd

first: Inmaculata

last: Hernandez-Gonzalez

first: Ignacio

last: Gonzalez-Robayna

first: Heng-Yu

last: Fan

first: Anthony

last: Zeleznik


title: Expression profiles from kidneys of rats treated with nephrotoxicants and with controls

status: Public on May 27 2009

city: Tel Aviv

first: yaron

last: kinar

address: 72 Pinchas Rosen st.

country: Israel

institute: Compugen

summary:
The objective of the study described here was to discover a genetic biomarker signature that can predict the occurrence of drug-induced renal toxicity before it is detected by clinical chemistry examination or histopathology. In order to identify the biomarker signature, Sprague-Dawley Crl:CD(SD) rats were treated  with well-known renal toxins:  Gentamicin, Cisplatin, Tobramycin, Cadmium Chloride, and Doxorubicin, and with controls - valproic acid, and saline.
The substances were administrated daily for 1, 5 or 28 days at doses that are expected to induce kidney-specific histopathological and clinical chemistry changes not before 28 days of repetitive dosing. At the end of treatment, kidneys from the treated animals were removed; the RNA from these kidneys, and from kidneys of several naive animals was extracted and subjected to microarray expression analysis. Twenty candidate genes which showed significant changes from control were identified using microarray experiments.

overall_design: Rats were treated with 7 different compounds - 5 known nephrotoxicants and 2 controls. Each compound was administrated daily for 1,5 and 28 days. The microarray expereiments were done for the 1 and 5-days groups, and for an additional control group of naive (untreated) rats. Each group contained 3 males and 3 females. Half of the apical parts of each kidney of each animal was taken, and the two halves were homogenized prior to RNA extraction

first: Yaron

last: Kinar


title: Expression data from normal atria and ventricles

status: Public on Aug 24 2009

city: Ottawa

first: Adolfo

last: de Bold

state: ON

address: 40 Ruskin St.

department: Cardiovascular Endocrinology

country: Canada

institute: University of Ottawa Heart Institute

summary:
Pharmacological and gene ablation studies have demonstrated a crucial role of the cardiac natriuretic peptides (NP) hormones ANF and BNP in the maintenance of cardiovascular homeostasis.  In addition, hypertension and chronic congestive heart failure are  clinical entities that may be regarded as states of relative NP deficiency. Hence the study of the function of the endocrine heart is highly relevant.
To identify genes that are related to the endocrine function of the heart we have conducted differential gene expression studies of the rat atria and ventricles using oligonucleotide arrays.
Keywords: comparative genomic hybridization

overall_design: The atrial appendages and the ventricular free walls were obtained from thirteen normal male Sprague Dawley rats. The total RNA was obtained from four pools of atrial and four pools of ventricular tissues. Four biological replicates for each muscle type were generated, i.e. 4 atrial replicates and 4 ventricular replicates.

first: Monica

middle: F

last: McGrath


title: Genome-wide Profiling of Gene Expression in a New Rat Model of Cholangiocarcinoma Progression Mimicking the Human Cancer

status: Public on Apr 02 2009

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

summary:
Validation of preclinical models of intrahepatic cholangiocarcinoma progression that reliably recapitulate altered molecular features of the human disease would provide an important resource for suggesting and testing of novel target-based therapies against this devastating cancer. In this study, comprehensive gene expression profiling in a novel orthotopic rat model of intrahepatic cholangiocarcinoma progression was carried out in an effort to identify potential therapeutic targets relevant to the progressive human cancer.
Microarray analysis was performed on intrahepatic cholangiocarcinomas formed at 10, 15, and 25 days after bile duct inoculation of neu-transformed rat cholangiocytes (BDEneu cells) into rat liver and on peritoneal metastases at the 25 day time period, compared with non-cancerous right liver lobe from the same animals.

overall_design: Tumors were collected at 10, 15, 25 days post inoculation from biological triplicates (different rats innoculated simultaneously). Also, biological triplicates of metastatic tumors (Mets) at day 25 were analyzed. Biological triplicates of paired normal right liver lobe (RLL) from the same animals from which tumors/mets were obtained were also analyzed in this study. Thus, a total of 9 rats were used for this study.

first: Jorge

last: Almenara

first: Alphonse

last: Sirica


title: Gene Expression Changes in Response to UV Inactivated Baculoviral Vector Transduction of the Rat Brain In Vivo

city: Singapore

first: Jerome

last: Boulaire

address: 31 Biopolis Way

department: Gene Delivery

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

summary:
Recombinant baculoviral vectors efficiently transduce several types of cells in the brain. To characterize host responses to viral challenge, thus verifying the suitability of using the virus for the development of gene therapy strategies in the central nervous system, we used cDNA microarray technology to examine in vitro and in vivo global cellular gene expression profiles after viral transduction. We demonstrated that the transduction induced host antiviral responses as a major reaction in all three types of samples profiled, including the rat brain, cultured human astrocytes and human neuronal cells. The related genes were mainly those associated with innate immunity. Several genes of the major histocompatibility complex molecules, an important component of the host adaptive immunity to exogenous pathogens, were up-regulated in the rat brain and human astrocytes, but not in neuronal cells. We also observed that genes related to cell death and apoptosis were up-regulated and genes related cell cycle regulation were down-regulated in neuronal cells, but not obviously affected in astrocytes. These findings should be useful in understating the molecular basis for neural cell response to baculoviral transduction and guiding rational applications of baculoviral vectors in the central nervous systems
Keywords: Baculovirus, brain, astrocytes, neurons, transduction, Infection, gene expression analysis, DNA microarray

overall_design:
For in vivo viral inoculation, adult male Wistar rats (weighing 250–300 g) were used. Five μl of baculovirus vectors (5 x 107 viral particles) was injected stereotaxically into the striatum at two injection sites (AP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis. Five μl of PBS was injection into the contralateral striatum and the tissues were collected and used as controls.
Seven rats were used for the study.
Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer. One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands). Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the human GeneChip Human Genome U133 Plus 2.0 or GeneChip Rat Genome 230 2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions. Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software.

Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 5 out of 7 brain samples or 2 out of 3 cell replicates had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition. The volcano plot was sometime used to filter the data further with the following cut-off (2-fold difference in expression level and t-test p-value of less than 0.05). Further data manipulation for comparison purposes are described in the text.

first: Shu

last: Wang


title: Expression data from 28 day sham and shunt atrial and ventricular tissues (set 1)

status: Public on Aug 01 2010

summary:
Pharmacological and gene ablation studies have demonstrated a crucial role of the caridac natriuretic peptides (NP) hormones ANF and BNP in the maintenance of cardiovascular homeostasis. Considerable effort has been focused on the elucidation of the mechanistic underlying increased atrial ANF and BNP expression and secretion. These investigations are important because under chronic congestive heart failure, the secretion of NPs although increased and beneficial, is relatively insufficient as demonstrated by the fact that patients  benefit form the unloading of the heart induced by therapeutic administration of either ANF or BNP.
To identify genes involved in the transcriptional response of the endocrine heart under normal and stimulated states, we conducted differential gene expression studies of the rat atria and ventricles under normal or chronic volume overload, induced by aorto-caval shunt.

overall_design: The left atrial appendages and left ventricular free walls were obtained from 28 day sham and shunt operated male Sprague Dawley rats. Total RNA was obtained from three pools (of two tissues) of left atria and left ventricles under sham and shunt conditions. Three biological replicates for each muscle type and condition were generated.

last: Forero

first: Tsuneo

last: Ogawa


title: Expression data from GLI1-transformed RK3E cells

status: Public on Mar 25 2009

city: Chicago

first: Joon Won

last: Yoon

state: IL

address: 2430 N Halsted

institute: Children's Memorial Reseach Center

summary:
SHH signaling pathway is activated in many type of cancers.  However, the role of its activation in particular type of cancer was poorly understood.  The GLI family transcription factor GLI1 is the effector of Shh pathway activation and functions as oncogene.  Our goal of research is to identify the GLI1 targets in desmoplastic medulloblastomas.
We used microarrays to obtain the global gene expression profiles in cells transformed by GLI1 and identified distinct classes of genes by comparing with those of desmoplastic medulloblastomas

overall_design: RK3E cells were transformed by GLI1 and the gene expression profiles were compared with control RK3E cells.  Genes obtained from this analysis were compared with those of desmoplastic medulloblastomas

first: Joon

first: Steve

last: Iannaccone

first: David

last: Walterhouse

first: Philip


title: Gene expression studies in IEC-6 cells induced by non-steroidal anti-inflammatory agents

status: Public on Mar 21 2009

city: Manhattan

first: Daniel

last: Marcus

state: KS

address: 228 Coles Hall

department: Anatomy & Physiology

institute: Kansas State University

summary:
Non-steroidal anti-inflammatory drugs (NSAIDs) are used extensively as therapeutic agents, despite their well-documented gastrointestinal (GI) toxicity. Presently, the mechanisms responsible for NSAID-associated GI damage are incompletely understood. In this study, we used Microarray analysis to generate a novel hypothesis about cellular mechanisms that underlie the GI toxicity of NSAIDs. Monolayers of intestinal epithelial
cells (IEC-6) were treated with NSAIDs that either exhibit indomethacin, NS-398) or lack (SC-560) inhibitory effects on intestinal epithelial cell migration. Bioinformatic analysis of array data suggested that NSAIDs with adverse GI effects either decrease the gene expression of the calpains or increase the gene expression of the calpain engodenous
inhibitor, calpastatin. Calpains have been shown previously to modulate the migration of a variety of cells in different physiological contexts. Our experimental results suggest that the altered expression of calpain genes may contribute to the adverse effects of NSAIDs on intestinal
epithelial restitution. Microarray analysis has generated the novel hypothesis that the GI toxicity of NSAIDs may be attributed in part to drug-induced changes in the expression and activity of calpains.
Keywords: dose response

overall_design: Monolayers of intestinal epithelial cells (IEC-6) were treated with NSAIDs that either exhibit (indomethacin, NS-398) or lack (SC-560) inhibitory effects on intestinal epithelial cell migration. Samples were then pooled to obtain sufficient material for gene array analysis.  The pooled samples were used to hybridize 4 gene array chips for each biological sample.

first: Nithya

last: Raveendran

first: James

last: Lillich

first: Lisa

last: Freeman


title: Influence of hyperthyroid conditions on gene expression in rat

status: Public on Mar 06 2009

first: Thomas

last: Postler

address: 421 Curie Boulevard

department: Cell and Developmental Biology


title: Effect of corticosterone treatment on rat neuronal progenitor cells

status: Public on Mar 31 2009

city: Suita

first: Taira

last: Mayanagi

state: Osaka

address: Yamadaoka 2-2

institute: Osaka University Graduate School of Medicine

summary:
Exposure to excessive glucocorticoids, which are major mediators of the stress reaction, is detrimental to brain development related to an increased risk of psychiatric disorders. However, the molecular mechanism underlying the effect of excessive glucocorticoids on the developing brain remains largely unclear. To clarify the mechanism, we examined the effects of glucocorticoids on cultured neuronal progenitor cells (NPCs) from cerebral cortices from rat embryo. We performed comparative analysis using gene expression profiling of corticosterone- or vehicle-treated NPCs. Results provide insight into the effects of glucocorticoids in regulating genetic programs important for controlling NPCs’ properties.
Keywords: expression analysis, corticosterone, neuronal progenitor, cortex

overall_design: Three couples of RNA samples from corticosterone- or vehicle-treated neuronal progenitor cells were analyzed.

first: K

last: Fukumoto

first: T

last: Sobue


title: Xenobiotic-responsive Nuclear Receptors in Transcriptional Effects Upon Perfluoroalkyl Acid Exposure in Diverse Species

status: Public on Feb 07 2009

city: RTP

first: Hongzu

last: Ren

state: NC

address: 109 TW Alexander Dr

institute: US Environmental Protection Agency

summary:
Humans and ecological species have been found to have detectable body burdens of a number of perfluorinated alkyl acids (PFAA) including perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS). In mouse and rat liver these compounds elicit transcriptional and phenotypic effects similar to peroxisome proliferator chemicals (PPC) that work through the nuclear receptor peroxisome proliferator activated receptor alpha (PPARalpha). Recent studies indicate that along with PPARalpha other nuclear receptors are required for transcriptional changes in the mouse liver after PFOA exposure including the constitutive activated receptor (CAR) and pregnane X receptor (PXR) that regulate xenobiotic metabolizing enzymes (XME). To determine the potential role of CAR/PXR in mediating effects of PFAAs in rat liver, we performed a meta-analysis of transcript profiles from published studies in which rats were exposed to PFOA or PFOS.  We compared the profiles to those produced by exposure to prototypical activators of CAR (Phenobarbital (PB)), PXR (pregnenolone 16 alpha-carbonitrile (PCN)), or PPARalpha (WY-14,643 (WY)). As expected, PFOA and PFOS elicited transcript profile signatures that included many known PPARalpha target genes. Numerous XME genes were also altered by PFOA and PFOS but not WY. These genes exhibited expression changes shared with PB or PCN. Reexamination of the transcript profiles from the livers of chicken or fish exposed to PFAAs indicated that PPARalpha, CAR, and PXR orthologs were not activated. Our results indicate that PFAAs under these experimental conditions activate PPARalpha, CAR, and PXR in rats but not chicken and fish. Lastly, we discuss evidence that human populations with greater CAR expression have lower body burdens of PFAAs.

Keywords: gene expression/microarray

overall_design: We used published and unpublished microarray gene expression profiling data to perform a meta-analysis to reveal the activation of CAR and PXR regulated genes in rat liver exposed to PFAA. This file contains part of data being analyzed.

first: Beena

last: Vallanat

last: Nelson

first: Leo

last: Yeung

first: Keerthi

last: Guruge

first: Paul

middle: K

last: Lam

first: Lois

last: Lehman-McKeeman

first: J

last: Corton


title: Rat exposure to RDX (3mg/kg or 18mg/kg; 0, 4, 24, 48 hr)

status: Public on Mar 13 2009

city: Aberdeen Proving Ground

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

institute: U.S. Army Medical Research Institute of Chemical Defense

summary:
RDX (Hexahydro-1,3,5-trinitro-1,3,5-triazine) is a synthetic, high-impact, relatively stable explosive that has been in use since WWII.   Exposure to RDX can occur either occupationally or through ordnance that lays unexploded on training ranges.  The toxicology of RDX is dominated by acute tonic-clonic seizures at high doses, which remit when exposure is removed and internal RDX levels decrease.  Sub-chronic studies have revealed few other toxic effects.  The objective of this study was to examine the effect of a single oral dose of RDX on global gene expression in the mammalian brain and liver, using a rodent model.

Keywords: time course, dose response

overall_design: Male Sprague-Dawley rats were given a single, oral, non-seizure inducing dose of either 3 or 18 mg/kg RDX in a gel capsule.  Rats were euthanized at times 0, 4, 24, and 48 hours. RNA purified from brain cortex or liver was hybridized to Affymetrix rat 230.2 arrays.

first: Desmond

last: Bannon

first: Edward

last: Perkins


title: ChIP-on-chip experiments of normal and failed hearts of Dahl rat

status: Public on Feb 19 2009

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

institute: Jichi Medical University

type: Genome binding/occupancy profiling by array

summary:
Left ventricle myocytes from Dahl rats with a normal or failed heart was subjected to mRNA quantitation or ChIP-on-chip experiments with Affymetrix Rat Genome 230 2.0 microarrays.
Keywords: ChIP-chip

overall_design: One left venctricle specimen was used for each mRNA quantitation/ChIP-on-chip experiment with a normal or failed heart.


title: Influence of hyperthyroid conditions on gene expression in rat tibialis anterior

summary:
Extraocular muscles (EOMs) are a highly specialized type of tissue with a wide range of unique properties, including characteristic innervation, development, and structural proteins. Even though EOMs are frequently and prominently involved in thyroid-associated diseases, little is known about the immediate effects of thyroid hormone on these muscles. In order to create a comprehensive profile of changes in gene expression levels in EOMs induced by thyroid hormone, hyperthyroid conditions were simulated by treating adult Sprague-Dawley rats with intraperitoneal injections of 25  μg T3 per 100 g body weight over the course of six weeks; subsequently, microarray analysis was used to determine changes in mRNA levels in EOMs from T3-treated animals relative to untreated controls.
RNA isolated from tibialis anterior muscles of the same animals was used as a reference fast-twitch muscle.

overall_design:
Adult Sprague-Dawley rats (initial body weight 200 ± 40 g) were fed ad libitum with standard laboratory diet and tap water. Eight rats were randomly divided into a T3-treated and a control group, three males and one female each.
To simulate a chronically hyperthyroid state, T3 treatment was administered by intraperitoneal injections of 25 µg T3 (Sigma-Aldrich, St. Louis, MO, U.S.A.) per 100 g body weight. Injections were administered every second day over a period of six weeks. 24 hours after the last injection, the animals were sacrificed by CO2 asphyxiation, muscles were dissected immediately after death.
Each of the four biological replicates in each group was used for a single microarray each.
RNA from EOMs was used. Tibialis anterior RNA from the same animals served as a fast-twitch reference muscle.

first: Murat

middle: T

last: Budak

first: Neal

last: Rubinstein


title: Expression data from rat kidney: pathophysiology of proteinuria

status: Public on Feb 03 2009

city: Ashkelon

first: Yoram

last: Yagil

address: Hahistadrut

institute: Ben-Gurion University, Barzilai Medical Center Campus

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Chana

first: Martin

last: Hessner


title: Expression data from female rat kidney: pathophysiology of proteinuria

status: Public on Jan 31 2009

summary:
This study was designed to investigate gene expression in kidneys of adult female Sabra rats (SBH/y and SBN/y rat strains) with two indwelling kidneys or after uni-ninephrectomy, seeking those genes that are differentially expressed between the two strains, and between animals with one or two kidneys. SBH/y after uninephrectomy develop proteinuria to a much greater extent than SBN/y. The study was performed as part of an overall effort to detect the genes that are associated with the pathophysiology of proteinuria.

Keywords: Analysis of genes that are differentially expressed in the kidneys, contrasting between an animal strain that tends to develop proteinuria which is amplified by uninephrectomy and another strain that is relatively resistant to the development of proteinuria

overall_design: The experiment was performed in female animals after weaning. Four groups were studied: SBN/y with 2 kidneys (sham uni-nephrectomy), SBN/y after uni-nephrectomy, SBH/y with 2 kidneys (sham uninephrectomy) and SBH/y after uni-nephrectomy. Animals were provided rat chow ad libitum. At age 5 months, 4 months after uninephrectomy or sham operation, animals were sacrificed under ether anesthesia, killed by exsanguination and the kidneys were rapidly removed and snap frozen with liquid nitrogen. The kidneys were stored at -800C until RNA was extracted for the differential expression experiment.


title: Influence of hyperthyroid conditions on gene expression in rat extraocular muscles

first: Thomas

last: Postler

summary: Extraocular muscles (EOMs) are a highly specialized type of tissue with a wide range of unique properties, including characteristic innervation, development, and structural proteins. Even though EOMs are frequently and prominently involved in thyroid-associated diseases, little is known about the immediate effects of thyroid hormone on these muscles. In order to create a comprehensive profile of changes in gene expression levels in EOMs induced by thyroid hormone, hyperthyroid conditions were simulated by treating adult Sprague-Dawley rats with intraperitoneal injections of 25  μg T3 per 100 g body weight over the course of six weeks; subsequently, microarray analysis was used to determine changes in mRNA levels in EOMs from T3-treated animals relative to untreated controls.

overall_design: Adult Sprague-Dawley rats (initial body weight 200 ± 40 g) were fed ad libitum with standard laboratory diet and tap water. Eight rats were randomly divided into a T3-treated and a control group. To simulate a chronically hyperthyroid state, T3 treatment was administered by intraperitoneal injections of 25 µg T3 (Sigma-Aldrich) per 100 g body weight. Injections were administered every second day over a period of six weeks. 24 hours after the last injection, the animals were sacrificed by CO2 asphyxiation. For RNA isolation, the extraocular muscles (EOMs) were removed, flash-frozen in liquid nitrogen and stored at -80 °C until further use.


title: Profiling of Transcripts in Rat Kidney Medullary Thick Ascending Limb

status: Public on Jan 26 2009

city: Taipei

first: Ming-Jiun

last: Yu

address: Rm 816, No. 1 Ren-Ai Road Section 1

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Taiwan University College of Medicine

summary: Freshly isolated rat kidney medullary thick ascending limbs were subjected for transcript profiling.

overall_design: Three microarray experiments were done to obtain the kidney medullary thick ascending limb transcriptome.


title: Profiling of Transcripts in Rat Proximal Tubule

summary: Freshly isolated rat kidney proximal tubules were subjected for transcript profiling.

overall_design: Three microarray experiments were done to obtain the kidney proxmial tubule transcriptome.

first: Panapat

last: Uawithya


title: Effect of BDNF on aging-related gene expression changes in young and aged rats

status: Public on Jan 23 2009

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary:
Patterns of gene expression in the aged entorhinal cortex and hippocampus were examined one month after entorhinal administration of BDNF lentivirus. Whole-genome patterns of expression were examined using Affymetrix arrays four weeks after entorhinal injection of lentiviral-BDNF or GFP injection compared to control subjects.

Keywords: Treatment effect

overall_design: 27 Samples total: 4 biological replicates of Age rats BDNF treated, 3 biological replicates of Age rats eGFP treated, and 4 biological replicates each of Aged and Young rats controls for the Entorhinal cortex tissue. 2 biological replicates of Age rats BDNF treated, 2 biological replicates of Age rats eGFP treated, and 4 biological replicates each of Age and Young rats controls for the hippocampus tissue.

first: A

middle: H

last: Nagahara

first: D

last: Merrill

first: G

first: S

last: Tsukada

first: B

middle: E

last: Schroeder

last: Shaked

first: L

last: Wang

last: Blesch

last: Kim

last: Conner

first: E

last: Rockenstein

first: M

middle: V

last: Chao

last: Koo

last: Geschwind

last: Masliah

last: Chiba

last: Tuszynski


title: Expression data from male rat kidney: pathophysiology of proteinuria

last: Yagil

summary:
This study was designed to investigate gene expression in kidneys of adult Sabra rats (SBH/y and SBN/y rat strains) with two indwelling kidneys or after uni-ninephrectomy, seeking those genes that are differentially expressed between the two strains, and between animals with one or two kidneys. SBH/y after uninephrectomy develop proteinuria to a much greater extent than SBN/y. The study was performed as part of an overall effort to detect the genes that are associated with the pathophysiology of proteinuria.

Keywords: Analysis of genes that are differentially expressed in the kidneys, contrasting between an animal strain that tends to develop proteinuria which is amplified by uninephrectomy and another strain that is relatively resistant to the development of proteinuria

overall_design: The experiment was performed in male animals after weaning. Four groups were studied: SBN/y with 2 kidneys (ham uni-nephrectomy), SBN/y after uni-nephrectomy, SBH/y with 2 kidneys (sham uninephrectomy) and SBH/y after uni-nephrectomy. Animals were provided rat chow ad libitum. At age 4 months, 3 months after uninephrectomy or sham operation, animals were sacrificed under ether anesthesia, killed by exsanguination and the kidneys were rapidly removed and snap frozen with liquid nitrogen. The kidneys were stored at -800C until RNA was extracted for the differentiale xpression experiment.

last: Hessner


title: Gene Expression Profiling of Rat Hippocampus Following Exposure to the Acetylcholinesterase Inhibitor Soman

first: James

last: Dillman

summary:
Soman (O-Pinacolyl methylphosphonofluoridate) is a potent neurotoxicant.  Acute exposure to soman causes profound inhibition of the critical enzyme acetylcholinesterase, resulting in excessive levels of the neurotransmitter acetylcholine.  Excessive acetylcholine levels cause convulsions, seizures, and respiratory distress.  The initial cholinergic crisis can be overcome by rapid anti-cholinergic therapeutic intervention, resulting in increased survival.  However, conventional treatments do not protect the brain from seizure-related damage, and thus neurodegeneration of soman-sensitive areas of the brain is a potential post-exposure outcome.  We performed gene expression profiling of rat hippocampus following soman exposure to gain greater insight into the molecular pathogenesis of soman-induced neurodegeneration.

Keywords: Time-course; toxicant exposure

overall_design: Male Sprague-Dawley rats were pretreated with the oxime HI-6 (l-(((4-aminocarbonyl)pyridinio)methoxyl)methyI)-2-((hydroxyimino)methyl)-pyridinium dichloride; 125 mg/kg, ip) 30 min prior to challenge with soman (180 μg/kg, sc; diluted with 0.9% sodium chloride).  One minute after soman challenge, animals were treated with atropine methyl nitrate (2.0 mg/kg, im).  Vehicle control animals (n=4; 2 euthanized at 1h, 1 euthanized at 12h, and 1 euthanized at 24h) received an equivalent volume of vehicle (0.9% sodium chloride), HI-6 and atropine. Naïve animals (n=3) were also included in the study and received no treatments.  Hippocampal tissue was harvested 1, 3, 6, 12, 24, 48, 72, 96, and 168h after soman exposure.  A sample size of n=3 was used for all time points except 3h (n=6) and 72h (n=4).  RNA was extracted from the hippocampal tissue and used to generate oligonucleotide microarray probes for gene expression profiling using Affymetrix Rat 230 2.0 microarrays.

last: Dillman III

first: Christopher

last: Phillips


title: MEF2 Activated Genes

status: Public on Jan 12 2009

city: Boston

first: Steven

middle: Willem

last: Flavell

state: MA

address: CLS 12260, 300 Longwood Avenue

department: Neurology

institute: Children's Hospital Boston

summary:
Expression profiling in hippocampal neurons to identify genes upregulated in response to ectopic MEF2 activation by MEF2-VP16-ER
Experiments were conducted to identify activity-regulated MEF2 target genes.

Keywords: Gene activation time course

overall_design: Neurons expressed either control MEF2deltaDBD-VP16-ER or MEF2-VP16-ER and expression profiling was conducted before and after 4-OH-Tamoxifen (4OHT) application.

first: Michael

last: Greenberg


title: TNF-a-induced MEK/ERK-dependent regulation of Cartilage Matrix Genes

status: Public on Jan 14 2009

city: London

first: Jason

middle: Scott

last: Rockel

state: Ontario

address: The University of Western Ontario

department: Anatomy and Cell Biology

institute: CIHR Group in Skeletal Development and Remodeling

summary:
TNF-a is increased in the synovial fluid of patients with rheumatoid arthritis and osteoarthritis.  TNF-a activates MEK/ERK in chondrocytes; however the overall functional relevance of MEK/ERK to TNF-a-regulated gene expression in chondrocytes is unknown. Chondrocytes were treated with TNF-a with or without the MEK1/2 inhibitor U0126 for 24 h. Microarray analysis was used to identify genes regulated by TNF-a in a MEK1/2-dependent fashion.

Keywords: compound, signalling response

overall_design: Primary chondrocytes from the femoral condyles of neonatal rats were treated with DMSO (control sample), TNF-a, U0126 (selective MEK1/2 inhibitor) or TNF-a and U0126.  Two biological replicates were collected for each treatment.  Total RNA was collected and analyzed by Affymetrix Microarray.

first: Suzanne

last: Bernier

first: Andrew

last: Leask


title: Epileptogenesis alters gene expression pattern in rats subjected to amygdala-dependent emotional learning

status: Public on Feb 13 2009

city: Gdansk

first: Katarzyna

last: Majak

address: Debinki 1

department: Department of Anatomy and Neurobiology

country: Poland

institute: Medical University of Gdansk

summary: Here we tested a hypothesis that epileptogenesis influences expression pattern of genes in the basolateral amygdala that are critical for fear conditioning. Whole genome molecular profiling of basolateral rat amygdala was performed to compare the transcriptome changes underlying fear learning in epileptogenic and control animals. Our analysis revealed that after acquisition of fear conditioning 26 genes were regulated differently in the basolateral amygdala of both groups. Thus, our study provides the first evidence that not only the damage to the neuronal pathways but also altered composition or activity level of molecular machinery responsible for formation of emotional memories within surviving pathways can contribute to impairment in emotional learning in epileptogenic animals. Understanding the function of those genes in emotional learning provides an attractive avenue for identification of novel drug targets for treatment of emotional disorders after epileptogenesis-inducing insult.

overall_design:
Experiment description:
Array: Rat Genome 230-2.0 (Affymetrix).
Samples: 2 biological replicates from 4 experimental groups (control unpaired = CU, CU1, control paired = CP, CP1, epileptogenic unpaired = EU, EU1, epileptogenic paired = EP, EP1).
Animals&model: Amygdala stimulation model (Nissinen et al., 2000):
control (C) animals = operated, not stimulated;
epileptogenic (E) animals = stimulated, responded with "good" status epilepticus (at least 40HAFDs within first 3h of SE), not expressing spontaneous seizures through the whole study.
All animals received 5 habituation session to the fear conditioning apparatus lasting 10 min, starting on day 5 (2 sessions on day 5 and 6 and 1 session on day 7) after stimulation (induction of SE).
On 8th day after stimulation:
unpaired (U) = twice received: 2min in apparatus → footshock (1.5mA, 1s)→ tone (75dB for 20 sec)
paired (P) = twice received: 2min in apparatus → tone (75dB for 20 sec) co-terminated by footshock (1.5mA, 1s).
RNA isolation: decapitation → ipsilateral temporal lobe isolated, embed in OCT and frozen in -70C. Cut into 10µm sections, thionin stained (Ambion protocol), basal and lateral nuclei of the amygdala laser-microdissected; total cellular RNA isolated with PicoPure RNA isolation kit (Arcturus).
RNA amplification: 30ng of of total cellular RNA from each rat underwent of 2 rounds of amplification using MessageAmp II aRNA kit (Ambion), according to manufacturer protocol (in vitro transcription time 14h in both rounds).
Sample pooling: aRNA from 2 animals was pooled (10µg in total = 2x5µg) and 8 samples were labeled and hybridized: CP, CP1, CU, CU1, EP, EP1, EU, EU1; (altogether aRNA from 16 rats was used).

first: Michal

last: Dabrowski

first: Asla

last: Pitkanen


title: Expt. C; Daily Rhythm in Expression of >600 Genes in the Rodent Pineal Gland: Dominant Role of Adrenergic/cAMP Signaling

status: Public on Jan 15 2009

city: Bethesda

first: David

middle: C.

last: Klein

address: 49 Convent Dr.

department: PDEGEN

institute: NICHD/NIH

summary:
Biological processes are optimized by circadian and circannual biological timing systems.  In vertebrates, the pineal gland plays an essential role in these systems by converting time into a hormonal signal, melatonin; in all vertebrates, circulating melatonin is elevated at night, independent of lifestyle. At night, sympathetic input to the pineal gland, originating from the circadian clock in the suprachiasmatic nucleus, releases norepinephrine. This adrenergic stimulation causes an elevation of cAMP, which is thought to regulate many of the dramatic changes in genes expression known to occur at night. In many aspects, the adrenergic/cAMP effects on gene expression can be recapitulated in primary organ culture.
We have analyzed the rat pineal transcriptome at mid-day and mid-night to identify genes that exhibit night/day changes in expression. The pineal transcriptome was compared to that of other rat tissues processed in parallel. In addition, pineal glands were cultured in control conditions, or stimulated with norepinephrine, dibutyryl-cAMP (DBcAMP), or forskolin; the transcriptomes of these glands were then analyzed.

Keywords: Time course (2 points) for in vivo pineal glands and various tissues; Treatment groups for cultured pineal glands

overall_design: Total RNA was extracted from various rat tissues, and from both in vivo and cultured rat pineal glands, for processing and hybridization to Affymetrix microarrays. Quadruplicates of pooled in vivo pineal glands were analyzed at each timepoint. Single day and night samples of retina, cortex, cerebellum, hypothalamus, liver, and heart were analyzed. Triplicates of  control and treated cultured pineal glands were analyzed.

middle: J

last: Bailey

middle: L

last: Coon

last: Carter

first: Ann

last: Humphries

first: Jong-so

last: Kim

first: Qiong

last: Shi

first: Pascaline

last: Gaildrat

first: Fabrice

last: Morin

first: Surajit

last: Ganguly

first: John

middle: B

last: Hogenesch

first: Joan

last: Weller

first: Martin

last: Rath

first: Morten

last: Møller

first: Ruben

last: Baler

last: Sugden

first: Zoila

middle: G

last: Rangel

first: Peter

last: Munson

middle: C


title: Transgenerational epigenetic programming of the brain transcriptome and anxiety behavior

status: Public on Jan 03 2009

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary:
Embryonic exposure to the endocrine disruptor vinclozolin during gonadal sex determination promotes an epigenetic reprogramming of the male germ-line that is associated with transgenerational adult onset disease states. Further analysis of this transgenerational phenotype on the brain demonstrated reproducible changes in the brain transcriptome three generations (F3) removed from the exposure. The transgenerational alterations in the male and female brain transcriptomes were distinct. In the males, the expression of 92 genes in the hippocampus and 276 genes in the amygdala were transgenerationally altered. In the females, the expression of 1,301 genes in the hippocampus and 172 genes in the amygdala were transgenerationally altered. Analysis of specific gene sets demonstrated that several brain signaling pathways were influenced including those involved in axon guidance and long-term potentiation. An investigation of behavior demonstrated that the vinclozolin F3 generation males had a decrease in anxiety-like behavior, while the females had an increase in anxiety-like behavior. These observations demonstrate that an embryonic exposure to an environmental compound appears to promote a reprogramming of brain development that correlates with transgenerational sex-specific alterations in the brain transcriptomes and behavior. Observations are discussed in regards to environmental and transgenerational influences on the etiology of brain disease.

Keywords: expression analysis, transgenerational changes due to vinclozolin

overall_design: Male and female amygdala and hippocampus and male whole brain RNA samples from F3 generation control groups are compared to F3 generation vinclozolin-treated groups.

first: Mathew

last: Anway

first: Marina

last: Savenkova

first: A

last: Gore

last: Crews


title: Cluster analysis of rat pancreatic islet gene mRNA levels after culture in low, intermediate and high [glucose]

city: Brussels

first: Jean-Christophe

last: Jonas

address: Av. Hippocrate, 55

department: Physiology and Pharmacology

country: Belgium

institute: UCL, Faculty of Medicine

summary:
Background: Survival and function of insulin-secreting pancreatic β-cells are markedly altered by changes in nutrient availability. In vitro, culture in 10 rather than 2mM glucose improves rodent β-cell survival and function whereas glucose concentrations above 10mM are deleterious.  Aim-Method: To identify the mechanisms of such β-cell plasticity, we tested the effects of a 18h culture at 2, 5, 10 and 30mM glucose on the transcriptome of rat islets precultured for 1 week at 10mM glucose (Affymetrix Rat 230.2 arrays).  Results: Culture in either 2-5mM or 30mM instead of 10mM glucose markedly impaired β-cell function without affecting islet cell survival. Of ~16000 probe sets reliably detected in islets, ~5000 were significantly regulated at least 1.4-fold by glucose. Analysis of these probe sets with GeneCluster software identified 10 mRNA profiles with unidirectional up- or down-regulation between 2 and 10, 2 and 30, 5 and 10, 5 and 30 or 10 and 30 mM glucose, and 8 complex V-shaped or inverse V-shaped profiles with a nadir or peak level of expression in 5 or 10mM glucose. Analysis of genes belonging to these various clusters with Onto-express and GenMapp software revealed several signaling and metabolic pathways that may contribute to the induction of β-cell dysfunction and apoptosis after culture in low or high vs. intermediate glucose concentration.  Conclusion: We have identified 18 distinct mRNA profiles of glucose-induced changes in islet gene mRNA levels that should help understanding the mechanisms by which glucose affects β-cell survival and function under states of chronic hypo- or hyperglycemia.

Keywords: Dose response

overall_design: Effect of 18h culture in 2, 5, 10 and 30 mmol/l glucose on the transcriptome of rat pancreatic islets precultured for 1 week in 10 mmol/l glucose. Four experiments were done on different islet preparations over a two-months period.

first: Mohammed

last: Bensellam

first: Leentje

last: Van Lommel

first: Lut

last: Overbergh

first: Frans

last: Schuit


title: Novel Environment Expression Profiling

first: Steven

last: Flavell

summary:
Expression profiling in whole rat forebrain in response to exposure of animals to a novel environment
Experiments were conducted to identify genes upregulated in response to novel sensory experiences.

Keywords: Gene expression profiling

overall_design: Rats were either housed in a standard laboratory cage (control) or exposed to a novel environment containing objects of different shapes and colors (novel environment) for three hours.

middle: W

last: Greenberg


title: mRNAs in un-injured and injured rat cortical axons isolated after 13 days in culture

status: Public on Jan 01 2009

city: Pasadena

first: Anne

middle: M

last: Taylor

institute: Caltech

summary:
Efficient growth cone regeneration requires protein synthesis in the adult mammalian brain and spinal cord.  Recent evidence suggests that the local availability of protein synthesis machinery in adult mammalian axons may be an indicator of their regenerative capacity.  Here we investigated the local protein synthesis capacity in matured cortical axons, which have poor regenerative capacity, yet are critical for recovery following injury due to traumatic brain injury and stroke.  This work is the first to biochemically isolate and identify mRNA from mammalian cortical axons, making use of a unique microfluidic platform to isolate axons free of other cellular debris.  We first sought to identify mRNA in naïve axons that makes up the pool of mRNA available for translation initiated following axotomy.  Next, we investigated changes in the mRNA population localized to axons 2 days following axotomy and growth cone regeneration.

Keywords: axonal expression analysis; injury state analysis

overall_design: Cortical axons were harvested using the compartmentalized microfluidic platform after 13 days in culture at a time when they express mature synaptic proteins.  A total of 7 Genechips were used for the uninjured cortical axons from 3 different culture batches.  3 Genechips were used for neurons isolated from the neuronal compartment of the microfluidic platfrom.  The neuronal Genechip were used to compare mRNA populations with axonal Genechips and for quality control purposes.  3 Genechips were used for regenerating axons; for these, axons were axotomized at 11 days in culture, then allowed to regrow for 2 days before harvesting.

first: Carl

last: Cotman


title: Comparative genomic hybridization suggests a role for NRXN1 and APBA2 in schizophrenia

status: Public on Dec 25 2008

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

type: Genome variation profiling by genome tiling array

summary:
Copy number variations (CNVs) account for a substantial proportion of human genomic variation, and have been shown to cause neurodevelopmental disorders. We sought to determine the relevance of CNVs to the aetiology of schizophrenia. Whole genome, high resolution, tiling path BAC array comparative genomic hybridization (array CGH) was employed to test DNA from 91 individuals with DSM-IV schizophrenia. Common DNA copy number changes that are unlikely to be directly pathogenic in schizophrenia were identified by comparison to a reference dataset of 372 control individuals analysed in our laboratory, and a screen against the Database of Genomic Variants. The remaining aberrations were tested for inheritance from the parents, and validated with Affymetrix 250K SNP arrays or 244K Agilent oligo-arrays. Thirteen aberrations satisfied our criteria. Two of them are very likely to be pathogenic. A deletion at 2p16.3 disrupts NRXN1 and was present in an affected sibling. A de novo duplication at 15q13.1 spans APBA2. The proteins of these two genes interact directly and play a role in synaptic development and function. Both genes have been affected by CNVs in other neurodevelopmental disorders.
Keywords: Array CGH

overall_design:
We undertook a systematic search for CNVs in patients with schizophrenia using high resolution, whole genome tiling path BAC arrays. We selected 45 male and 48 female unrelated proband-parent trios from our sample of ~600 Bulgarian SZ trios recruited as described previously. In all cases IQ was > 70. The mean age of probands was 33.8 years (SD = 10.1, range 13-57 years). The mean age at onset of psychotic symptoms was 22.1 years (SD = 6.6, range 11-44 years).
Sonicated patient and reference DNA was labelled by random priming (Bioprime Array CGH, Invitrogen, Carlsbad, CA) with Cy3 and Cy5 (Amersham Biosciences, Piscataway, NJ), respectively, and hybridized onto a tiling path BAC array, consisting of ~36,000 BAC clones obtained from several sources as described on our website (http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/). All protocols are also provided on that website. For the analysis and visualization of array CGH data, our software-package CGHPRO was employed. For the assessment of copy number gains and losses, we used conservative log2 ratio thresholds of 0.3 and -0.3, respectively. Deviant signal intensity ratios involving three or more neighboring BAC clones were considered to be potentially pathogenic, unless they were covered by more than one known DNA copy number variant, as listed in the Database of Genomic Variants. No dye swap was done. Array CGH analysis was successful in 91 cases.


title: Detailed transcriptome atlas of the pancreatic beta cell

status: Public on Dec 31 2008

city: Seattle

first: Burak

last: Kutlu

address: 1441 North 34th Street

institute: Institute for Systems Biology

summary: The aim of the present study was to explore the transcriptome of pancreatic islets and, based on this information, to prepare a comprehensive and open access inventory of insulin-producing β-cell gene expression, the beta-Cell Gene Atlas (BCGA).

overall_design: INS-1 cells, primary rat beta-cells (>87% beta-cells) and non-beta-cells (<3% beta cells, mostly alpha) were isolated by FACS mediated purification of two different rat islet preparations.


title: Expression data from isolated perfused rat hearts exposed to doxorubicin

city: Zurich

last: Zaugg

address: Raemistrasse 100

department: Anesthesiology

country: Switzerland

institute: Anesthesiology, University Hospital Zurich

summary:
We used microarrays to detail transcriptional changes in the rat heart in response to doxorubicin, a chemotherapeutic drug known to induce cardiac disfunction/heart failure

Keywords: treatment vs control

overall_design: Langendorff perfusion of isolated hearts with/without doxorubicin

first: Eliana

last: Lucchinetti

first: Malgorzata

last: Tokarska-Schlattner


title: Daily Rhythm in Expression of over 600 Genes in the Rodent Pineal Gland: Dominant Role of Adrenergic/cAMP Signaling

first: David

last: Klein

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Azoxymethane induced changes in Rat proximal and distal colonic epithelium.

status: Public on Dec 05 2008

city: Sydney

first: Caroline

middle: Audrey

last: Kerr

state: NSW

address: 11 Julius Ave North Ryde

department: Moelcular health Technologies

country: Australia

institute: CSIRO

summary:
Comparison of global gene expression in the proximal and distal colonic epithelium in azoxymethane treated rats.

Keywords: disease state analysis

overall_design:
Ten male Sprague Dawley rats weighing approximately 245 ± 14.5 g were housed in wire-bottomed caging in a temperature controlled room (22-24°C) with a 12 h light/dark cycle. They were randomly allocated into two groups (n=5) with approximately equal body weights.  They were given free access to water and modified AIN-93G diet for 10 days when they were injected with 15 mg of AOM/kg subcutaneously (Sigma Chemical Co., St. Louis, MO, USA).  They were anaesthetised with isoflurane and killed by exsanguination six hours after injection. The large bowel (excluding the rectum) was removed, opened longitudinally along the mesenteric border and digesta removed. The colon was rinsed clean with PBS and transferred to a chilled ceramic plate.  The most distal and the most proximal 0.5 cm were discarded.  Mucosal samples for gene expression and protein analyses were collected by scraping the next 4 cm of proximal and distal colon with new microscope slides.
The mucosal scraping was transferred into RNAlater (Sigma Chemical Co., St. Louis, MO, USA) and stored at -80oC for later processing.  All instruments were replaced or cleaned thoroughly between animals.  All procedures involving animals were approved by the Commonwealth Scientific and Industrial Research Organisation (CSIRO) Human Nutrition Animal Ethics Committee and complied with the Australian code of practice (2004).
The distal and proximal colonic mucosal samples were removed from the RNAlater stabilisation reagent (Sigma, Australia) and placed in 1ml of TRIzol® Reagent (Invitrogen, Sydney, N.S.W., Australia). Samples were then homogenised using beads (mix of 2.5mm glass and 0.1 - 1.0mm diameter silicon-zirconian beads) in a MiniBeadbeater-8™ (BioSpec Products Inc. Oklahoma, US). Total RNA was then extracted according to the TRIzol® Reagent manufacturer’s instruction after which samples were further purified using RNAeasy mini spin columns (QIAGEN, Doncaster, Victoria, Australia) with a DNase on-column digestion as per the manufacture’s instructions.  The integrity of the RNA was checked using a Bioanalyzer 2100 (Agilent Technologies) and quantified using a NanoDrop® ND-1000 Spectrophotometer.
RNA (4.5ug) samples were processed for Microarray expression analysis using high-density oligonucleotide arrays (Affymetrix® GeneChip array, Affymetrix®, Santa Clara, CA, USA) commensurate with the manufacturer’s instructions.

middle: A

first: Barney

last: Hines

first: Siok

last: Hwee Tan

first: Rob

last: Dunne

first: Lauren

last: Bragg

first: Julie

last: Clarke

first: Trevor

last: Lockett

first: Richard

last: Head


title: MEF2 Regulated Genes

last: Flavell

summary:
Expression profiling in hippocampal neurons to identify activity-regulated genes controlled by MEF2
Experiments were conducted to identify activity-regulated MEF2 target genes.

Keywords: Gene knockdown and depolarization time course

overall_design: Neurons were depolarized with 55mM extracellular KCl for one or six hours in the presence of control or MEF2-specific shRNAs

first: Michael

last: Greenberg


title: Ghrelin treatment effects on hepatic gene expression in rats submitted to Bile Duct Ligation

status: Public on Dec 03 2008

city: Barcelona

first: Ramón

last: Bataller

address: C/Casanova, 143

department: Liver Unit

institute: Hospital Clínic, IDIBAPS

summary: Hepatic fibrosis, the wound-healing response to repeated liver injury, ultimately leads to cirrhosis. There is an urgent need to develop effective antifibrotic therapies. Ghrelin (encoded by Ghrl) is an orexigenic hormone that has pleiotrophic functions including protection against cell death1. Here we investigate whether ghrelin modulates liver fibrosis and protects from acute liver injury. Recombinant ghrelin reduced the fibrogenic response to prolonged bile duct ligation in rats. This effect was associated with decreased liver injury and myofibroblast accumulation as well as attenuation of the altered gene expression profile. Ghrelin also reduced fibrogenic properties in cultured hepatic stellate cells. Moreover, Ghrl-/- mice developed exacerbated hepatic fibrosis and liver damage after chronic injury. Ghrelin also protected rat livers from acute liver injury and reduced the extent of oxidative stress and the inflammatory response. In patients with chronic liver diseases, ghrelin serum levels decreased in those with advanced fibrosis and hepatic expression of the ghrelin gene correlated with expression of fibrogenic genes. Finally, in patients with chronic hepatitis C, single nucleotide polymorphisms of the ghrelin gene (-994CT and –604GA) influenced the progression of liver fibrosis. We conclude that ghrelin exerts antifibrotic effects on the liver and may represent a novel antifibrotic therapy.

overall_design: Rats were divided into three groups: control rats receiving saline (sham operation), rats with bile duct ligation receiving saline and rats with bile duct ligation receiving recombinant ghrelin (10 micrograms/Kg/day by a subcutaneous osmotic mimi-pump). For the microarray analysis samples from 6 rats were analyzed except for the ghrelin-treated group (5 rats).

first: Montserrat

last: Moreno

first: Fernando

last: Ramalho

first: Leandra

first: Laura

last: Conde

first: Pedro

last: Jares

first: Juan

last: Caballeria

last: Lozano

first: Ramon


title: Transcriptional profile of primary astrocytes expressing ALS-linked mutant SOD1.

status: Public on Dec 18 2008

city: Montevideo

first: Marcelo

middle: R.

last: Vargas

address: Av. Italia 3318

department: Neurobiología Celular y Molecular

country: Uruguay

institute: Instituto Clemente Estable

summary:
Amyotrophic lateral sclerosis (ALS) is caused by the progressive degeneration of motor neurons. Mutations in the Cu/Zn superoxide dismutase (SOD1) are found in about 20% of patients with familial ALS. Mutant SOD1 causes motor neuron death through an acquired toxic property. Although, molecular mechanism underlying this toxic gain-of-function remains unknown, evidence support the role of mutant SOD1 expression in non-neuronal cells in shaping motor neuron degeneration. We have previously found that in contrast to non-transgenic, SOD1G93A-expressing astrocytes induced apoptosis of co-cultured motor neurons. This prompted us to investigate whether the effect on motor neuron survival was related to a change in the gene expression profile. Through high-density oligonucletide microarrays we found changes in the expression of genes involved in transcription, signaling, cell proliferation, extracellular matrix construction, response to stress and steroid and lipid metabolism. Decorin, a small multifunctional proteoglycan, was the most up-regulated gene. Down-regulated genes included the insulin-like growth factor-1 receptor and the RNA binding protein ROD1. We also analyzed the expression of selected genes in purified motor neurons expressing SOD1G93A and in spinal cord of asymptomatic and early symptomatic ALS-rodent model.
The expression of mutated SOD1 in astrocytes cause gene expression changes with potential consequences for its interaction with motor neurons. The astrocyte-specific gene expression profile contributes to the identification of possible candidates for cell type-specific therapies in ALS
Keywords: Cell type comparison

overall_design:
Astrocytes were plated at a density of 2x104 cells/cm2 and maintained as described in Cassina P, et al.J Neurosci Res. 2002;67(1):21-9.
Confluent astrocytes monolayers were changed to supplemented L15 medium (Vargas et al., 2006) for 24h before RNA isolation. Total RNA was isolated with RNeasy kit/RNase-Free DNase Set (Qiagen, CA, USA). RNA quality was assessed with the A260/280 ratio and the 2100 Bioanalyzer  (Agilent Technologies, CA, USA) to ensure integrity of the samples used for microarray analysis.
Double-stranded cDNA was synthesized from 5 μg of total RNA and used for microarray analysis with the Rat Genome 230 2.0 array (Affymetrix, CA, USA). A total of six arrays divided in three control and three transgenic samples were used. Labeling was performed with one-cycle target labeling assay according to Affymetrix, including the eukaryotic poly-A RNA control and the eukaryotic hybridization control kit. Hybridization, washing and scanning were carried out as described in the Affymetrix GeneChip expression analysis technical manual at the Oregon State University’s Center for Genome Research and Biocomputing. Image processing was done using Affymetrix GCOS 1.4 software. The quality of hybridization and overall chip performance was determined by visual inspection of the raw scanned data and the GCOS-generated report file. Microarray data (.CEL files) was normalized using GC-RMA probe-level analysis in ArrayAssist 4.0 (Stratagene, CA, USA). Following variance stabilization and Log transformation, fold chance versus p-value was calculated using nontransgenic (NonTG) samples as base values.

middle: R

first: Mariana

last: Pehar

first: Joseph

middle: S

last: Beckman

first: Luis

last: Barbeito


title: Identification of a miRNA Regulatory Network in FACS-Purified Neuronal Progenitors at the Onset of Rat Neurogenesis

status: Public on Dec 01 2008

first: Joe

last: Nielsen

address: 49 Convent Drive BD49,5A75

institute: NIH/NINDS

summary:
Cortical development is a complex process involving the generation of neuronal progenitors, which proliferate and migrate to form the stratified layers of the maturing cortex. To identify microRNAs (miRNAs) and genes that may be important during early cortical development, we analyzed the expression profiles of rat neuronal progenitors obtained at embryonic day 11 (E11), E12 and E13 using microarrays.  Neuronal progenitors were purified from telencephalic dissociates with a positive-selection strategy using surface labeling tetanus-toxin and cholera-toxin and fluorescence-activated cell sorting.  We identified classes of miRNAs and mRNAs that were up-regulated or down-regulated in these neuronal progenitors as cortical development progressed from E11 to E13.  We present data that supports a regulatory role for miRNAs during the transition from neuronal progenitors into differentiating cortical neurons.
Keywords: Developmental

overall_design: Flow cytometry was used to isolate tetanus toxin+ and cholera toxin+ neuronal progenitors from embryonic days 11, 12 and 13 rat telencephalon.  4 biological replicates were obtained for each group using a pooled litters for each biological replicate on different prepararation days

first: Pierre

last: Lau

first: Dragan

last: Maric

first: Jeffery

last: Barker

first: Lynn

middle: D

last: Hudson


title: A Sphingosine 1-Phosphate 1 Receptor Agonist Modulates Brain Death-Induced Neurogenic Pulmonary Injury

status: Public on Jul 01 2010

city: Reno

first: Tong

last: Zhou

state: NV

address: 1664 N Virginia St

institute: University of Nevada School of Medicine

summary: Lung transplantation remains the only viable therapy for patients with end-stage lung disease; however, full utilization of this treatment strategy is severely compromised by the lack of donor lung availability. For example, the vast majority of donor lungs available for transplantation are obtained from brain death (BD) individuals. Unfortunately, the autonomic storm which accompanies BD often results in neurogenic pulmonary edema (NPE), thereby either producing irreversible lung injury or leading to primary graft dysfunction following lung transplantation. We previously demonstrated that sphingosine 1-phosphate (S1P), a phospholipid angiogenic factor and major barrier-enhancing agent, as well as S1P analogues serve to reduce vascular permeability and ischemia/reperfusion (I/R) lung injury in rodents via ligation of the S1P1 receptor, S1PR1. As primary lung graft dysfunction is induced by lung vascular endothelial cell barrier dysfunction, we hypothesized that SEW-2871, a S1PR1 agonist, may attenuate NPE when administered to the donor shortly after BD.  Significant lung injury was observed 4h after BD in a rat BD model with ~60% increases in BAL total protein, BAL cell counts, and lung tissue W/D weight ratios. In contrast, rats receiving SEW-2871 (0.1 mg/kg) 15 minutes after the induction of BD and assessed 4h later exhibited significant lung protection (~50% reduction, p=0.01) reflected by reduced BAL total protein, BAL cytokines concentrations, BAL albumin, BAL total cell count and lung tissue wet/dry (W/D) weights ratio. Microarray analysis at 4hrs revealed a global impact of both BD and SEW on lung gene expression with differential expression of a subclass of genes enriched in immune/inflammation response pathways across the 4 experimental groups. Overall, SEW served to attenuate the BD-mediated ie gene expression upregulation. Two potentially useful biomarkers, Tnf and Ccrl2, exhibited gene dysregulation by microarray analysis, which was validated by qPCR. We conclude that SEW-2871 significantly attenuates BD-induced lung injury and may serve as a potential candidate to improve human lung donor availability and transplantation outcomes.

overall_design: Animals were divided into four groups: sham, BD (A Fogarty catheter 4 Fr. was inserted and secured into the extradural space and inflated to induce BD), SEW (injection of SEW-2871), and BD/SEW. Three replicates each.

first: Saad

last: Sammani

first: Ki-Sung

last: Park

first: Rafe

last: Zaidi

first: Biji

last: Mathew

first: Ting

last: Wang

first: Yong

last: Huang

first: Yves

last: Lussier

first: Aliya

middle: N

last: Husain

first: Liliana

last: Moreno-Vinasco

first: Wickii

middle: T

last: Vigneswaran

last: Garcia


title: Expression from control subplate neurons with few synapses and cocultured subplate neurons with induced synaptogenesis

status: Public on Nov 24 2008

city: Ashburn

first: Claire

last: McKellar

state: VA

address: 19700 Helix Drive

institute: HHMI Janelia Farm Research Campus

summary:
The transcriptional events accompanying synaptogenesis are largely unknown, or have been studied in systems in which synapse formation occurs gradually over time.  With a system in which synaptogenesis is synchronized and controllable, molecular or biochemical techniques can be used to examine cellular events across cultures on a wide scale, as synapses develop.
Here, we have triggered synaptogenesis in immunopurified subplate neurons by coculturing with cortical feeder layers and have used microarrays to investigate the transcriptional events occuring in this more defined and controllable system.
Keywords: treatment type comparison, time course

overall_design: Affymetrix rat GeneChip microarrays were used to assess whether coculturing induces transcriptional changes in subplate neurons.  Subplate synapses develop rapidly following coculturing; an exposure to the feeder layer of only 48 hours is sufficient to detect a significant increase in the density of synapses, and is as effective as longer durations.  Within the first few minutes or hours of a cell's response to an exogenous signal, any primary transcriptional events are expected to involve activation of immediate early genes (IEGs), often transcription factors themselves, which may then turn on downstream target response genes encoding factors to be delivered to sites of action, such as synapses.  With the aim of searching for such downstream genes, microarrays were performed after 24 hours of coculturing, an intermediate timepoint between the likely phase of IEG transcription and the large wave of synaptogenesis seen between 24 and 48 hours of coculturing.  Additional microarrays were also performed after 96 hours of coculturing to assess transcriptional changes that might occur over longer timescales.  Five biological replicates of control and cocultured neurons at 24 and 96 hours were used, for a total of 20 microarrays.

middle: E

first: Carla

last: Shatz


title: Comparison of Environmental and Genetic models of ADHD

status: Public on Nov 21 2008

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: ADHD is the most common neurobehavioral disorder in school-aged children. In addition to genetic factors, environmental influences or gene x environmental interactions also play an important role in ADHD. One example of a well studied environmental risk factor for ADHD is exposure to polychlorinated biphenyls (PCBs). In this study, we investigated whether the well-established genetic model of ADHD based on the Spontaneously Hypertensive Rat (SHR) and a well established PCB-based model of ADHD exhibited similar molecular changes in brain circuits involved in ADHD. The brains from 28 male rats (8 SHR, 8 Sprague-Dawley (SD) controls, 8 Wistar-Kyoto (WKY) controls, and 4 PCB-exposed SD rats) were harvested at postnatal day 55-65 and RNA was isolated from six brain regions of interest. The RNA was analyzed for differences in expression of a set of 308 probe sets interrogating 218 unique genes considered highly relevant to ADHD or epigenetic gene regulation using the Rat RAE 230 2.0 GeneChip (Affymetrix).  Selected observations were confirmed by real time quantitative RT-PCR. The results show that the expression levels of genes Gnal, COMT, Adrbk1, Ntrk2, Hk1, Syt11 and Csnk1a1 were altered in both the SHR rats and the PCB-exposed SD rats. Arrb2, Stx12, Aqp6, Syt1, Ddc and Pgk1 expression levels were changed only in the PCB-exposed SD rats. Genes with altered expression only in the SHRs included Oprm1, Calcyon, Calmodulin, Lhx1 and Hes6.The epigenetic genes Crebbp, Mecp2 and Hdac5 are significantly altered in both models. The data provide strong evidence that genes and environment can affect different set of genes in two different models of ADHD and yet result in the similar disease-like symptoms.

first: Tania

last: DasBanerjee

first: David

middle: F

last: Berger

first: John

middle: P

last: Lombardo

first: Terje

last: Sagvolden

first: Stephen

middle: V

last: Faraone


title: Analyzing microarray data with transitive directed acyclic graphs

status: Public on Dec 30 2008

city: Memphis

first: Thomas

last: Sutter

state: TN

address: 3774 Walker Ave.

department: Biology

institute: University of Memphis

summary:
Test compound one, 5,6-benzoflavone (BNF), was known to act through both the Ah receptor and Nrf2 receptor pathways, while test compounds two and three, 3H-1,2-dithiole-3-thione (D3T) and 4-methyl-5-pyrazinyl-3H-1,2-dithiole-3-thione (OLT), were known to act through the Nrf2 receptor pathway.  Furthermore, D3T is known to be more potent and efficacious than OLT for Nrf2 activation.  OLT has been shown to exhibit 20-50% of the efficacy of D3T for inhibition of alfatoxin-induced heptic foci.  Nonetheless, because OLT is an approved drug, it is currently being evaluated in human phase II intervention trials of biomarkers of alfatoxin-related hepatocellular carcinoma.  More recently, BNF was shown to be an effective chemopreventive agent in the rat mammary carcinogen model, inhibiting 7,12-dimethylbenz(a)anthracene DNA adduct formation in liver and mammary cells by 96 and 83% respectively.
We used microarrays to study the structure activities that lie within the test compounds.
Keywords: treatment effect study

overall_design: Twenty female Sprague Dawley rats, were randomly divided into 4 groups of 5 each. Each group of rats were fed with Harlan Teklad Rodent diet, 4% mash diet (Control) or the same formulation containing either, 5,6-benzoflavone (BNF, 1650 mg/kg diet), 3H-1,2-dithiole-3-thione (D3T, 600 mg/kg diet), or 4-methyl-5-pyrazinyl-3H-1,2-dithiole-3-thione  (OLT, 500 mg/kg diet), for 24 days. The rats were sacrificed with carbon dioxide.  The livers were harvested within 3 min, rapidly frozen in liquid nitrogen, and stored at -80oC until they were processed


title: DNA topoisomerase IIbeta (topo IIbeta) regulates  gene expression in developing cerebellar granule cells (CGC)

status: Public on Nov 30 2008

city: Okayama

first: Kuniaki

middle: Sano

state: Okayama

address: 2-5-1, Shikata-cho

department: Department of Neurogenomics

institute: Okayama Univsersity

summary: We used microarrays to determine the global programme of gene expression regulated by topo IIbeta.

overall_design: We categorized the genes expressed in differentiating cerebellar neurons by analyzing the expression data on the basis of combination of two factors: induction during differentiation in vitro and susceptibility to a topo II-specific inhibitor, ICRF-193. The inhibitor not only inhibits the activity but also depletes the enzyme by selective degradation, practically knocking it down at the protein level. In addition, topo ΙΙbeta is the only target of topo II-specific inhibitors since these cells do not express topo IIalpha. raw data is missing

last: Sano

first: Kimiko

last: Tsutsui

first: Ken


title: Basal gene expression in bone

status: Public on Nov 15 2008

city: London

first: Simon

middle: Charles

last: Rawlinson

address: 4 Newark Street

institute: Bart's and The London School of Medicine and Dentistry

summary: Analysis of basal gene expression of the protective bones of the skull (parietals) and weight-bearing bones of the limb (ulnae)

overall_design: RNA extraction from normal bone


title: Microarray analysis of rat testis following combined fetal and postnatal DBP exposure

city: RTP

first: Longlong

last: Yang

address: 6 Davis Dr.

institute: CIIT Centers for Health Research

summary: Provided later

overall_design: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

first: Kamin

last: Johnson


title: Positional identification of Adamts16 variants linked to inherited hypertension

status: Public on Nov 01 2008

city: Washington, DC

first: Norman

middle: H

last: Lee

state: DC

address: 2300  I Street, N.W.

department: Pharmacology & Physiology

institute: The George Washington University Medical Center


title: Positional identification of Adamts16 variants linked to inherited hypertension: gene expression of congenic vs S rats

summary:
We used Affymetrix GeneChips to expression profile kidneys from Dahl salt-senstive hypertensive inbred strain and less hypertensive S.LEW(D1MCO4x1x3Bx1) congenic strain to identify genes downstream of Adamts16 (the function of Adamts16 has yet to be fully delineated). The S.LEW(D1MCO4x1x3Bx1) congenic animal is an S rat containing the LEWIS allele for Adamts16 instead of the S allele. It is hypothesized that allelic differences in Adamts16 in inbred rats is responsible for blood pressure variance. We further hypothesize that gene expression differences in the kidneys of S.LEW(D1MCO4x1x3Bx1) versus S result from sequence differences between the S and LEWIS alleles of Adamts16. Lastly, the downstream genes differentially regulated by the Adamts16 alleles may provide insight pertaining to the mechanism of blood pressure differences. Gene expression differences resulting from these kidney comparisons will be compared to the gene expression profiling experiments comparing siRNA-mediated knockdown of Adamts16 in NRK-52E kidney cells versus scrambled siRNA control.

Keywords: Genetic modification, disease state analysis

overall_design: Kidney RNA from 3 Dahl salt-sensitive rats was extracted for target preparation and hybridization onto Affymetrix GeneChips. We also isolated kidney RNA from 3 S.LEW(D1MCO4x1x3Bx1) congenic rats for target preparation and hybridization onto Affymetrix GeneChips.

first: Bryan

last: Frank

first: Bina

last: Joe