title: Assessing concordance of drug-induced transcriptional response in rodent liver and cultured hepatocytes

city: Indianapolis

first: Jeffrey

last: Sutherland

state: IN

address: Lilly Corporate Center

institute: Lilly Research Laboratories

summary:
The effect of drugs, disease and other perturbations on mRNA levels are studied using gene expression microarrays or RNA-seq, with the goal of understanding molecular effects arising from the perturbation.  Previous comparisons of reproducibility across laboratories have been limited in scale and focused on a single model.  The use of model systems, such as cultured primary cells or cancer cell lines, assumes that mechanistic insights derived with would have been observed via in vivo studies.  We examined the concordance of compound-induced transcriptional changes using data from several sources: rat liver and rat primary hepatocytes (RPH) from Drug Matrix (DM) and open TG-GATEs (TG), primary human hepatocytes (HPH) from TG, and mouse liver / HepG2 results from the Gene Expression Omnibus (GEO) repository.  Gene expression changes for treatments were normalized to controls and analyzed with three methods: 1) gene level for 9071 high expression genes in rat liver, 2) gene set analysis (GSA) using canonical pathways and gene ontology sets, 3) weighted gene co-expression network analysis (WGCNA).  Co-expression networks performed better than genes or GSA on a quantitative metric when comparing treatment effects within rat liver and rat vs. mouse liver.  Genes and modules performed similarly at Connectivity Map-style analyses, where success at identifying similar treatments among a collection of reference profiles is the goal.  Comparisons between rat liver and RPH, and those between RPH, HPH and HepG2 cells reveal low concordance for all methods.  We investigate differences in the baseline state of cultured cells in the context of drug-induced perturbations in rat liver and highlight the striking similarity between toxicant-exposed cells in vivo and untreated cells in vitro.
Gene expression studies in model systems are widely used for understanding the mechanism of drugs and other perturbations in biological systems.   Other researchers have examined the reproducibility of microarray studies between laboratories, or comparing microarrays and/or RNA sequencing.  However, no large scale studies have compared results from protocols which differ in minor details, or results generated in vivo vs. in vitro culture system thought to serve as useful models.   The rat liver is by far the most extensively studied model evaluating effects of drugs and other perturbations, and existing data allowed us to assess the level of concordance between rat liver and rat primary hepatocytes cultured in collagen-coated plates (i.e. “flat” culture) for hundreds of drugs.  We found that the mouse liver serves as a better model of the rat liver than do rat primary hepatocytes, even after allowing for differences due to pharmacokinetics.  The low concordance observed between rat liver and rat hepatocytes suggests that validating the utility of ‘omics data generated on emerging cell culture approaches (e.g. “organ-on-a-chip”, 3D-printed tissues) using rat cells and comparison to the rat liver may be necessary in order to gain confidence these approaches substantially improve on traditional culture models of human cells.

overall_design: To identify transcriptional changes in culture, rat primary hepatocytes (RPH) were isolated from three male Sprague Dawley rats. During the isolation and prior to perfusion, a lobe of liver was tied off to serve as the liver in situ reference sample.  Cells were isolated and samples from the cell pellet (time zero) and cells cultured for 4, 24 and 48 hours. Three biological replicates were generated for each group (one from each rat).  Each biological replicate was analyzed via 3 technical replicates, for a total of 9 array hybridizations per group.

last: Jolly

first: Keith

last: Goldstein

first: James

last: Stevens


title: A validated gene regulatory network and GWAS identifies early regulators of T-cell associated diseases (exon array)

status: Public on Nov 12 2015

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

summary: In this work we present an analytical strategy to systematically identify early regulators by combining gene regulatory networks (GRN) with GWAS.  We hypothesized that early regulators in T-cell associated diseases could be found by defining upstream transcription factors (TFs) in T-cell differentiation. Time series expression and DNA methylation profiling of T-cell differentiation identified several upstream TFs, of which TFs involved in Th1/2 differentiation were most enriched for disease associated SNPs identified by GWAS.

overall_design: Peripheral blood mononuclear cells (PBMCs) were prepared from fresh blood from 10 patients with seasonal allergic rhinitis and 10 healthy controls using Lymphoprep (Axis-Shield PoC, Oslo, Norway) according to the manufacturer’s protocol. PBMCs were stimulated with allergen extract (ALK-Abelló A/S; 100 μg/ml) or diluent (PBS) in RPMI 1640 supplemented with 2 mM L-glutamine (PAA Laboratories, Linz, Austria), 5% human AB serum (Lonza, Switzerland), 5 µM β–mercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, USA) and 50 µg/mL gentamicin (Sigma-Aldrich, St. Louis, Missouri, USA). After 17 hours of incubation, total CD4+ T cells were enriched from PBMCs by MACS negative sorting. Total RNA was extracted using a miRneasy Mini Kit (Qiagen, Valencia, CA, USA). The cRNA was prepared using a Low Input QuickAmp Labeling Kit. The expression microarray analyses were performed using Agilent SurePrint G3 Human Exon 4x180K Microarrays according to the manufacturer's instructions.

first: Mika

last: Gustafsson

middle: R

first: Sandra

last: Hellberg

first: Aelita

last: Konstantinell

first: Daniel

last: Eklund

first: Jan

last: Ernerudh

first: Antonio

last: Lentini

first: Robert

last: Liljenström

first: Johan

last: Mellergård

first: Hui

last: Wang

first: Colm

middle: E

last: Nestor

first: Huan

last: Zhang

first: Mikael

last: Benson


title: Expression data from adult wistar female rat 5mm spinal cord tissue

status: Public on Nov 02 2015

city: Los Angeles

first: Weihong

last: Ge

state: CA

address: 635 Charles E Young Dr South 355

country: USA

institute: UCLA

summary: We used microarray gene expression analyses to unveil the mechanisms underlying NT-3-chitosan-induced spinal cord regeneration.

overall_design: Complete transaction of thoracic spinal cord at T7/8 was performed, with a 5 mm segment of the spinal cord being removed. The emptied space where either refilled with a 5mm chitosan tube loaded with or without NT-3 (NT-3 or empty tube, ET, respectively) or left alone (lesion control, LC). At 1, 3, 10, 20, 30, 60, 90days post surgery, animals were sacrificed, and 5mm segments of spinal cord at the lesion site, as well as immediately caudal or rostral to the lesion segment were collected labeled with R for rostral, C for caudal, and M for lesion site

first: Xiaoguang

last: Li

first: Yi

last: Sun


title: Effect of LXR activation on LPS-induced inflammatory response in immortalized bone marrow macrophages from LXRa/b knockout mice stably expressing LXR wildtype, K328R/K434R or L439A/E441A mutant

status: Public on Oct 15 2015

first: Ayaka

last: Ito

state: California

address: 675 Charles E Young Dr. South

department: Pathology and Laboratory Medicine

institute: University of California, Los Angeles

summary: The liver X receptors (LXRs) are transcriptional regulators of lipid homeostasis that also have potent anti-inflammatory effects.  The molecular basis for their anti-inflammatory effects is incompletely understood, but has been proposed to involve indirect tethering of sumoylated LXRs to inflammatory gene promoters.  Here we demonstrate that the ability of LXRs to repress endogenous inflammatory gene expression in cells and mice derives from their ability to regulate lipid metabolism through transcriptional activation and does not require sumoylation or transrepression.  Moreover, we identify the putative lipid transporter ABCA1 as a critical mediator of LXR’s anti-inflammatory effects.  Ligand activation of LXR inhibits signaling from TLR4 to its downstream NF-κB and MAPK effectors through ABCA1-dependent changes in membrane lipid composition and organization that disrupt the recruitment of MyD88 and TRAF6.  These data suggest that a common mechanism–direct transcriptional activation–underlies the dual biological functions of LXRs in metabolism and inflammation.

overall_design: Cells were placed in DMEM containing 0.5% FBS, 5 μM simvastatin, 100 μM mevalonic acid and 1μM GW3965 or DMSO overnight.  Cells were then stimulated with 10ng/ml LPS or vehicle for 4 hours. Each sample contains pooled RNA from n=3-4 biological replicates.

first: Peter

last: Tontonoz


title: Identification of a potent and selective chemical probe for exploring the role of Mediator complex-associated protein kinases CDK8 and CDK19 in human disease [beta-catenin organoids]

status: Public on Oct 26 2015

city: Sutton

middle: te

last: Poele

state: Surrey

address: 15 Cotswold Road

department: Cancer Reserach UK Unit for Cancer Therapeutics

country: United Kingdom

institute: The Institute of Cancer Research

summary:
There is an unmet need for chemical tools to explore the role of the Mediator complex in human pathologies ranging from cancer to cardiovascular disease.  Here we determine that CCT251545
a WNT-pathway inhibitor discovered by cell-based screening
is a potent and selective chemical probe for the Mediator complex-associated protein kinases CDK8 and CDK19.  CCT251545 is an ATP competitive inhibitor with >100-fold selectivity over 291 other kinases. X-ray crystallography demonstrates Type 1 binding involving insertion of the CDK8 C-terminus into the ligand binding site.  In contrast to Type II inhibitors of CDK8/19
CCT251545 displays potent cell-based activity.  We show that CCT251545 and close analogues not only alter WNT-pathway regulated gene expression
but also other CDK8/19 targets including STAT1-regulated gene expression.   Consistent with this we find that phospho-STAT1SER727 is a biomarker of CDK8 kinase activity in vitro and in vivo.  Finally
we demonstrate in vivo activity of CCT251545 in WNT-dependent tumours.
Compound 1,2, 6 and 9 are close analogues of a 3,4,5-trisubstituted pyridine series identified from a high-throughput cell-based reporter assay of WNT signalling. They were shown to be potent and selective inhibitors of the Mediator complex-associated protein kinases CDK8 and CDK19.  They are ATP competitive inhibitors with >100-fold selectivity over 291 other kinases. X-ray crystallography demonstrates Type 1 binding involving insertion of the CDK8 C-terminus into the ligand-binding site.

overall_design:
A 3D culture model of murine intestinal-derived organoids expressing a transgenic doxycycline-inducible mutant beta-catenin expression following removal of doxycycline results in reduced WNT signalling and was compared to treatment for 24 hours with coumpound 2,  6 and 9. Compound 2 (n=3), compound 6 (n=4), compound 9 (n=3), doxycycline removal (n=4), doxycycline treatment (n=7). Samples were hybridized agianst mouse reference.
Compounds 2, 6 and 9 are close analogues of a 3,4,5-trisubstituted pyridine series identified from a high-throughput cell-based reporter assay of WNT signalling. They were shown to be potent and selective inhibitors of the Mediator complex-associated protein kinases CDK8 and CDK19.  They are ATP competitive inhibitors with >100-fold selectivity over 291 other kinases. X-ray crystallography demonstrates Type 1 binding involving insertion of the CDK8 C-terminus into the ligand-binding site.

first: Trevor

last: Dale

first: Paul

middle: A

last: Clarke

first: Christina

last: Esdar

first: Dennis

last: Waalboer

first: Olajumoke

last: Adeniji-Popoola

first: Maria-Jesus

last: Ortiz-Ruiz

first: Aurelie

last: Mallinger

first: Rahul

last: Samant

last: Czodrowski

first: Djordje

last: Musil

last: Schwarz

first: Klaus

last: Schneider

first: E

middle: V

first: A

last: Lammens

first: Mark

last: Stubbs

first: Ken

last: Ewan

first: Elizabeth

last: Fraser

middle: H

last: te Poele

first: Will

last: Court

first: Gary

last: Box

first: Melanie

last: Valenti

first: Alexis

last: de Haven Brandon

first: Sharon

last: Gowan

first: Felix

last: Rohdich

first: Florence

last: Raynaud

first: Richard

first: Oliver

last: Poeschke

first: Andree

last: Blaukat

last: Workman

first: Kai

last: Schiemann

first: Suzanne

last: Eccles

first: Dirk

last: Wienke

first: Julian

last: Blagg


title: Pramipexole induced place preference promoted after L-dopa therapy and nigral dopaminergic loss: linking behavior to transcriptional modifications

status: Public on Oct 28 2015

city: Clermont-Ferrand

first: Simon

last: Loiodice

address: 28 Place Henir Dunant

department: Faculté de médecine

country: France

institute: Université d'Auvergne

summary:
Symptoms of the dopamine dysregulation syndrome in patients with Parkinson’s disease (PD) are close to those observed in psychostimulant addiction. This suggests that dopamine replacement therapy shares some properties with potentially addictive drugs. A remaining challenge is to understand the neuroadaptations leading to compulsive dopaminergic medication use.
To this end,  the reinforcing properties of the D2/D3 agonist pramipexole (PPX) were assessed after chronic exposure to L-dopa in an alpha-synuclein PD rat model.

overall_design: Individual male rats underwent a bilateral nigral loss induced by AAV-mediated alpha-synuclein overexpression. Control sham animals received stereotaxic injection of the same AAV vector enabeling expresion of the GFP. Five weeks after lesion induction, animals received a subcutaneous daily administration of L-dopa methyl-ester (50mg/kg) plus benserazide (12,5mg/kg) or a saline solution. Following this 3 weeks period of chronic treatment, the reinforcing properties of the D2/D3 agonist pramipexole were assessed using a place conditioning paradigm. This procedure consists in pairing a drug with a specific environment and vehicle with another environment during a conditioning period. The first day, animals received an intraperitoneal injection of saline solution before a 20min habituation period that allowed exploration of the apparatus (pre-test). Time spent in each chamber was analyzed. The compartment less occupied by the animal was determined as the drug paired side. The following days, animals received either pramipexole 2mg/kg on days 1, 3, 5 and 7 or vehicle on days 2, 4, 6 and 8 and were placed in the paired-chamber for 40 minutes. Controls groups received saline solution during all conditioning sessions. The day following the last conditioning session, a probe test (post test) was performed with 20min free access to the apparatus after an ip injection of saline solution. Place preference scores were calculated as the difference in time spent in the drug-paired chamber between post-test and pre-test.

first: Poppy

last: Winlow

first: Sarah

last: Dremier

first: Etienn

last: Hanon

first: Aziz

last: Hafidi

first: André

last: Nogueira da Costa

first: Franck

last: Durif


title: Effect of LXR activation on LPS-induced inflammatory response in primary bone marrow macrophages from ABCA1fl/fl LysM Cre and control wildtype mice

first: Ayaka

last: Ito

overall_design: Cells were placed in DMEM containing 0.5% FBS, 5 μM simvastatin, 100 μM mevalonic acid and 1μM GW3965 or DMSO overnight.  Cells were then stimulated with 10ng/ml LPS or vehicle for 4 hours.Each sample contain contains pooled RNA from n=3-4 biological replicates.

first: Peter

last: Tontonoz


title: Gene expression profiling of novel glucocorticoids in RAW264.7 cells

status: Public on Oct 06 2015

city: Grand Rapids

first: Eric

last: Xu

state: MICHIGAN

address: 333 Bostwick Ave

institute: Van Andel Institute

summary: To investigate the anti-inflammation activity of novel glucocorticoids on gene expression of macrohpage cells, we use mouse macrophage RAW264.7 cells to profiling gene expression pattern of novel glucocorticoids upon the onset of inflammation response.

overall_design: Pretreated cells with various glucocorticoids (Dexamethasone, VSG22, VSGC12 and Fluticasone Furoate) one hour before induction of inflammation resposne via LPS for overnight, each treatment has two replicate. 16 hours after treatment, harvest total RNA for gene profiling.

first: Xiang

last: Gao

first: Yuanzheng

last: He


title: Whole genome amplification effect on segmental copy-number changes and copy-number neutral loss of heterozygosity analysis by oligonucleotide-based array-comparative genome hybridization

status: Public on Sep 29 2015

city: Newcastle upon Tyne

first: Aneta

last: Mikulasova

address: Brewery Lane

department: Biosciences Institute

institute: Newcastle University

type: Genome variation profiling by genome tiling array

summary:
Background: Insufficient quantities of human genomic DNA are a limiting factor for many clinical applications. Whole genome amplification (WGA) is an approach designed to overcome small amount of DNA for genome-wide genetic tests as it allows amplification of the entire genome from picogram or nanogram quantities of DNA. Various strategies of WGA have been developed; however, none of them can guarantee the absence of amplification bias. High-quality genome-representative amplified DNA is crucial for WGA use in basic research and clinical genetics. Thus, systematic evaluation of WGA effect on downstream methods is necessary.
Results: In this paper, 4 multiple displacement amplification (MDA) -based and 2 PCR-based WGA kits were compared in their effect on segmental copy-number changes as well as copy-number neutral loss of heterozygosity detection by high-density oligonucleotide DNA arrays. We described outcomes and limits for each individual WGA; however, the main goal of this study was chiefly to show a general compatibility and features specific for particular WGA strategy. The main outcomes are as follows: 1) MDA-based WGAs showed higher tendency to generate false positive imbalances in contrast to PCR-based WGAs with higher risk of false negativity; 2) the specific risk of false positivity and/or negativity increased with decreasing copy-number segments size; 3) single-cell WGAs showed significantly worse effect on results in comparison to WGAs with nanogram level of DNA as input; 4) PCR-based WGAs were not compatible with copy-number neutral loss of heterozygosity analysis based on single nucleotide polymorphisms in restriction digestion sites and also showed higher risk of copy-number neutral loss of heterozygosity false negativity if combined with analysis based on simple hybridization.
Conclusions: This study gives a comprehensive insight into the WGA effect on DNA array analysis. The results of this study help to choose WGA according to individual user requirements and options. Moreover, we show a strategy to verify and validate segmental copy-number changes detection by DNA array protocol including any WGA for any purpose to attain the highest efficiency without an unnecessary WGA bias.

overall_design: 6 WGAs were tested and compared to unamplified control by 3 aCGH platforms. Experiments were performed in duplicates. Taken together, 42 hybridizations were done.

first: Jan

last: Smetana

first: Marketa

last: Wayhelova

first: Helena

last: Janyskova

first: Roman

last: Hajek

first: Petr

last: Kuglik


title: Gene expression profiles of rat liver tissues after high-fat emulsion feeding

city: Xinxiang

first: Cunshuan

address: No. 46, Construction East Road

country: China

institute: Henan Normal University

summary:
Nonalcoholic fatty liver disease (NAFLD) is a common disorder characterized by excessive hepatic fat accumulation, and potentially resulting in non-alcoholic steatohepatitis (NASH), liver cirrhosis (LC) and end-stage liver disease
We used Rat Genome 230 2.0 microarray to further highlight the rat liver tissues after high-fat emulsion feeding.

overall_design: The rat model of nonalcoholic fatty liver disease (NAFLD) was established, and the expression profiles of liver tissues from NAFLD were detected at  2, 4, and 6 weeks using Rat Genome 230 2.0 array. Then the significantly changed genes related to NAFLD were identified. The relevance of gene expression profiles and biological processes was analyzed by bioinformatics and systems biology.

first: Gaiping

last: Wang

first: Yunpeng

last: Hao

first: Jia

last: Zhi

first: Shasha

last: Chen


title: Identification of differential expressed genes among P-RPC, rESC-RPC1 and rESC-RPC2 through genome-wide transcript profiling

status: Public on Oct 01 2015

city: Shanghai

first: Zepeng

last: Qu

address: 280 South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Degenerative retinal diseases like age-related macular degeneration (AMD) are the leading cause of blindness. Cell transplantation showed promising therapeutic effect for such diseases, and retinal progenitor cell (RPC) derived from embryonic stem cell (ESC) is one of the sources of such donor cells. Here, we established two protocols through which two types of rat ESC-derived RPCs (rESC-RPCs) were obtained and both contained some NPCs and committed retina lineage cells. As P-RPCs have been reported to successfully integrate into host eyes, we sough to identify differentially expressed genes among P-RPCs, rESC-RPC1s and rESC-RPC2s through genome-wide transcript profiling. rESC-RPC2 can integrate into the host retina, form synaptic connections and restore visual function after transplanted into the degenerative retinal disease model RCS rat.

overall_design: RPCs differentiated from rESCs following two different protocols were divided into two groups for RNA extraction and hybridization on Affymetrix microarrays. For rESC-RPC1, the cells were switched to adherent culture at D10, while for rESC-RPC2, the suspension culture was maintained to D14. Both RPCs were harvested at D16. P-RPCs derived from the newborn (P1) SD rat retina were applied as positive control. Each group above had three independent biological repeats.


title: Gene expression profiles of rat liver tissues after diethylnitrosamine treatment

summary:
Hepatic cancer (HC), as one of the common malignancies in the world, is characterized by malignant cell prolifeHCion and growth, and hepatocarcinogenesis covers the stages of non-specific liver injury, liver fibrosis, liver cirrhosis, dysplasia nodules and finally liver carcinoma
We used HC Genome 230 2.0 microarray to further highlight the regulatory role of rat liver tissues after diethylnitrosamine treatment.

overall_design: The rat model of hepatic cancer (HC) was established, and the expression profiles of liver tissues from HC were detected at 5, 8, 12, 16 and 18 weeks using Rat Genome 230 2.0 array. Then the significantly changed genes related to HC were identified. The relevance of gene expression profiles and biological processes was analyzed by bioinformatics and systems biology.


title: Quercetin showed no genotoxicity by transcriptomic analysis in liver and small intestine of mice

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: Given the positive results of quercetin in in vitro genotoxicity studies, it is of interest to test the in vivo genotoxicity of this important dietary flavonoid, especially considering possible high intake by widely available supplements. In the present study quercetin was tested in a transcriptomic analysis for genotoxicity in liver and small intestine of mice.    Quercetin (0.33%) supplemented to a high-fat diet was administered to mice during 12 weeks and compared with high-fat diet feeding. Serum ALT and AST levels revealed no indications for hepatotoxicity. General microarray pathway analysis of liver and small intestinal tissue samples showed no regulation of genotoxicity related pathways. In addition, analysis of DNA damage pathways in these samples, also did not point at genotoxicity. Furthermore, comparison with a published classifier set of transcripts for identifying genotoxic compounds did not reveal any similarities with the regulation of these classifier set of transcripts by quercetin, except for two of the transcripts which were regulated in opposite direction. Available microarray datasets of known genotoxic compounds, 2-acetylaminofluorene (2-AAF) and aflatoxin B1 (AFB1) in mice were taken along as positive controls for comparison, and indeed showed genotoxic properties (regulation of genotoxic related genes) in the analyses.  This transcriptomic study showed that supplementation with quercetin at ~350 mg/kg bw/day for 12 weeks in mice gave no indications of quercetin-induced genotoxicity in liver and small intestine.

overall_design: Small intestinal samples were obtained from 24 C57BL/6J male adult mice. All mice started with a three week adaptation phase, in which they were fed a normal-fat diet.  During the intervention of 12 weeks, the mice received a high-fat diet without (HF) or with supplementation of 0.33% (w/w) quercetin (HF-Q). One quercetin fed mouse was excluded from all analyses, because a nasal abscess developed in week 6.

first: Elise

middle: F

last: Hoek-van den Hil

middle: M

first: Jaap

last: Keijer


title: Gene expression profiles of rat liver tissues after carbon tetrachloride treatment

last: Xu

summary:
Acute hepatic failure (AHF) usually occurs due to the rapid necrosis of liver cells or serious liver injury induced by a variety of pathogenic factors.
We used Rat Genome 230 2.0 microarray to further highlight the rat liver tissues after carbon tetrachloride treatment.

overall_design: The rat model of acute hepatic failure (AHF) was established, and the expression profiles of liver tissues from AHF were detected at 3, 6, 12, 24, 48 and 72 hours using Rat Genome 230 2.0 array. Then the significantly changed genes related to AHF were identified. The relevance of gene expression profiles and biological processes was analyzed by bioinformatics and systems biology.


title: Gene expression signature of HoxA9-Meis1 AML cells treated with Pyrydopyrazine

status: Public on Sep 02 2015

city: Dijon

first: ronan

last: quere

address: 7 bd Jeanne d'Arc

institute: Inserm U866

summary: Pyrydopyrazine A2 induced in vitro the differentiation of leukemic cells (HoxA9-Meis1) into macrophages, we decided to perform a transcriptomic study in order to analyze the GM-CSF pathway regulation. We therefore compared effect with A2 to cells treated with Retinoic acid and D3 Vitamin, a combination known to induce also differentiation of leukemic cells.

overall_design:
HoxA9-Meis1 murine AML cells were treated in vitro during 24h, with Pyrydopyrazine( A2) at 3.4μM or a combination of all-trans Retinoic Acid (RA) and 1α-hydroxy-D3 Vitamin (D3V), 10μM each. Gene expression signature was compared to untreated control.
One sample was tested for each condition

first: Ronan

last: Quéré


title: Identification of s-RNYs targets in bone marrow-derived macrophages

status: Public on Sep 16 2015

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Bone marrow-derived macrophages (BMDMs) were collected from 4 C57BL/6J males and transfected with siRNAs against the terminal loop of mouse RNYs and control. 48 hr after transfection, the total RNA was isolated by using RNAeasy kit (Qiagen) and mRNA profiling was performed on Agilent Sureprint whole genomemicroarrays. The normalized data were analyzed with Biometric Research Branch (BRB) array tools 3.8.0. Log2-transformed signal intensities were used to identify probes with at least 1.2 fold change of expression difference between BMDMs overexpressing s-RNYs and control, and with a statistically significant p-value (p<0.05).

overall_design: One color design, corresponding to 2 conditions performed on 4 mice: siRNA against terminal loop of RNY versus Control (Ct) siRNA for a total of 8 samples.

first: Michelle

last: Trabucchi

first: B

last: Mari

first: P

last: Barbry

first: K


title: Effect of exogenous FABP4 (A-FABP/aP2) with and without palmitic acid on gene expression in RAW264.7 macrophages

status: Public on Sep 19 2015

city: Sapporo

first: Masato

last: Furuhashi

country: Japan

institute: Sapporo Medical University School of Medicine

summary: Gene expression profile of FABP4 treatment in RAW264.7 macrophages was examined to show a ligand (palmitic acid)-dependent and a ligand-independent effect of FABP4.

overall_design: RAW264.7 macrophages were treated with and without 200 nM recombinant FABP4 in the absence and presence of 0.2 mM palmitic acid.


title: Expression data from predose and postdose rat blood after acetaminophen treatment

status: Public on Sep 07 2015

city: Hangzhou

first: Xiaoyan

last: Lu

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

summary:
Predose and postdose gene expression profiles of blood samples of five most susceptible and five most resistant rats to acetaminophen-induced hapatotoxicity were determined by microarray analysis.
Four out of ten selected genes were found to be reproducibly in real-time PCR with independent set animals to predict the susceptible individuals to acetaminophen-induced hapatotoxicity.

overall_design: We combined gene expression profiles of predose and postdose rat blood to predict the susceptible individuals to acetaminophen-induced hapatotoxicity.

first: Bin

last: Hu

first: Cai

last: Ji

first: Xiaohui

last: Fan


title: Expression profile of control, Drosha or Dicer deleted LSKs

status: Public on Sep 10 2015

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

summary: To determine genes regulated independently of microRNAs in early haematopoietic progenitors (LSKs) we compared the expression profiles of Drosha or Dicer deficient LSKs and control. Those genes differentially expressed between Drosha or Dicer deficient LSKs are likely regulated indepedently of microRNAs as either Drosha or Dicer deletion will lead to a complete and equivalent loss of microRNAs.

overall_design: LSKs were sorted from control, Drosha fl/fl of Dicer fl/fl mice.These cells were activated in vitro for 72 hours to induce total and equivalent deletion of Drosha or Dicer. RNA was extracted after 72 hours.3 repeats of the three groups were analyzed.

first: Tim

last: Johanson

first: Marek

last: Cmero

first: Amit

last: Kumar

first: Yifan

last: Zhan

first: Andrew

last: Lew


title: Transcriptomic Responses to Prion Disease in Rats

status: Public on Sep 01 2015

city: Edmonton

first: Allen

last: Herbst

state: AB

address: 114C BARB

country: Canada

institute: University of Alberta

summary: While prion infections have been extensively characterized in the laboratory mouse, little is known regarding the molecular responses to prions in other rodents. To explore these responses and make comparisons, we generated a prion disease in the laboratory rat by successive passage of mouse RML prions. Here we describe the accumulation of prions and associated pathology in the rat and describe the transcriptional impact throughout prion disease.  Comparative transcriptional profiling between laboratory mice and rats suggests that similar molecular processes are unfolding in response to prion infection. At the level of individual transcripts, however, variability exists between mice and rats and many genes deregulated in mouse scrapie are not affected in rats. Notwithstanding these differences, many transcriptome responses are conserved between mice and rats infected with scrapie. Our findings highlight the usefulness of comparative approaches to understanding neurodegeneration and prion diseases in particular.

overall_design: We Adapted RML Mouse Scrapie into Rats and measured the resulting gene expression changes in brain as a result of disease progression. Rats were infected by intracranial inoculation with prion isolates obtained by adaptation of mouse RML scrapie prions into rats. Brain samples were collected from third and fourth passage infected rats and age-matched controls at specified timepoints and gene expression profiles obtained. For each time point, 3 diseased and control brain samples were profiled.

first: Judd

last: Aiken


title: Gata6 induced XEN-like cells w/o Sox7

status: Public on Sep 14 2015

city: Kobe

first: Hitoshi

last: Niwa

state: Hyogo

address: 2-2-3 Minatojima-minamimachi,Chuo-ku

department: Center for Developmental Biology

institute: RIKEN

summary: To understand the role of Sox7 in primitive endoderm differentiation, we compare the gene expression pattern of Sox7 (+/-) and Sox7 (-/-) ES cells with or without dexamethasome (Dex) treatment. Because these ES cells harbour Gata6-GR transgene, Dex treatment forces ES cells differentate into XEN-like cells. As Sox7 (-/-) ES cells can differentiate into XEN-like cell by morphology,  we assessed genome wide gene expression pattern.

overall_design: Sox7 (+/-) ES cells and Sox7 (-/-) ES cells are forced to differentiate into XEN-like cells by Gata6-GR transgene. To compare the gene expression, we collected RNA samples at day4 with or without dexamethasone treatment from each genotype.

first: Masaki

last: Kinoshita

first: Mariko

last: Yamane


title: Gene expression changes associated with exposure to BHPF in mice

status: Public on Oct 16 2015

city: Beijing

first: Zhaobin

last: Zhang

address: Yiheyuan Road 5#

institute: Peking Univ

summary: To identify the gene expression changes associated with exposure to fluorene-9-bisphenol (BHPF), analysis of global gene expression profiles in the uteri, ovaries, and livers of mice treated with 50 mg/kg/day of BHPF for 3 days compared with those of control mice was performed by means of an Agilent mouse gene expression microarray.

overall_design: Gene expression changes in in the uteri, ovaries, and livers of immature mice treated with 50 mg/kg/day of BHPF for 3 days was compared with those of control mice.

first: Zhang

last: Zhaobin


title: Transcriptomic analysis of early response of rat brain orthotopic tumors after synchrotron microbeam irradiation (MRT)

city: LA TRONCHE

first: Michèle

last: EL ATIFI

address: Chemin fortuné ferrini

institute: INSERM

summary: The aim of this study was to identify the transcriptomic response 6 hours after the MRT irradiation, in normal brain tissue (11 samples) and in glioma tissue (11 samples), in rat.

overall_design: The orthotopic tumor-bearing rats were either treated with MRT radiation (six MRT-tumors), or untreated (five No irradiated tumors). The contralateral half hemisphere without tumor received the MRT treatment for six rats (6 MRT-Contralateral samples) and no irradiation for five rats (5 Untreated contralateral samples). Six hours after treatment, the tumors and their controlateral regions were resected and analysed for transcriptomic response.

first: Audrey

last: Bouchet

first: Nathalie

last: Sakakini

last: El Atifi

first: Céline

last: Le Clec’h

first: Elke

last: Brauer

first: Anaïk

last: Moisan

first: Pierre

last: Deman

first: Pascal

last: Rihet

first: Géraldine

last: Le Duc

first: Laurent

last: Pelletier


title: Gene expression analysis of WT, HBZ-Tg, IFNgKO, and HBZ-Tg/IFNg KO mice.

status: Public on Aug 25 2015

city: Kyoto

first: Yu

last: Mitagami

address: Sakyo-ku

institute: IVR

summary: Comprehensive analysis of gene expression in CD4+ T cells of WT, HBZ-Tg, IFNgKO, and HBZ-Tg/IFNg KO mice.

overall_design: CD4+ T cells were isolated from splenocytes of each strain. From isolated CD4+ T cells, RNAs were extracted and used for microarray analysis.

first: Jun-ichirou

last: Yasunaga


title: Time course expression data from Brown Norway rat livers treated with nevirapine or galactosamine or both

status: Public on Aug 15 2015

city: Research Triangle Park

first: Neal

last: Cariello

state: NC

address: 5 Moore Drive, Bldg 9, Rom 2011

department: Safety Assessment

institute: GlaxoSmithKline

summary:
Nevirapine alone produces only mild hepatic hypertrophy in the rat. Single ip dose galactosamine produces transient hepatocellular apoptotic and oncotic cell death mimicking viral hepatitis with portal inflammatory infiltrate and biliary hypertrophy and hyperplasia. Damage is typically resolved within 7-10 days. However if rats are pretreated with nevirapine at specific doses for 7 days prior to the single galactosamine dose, bridging fibrosis is observed, 8 days after the single galactosamine dose is given.
We used microarrays to detail the global programme of gene expression underlying the sequential responses of nevirapine alone, galactosamine alone, and the identified distinct classes of up-regulated genes during this process.

overall_design: 50 liver samples were analyzed.  Liver samples were snap frozen in liquid nitrogen from rats dosed with nevirapine (150, 100,75 mg/kg) for 7 days before a single ip dose of galactosamine at 750 mg/kg and then euthanized eight days later (nevirapine group). Comparisons were made to rats dosed with nevirapine (75 mg/kg) only for 15 days (nevirapine group) and to rats dosed with a single ip galactosamine only dose (750 mg/kg) and euthanized after 8 days (galactosamine group). The purpose was to examine the 8 day period over which fibrosis occurred when the nevirapine and galactosamine co-administration produced fibrosis and the single drug dosages did not. Time points after galactosamine administration (3 hr, 24 hr, 48 hr and 8 days) were chosen for sampling.

first: Lawrence

last: Yoon

first: Roger

last: Brown


title: Whole genome microarray gene expression profiling of hippocampal genes from aged rats subjected to chronic unpredictable mild stress

status: Public on Aug 13 2015

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

summary: Psychological, psychosocial and physical stress are major risk factors, which enhance the development of sporadic late-onset Alzheimer`s disease. The chronic unpredictable mild stress model mimics those risk factors and triggers signs of neurodegeneration and neuropathological features of sporadic AD such as tau hyperphosphorylation and enhanced amyloid beta generation. The study investigated the impact of chronic unpredictable mild stress on signs of neurodegeneration by analyzing hippocampal gene expression with whole genome microarray gene expression profiling.

overall_design: Whole genome microarray gene expression profiling was performed to study the impact of stress on hippocampal gene expression. Aged male rats (15 months of age) were subjected to the chronic unpredictable mild stress (CUMS) battery for four weeks. Thereafter at an age of 16 months, 4 h before the beginning of the dark phase, rats were anesthetized, the hippocampus was dissected out on ice and processed for whole genome microarray gene expression profiling according to the protocol of the manufacturer (Affymetrix). The study used the GeneChip Rat Genome 230 2.0 Array for whole genome gene expression analysis of hippocampal genes from stressed rats relative to age-matched non-stressed controls.Two biological replicates were made of each group, and total hippocampal RNA of three rats was pooled for one gene chip.

first: Said

last: AbdAlla


title: Transcription Dynamically Patterns the Meiotic Chromosome-Axis Interface [ChIP-chip]

status: Public on Aug 06 2015

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

type: Genome binding/occupancy profiling by genome tiling array

summary: Meiotic chromosomes are highly compacted yet remain transcriptionally active. To understand how chromosome folding accommodates transcription, we investigated the assembly of the axial element, the proteinaceous structure that compacts meiotic chromosomes and promotes recombination and fertility. We found that the axial-element proteins of budding yeast are flexibly anchored to chromatin by the ring-like cohesin complex and biased towards small chromosomes by a separate modulating mechanism that requires the conserved axial element component Hop1. The ubiquitous presence of cohesin at sites of convergent transcription provides well-dispersed points for axis attachment and thus compaction. Axis protein enrichment at these sites directly correlates with the propensity for recombination initiation nearby. Importantly, axis anchoring by cohesin is adjustable and readily displaced in the direction of transcription by the transcriptional machinery. We propose that such robust but flexible tethering allows the highly structured axial element to promote recombination while easily adapting to changes in chromosome activity.

overall_design: Two types of study were undertaken to understand the meiotic chromosomal axes assembly and its importance in DSB regulation in yeast. First, DSBs were mapped using ssDNA enrichment in strains isogenic for a dmc1 mutation, and also including rec8 deletion and pREC8-SCC1 in rec8 deletion. Second, the genome-wide distribution of meiotic or mitotic cohesin in meiosis was measured by ChIP-chip analysis in wild-type and pREC8-SCC1 in rec8 deletion.

first: Xiaoji

last: Sun

first: Hannah

middle: G

last: Blitzblau


title: mRNA expression data for rat liver treated for 24h with RG3487 (180mg/kg po.) vs vehicle only (deionized water)

status: Public on Aug 26 2015

city: Basel

first: Laura

last: Badi

address: Grenzacherstrasse

institute: Hoffmann La Roche LTD

summary:
Gene expression analysis followed by gene onthology pathway analysis revealed that “cell cycle” and “growth and proliferation” pathways were significantly affected in the high dose group at the 24h time point.
No consistent gene expression changes related to nuclear receptor activation, in particular target genes of CAR, PXR or PPAR were observed at the 24h time point

overall_design: Rat liver tissue was harvested 2h hours after treatment of rats with test compound or vehicle. Tissue was harvested in RNA-Later (Ambion Cat No 7021) for RNA extraction and hybridization to Affymetrix microarrays

first: Adrian

middle: B

last: Roth

first: Franziska

last: Boess


title: Cell stage dependent transcriptional response to leukemic oncogene

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

summary: Acute myeloid leukemia (AML) is characterized by a block in myeloid differentiation the stage of which is dependent on the nature of the transforming oncogene and the developmental stage of the oncogenic hit. This is also true for the t(8;21) translocation which gives rise to the RUNX1/ETO fusion protein and initiates the most common form of human AML. To understand the molecular principles governing this differential action, we used the differentiation of mouse embryonic stem cells expressing an inducible RUNX1/ETO protein into blood cells as a traceable model combined with genome-wide analyses of transcription factor binding and gene expression. We found that RUNX1/ETO interferes with both the activating and repressive function of its normal counterpart, RUNX1, at early and late stages of blood cell development. However, the response of the transcriptional network to RUNX1/ETO expression is stage-specific, highlighting the molecular mechanisms determining specific target cell expansion after an oncogenic hit.

overall_design: Microarray data have been used to study RUNX1/ETO role in hematopoietic system

first: Kakkad

last: Regha

first: Olga

last: Tsoulaki

first: Georges

last: Lacaud

first: Constanze

last: Bonifer


title: Gene expression profiles of rat liver tissues after carbon tetrachloride administration

city: Xinxiang

first: Cunshuan

last: Xu

address: No. 46, Construction East Road

institute: Henan Normal University

summary:
Liver cirrhosis (LC) is pathologically characterized with abnormality and necrosis of hepatic cells, proliferation of fibrous tissue, nodular regeneration and pseudolobule formation.
We used Rat Genome 230 2.0 microarray to further highlight the rat liver tissues after carbon tetrachloride administration

overall_design: The rat model of liver cirrhosis (LC) was established, and the expression profiles of liver tissues from LC were detected at  3, 6, and 9 weeks using Rat Genome 230 2.0 array. Then the significantly changed genes related to LC were identified. The relevance of gene expression profiles and biological processes was analyzed by bioinformatics and systems biology.

first: Gaiping

last: Wang

first: Yunpeng

last: Hao

first: Jia

last: Zhi

first: Shasha

last: Chen


title: Overexpression of the Growth arrest specific 1 (Gas1) gene reduces the in vivo progression of murine hepatocellular carcinoma and restores gene expression level

status: Public on Jul 31 2015

city: Valencia

first: Angela

middle: L.

last: Riffo-Campos

state: Valencia

address: Avda. Blasco Ibáñes, 17

department: Department of Biochemistry and Molecular Biology

country: Spain

institute: University of Valencia, and INCLIVA

summary: Mice developing diethylnitrosamine (DEN)-induced hepatocellular carcinoma were transfected in vivo with Gas1 by hydrodynamic gene delivery. The treatment significantly (p < 0.05) reduced the number of large tumors (more than 2 mm diameter) and histological analyses revealed that the number of carcinoma foci in liver was reduced in favor of less malignant lesions, such as hyperplastic areas, and that the number of lung metastases was also diminished. To study the effects of DEN and the subsequent transfection with Gas1, an expression microarray experiment was designed in which the transcription of 20758 genes in liver was determined. A triangular analysis of microarray data shows that transfection with Gas1 restores the level of transcription level of 182 out of the 698 genes, whose expression was affected by DEN. Therefore, transfection of liver tumor-bearing animals with Gas1 significantly reduces the size and proliferative activity of tumors and restores the transcriptional profile of the liver.

overall_design: Here we studied effects of diethylnitrosamine treatment of mice on the transcription of 20758 liver genes and the consequences of transfecting the livers with Gas1.

first: Ángela

middle: L

first: Josefa

last: Castillo

first: Luis

last: Franco

first: Gerardo

last: López-Rodas


title: Expression data from the liver of rat treated by Piperonyl butoxide and Dammar resin

status: Public on Jul 29 2015

city: Osaka

first: Masayuki

last: Kanki

address: 2-1-6, Yodogawa-ku

institute: Astellas Pharma Inc.

summary:
Several studies have successfully detected hepatocarcinogenicity in rats based on gene expression data. Here, we constructed a model for detecting non-genotoxic (NGTX) hepatocarcinogens and predicted their MOAs in rats.
Piperonyl butoxide (PBO) and Dammar resin (DAM) are NGTX hepatocarcinogens. Gene expression data in the liver treated by PBO and DAM was used for validation of constructed model.

overall_design: There are four and three dosing groups including control group in PBO and DAM, respectively. The replicates is three samples in each dosing group. Doses for PBO are 0, 500, 1000 and 1500 mg/kg and those for DMA are 0, 800 and 2000 mg/kg.

first: Masaki

last: Fujioka


title: Effects of a Tricaprylin Emulsion on Anti-glomerular Basement Membrane Glomerulonephritis in Rats

status: Public on Jul 14 2015

first: Akira

last: Hirasawa

state: Kyoto

address: 46-29 Yoshida Shimoadachi-cho, Sakyo-ku

department: Genomic Drug Discovery Science

institute: Kyoto University Graduate School of Pharmaceutical Sciences

summary: Expression data from rat with anti-glomerular basement membrane nephritis (anti-GBM). We used microarrays to analyze the transcriptome of kidney from anti-GBM model rat with or without drug treatment

overall_design: RNA from whole kidneys was extracted and processed for hybridization on Affymetrix microarrays.

first: Keiko

last: Iida

first: Naoya

last: Umeda


title: Endothelin-Mediated Changes in Gene Expression in Isolated Purified Rat Retinal Ganglion Cells

status: Public on Jul 17 2015

city: Fort Worth

first: Shaoqing

last: He

state: TX

address: 3500 Camp Bowie BLVD

department: Cell Biology and Immunology

institute: UNTHSC

summary:
A growing body of evidence suggests that the vasoactive peptides endothelins (ETs) and their receptors (primarily the ETB receptor) are contributors to neurodegeneration in glaucoma. However, ET’s actions in retinal ganglion cells (RGCs) are not fully understood. The purpose of this study was to determine ETs effects on gene expression in primary RGCs.
Primary RGCs treated with 100nM of ET-1, ET-2 or ET-3 for 24 hours was used as cell model to investigation the role of endothelins in gene expression.

overall_design: Primary RGCs isolated from rat pups were treated with 100nM of ET-1, ET-2 or ET-3 for 24 hours. Total RNA was extracted followed by cDNA synthesis. Changes in gene expression in RGCs was detected using Affymetrix Rat Genome 230 2.0 microarray and categorized by DAVID analysis.

first: Yong

last: Park

first: Thomas

last: Yorio

first: Raghu

last: Krishnamoorthy


title: Expression data from kidneys of rats with and without glomerulonephritis

status: Public on Jul 06 2015

city: Wuppertal

first: Heidrun

middle: Christine

last: Ellinger-Ziegelbauer

address: Aprather Weg 18a

country: Germany

institute: Bayer Pharma AG

summary:
We investigated a glomerulonephritis (GN) model in rats induced by nephrotoxic serum (NTS) which contains antibodies against the glomerular basement membrane (GBM). The anti-GBM GN model in rats is widely used since its biochemical and histopathological characteristics are similar to crescentic nephritis and Goodpasture's disease in humans. Male Wistar Kyoto (WKY) and Sprague Dawley (SD) rats were dosed once with 1, 2.5 and 5 ml/kg nephrotoxic serum (NTS) or 1.5 and 5 ml/kg NTS, respectively. GN and tubular damage were observed histopathologically in all treated rats after 14 days.
To obtain insight into molecular processes during GN pathogenesis, mRNA  expression was investigated in WKY and SD kidneys. The immunopathological processes during GN are still not fully understood and likely involve both innate and adaptive immunity. In the present study, several hundred mRNAs were found deregulated, which functionally were mostly associated with inflammation and regeneration.   The β-chain of the major histocompatibility complex class II RT1.B (Rt1-Bb) and complement component 6 (C6) were identified as two mRNAs differentially expressed between WKY and SD rat strains which could be related to known different susceptibilities to NTS of different rat strains; both were increased in WKY and decreased in SD rats. Increased Rt1-Bb expression in WKY rats could indicate a stronger and more persistent cellular reaction of the adaptive immune system in this strain, in line with findings indicating adaptive immune reactions during GN. The complement cascade is also known to be essential for GN development, especially terminal cascade products like C6.

overall_design: Two different rat strains (WKY and SD) were dosed with different doses of NTS and after 14 days rats were euthanized and kidneys were removed for RNA extraction and hybridization on Affymetrix microarrays. We sought to analyze the deregulation of gene expression during NTS-induced glomerulonephritis and to compare the effect in the two rat strains.

first: Mira

last: Pavkovic

first: Bjoern

last: Riefke

first: Anna-Lena

last: Frisk

first: Ina

last: Groetike


title: Expression data from rat Achilles tendon-derived stem cells during development

status: Public on Jul 10 2015

city: Hangzhou

first: Jialin

last: Chen

address: Yuhangtang Road

institute: Zhejiang University

summary: We have compared the gene expression profile of rat Achilles tendon-derived stem cells in post-natal tendon development. Rat tendon stem/progenitor cells (TSPCs) were isolated at different stages of post-natal development: TSPCs-1d, TSPCs-7d and TSPCs-56d.

overall_design: TSPCs at different post-natal development stages (1d, 7d and 56d) were isolated, cultured and used for microarray analyses at passage 2. All TSPCs in this study were of isolated from more than one individual. Total RNA was extracted and fragmented biotin-tagged cRNA was hybridized to Rat Genome 230 2.0 Array.


title: Genome-wide expression analysis of quiescent versus activated muscle stem cells (satellite cells)

status: Public on Jun 30 2015

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

institute: UPF

summary: We performed genome-wide gene expression analysis of quiescent/activated muscle stem cells isolated from mouse skeletal muscle by flow cytometry.

overall_design: We analyzed the global changes in gene expression occurring within muscle stem cells (satellite cells) in homeostatic conditions or after cardiotoxin (CTX) injury (3 days).  Pure satellite cell populations from dissociated skeletal muscle from mice were isolated using a well-established flow cytometry protocol gating on integrin a7(+) (positive selection) and Lin- (CD31, CD45, CD11b, Sca1) (negative selection).

first: Pura

last: Munoz-Canoves


title: Gene expression profile of Mef2d KO retina at P14

status: Public on Jul 01 2015

city: Suita

first: Takahisa

last: Furukawa

state: Osaka

address: 6-2-4 Furuedai

department: Developmental Biology

institute: Osaka Bioscience Institute

summary: To analyze the expression profile in the Mef2d KO retina, we performed a microarray analysis using wild-type and Mef2d KO retina at P14.

overall_design: We performed a microarray analysis using wild-type and Mef2d KO retina at P14, and compared the expression profiles.

first: Yoshihiro

last: Omori


title: Transcriptome profiling of control and FOSL1 knockdown Rcho-1 trophoblast stem (TS) cells

city: Kansas City

first: Kaiyu

last: Kubota

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

summary: In hemochorial placentation, trophoblast stem cells differentiate into multiple lineages to aquire specific functions, such as invasive and endocrine phenotype. FOSL1 has been identified as a key regulator for trophoblast differentiation. We used microarray to detail mechanisms underlying FOSL1 signaling pathway in trophoblast differentiation.

overall_design: 3 replicates of differentiated Rcho1 TS cells expressing control shRNA; 3 replicates of differentiated Rcho1 TS cells expressing Fosl1 shRNA

first: Lindsey

middle: N

last: Kent

first: Michael

middle: J

last: Soares


title: Expression data from NRK-52E cells treated with aristolochic acids for 6h, 24h and 72h

status: Public on Jul 02 2015

city: Manchester

first: Kate

last: Bloch

address: Alderley Park, Alderley Edge

institute: Manchester University

summary:
In this study we have examined the effect of sub-cytotoxic exposure to aristolochic acids (1.65µM) at 6h, 24h and 72h on the whole-genome expression profile in a rat proximal renal tubule cell line (NRK-52E).
We used microarrays to detail the mechanism of toxicity and possibly carcinogenicity of aristolochic acids in rat renal proximal cells.

overall_design: NRK-52E cells were cultured to confluence on 6-well plates. Cells were then exposed to aristolochic acid dissolved in DMSO (0.1%) at the IC10 concentration at 72h (1.65 μM) or DMSO only as control. After 6h, 24h and 72h the medium was removed and RNA was extracted from the cells. Three studies were conducted at each time point.

first: Katarzyna

first: Edward

last: Lock


title: The C-terminal region of Xpc is dispensable for the transcriptional activity of Oct3/4 in mouse embryonic stem cells

status: Public on Jun 09 2015

city: Kobe

first: Hitoshi

last: Niwa

address: 2-2-3 Minatojima-minamimachi,Chuo-ku

institute: RIKEN

summary: The transcription factor Oct3/4 is essential to maintain pluripotency in mouse embryonic stem (ES) cells. It was reported that the Xpc DNA repair complex is involved in this process. Here we examined the role of Xpc on the transcriptional activation of the target genes by Oct3/4 using the inducible knockout strategy. We found that the removal of the C-terminal region of Xpc, including the interaction sites with Rad23 and Cetn2, showed faint impact on the gene expression profile of ES cells and the functional Xpc-ΔC ES cell lines retained proper gene expression profile as well as pluripotency to contribute chimeric embryos. These data indicated that the C-terminal region of Xpc is dispensable for the transcriptional activity of Oct3/4 in mouse ES cells.

overall_design: An inducible knockout ES cell line of Xpc with the Cre-loxP system was generated and gene expression was measured without  Xpc deletion, after 4 days of Xpc deletion or constitutive knocked out cells. Each sample was prepared in triplicate.

first: Shunsuke

last: Ito

first: Mariko

last: Yamane

first: Satoshi

last: Ohtsuka


title: Expression profiling of microRNA and mRNA on hepatic inflammation in high-fat induced murine model

status: Public on Jun 22 2015

city: Los Angeles

first: Minhyung

last: Kim

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

summary: The goal of this study was to identify and characterize of miRNA in the regulation of inflammatory responses of high-fat induced inflammation mouse model.  In this study, we established a mouse model of high-fat-diet-induced inflammation to gain understanding on the biological functions deregulated by aberrant gene expression based on miRNA and mRNA expression profiling analysis. And then we looked for direct miRNA targets by performing pair-wise correlation coefficient analysis on expression levels of mRNAs and by comparing these results with predicted miRNA targets from TargetScan5.1.

overall_design: A subset of the mice from the Chow and HFD groups were killed after 3 months and 9 months. All animals were weighed and anesthetized with ether. Serum was then obtained from the retro-orbital cavity, and mice were killed before  liver tissue collection.

first: Wonhee

last: Hur

first: Sung

middle: W

first: Seung

middle: K

last: Yoon


title: Effect of a DP1 agonist BW245C on concanavalin A-induced hepatitis

status: Public on Jun 01 2015

city: Kyoto

first: Tomoko

last: Fujita

address: Yoshida Konoe-Cho

department: Medicine

institute: Kyoto University

summary: To elucidate the effect of a prostaglandin D2 receptor DP1 agonist BW245C on concanavalin A (ConA) hepatitis, we performed DNA microarray using SurePrint G3 Mouse GE 8x60K Microarray. Mice were treated with ConA for 3 or 24 hr with vehicle or BW245C . Livers were collected, homogenized, and subjected to total RNA extraction.

overall_design: Mice were injected with 10 mg/kg ConA, followed by i.p. administration of vehicle or 1mg/kg BW245C 15 min later. Livers were collected at 3hr and 24hr, homogenized, and totalRNA was extracted. Each group consists of five mice (#1 to #5).

first: Shuh

last: Narumiya


title: Expression data from pregnant rat hearts

status: Public on Jun 12 2015

city: Valhalla

first: Caroline

last: Ojaimi

institute: New York Medical College

summary:
Hyperhomocysteinemia (HHcy) causes cardiovascular dysfunction and is associated with many complications during pregnancy related to reduced NO bioactivity. The mechanisms of HHcy on the NO-dependent control of myocardial metabolism was compared with L-NAME, which directly inhibits NO bioavailability, treated animals.
We used microarrays to detail the global programme of gene expression underlying hyperhomocysteinemia during pregnancy and identified distinct classes of differentially regulated genes.

overall_design: Female SD rats were mated with male SD rats. Methionine was used to generate hyperhomocysteinemia model. L-NAME was used to generate NO restricted model. After treatment, the left ventricles were harvested for RNA extraction and hybridization on Affymetrix microarrays.

first: Su

last: Song

first: Thomas

last: Hintze


title: Expression data of sandwich cultured primary rat hepatocytes incubated to piperazine designer drugs

status: Public on May 13 2015

city: Porto Alegre

first: Marcelo

middle: Dutra

last: Arbo

address: Avenida Paulo Gama, 110

department: Departamento de Análises

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

summary:
The piperazine derivatives most frequently consumed for recreational purposes are 1-benzylpiperazine (BZP), 1-(3,4-methylenedioxybenzyl)piperazine (MDBP), 1-(3-trifluoromethylphenyl)piperazine (TFMPP), and 1-(4-methoxyphenyl)piperazine (MeOPP). Currently it is unclear whether piperazine designer drugs induce mechanisms of hepatotoxicity and, if so, whether they act by a common mechanism.
We performed a gene array study with rat hepatocytes incubated with the four designer drugs for 24 h in order to detail the global programme of gene expression

overall_design: Primary rat hepatocytes were cultured in collagen sandwich and incubated with the piperazine designer drugs. After 24 h, the RNA was extracted and the Affymetrix microarray analysis was performed.

middle: D

first: Jan

last: Hengstler


title: Lentiviral vector-based microRNA sponges identifies miR-155 and miR-802 target genes in the hippocampus of Ts65Dn mice

status: Public on May 16 2015

city: Frederick

first: Xavier

last: Bofill-De Ros

state: MD

address: 1050 Boyles St., blg 560

department: RNA Biology Laboratory

institute: National Cancer Institute

summary: A major challenge in Down syndrome (DS) is to understand how the extra-dose of functional chromosome 21  (HSA21) genetic elements can impact on the tissue-specific transcriptome to contribute to phenotypic alterations. MiRNAs are post-transcriptional modulators with genome-wide regulatory effects. Five microRNAs have been identified in HSA21 that are present in triple copy in DS individuals. Interestingly, in the Ts65Dn mouse model of DS two of these miRNAs, miR-155 and miR-802, are also triplicated resulting in its overexpression. In the current work, we have developed a lentiviral miRNA-sponge genetic strategy for miR-155 and miR-802 (Lv-miR155-802T) to identify novel mRNA targets involved in hippocampal function. Hippocampal injection of the lentiviral sponge in Ts65Dn mice reduced miR-155 and miR-802 overexpression. Noticeable lentiviral sponge rescued the expression of the miRNA predicted targets showing the potential of the strategy to identify miRNA dosage-sensitive genes with potential involvement in DS-hippocampal phenotypes.

overall_design: Euploid and trisomic adult mice were bilaterally injected at the level of the ventral hippocampus at selected coordinates (AP=-3.3mm, L=+/- 3mm, DV=-3.3mm and -2.3mm relative to bregma). Up to 108 transducing units (3µl of viral suspensions of Lv-Contol or Lv-miR155-802T) were injected into each hemisphere at a rate of 0.2 µl/min, under the precise control of an infusion pump (Ultramicropump, World Precision Instruments). Mice were euthanized for hippocampus collection at day 23 after administration. Transcriptome of hippocampus of euploid and trisomic mice treated with Lv-Control or Lv-miR155-802T was analysed using an Agilent SurePrint G3 Mouse gene expression 8x60K Microarray (ID 028005). A total RNA 100 ng, obtained using miRNeasy Mini Ki (QIAGEN), were labeled using LowInputQuick Amp Labeling kit (Agilent 5190-2305) following manufacturer instructions. Briefly, mRNA was reverse transcribed in the presence of T7-oligo-dT primer to produce cDNA. cDNA was then in vitro transcribed with T7 RNA polymerase in the presence of Cy3-CTP to produce labeled cRNA. The labeled cRNA was hybridized to the Agilent SurePrint G3 Mouse gene expression 8x60K Microarray (ID 028005) according to the manufacturer's protocol. The arrays were washed, and scanned on an Agilent G2565CA microarray scanner at 100% PMT and 3µm resolution. Intensity data was extracted using the Feature Extraction software (Agilent). Replicates from each genotypes and treatment group were distributed as follows: EU+Lv-Contol n=4, EU+Lv-miR155-802T n=4, TS+Lv-Contol n=5, TS+Lv-miR155-802T n=3.

first: Monica

last: Santos

first: Mara

last: Dierssen

first: Cristina

last: Fillat


title: Host responses contributing to the attenuation of severe acute respiratory syndrome coronaviruses missing E protein domains

status: Public on May 19 2015

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

summary: Severe acute respiratory syndrome coronavirus (SARS-CoV) causes a respiratory disease leading to death in 10% of the infected people. A mouse adapted SARS-CoV lacking the envelope (E) protein (rSARS-CoV-MA15-ΔE) is attenuated in vivo. To identify E protein domains and host responses that contribute to rSARS-CoV-MA15-ΔE attenuation, several mutants (rSARS-CoV-MA15-E*) containing point mutations or deletions in the amino-terminal or the carboxy-terminal regions of E protein, respectively, were generated. Amino acid substitutions in the amino terminus, or deletion of domains in the internal carboxy terminal region of E protein led to viral attenuation. Attenuated viruses induced minimal lung injury and limited neutrophil influx to the lungs but, interestingly, increased CD4+ and CD8+ T cell counts in BALB/c mice. To analyze the host responses leading to rSARS-CoV-MA15-E* attenuation, the differential gene expression elicited by the native virus and the mutant ones in infected cells was analyzed. The expression levels of a large number of proinflammatory cytokines inducing lung injury was reduced in the lungs of rSARS-CoV-MA15-E* infected mice, whereas the levels of anti-inflammatory cytokines were increased, both at the mRNA and protein levels. These results suggested that the reduction in lung inflammation together with a specific antiviral T cell response, contributed to rSARS-CoV-MA15-E* attenuation. Interestingly, the attenuated viruses completely protected mice against the challenge with the lethal parental virus, being promising vaccine candidates.

overall_design: Three biological replicates were independently hybridized (one channel per slide) for each sample type (rSARS-CoV-MA15-wt, rSARS-CoV-MA15-∆E, rSARS-CoV-MA15-∆3, rSARS-CoV-MA15-∆5, Mock). Slides were Sure Print G3 Agilent 8x60K Mouse (G4852A-028005)

last: Regla-Nava

first: José

last: Nieto-Torres

last: Jiménez-Guardeño

first: Raúl

last: Fernandez-Delgado

first: Craig

last: Fett

first: Carlos

last: Castaño-Rodríguez

first: Stanley

last: Perlman

first: Luis

last: Enjuanes

first: Marta

last: DeDiego


title: Temporal Changes in Rat Liver Gene Expression after Acute Cadmium and Chromium Exposure

status: Public on May 21 2015

city: Fort Detrick

first: Michael

middle: Scott

last: Madejczyk

address: 568 Doughten Dr

department: Environmental Health Program

institute: US Army Center for Environmental Health Research

summary: U.S. Service Members and civilians are at risk of exposure to a variety of environmental health hazards throughout their normal duty activities and in industrial occupations. Metals are widely used in large quantities in a number of industrial processes and are a common environmental toxicant, which increases the possibility of being exposed at toxic levels. While metal toxicity has been widely studied, the exact mechanisms of toxicity remain unclear. In order to further elucidate these mechanisms and identify candidate biomarkers, rats were exposed via a single intraperitoneal injection to three concentrations of CdCl2 and Na2Cr2O7, with livers harvested at 1, 3, or 7 days after exposure. Cd and Cr accumulated in the liver at 1 day post exposure. Cd levels remained elevated over the length of the experiment, while Cr levels declined. Metal exposures induced ROS, including hydroxyl radical (•OH), resulting in DNA strand breaks and lipid peroxidation. Interestingly, ROS and cellular damage appeared to increase with time post-exposure in both metals, despite declines in Cr levels. Differentially expressed genes were identified via microarray analysis. Both metals perturbed gene expression in pathways related to oxidative stress, metabolism, DNA damage, cell cycle, and inflammatory response. This work provides insight into the temporal effects and mechanistic pathways involved in acute metal intoxication, leading to the identification of candidate biomarkers.

overall_design: Rats (5 per group) were exposed via a single intraperitoneal injection to three concentrations of CdCl2, Na2Cr2O7, or vehicle control,with livers harvested at 1, 3, or 7 days after exposure. Only the Cd mid dose and Cr high dose were selected for microarray analysis.

middle: S

first: Christine

middle: E

last: Baer

first: William

last: Dennis

first: Valerie

middle: C

last: Minarchick

first: Stephen

last: Leonard

first: David

middle: A

last: Jackson

first: Jonathan

last: Stallings

first: John

last: Lewis


title: Microarray analysis of Wild-type vs. Brpf1-deficient E8.75 mouse embryo

status: Public on May 15 2015

city: Montreal

first: Xiang-Jiao

last: Yang

state: Quebec

address: 1160 Pine Ave W

institute: McGill University

summary: RNA was isolated from three pairs of wild-type and Brpf1-deficient E8.75 mouse embryos for microarray analysis.

overall_design: The cDNA samples were then labeled and mixed for hybridization with one array. The data from three arrays were obtained and used for bioinformatic analysis.

first: Linya

last: You

first: Jinfeng

last: Zhou

first: Hong

last: Zhao

first: Nicholas

middle: R

last: Bertos

first: Morag

last: Park

first: Edwin

last: Wang


title: Mapping genetic modifiers of ARPKD

status: Public on Jun 06 2015

city: Milwaukee

first: Carol

last: Moreno

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Autosomal recessive polycystic kidney disease (ARPKD) is caused by mutations in the PKHD1 gene in both humans and the orthologous PCK rat model. Although ARPKD results solely from PKHD1 mutations, the disease onset and severity are highly variable, indicating that other unknown genetic risk factor(s) modify ARPKD-associated phenotypes. To identify genetic modifiers of ARPKD severity, we created two genetically distinct Pkhd1 congenic rat strains on the Fawn-Hooded Hypertensive (FHH) and the Dahl S (SS) rat backgrounds (denoted FHH.Pkhd1 and SS.Pkhd1, respectively) that harbor the PCK-derived Pkhd1 allele. The FHH.Pkhd1 and SS.Pkhd1 strains had lower renal cyst formation at 30 days-of-age (5±2% and 8±2% cystic, respectively; P<0.001) compared to the PCK kidneys (26±4% cystic), which coincided with significantly reduced kidney weights in the FHH.Pkhd1 and SS.Pkhd1. Liver cyst formation and liver weight did not differ between PCK, FHH.Pkhd1, and SS.Pkhd1. These data indicated that the PCK genome harbors genetic modifier(s) of ARPKD severity that are not present in the FHH and SS genomes. Using high density SNP array genotyping and microarray expression analysis, we identified 50 potential modifiers of ARPKD severity in the PCK rat. Of these candidates, a damaging nonsynonymous variant in Nphp4 stood out as the most likely candidate based on variant segregation, protein modeling, network analysis, and gene ontology. Nphp4 is widely associated with the autosomal recessive cilliopathy and nephronopthisis, but had not been previously implicated in the molecular or cellular pathophysiology of ARPKD. Collectively, these data provide genetic evidence of disease modifier(s) in the PCK model of ARPKD and prioritized multiple candidates, including NPHP4, for further investigation in ARPKD pathogenesis.

overall_design: In this study, we used microarray to analyze transcript expression in the kidneys of 30 day old SD (n=4), PCK (n=4), FHH (n=4), FHH.Pkhd1 (n=4), SS (n=4), and SS.Pkhd1 (n=4). Samples were pooled and the pooled samples were run in triplicate. The 30 day timepoint was chosen because the differences in renal cyst formation between PCK, FHH.Pkhd1, and SS.Pkhd1 were greatest at this timepoint. To account for genetic strain differences that do not contribute to ARPKD severity, gene expression of each cystic rat strain was compared to its parental strain.

first: Bradley

middle: T

last: Endres

last: Flister

first: Jeremy

last: Prokop

first: Matthew

last: Hoffman

first: Marc

last: Casati

first: Shirng-Wern

last: Tsaih

first: Martin

last: Hessner

first: Aron

middle: M

last: Geurts

first: Howard

last: Jacob

last: Sweeney

first: Ellis

last: Avner


title: Neuronal changes induced by Varicella Zoster Virus in a rat model of Post Herpetic Neuralgia

status: Public on Mar 31 2015

city: Pittsburgh

first: Stephen

middle: Alan Kenneth

last: Harvey

state: PA

address: 203 Lothrop St

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

summary:
Neuronal reactivation of latent varicella zoster virus (VZV) causes debilitating and protracted pain (post herpetic neuralgia: PHN) in a significant fraction of patients.
Productive infection of VZV seems to occur only in humans and primates, so VZV-infected human cells (e.g., MEWO cell line) are used to transmit VZV to rodents.
A commonly accepted method of assessing nociception is ipsilateral nocifensive (pain avoidance) behavior in rats which have been injected in a footpad. No such behavioral change is associated with the contralateral  (uninjected) footpad.
Uninfected MEWO cells or VZV-infected MEWO cells were inoculated into the glabrous region of the right rear footpad of male Sprague-Dawley rats.
By 9 days post-inoculation, there was a VZV-dependent decrease in the frequency of neurites that extend from the dermis past the stratum basale layer of the footpad epidermis.
Between 7 days and 21 days post-inoculation there was a VZV-dependent increase in nocifensive behaviours in the rats.
All VZV-dependent effects occurred in the absence of the productive VZV infection. That is, the virus entered rodent cells and expressed immediate early and early genes, but did not express late genes, synthesize viral DNA, or release infectious virions.
Animals which had developed VZV-dependent nocifensive behaviours at 10 days were euthanized, and dorsal root ganglia (L4,5) ipsilateral to inoculation were taken for microarray analysis. Dorsal root ganglia from matching control animals were also analyzed.

overall_design: Control (uninfected MEWO cells) or VZV-infected MEWO cells were inoculated into the glabrous region of the right rear footpad of male Sprague-Dawley rats. After development of ipsilateral nocifensive behaviour in the VZV-infected animals, the ipsilateral dorsal root ganglia (L4,5) from infected and control animals were taken for microarray analysis.

first: Jean-Marc

middle: G

last: Guedon

first: Michael

middle: B

last: Yee

first: Mingdi

last: Zhang

first: William

middle: F

last: Goins

first: Paul

last: Kinchington


title: Fibrogenic cell plasticity blunts tissue regeneration and aggravates muscular dystrophy

status: Public on Apr 09 2015

first: Patrizia

last: Pessina

address: C/ Dr. Aiguader 88

institute: University Pompeu Fabra

summary: Preservation of cell identity is necessary for homeostasis of most adult tissues. This process is challenged every time a tissue undergoes regeneration after stress or injury. In the lethal Duchenne muscular Dystrophy (DMD), skeletal muscle regenerative capacity declines gradually as fibrosis increases. Using genetically engineered-tracing mice, we demonstrate that in dystrophic muscle, specialized cells of muscular, endothelial and hematopoietic origins gain plasticity towards a fibrogenic fate via a TGFβ-mediated pathway. This results in loss of cellular identity and normal function, with deleterious consequences for regeneration. Furthermore, this fibrogenic process involves acquisition of a mesenchymal progenitor multipotent status, illustrating a link between fibrogenesis and gain of progenitor cell functions. As this plasticity was also observed in DMD patients, we propose that mesenchymal transitions impair regeneration and worsen diseases with a fibrotic component.

overall_design: TGFb exposure induced gene expression was measured after 4 days of treatment compared to untreated cells. Three independent experiments were performed both for the treatment and for the control


title: Analysis of the placental tissue transcriptome from normal and testosterone treated rat pregnancy

status: Public on Apr 20 2015

city: Madison

first: Sathish

last: Kumar

address: 2015 Linden Dr

department: Comparative Biosciences

institute: University of Wisconsin

summary: Elevated testosterone levels increase maternal blood pressure and decrease uterine blood flow in pregnancy, resulting in abnormal perinatal outcomes. The placenta is the key in understanding the pathophysiological processes associated with pregnancy. The current study is designed to characterize the genes essential for placental function to understand the mechanisms underlying normal and pathological gestation.

overall_design: Timed pregnant Sprague-Dawley rats (day 12 of gestation; copulation plug on day 1; Charles River, Wilmington, MA) were selected. After acclimatization, on gestational day (GD) 13, dams were randomly divided into 2 groups. Dams in the treatment group were subcutaneously injected with testosterone propionate (0.5 mg/Kg/day, n=12) for 5 days from GD 15–19. The control group received vehicle (sesame oil, n=12).The animals were housed in a room with a controlled temperature and a 12-hour light-dark cycle. During 8-10 am on days 20 of pregnancy, rats were anaesthetized with carbon dioxide, three placentas each from male and female fetuses in control and testosterone-treated rats were disected and total RNAs were isolated. The isolated RNA from each animal was used for the cRNA preparation. cRNA was prepared and fragmented as suggested by Affymetrix technical manual, and simultaneously hybridized  to Affymetrix Rat Expression Array 230 2.0. The data were analyzed with R statistical package (version 2.8.1), GeneSpring GX - Agilent Technologies and Ingenuity pathway analysis .

first: Gopalakrishnan

last: Kathirvel

first: Vijayakumar

last: Chinnathambi

first: Kunju

last: Sathishkumar


title: Nitric oxide signaling and its role in oxidative stress response in Schizosaccharomyces pombe

status: Public on Mar 26 2015

city: Ikoma

first: Daisuke

last: Watanabe

state: Nara

address: 8916-5 Takayamacho

institute: Nara Institute of Science and Technology

summary: In examining NO signaling in the fission yeast Schizosaccharomyces pombe, we found that the putative NO dioxygenase SPAC869.02c (named Yhb1) and the S-nitrosoglutathione reductase Fmd2 cooperatively reduced intracellular NO levels as NO-detoxification enzymes. Although both protein levels were increased with exogenous NO, their expression patterns were different during growth phases. While expression of Yhb1 in the log phase was abrogated by treatment with an NO synthase inhibitor, induction of Fmd2 in the stationary phase was correlated with elevated mitochondrial respiratory chain (MRC) activity and reactive oxygen species (ROS) generation. Moreover, NO was localized in the mitochondria specifically in the stationary phase, suggesting that there are at least two distinctive types of NO signaling in S. pombe cells. For mitochondrial NO signaling, pretreatment with an NO donor effectively rescued the cell viability by repressing generation of ROS under oxidative stress. DNA microarray analysis revealed that exogenous NO contributes to tolerance to hydrogen peroxide (H2O2) stress by (i) inhibition of Fe3+ to Fe2+conversion, (ii) upregulation of the H2O2-detoxifying enzymes, and (iii) downregulation of the MRC genes. Therefore, NO is suggested to play a pivotal role in the negative feedback system to regulate ROS levels under oxidative stress in S. pombe cells.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: We examined the effects of DETA NONOate treatment on gene expression of log-phase Scizosaccharomyces pombe cells by using Affymetrix Yeast Genome 2.0 Array. Total RNA samples were extracred from untreated cells (DetaNONOate 0) and cells treated with 0.5 mM DETA NONOate for 2 h (DetaNONOate 0.5) and were subjected for this DNA microarray analysis.

first: Rika

middle: I

last: Astuti

first: Hiroshi

last: Takagi


title: The Mitochondrial Calcium Uniporter controls skeletal muscle mass in vivo

status: Public on Mar 05 2015

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary: Muscle atrophy contributes to the poor prognosis of many physiopathological conditions, but pharmacological therapies are still limited. Muscle activity leads to major swings in mitochondrial [Ca2+] which control aerobic metabolism, cell death and survival pathways. We have investigated in vivo the effects of mitochondrial Ca2+ homeostasis in skeletal muscle function and trophism, by overexpressing or silencing the Mitochondrial Calcium Uniporter (MCU). The results coherently demonstrate that both in developing and in adult muscles MCU-dependent mitochondrial Ca2+ uptake has a marked trophic effect that does not depend on autophagy or aerobic control, but impinges on two major hypertrophic pathways of skeletal muscle, PGC-1α4 and Igf1-Akt/PKB. In adult mice, MCU overexpression protects from denervation-induced atrophy. These data reveal a novel Ca2+-dependent organelle-to-nucleus signaling route, which links mitochondrial function to the control of muscle mass and may represent a possible pharmacological target in sarcopenia.

overall_design: Experiments were performed on biological replicates of single skeletal muscle fibres. Seven fibres were chosen for their Mutochondrial Calcium Uniporter (MCU) overexpression and other seven fibres because MCU was silenced. Overexpression and silencing were performed injecting skeletal muscle with AAV containing MCU gene or short interfering oligos specific for MCU. As control was profiled eigth fibres transfected with AAV and eigth wild type fibres. Analyses were performed 7 days and 14 days after the AAV injection (3 fibers after 7 days and 4 fibers after 14 days for MCU overexpression and silencing, four fibres after 7 days and four after 14 days for control).

first: Stefano

last: Cagnin

first: Francesco

last: Chemello

first: Cristina

last: Mammucari

first: Rosario

last: Rizzuto

first: Gaia

last: Gherardi

first: Anna

last: Raffaello

first: Giorgia

last: Pallafacchina

first: Sofia

last: Zanin

first: Alessandra

last: Braga

first: Diego

last: De Stefani

first: Ilaria

last: Zamparo


title: Development of gene expression signatures for colonic lamina propria DCs of CD300a deficient mice

status: Public on Apr 10 2015

city: Tsukuba

first: Chigusa

last: Nakahashi-Oda

state: Ibaraki

address: 1-1-1 Tennoudai

institute: University of Tsukuba

summary: To further development of our gene expression approach to CD300a deficiency on dendritic cells (DCs) in colonic lamina propria, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish CD300a deficiency on DCs in colonic lamina propria from those of WT mice.  Colonic lamina propria DCs were obtained by cell sorter from WT and CD300a deficient mice raised under SPF and GF condition. Expression of Ifnb1 was significantly higher in CD300a deficient DCs, quantified in the same RNA samples by real-time PCR.

overall_design:
Gene expression in WT and CD300a colonic lamina propria DCs raised under SPF and GF conditions were measured.  Colonic lamina propria cells were obtained from 5 mice in each conditions.
Takara-Bio

first: Shuichi

last: Iino


title: Microarray analysis of Wild-type vs. Brpf1-deficient P4 mouse brain

status: Public on Apr 08 2015

first: Xiang-Jiao

last: Yang

summary: RNA was isolated from three pairs of wild-type and Brpf1-deficient mouse brains (the dorsal cortex part) at postnatal day 4 for microarray analysis.

first: Linya

last: You

first: Jinfeng

last: Zhou

first: Hong

last: Zhao

first: Nicholas

last: Bertos

first: Morag

last: Park

first: Edwin

last: Wang


title: Transcriptome study of P5424 T-cell line

city: Marseille - cedex 09

first: Aurélien

last: Griffon

address: 163, Avenue de Luminy - case 928

institute: TAGC - Inserm U1090

summary: P5424 T-cell line was observed transcriptome in two replicates

overall_design: Total RNAs were extracted from 2 samples of P5424 T-cell line and were profiled in replicate after hybridization with Agilent SurePrint G3 Mouse GE 8x60K

first: Laurent

last: Vanhille

first: Lan

last: T Dao

first: Nicolas

last: Fernandez

first: Salvatore

last: Spicuglia


title: Expression data from rat with different quantities of PS

status: Public on Mar 29 2015

city: LYON

first: leslie

last: renouard

address: 7 rue Guillaume Paradin

institute: Inserm U1028 - CNRS UMR5292

summary: Paradoxical sleep function remains unknown although several studies indicate that it might play a role in learning and memory. To investigate what modifications paradoxical sleep may bring at the molecular level in neocortex and in hippocampal formation, we profiled gene expression in these structures in rats with different quantities of PS by cDNA microarrays approach.

overall_design: The first group of rats (n=12) was deprived of PS (PSD) by the multiple platform method during 78h, the second group of rats was allowed to recover from this deprivation (PSR) during 6 hours (n=12), the third group of rats remained in their home cage during all the protocol PSC (n=12). All animals were euthanasied at 16h. An equal mass amount of total RNA from the right neocortex and hippocampal formation was pooled from two sets of 6 rats from each experimental group (PSC, PSD, PSR). For the first set of animals, two independent pools of total RNA from both structures were made for each condition to control for the technical variability of the microarray method.

first: Pierre-Hervé

last: Luppi

first: Leslie

last: Renouard

first: Patrice

last: Fort

first: Nutabi

last: Camargo

first: Mouaadh

last: Abdelkarim

first: Nadine

last: Gay

first: Celine

last: Scoté

first: Lucienne

last: Leger

first: Christelle

last: Peyron


title: Gene expression in 2,3-Pentanedione Induced Bronchiolitis Oblliterans

status: Public on Mar 03 2015

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Fibrotic and nonfibrotic bronchial tissues were collected from lungs of pentandione exposed rats by laser capture microdissection. Analogous tissue was collected from air-exposed controls. Miroarray analysis revealed a number of DEGs

overall_design: Male Wistar Han rats were exposed to either air or 200 ppm 2,3-pentanedione for 2 wks. Fibrotic bronchial lesions were collected form exposed rats and analogous bronchial tissue was collected from controls.  RNA was extracted and amplified to cDNA which was hybridized to Affymetrix microarrays to Rat Gene 1.0 ST Array. Transcript profiles from control and treated rats were compared.

first: Daniel

middle: L

last: Morgan

first: B

last: Merrick

first: Kevin

last: Gerrish

first: Patricia

last: Stockton

first: Julie

last: Foley

first: William

last: Gwinn

first: Francine

last: Kelly

first: Scott

last: Palmer

first: Thai

last: Ton

first: Mark

middle: J

last: Hoenerhoff

first: Gordon

middle: P

last: Flake


title: Cell intrinsic expression of TLR9 in autoreactive B cells constrains BCR/TLR7-dependent responses

status: Public on Mar 04 2015

city: Bethesda

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

summary: Endosomal Toll-like receptors (TLRs) play an important role in the etiology of systemic autoimmune diseases such as SLE, where DNA- and RNA-associated autoantigens activate autoreactive B cells through TLR9- and TLR7-dependent pathways, respectively. Nevertheless, TLR9-deficient autoimmune prone mice develop more severe clinical disease, while TLR7-deficient and TLR7/9-double deficient autoimmune-prone mice develop less severe disease. To determine whether the regulatory activity of TLR9 is B cell intrinsic, we have now directly compared the functional properties of autoantigen activated WT, TLR9-deficient and TLR7-deficient B cells, in an experimental system where proliferation depends on BCR/TLR co-engagement. In vitro, TLR9-deficient cells are less dependent on survival factors for a sustained proliferative response than either WT or TLR7-deficient cells. The TLR9-deficient cells also preferentially differentiate toward the plasma cell lineage, as indicated by expression of CD138, sustained expression of IRF4, and other molecular markers of plasma cells. In vivo, autoantigen-activated TLR9-deficient cells give rise to greater numbers of autoantibody producing cells. Our results identify distinct roles for TLR7 and TLR9 in the differentiation of autoreactive B cells that explain the capacity of TLR9 to limit, and TLR7 to promote, the clinical features of SLE.

overall_design: AM14 WT, Tlr7-/-, Tlr9-/- and Tlr7/9-/- B cells were stimulated with PL2-3 for 0, 6, 24, and 42 hours, for a total of 16 samples.


title: Gene expression profile after Dax1 deletion in ES cells

city: Kobe

first: Hitoshi

last: Niwa

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

institute: RIKEN

summary: To investigate the function of Dax1 in mouse ES cells, whole genome microarray expression profiling was employed to identify genes that are potentially affected by the deletion of Dax1.

overall_design: An inducible knockout ES cell line of Dax1 with the Cre-loxP system was generated and gene expression was measured (i) without Dax1 deletion, (ii) after 4 days of Dax1 deletion, or (iii) after several passags of Dax1 deletion. Each sample was prepared in triplicate.

first: Setsuko

last: Fujii


title: Knockout of Vdac1 activates the HIF signaling pathway and induces tumor development in vivo by promoting vascular remodeling and inflammation

status: Public on Apr 27 2015

city: Valbonne - Sophia-Antipolis

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Mitochondria are subcellular organelles that are more than just the powerhouse of cells, they also dictate if a cell dies or survives. The mitochondrial outer-membrane voltage-dependent anion channel 1 (VDAC1) has been shown to play a crucial role in metabolism and apoptosis, however its involvement in ischemic pathologies and cancer is not clear. Transcriptome analysis of Vdac1-/- mouse embryonic fibroblasts (MEF) highlighted cancer and inflammation as top diesases but also activation of the HIF-1 signaling pathway in normoxia. HIF-1α protein was stable due to ROS accumulation that decreased respiration and glycolysis and maintained basal apoptosis. However, in hypoxia increased activation of ERK  in combination with maintenance of respiration and increased glycolysis counterbalanced the deleterious effects of ROS, thereby allowing Vdac1-/- MEF to proliferate better than wild-type MEF. Xenografts of RAS-transformed Vdac1-/- MEF in mice showed stabilization of both HIF-1α and HIF-2α which led to blood vessel destabilization and a strong inflammatory response. Moreover, expression of Cdkn2a, a HIF-1-target and tumor suppressor gene, was strongly decreased. Consequently RAS-transformed Vdac1-/- MEF tumors grew faster than wild-type MEF tumors. These findings provide new perspectives into the understanding of VDAC1 in the function of mitochondria not only in cancer but also in inflammatory diseases.

overall_design: Profiling of VDAC1-/-  and wild-type (Wt) Mouse Embryonic Fibroblasts (MEFs) was performed using whole genome mouse microarrays. in normoxic  or hypoxic  conditions.  MEF (Wt and Vdac1-/-) were incubated in normoxia (Nx, ie: 20% O2) or hypoxia (Hx, ie: 1% O2) for 72h and then lysed prior to RNA isolation, labelling and hybridization on microarrays. One color experiment with 2 biological replicates (marked 1 or 2) of the 4 experimental conditions. One condition (MEF WT Nx2) has been removed from the statistical analysis after microarray quality check due to high background. Total of 7 samples.

first: N

last: Mazure

last: Mari

first: K

first: P

last: Barbry


title: Differential gene expression is not correlated to age-related vascular pathology in aorta and mesenteric artery of Brown Norway and Fischer344xBrown Norway rats

status: Public on Mar 02 2015

city: Boston

first: Gabriel

last: Gruionu

state: MA

address: 149 13th Street, Room 3316

department: Radiation Oncology

institute: Massachusetts General Hospital

summary:
Novel genetic pathways associated with successful and/or unsuccessful vascular aging
Customized therapies for vascular disease will require matching the vessel type and genetic background of the patient. Our previous studies showed that progressive age-related vascular pathology is strain specific in the thoracic aorta (TA) and mesenteric arteries (MA) of the Brown Norway (BN) and the Fisher344/Brown Norway F1 hybrid (F1) rats. The purpose of this study was to identify novel genetic pathways associated with successful and/or unsuccessful vascular aging.  TA and MA were collected from anesthetized 6, 15 and 24 month old age-matched F1 and BN rats for total RNA isolation. The gene microarrays were generated using the Affimetrix GeneChip Rat Expression 230A Array. Gene expression data was analyzed with the Ingenuity Pathway Analysis and proprietary software. Despite more pronounced age-related vascular pathology in the F1 strain, more genes were differentially expressed in the BN strain during aging. A sample of common key genes (KLB1, TRIO, HLA-C and PCP4) showed similar expression at 6 and 15 months and downregulation at 24 months in F1 vs. upregulation in BN rats. Among the top 50 canonical pathways there was only a 10 and 30% overlap, respectively, between the F1 and BN strains in MA and TA. Most of the overexpressed molecules associated with the same vascular-related biological functions are different between strains. The data suggest that age-related vascular pathology and decrement in function is both strain and vessel-dependent and different genetic programs could be employed to accomplish both normal and pathological physiological processes in conduit and resistance arteries.

overall_design: two strains: two vessel types, 3 different ages

first: Steven

last: Miller

first: Jeanette

middle: N

last: McClintick


title: Gene expression alteration in chondrocyte by HES1 overexpression

city: TOKYO

first: Taku

last: Saito

address: 7-3-1 Hongo, Bunkyo-ku

department: Orthopaedic Surgery, Faculty of Medicine

institute: The University of Tokyo

summary: To investigate target molecules of HES1, we transduced GFP or HES1 into mouse chondrocyte cell line ATDC5, and performed the microarray analysis. HES1 overexpression increased inflammation-related genes including Il6 and Il1rl1.

overall_design: We established stable ATDC5 cells overexpressing GFP or HES1 by lentiviral transduction. We harvested mRNA from these cells, and performed microarray analysis.

first: Shurei

last: Sugita


title: Expression data from NRK-52E cells treated with monuron for 6h, 24h and 72h and rats exposed to monuron for 72h.

status: Public on Feb 16 2015

city: Manchester

first: Kate

last: Bloch

address: Alderley Park, Alderley Edge

institute: Manchester University

summary:
Monuron (1,1-dimethyl-3-(4-chlorophenyl) urea) is a non-selective phenylurea herbicide, widely used in the developing countries, however concerns have been raised about it toxicity and carcinogenicity. Monuron was evaluated by the National Toxicology Program (1988) and shown to be a male rat-specific renal carcinogen; however the mechanism of carcinogenesis is unknown. In this study we have examined the effect of sub-cytotoxic exposure to monuron (250µM) at 6h, 24h and 72h on the whole-genome expression profile in a rat proximal renal tubule cell line (NRK-52E). In addition we examined the short term exposure of MON in kidney and liver of exposed rats.
We used microarrays to detail the mechanism of toxicity and possibly carcinogenicity of monuron.

overall_design: NRK-52E cells were cultured to confluence on 6-well plates. Cells were then exposed to chlorothalonil dissolved in DMSO (0.1%) at the IC10 concentration at 72h (1.1 μM CHL) or DMSO only as control. After 6h, 24h and 72h the medium was removed and RNA was extracted from the cells. Three studies were conducted at each time point. Eight Wistar-derived rats where bred in the Life Science Support Unit at Liverpool John Moores University male rats (190-240g) 7-9 weeks of age were used in this study. Four rats being dosed with MON at 40mg/kg body weight on day 1 and 400mg/kg body weight on days 2 and 3, at 5ml/kg in corn oil. Four control animals were dosed with corn oil at 5ml/kg. Seventy two hours after the last dose all rats were killed by a rising concentration of carbon dioxide, the liver and kidneys quickly removed and immersed in RNAlater.

first: Katarzyna

first: Edward

last: Lock


title: mRNA expression in parotid acinar cells during terminal differentiation

status: Public on Feb 03 2015

city: Louisville

first: Douglas

last: Darling

state: KY

address: 501 S. Preston St.

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

summary:
Terminal differentiation in parotid acini relies on sustained changes in gene expression during the first few postnatal weeks. Little is known about what drives these changes. Expression measurements along with knowledgebased network analysis was used to develop a prospective gene regulatory network that drives differentiation.
We used expression measurements along with knowledgebased network analysis was used to develop a prospective gene regulatory network that drives differentiation.

overall_design: laser capture microdissection was used to isolate acinar cells from the parotid at nine timepoints in triplicate (E18, E20, P0, P2, P5, P9, P15, P20, and P25). RNA was isolated, and applied to the affymetrix rat genome array 230.

middle: S

first: Venkatesh

last: Srirangapatnam