title: Distinct Gene Expression Patterns in Biomechanically Stretched Cardiomyocytes

status: Public on Dec 01 2007

city: Heidelberg

first: Derk

last: Frank

address: Im Neuenheimer Feld 350

department: Dept. of Internal Medicine III

institute: University of Heidelberg

summary:
Neonatal rat ventricular cardiomyocytes (NRVCMs) were stretched biaxially (112%/24h) or stimulated with phenylephrine (PE, 50 uM), both resulting in a similar degree of hypertrophy. Unstretched NRVCMs served as negative control. Affymetrix microarray analysis revealed 164 genes more than 2.0-fold up- and 21 genes less than 0.5-fold downregulated (p<0.01). Differential expression was confirmed by real-time PCR. Several genes of the “fetal gene program”, i.e. BNP (4.2-fold, all p<0.05) were induced by stretch as well as PE. We also verified the upregulation of known stretch-responsive genes, including HSP70 (20.9x) and c-myc (3.0x). Moreover, we identified genes exclusively induced by stretch, such as the cardioprotective and antihypertrophic cytokine GDF15 (24.8x) and the antihypertrophic factor heme oxygenase 1 (Hmox1, 10.8x; both confirmed on protein level). Of note, neither PE nor endothelin-1 were able to upregulate GDF15 and Hmox1, while angiotensin II significantly induced both genes. Conversely, addition of the AT1 receptor blocker irbesartan markedly blunted stretch-mediated GDF15 and Hmox1 induction, suggesting that the angiotensin II receptor mediates stretch-dependent signals.
In conclusion, we report a comprehensive gene expression profile of cardiomyocytes subjected to biomechanical stress in comparison to pharmacologically induced hypertrophy. Our data imply that a stretch-specific gene program exists, that is mediated, at least in part, by angiotensin-II-dependent signalling.
Keywords: stress response

overall_design:
Three conditions were compared with two replicates each. These are:
(1) control, i.e. no treatment; (2) induction by phenylephrine (50 uM); (3) induction by biomechanical stretch (112%/24h)

first: Christian

last: Kuhn

first: Benedikt

last: Brors

first: Hugo

last: Katus

first: Norbert

last: Frey


title: Comparison of Renal Gene Expression from Dahl Salt-Sensitive (S) and the Renal Protective S.SHR(2) Congenic Strain

status: Public on Nov 01 2007

city: Toledo

first: Michael

middle: R

last: Garrett

state: OH

address: 3000 Arlington Ave, MS#1009

department: Physiology and Pharmacology

country: USA

institute: University of Toledo-Health Science Campus

summary:
The study sought to investigate differences in onset and progression of renal disease in the Dahl salt-sensitive (S), S.SHR(2) congenic, and spontaneously hypertensive rat (SHR) using a time-course. The data clearly demonstrates that the locus on chromosome 2 has a major and sustained ability to attenuate renal damage. As early as week 4, significant interstitial changes were observed between the S and the congenic which preceded any significant difference in proteinuria. Gene expression profiling was performed at week 4, 12, and 20 using kidney from the S and S.SHR(2) congenic to: (1) identify expression differences of positional candidates within the QTL region; (2) correlate temporal gene expression changes between the S and congenic with degree of renal damage; and (3) identify biochemical pathways potentially involved in the attenuated renal damaged observed in the congenic.  Gene pathway analysis (Ingenuity® Systems) performed at week 4, 12, and 20 revealed that pathways involved in cellular assembly and organization, cellular movement, and immune response were controlled differently between the S and congenic. Considering all the data, the chromosome 2 congenic appears to attenuate renal damage primarily through an altered fibrotic response.
Keywords: time course

overall_design:
DNA microarray analysis was performed using Affymetrix Genechip® Rat  Genome 230 2.0 array at three timepoints. The chip contains 31,000 probe sets from more than 30,000 transcripts on one array.  Three male S and three male S.SHR(2) congenic were selected at random from each group test for proteinruia at week 4, 12 and 20. Kidney was cut into ~ 0.5cM size cubes, suspended in RNAlater (Ambion, Austin, TX) and stored overnight at 4ºC.  RNA was extracted using Trizol® reagent (Invitrogen, Carlsbad, CA) and purified using Mini RNeasy kit (Qiagen,Valencia, CA ) according to manufacturer’s protocols. RNA quality was assessed by an OD260/280 ratio > 2.0 and visually by ethidium bromide staining on an agarose gel.
Biotinylated cRNA was synthesized from 10 ug of total RNA using the One-Cycle Target Labeling Kit (Affymetrix, Santa Clara, CA) as directed by the user manual. cRNA quality for each sample was assessed by hybridization of 5ug adjusted kidney cRNA to Affymetrix Genechip® Test3 array. Subsequently, 15ug adjusted kidney cRNA was hybridized to the Genechip® Rat 230 2.0 array. Hybridized chips were automatically washed, stained and scanned at the Medical University of Ohio Bioinformatics & Proteomics/Genomics Program gene array facility using Affymetrix equipment.


title: Infarcted rats teated with rhNRG-1(recombinant human NRG-1)

status: Public on Oct 18 2007

city: shanghai

first: zensun

last: biology

address: shanghai zhangjiang

country: China

institute: zensun biology

summary:
The ErbB famliy of erceptor tyrosine kinases and their ligands, neuregulins(NRGs), are crtical involved not only in cardiac development but also in the maintenace of structural and functional integrity of the adult heart. rhNRG-1(recombinant human NRG-1) Improves cardiac function and sruvival in models of ischemic, dilated, and viral cardiomyopathy with the ErbB-activation. But the mechanism is still unknown
Keywords: Genechips

overall_design: Three individual samples in each group (vehicle, rhNRG-1 treated or sham operated rats) were hybridized with 9 GeneChip® Rat Genome 230 2.0 Arrays (Affymetrix) separately.A total of 1950 genes (at least a 1.5-fold change in expression level compared with any another groups, all p <0.05),were selected and used as input for hierarchical clustering, a computational method that groups experimental samples according to similarity in patterns of gene expression across a large number of genes.


title: Triazole Antifungal Toxicogenomics: rat_primary_hepatocyte_CellzDirect

status: Public on Oct 21 2007

city: Research Triangle Park

first: David

last: Dix

state: NC

address: 109 TW Alexander Drive

department: ORD/NCCT

institute: US EPA

summary:
The triazole antifungals myclobutanil (MYC), propiconazole (PPZ) and triadimefon (TDF) all disrupt steroid hormone homeostasis and cause varying degrees of hepatic toxicity. To identify biological pathways consistently activated across various study designs, gene expression profiling was conducted on livers from rats following acute, repeated dose, or prenatal to adult exposures. To explore conservation of responses across species, gene expression from these rat in vivo studies were also compared to in vitro data from rat and human primary hepatocytes exposed to MYC, PPZ, or TDF. Pathway and gene level analyses across time of exposure, dose, and species identified patterns of expression common to all three triazoles, which were also conserved between rodents and humans. Pathways affected included androgen and estrogen metabolism, xenobiotic metabolism signaling through CAR and PXR, and CYP mediated metabolism.  Many of the differentially expressed genes are regulated by the nuclear receptors CAR, PPAR alpha and PXR, including ABC transporter genes (Abcb1 and MDR1), genes significant to xenobiotic, fatty acid, sterol and steroid metabolism (Cyp2b2 and CYP2B6; Cyp3a1 and CYP3A4; Cyp4a22 and CYP4A11) and xxx (Ugt1a1 and UGT1A1). Modulation of hepatic sterol and steroid metabolism is a plausible mechanism for triazole induced increases in serum testosterone. The gene expression changes caused by all three triazoles appear to focus on pathways regulating lipid and testosterone homeostasis, identifying potential common mechanisms of triazole hepatotoxicity that are conserved between rodents and humans.
Keywords: dose response, time course, comparative toxicogenomics

overall_design: A total of 35 samples were analyzed.  Three biological replicates for the controls (DMSO 0.1%), 2 biological replicates for positive control PCN, 3 biological replicates for positive control phenobarbital, 3 biological replicates for low dose myclobutanil, 3 biological replicates for mid dose myclobutanil, 3 biological replicates for high dose myclobutanil.  Three biological replicates each for low, mid, and high dose propiconazole, and 3 biological replicates each for low, mid, and high dose triadimefon.

middle: J

first: Amber

middle: K

last: Goetz


title: Changes in gene expression profile in mammalian cells upon Raf activation

status: Public on Sep 18 2007

city: LONDON

first: ALISON

middle: C

last: LLOYD

address: GOWER STREET

department: LMCB

country: United Kingdom

institute: UNIVERSITY COLLEGE LONDON

summary:
Comparison of  the changes in the gene expression profile of cells in which there is an activation of the Raf oncogene in the absence of any other extracellular signals
Keywords: Response to oncogenic activation of the MAPK pathway

overall_design: Primary rat Schwann cells containing an inducible RafER allele were plated on poly-L-lysine plus fibronectin coated dishes on DMEM + 3% FCS containing medium. Next day cells were transferred to minimal medium (DMEM  containing 100 μg ml-1 transferrin, 100 μg ml-1 bovine serum albumin, 16.1 μg ml-1 putrescine, 39 ng ml-1 selenium) for 24 h. Cells were then treated with either the vehicle (EtOH) or with Tamoxifen for 24 h. Three independent experiments were performed.

first: Pedro

last: Echave

first: Alison

last: Lloyd


title: Acute Gene Induction by Tienilic Acid in the Male Sprague Dawley Rat: Possible Role for Danger

status: Public on Jun 23 2007

city: Toronto

first: Paul

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary:
Tienilic acid (TA) was withdrawn from the US market due to numerous cases of liver necrosis.  Two major hypotheses currently used to understand the mechanisms of idiosyncratic reactions such as TA-induced hepatotoxicity are the hapten and danger hypotheses. Both human cytochrome (CYP) P450 2C9 and the rat ortholog CYP 2C11 metabolize TA, and it was reported that a reactive metabolite of TA binds almost exclusively to these enzymes, thus acting as a mechanism-based inhibitor.  TA-induced liver toxicity is associated with antibodies against CYP 2C9, thus TA appears to act as a hapten.  However, if the binding were limited to CYP 2C, it is unlikely that this would lead to significant cell stress.  Thus, if TA does not cause cell stress it would suggest that a drug does not have to generate a “danger signal” in order to cause an idiosyncratic drug reaction and acting as a hapten is sufficient.  In order to test whether TA can cause cell stress, male Sprague Dawley rats were orally dosed with TA, and hepatic gene expression was profiled at 6 and 24 h after drug administration.
Results showed that TA induced robust changes in genes involved in oxidative stress (e.g. aldo-keto reductase, glutathione-S-transferase, thioredoxin reductase, epoxide hydrolase), inflammation and cytotoxicity (e.g. IL-1b, interferon regulatory factor 1, macrophage stimulating protein 1, caspase-12), as well as those promoting liver regeneration (e.g. p27Kip1, DUSP6, serine dehydratase, spectrin bII, inhibin bA).  These data support the hypothesis that danger signals in the form of cell-stress proteins and the generation of oxidative stress may be involved in initiating the immune response observed in TA-induced toxicity.  Other recent data also indicate that the reactive metabolite of TA binds to other proteins in addition to CYP 2C
Keywords: time course, stress response

overall_design: Rats were orally dosed with TA or control sodium bicarbonate. Eight animals were divided into two groups: Group 1 consisted of two animals that received a single dose of TA, and the two control animals received only sodium bicarbonate.  Group 1 was sacrificed 6 h after drug/vehicle administration.  Group 2 also comprised of two animals, and they were given two doses of TA (given at t=0 and t=16 h) and sacrificed at 24 h.  Control rats in group 2 received two oral doses of sodium bicarbonate.  For microarray analysis, six Affymetrix chips were used: Group 1 samples (3 chips) was comprised of pooled RNA from control rats C1 and C2, and an individual chip for each treated animal T1 and T2; Group 2 (3 chips) pooled RNA from control rats C3 and C4, and an individual chip for each treated animal T3 and T4.

first: Stephanie

last: Pacitto

first: Jack

middle: P

last: Uetrecht


title: Interactions Between Progesterone and Tumor Necrosis Factor-alpha in the Regulation of Primordial Follicle Assembly

status: Public on Jun 22 2007

city: Pullman

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary:
Follicle assembly is the process by which groups or ‘nests’ of oocytes break down to form primordial follicles.  The size of the primordial follicle pool is the major determinant of the reproductive lifespan of a female.  Previously, progesterone (P4) has been shown to inhibit follicle assembly, while tumor necrosis factor alpha (TNF-alpha) has been shown to promote the apoptosis that is necessary for follicle assembly. The current study examines how TNF-alpha and progesterone interact to regulate primordial follicle assembly.  Ovaries were collected from newborn rats and placed in organ culture to examine the actions of P4 and TNF-alpha.  P4 was found to decrease primordial follicle assembly and increase the percentage of un-assembled oocytes both in vitro and in vivo.  TNF-alpha treatment did not change the proportion of assembled follicles in cultured ovaries, but did block the ability of P4 to inhibit follicle assembly.  Microarray analysis of  the ovarian transcriptome  revealed that progesterone treatment of the ovaries altered the expression of 513 genes with 132 only expressed after P4 treatment and 16 only expressed in control ovaries.  The majority of genes were up-regulated greater than 2-fold over control, with a small subset of 16 genes down-regulated.  Categories of genes affected by P4 are described including a group of extra-cellular signaling factors.  The progesterone receptors expressed at the time of follicle assembly included the surface membrane progesterone receptors PGRMC1, PGRMC2 and RDA288.  The nuclear genomic P4 receptor was not expressed at appreciable levels.  Progesterone increased the expression of several genes (TANK, NFkappaB, Bcl2l1 and Bcl2l2) involved in a signaling pathway that promotes cell survival and inhibits apoptosis.  Observations indicate that P4 acts through the surface membrane progesterone receptors to regulate primordial follicle assembly, and that TNF-alpha can over-ride the inhibitory actions of P4 on follicle assembly.  A major mechanism involved in the actions of P4 is an increase in cell survival genes and inhibition of the apoptosis pathway.  Observations provide insight into the hormonal regulation of primordial follicle assembly and lead to novel approaches to potentially manipulate follicle assembly and reproductive capacity.
Keywords: expression analysis, progesterone, TNFa, follicle assembly, ovary

overall_design: RNA samples from two control groups (pooled untreated cultured ovaries) are compared to two treated groups (pooled cultured ovaries treated with progesterone)

first: Eric

last: Nilsson

first: Jacob

last: Stanfield


title: Expression data from epididymal fat tissues of diet induced obese rats

status: Public on Aug 07 2007

city: Indianapolis

first: Dan

last: Li

state: IN

address: Lilly Corporate Center

institute: Eli Lilly & Company

summary:
Analysis of gene expression profiles of epididymal fat from DIO rats
We applied a comparative functional genomics approach to evaluate diet-induced obese (DIO) rats as an obesity model
Keywords: single time point, comparison control animal vs. diet induced obese animal

overall_design: Gene expression profiles from DIO and lean rats were generated and compared. A private colony of male Long-Evans rats was set up at Harlan (Harlan-Sprague Dawley, Indianapolis, IN).  The animals had been on either a high fat/high sucrose diet (TD95217, Harlan Takled, Madison, WI) or a regular chow (Purina 5008; Ralston-Purina, St. Louis, MO) since weaning.  Rats were shipped at 14-weeks of age to our facility and maintained on a 12:12-hour light-dark photoperiod (light on 10:00 PM).  They were individually housed throughout the study at ambient temperature, and had free access to diets and water.  After 2 weeks acclimation to the facility, body weight of the rats and weight of food consumed in the last 7 days were measured once a week.  Body fat mass was analyzed by nuclear magnetic resonance (NMR) using an Echo Medical System (Houston, TX) instrument 3 times throughout the study.  Fat free mass is the difference between body mass and fat mass.  All animal studies were conducted in compliance with approved institutional animal care and use protocols according to NIH guidelines (NIH publication No. 86-23, 1985). OGTT was conducted after an overnight fasting when animals were 21 weeks of age.  After a baseline blood collection (time 0), animals were dosed orally with 1.5 gram/kg glucose.  Subsequence blood samples were collected at 30, 60, and 120 minutes post glucose challenge for the determination of plasma glucose and insulin levels. At 25 weeks of age, blood was collected by tail bleeding after overnight fasting.  Rats were killed a week later at 09:00am by rapid decapitation.  Trunk blood was collected and epididymal fat tissue excised.   Various circulating metabolic parameters were measured under fasted (week 25) and fed conditions (week 26). Total RNA from rat epididymal fat was isolated with RNA STAT-60 (Tel-Test) according to the manufacturer's protocol.  5 micrograms of total RNA were labeled and hybridized to Affymetrix RAE230_2 arrays according to the Affymetrix protocol.

first: Shuyu

first: Yanyun

last: Chen


title: Making a predictive heart failure expression profile in Ren2 rat left ventricles

status: Public on Oct 05 2007

city: Maastricht

first: Arie

last: van Erk

address: PO Box 616

department: BiGCaT Bioinformatics

country: Netherlands

institute: University Maastricht

summary:
The intercalated disc of cardiac myocytes is emerging as a crucial structure in the heart. Loss of intercalated disc proteins like N-cadherin causes lethal cardiac abnormalities, mutations in intercalated disc proteins cause human cardiomyopathy. A comprehensive screen for novel mechanisms in failing hearts demonstrated that expression of the lysosomal integral membrane protein-2 (LIMP-2) is increased in cardiac hypertrophy and heart failure in both rat and human myocardium. Complete loss of LIMP-2 in genetically engineered mice did not affect cardiac development; however these LIMP-2 null mice failed to mount a hypertrophic response to increased blood pressure but developed cardiomyopathy. Disturbed cadherin localization in these hearts suggested that LIMP-2 has important functions outside lysosomes. Indeed, we also find LIMP-2 in the intercalated disc, where it associates with cadherin. RNAi-mediated knockdown of LIMP-2 decreases the binding of phosphorylated b-catenin to cadherin, while overexpression of LIMP-2 has the opposite effect. Taken together, our data show that lysosomal integrated membrane protein-2 is crucial to mount the adaptive hypertrophic response to cardiac loading. We demonstrate a novel role for LIMP-2 as an important mediator of the intercalated disc.
Keywords: heart failure, comparison

overall_design:
overall design:
3 groups of rats, 1 sample per rat:
- compensated = Ren2 rat, hypertensive, no heart failure (N=6)
- failure = Ren2 rat, hypertensive, no heart failure (N=4)
- SD = control group, non-hypertensive (N=4)

first: Blanche

last: Schroen

first: Yigal

last: Pinto


title: Gene expression data from hypothalamus of normal sexual development of the female rat

status: Public on Jun 27 2007

city: Beaverton

first: Alejandro

last: Lomniczi

state: OR

address: 505 NW 185th Ave

department: Neuroscience

institute: Oregon National Primate Research Center - OHSU

summary:
To determine the global changes in hypothalamic gene expression that may occur at the time of female puberty in this species, animals were euthanized at three different stages, juvenile (25-days of age), early puberty (30-35 days of age) and on the day of the first proestrus (32-37 days of age). According to criteria previously established (Ojeda,S.R.; Urbanski,H.F. Puberty in the rat pp.363-409. The Physiology of Reproduction, 2nd Edition, Vol 2. Edited by  Knobil,E.; Neill,J.D. Raven Press, 1994), 25-day-old animals are in the mid- juvenile phase of prepubertal development (JUV). At this time, the vagina is not yet patent and the uterine weight is 60 mg or less, with no accumulation of intrauterine fluid. Older rats showing a closed vagina, accumulation of intrauterine fluid and an uterine weight less that 180 mg are considered to be in the early proestrous (EP) phase of puberty. Finally, rats still exhibiting a closed vagina, but showing a uterus ballooned with fluid and a uterine weight of at least 200 mg are considered to be in late proestrus (LP), i.e., the phase of puberty when the first preovulatory surge of LHRH and gonadotropins takes place. The first ovulation occurs the following day.  All animals were sacrificed between 1600-1700 h, and the medial basal hypothalamus (MBH) was immediately dissected, as previously described (Rogers,L.C.; Junier,M-P.; Farmer,S.R.; Ojeda,S.R. A sex-related difference in the developmental expression of class II -tubulin messenger RNA in rat hypothalamus. Mol.Cell.Neurosci., 2: 130-138, 1991) and stored in RNAlater according to manufacturer’s instructions.
Keywords: comparison between Early pubertal and Juvenile or Late pubertal and Juvenile stages of sexual development in the female rat

overall_design: Affymetrix arrays were used to detect global changes in gene expression in the hypothalamus of normal sexual development of the female rat.

first: Claudio

middle: A

last: Mastronardi

first: Sergio

last: Ojeda


title: A Multi- Kinase Inhibitor Modulates Pulmonary Hypertension in a Rodent Model 2

status: Public on Jun 15 2007

city: Chicago

first: Ankit

last: Desai

state: IL

address: 929 East 57th Street, Room W403R

department: Medicine

institute: The University of Chicago

summary:
Pulmonary hypertension (PH) and cancer pathophysiology share common signal transduction pathways leading to abnormal endothelial and smooth muscle cell interactions and angioproliferative vasculopathy. Sorafenib (Sor) a drug in clinical trials for cancer treatment, is an inhibitor of multiple kinases important in angiogenesis (Raf-1 kinase, VEGFR-2, VEGFR-3, PDGFR-beta). In this study, we assessed the efficacy of Sor as a potential therapy for PH, and hypothesized that Sor prevents the development of both a conventional and an augmented rodent model of PH.  We performed studies in Dahl Salt-Sensitive rats (SS) exposed to hypoxia alone and in combination with the VEGFR-2 inhibitor, SU5416, known to induce a well-characterized augmented PH  phenotype. Rats were, thus, divided into 5 groups: normoxia/vehicle (Norm), hypoxia/vehicle (H), hypoxia/ SU5416 (H-SU), hypoxia/Sorafenib (H-Sor) and hypoxia/ SU5416/ Sorafenib (H-SU-Sor). Except for the Norm group, all rats were maintained in a hypoxia chamber with a FiO2 of 10%. Rats received a single injection of SU5416 on Day 1 (20 mg/kg) and Sor solution was administered daily by gavage (2.5mg/kg). After 3.5 weeks, all rats were assessed by open chest catheterizations for pulmonary vascular and right ventricular pressures. Lung and heart tissue were harvested for histological and microarray analyses. Our results showed H-SU rats developed severe PH with changes in hemodynamic and histologic parameters when compared to Norm controls while rats exposed to H alone only displayed mildly elevated pressures compared with Norm. There was no significant change in pressures in the H-Sor or H-SU-Sor compared to Norm. Histopathology demonstrated a dramatic prevention of the PH phenotype in the H-SU-Sor rats with no significant remodeling compared with H-SU rats. Expression profiling data from H (n=4) and H-SU (n=3) rat lungs were compared to Norm (n=4) using normalization in R and SAM (δ>.639,) (minimum fold change >1.4). With false discovery rates (FDR) of 6.5% in hypoxia and 1.6% in H-SU, 1019 and 465 genes, respectively, were differentially-regulated compared to Norm. In addition, 38 genes were differentially expressed between H-SU and H-SU-Sor (n=4, FDR 6.7%) revealing  a molecular signature with potentially novel target genes of Sor. Five differentially expressed genes (Tgfbeta3, C1qg, Nexn, Frzb, and Plaur) were examined by real-time RT-PCR and three were further validated by immunohistochemistry confirming the regulation on protein level. Based on the known pathways of hypoxic-induced PH and Sor, we further utilized immunohistochemistry to show the up-regulation of mediators of the MAPK cascade in the H and H-SU models of PH with subsequent, down-regulation by Sor. We therefore present Sor as a novel treatment for the development of severe PH and theorize that the MAPK cascade is a canonical pathway involved both in the development of PH and in the attenuation by Sor.
Keywords: Drug Effect

overall_design: Rats were divided into 5 groups of which 4 groups were analyzed by microarrays: normoxia/vehicle (n=4), hypoxia/vehicle (n=4), hypoxia/ SU5416 (n=3), and hypoxia/ SU5416/ Sorafenib (n=4). RNA was harvested from lung tissue at 3.5 weeks.Expression profiling data from H and H-SU rat lungs were compared to Norm using normalization in R and SAM (δ>.639,) (minimum fold change >1.4). With false discovery rates (FDR) of 6.5% in hypoxia and 1.6% in H-SU, 1019 and 465 genes, respectively, were differentially-regulated compared to Norm. In addition, 38 genes were differentially expressed between H-SU and H-SU-Sor (FDR 6.7%) revealing  a molecular signature with potentially novel target genes of Sor.

first: Liliana

last: Moreno-Vinasco

first: Patrick

last: Singleton

first: Sam

last: Lee

first: Yves

last: Lussier

first: Mardi

last: Gomberg-Maitland

first: Michael

last: Maitland

first: Alyna

last: Hussein

first: Ye

last: Liu

first: Keith

last: Collins

first: Saad

last: Sammani

first: Roberto

last: Lang

first: Joe

middle: G

last: Garcia


title: Skeletal muscle after fine needle stimulation

status: Public on Sep 01 2007

city: Suita

first: Osamu

last: Ishida

state: Osaka

address: 5-7-1 Fujishorodai

department: Regenerative Medicine

country: Japan

institute: National Cardiovascular Center

summary:
Fine needle stimulation also known as acupuncture is a traditional Chinese medical practice which causes relief of pain.  We demonstrated that it caused neovascularization and enhanced recovery of blood perfusion in a ischemic portion of skeletal muscle in rats with  hindlimb ischemia.  Therefore we evaluated the effect of fine needle stimulation on skeletal muscle at gene expression level
Keywords: Evaluation of physical stimulation

overall_design: With 0.14mm diameter stainless steel needle, a hundred pricks were applied in a 100 square mili-meter region on addductor portion of the left rat hindlimb.  Right hindlimb was left intact as control.  24 hrs after fine needle stimulation, skeletal muscle sample was resected from adductor muscle of fine needle stimulated left hindlimb and non-stimulated right hindlimbs, respectively.  Then gene expression analysis with microarray was conducted on each skelatal muscle sample.


title: Characterization of weight loss and weight regain mechanisms after Roux-en-Y gastric bypass in rats

status: Public on Jun 30 2007

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary:
Roux-en-Y gastric bypass (RYGB) is the most effective therapy for morbid obesity, but it has a ~20% failure rate. We used our established RYGB model in diet-induced obese (DIO) Sprague-Dawley rats, which reproduces human bi-phasic body weight (BW) loss pattern, to determine mechanisms contributing to success (RGYB-S) or failed (RYGB-F) RYGB. DIO rats were randomized to RYGB, sham operated Obese, and sham operated obese pair fed-linked to RYGB (PF) groups. BW, caloric intake (CI) and fecal output (FO) were recorded daily for 90 days, food efficiency (FE) was calculated, and morphologic changes were determined. Gut, adipose and thyroid hormones were measured in plasma. Mitochondrial respiratory complexes in skeletal muscle, expression of energy-related hypothalamic and fat peptides, receptors and enzymes were quantified. A 25% failure rate occurred. RYGB-S, RYGB-F and PF rats vs. Obese showed rapid BW decrease, followed by sustained BW loss in RYGB-S. RYGB-F and PF gradually increased BW. Expression profiling of both CNS (hypothalamus) and peripheral tissues (subcutaneous abdominal fat) strongly supported the involvement of a number of metabolic and feeding-related genes in the differential outcomes.
Keywords: gene expression analysis

overall_design: 3 biological replicate RNA samples were prepared from 2 tissues (the subcutaneous abdominal fat or the hypothalamus) from rats in 3 treatment groups (rats losing weight successfully after gastric bypass surgery, rats gaining weight, and rats that were fed the same amount as the treated rats)

first: Ana

last: Guijarro

first: Susumu

last: Suzuki

first: Chung

last: Chen

first: Henriette

last: Kirchner

first: Sergiy

last: Nadtochiy

first: Paul

middle: S

last: Brookes

first: Akira

last: Niijima

first: Akio

last: Inui

middle: M

last: Meguid


title: Expression data from metanephric mesenchyme induced to convert into nephron epithelia

status: Public on Jul 01 2007

city: Berlin

first: Kai

middle: Martin

last: Schmidt-Ott

address: Robert-Roessle-Str. 10

department: Differentiation and Regeneration of Kidney Epithelia

country: Germany

institute: Max-Delbrueck Center for Molecular Medicine

summary:
During kidney development segmented epithelia of the nephron derive from progenitor cells in the metanephric mesenchyme after induction by secreted molecules from the ureteric bud. We have identified three distinct inductive activities from a ureteric bud cell line. These include leukemia inhibitory factor (LIF), neutrophil gelatinase-associated lipocalin (NGAL) and an active fraction currently referred to as ANX. Each of these activities induces segmented nephron epithelia in isolated rat metanephric mesenchyme over a time period of 7 days. This study was designed to characterize the temporal sequence of gene expression in the course of the conversion process induced by each of the distinct inducers.
Keywords: time course

overall_design: Metanephric mesenchymes were microdissected from rat E13.5 embryos. Mesenchymes were cultured on transwells in the presence of either LIF, NGAL or the ANX fraction and RNA was harvested after 1, 2, 3, 4, 5, and 7 days for RNA extraction. Freshly dissected mesenchymes and mesenchymes cultured in the absence of inducers for 1 and 2 days, respectively, served as controls. Each condition was analyzed in duplicate (biological replicates). Biotinylated cRNA was prepared and hybridized to Affymetrix Rat Genome 230 2.0 Microarrays. Expression values were obtained by robust multichip analysis.

first: Xia

first: Benjamin

last: Hirsh

first: Abby

last: Sarkar

first: Jun

last: Yang

first: Jonathan

last: Barasch


title: A Multi- Kinase Inhibitor Modulates Pulmonary Hypertension in a Rodent Model

first: Ankit

last: Desai

summary:
Pulmonary hypertension (PH) and cancer pathophysiology share common signal transduction pathways leading to abnormal endothelial and smooth muscle cell interactions and angioproliferative vasculopathy. Sorafenib (Sor) a drug in clinical trials for cancer treatment, is an inhibitor of multiple kinases important in angiogenesis (Raf-1 kinase, VEGFR-2, VEGFR-3, PDGFR-beta). In this study, we assessed the efficacy of Sor as a potential therapy for PH, and hypothesized that Sor prevents the development of both a conventional and an augmented rodent model of PH.  We performed studies in Dahl Salt-Sensitive rats (SS) exposed to hypoxia alone and in combination with the VEGFR-2 inhibitor, SU5416, known to induce a well-characterized augmented PH  phenotype. Rats were, thus, divided into 5 groups: normoxia/vehicle (Norm), hypoxia/vehicle (H), hypoxia/ SU5416 (H-SU), hypoxia/Sorafenib (H-Sor) and hypoxia/ SU5416/ Sorafenib (H-SU-Sor). Except for the Norm group, all rats were maintained in a hypoxia chamber with a FiO2 of 10%. Rats received a single injection of SU5416 on Day 1 (20 mg/kg) and Sor solution was administered daily by gavage (2.5mg/kg). After 3.5 weeks, all rats were assessed by open chest catheterizations for pulmonary vascular and right ventricular pressures. Lung and heart tissue were harvested for histological and microarray analyses. Our results showed H-SU rats developed severe PH with changes in hemodynamic and histologic parameters when compared to Norm controls while rats exposed to H alone only displayed mildly elevated pressures compared with Norm. There was no significant change in pressures in the H-Sor or H-SU-Sor compared to Norm. Histopathology demonstrated a dramatic prevention of the PH phenotype in the H-SU-Sor rats with no significant remodeling compared with H-SU rats. Expression profiling data from H (n=4) and H-SU (n=3) rat lungs were compared to Norm (n=4) using normalization in R and SAM (δ>.639,) (minimum fold change >1.4). With false discovery rates (FDR) of 6.5% in hypoxia and 1.6% in H-SU, 1019 and 465 genes, respectively, were differentially-regulated compared to Norm. In addition, 38 genes were differentially expressed between H-SU and H-SU-Sor (n=4, FDR 6.7%) revealing  a molecular signature with potentially novel target genes of Sor. Five differentially expressed genes (Tgfbeta3, C1qg, Nexn, Frzb, and Plaur) were examined by real-time RT-PCR and three were further validated by immunohistochemistry confirming the regulation on protein level. Based on the known pathways of hypoxic-induced PH and Sor, we further utilized immunohistochemistry to show the up-regulation of mediators of the MAPK cascade in the H and H-SU models of PH with subsequent, down-regulation by Sor. We therefore present Sor as a novel treatment for the development of severe PH and theorize that the MAPK cascade is a canonical pathway involved both in the development of PH and in the attenuation by Sor.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptional response of rat cerebrocortical tissue following acute exposure to permethrin or deltamethrin.

status: Public on Oct 15 2007

first: Joshua

last: Harrill

department: Curriculum in Toxicology

institute: University of North Carolina

summary:
Pyrethroids are neurotoxicants that disrupt nervous system function by interacting with a variety of membrane bound ion channels on neuronal plasma membranes.  This study is designed to investigate the transcriptional events downstream of pyrethroid-induced disruption of nervous system excitability.  Adult, male Long-Evans rats were orally dosed in vivo with a single dose of either permethrin (1, 10, or 100 mg/kg) or deltamethrin (0.3, 1, 3 mg/kg) at levels that produce only modest behaviroal effects in the whole animal (Wolansky et al. 2006).  Transcriptional profiles were obtained from frontal cerebrocortical tissue 6 hours after acute exposure.  The primary goals were 1) to identify dose-responsive biomarkers of effect for pyrethroids and 2) identify sensitive intracellular signaling or metabolic pathways sensitive to pyrethroid compounds.
Keywords: dose response

overall_design:
In total 60 samples were analyzed in the present study: vehicle control (n = 12), 1 mg/kg permethrin (n=8), 10 mg/kg permethrin (n = 8), 100 mg/kg permethrin (n = 8), 0.3 mg/kg deltamethrin (n = 8), 1 mg/kg deltamethrin (n = 8), 3 mg/kg deltamethrin (n = 8).  Transcriptional profiles for each test subject were obtained independently, without sample pooling.

The publication will include an Appendix Table comparing the variability of RMA values (see Sample VALUE columns) to that of GCOS values (see Sample .CHP files).

first: Zhen

last: Li

first: Fred

last: Wright

first: Kevin

last: Crofton


title: Global analyses of gene expression in early experimental knee osteoarthritis

status: Public on Jul 10 2007

city: London

first: Tom

last: Appleton

state: ON

address: Rm 0061 DSB The University of Western Ontario

department: Physiology & Pharmacology

institute: The University of Western Ontario

summary:
OBJECTIVE: To analyze genome-wide changes in chondrocyte gene expression in a surgically induced model of early osteoarthritis (OA) in rats, to assess the similarity of this model to human OA, and to identify genes and mechanisms leading to OA pathogenesis. METHODS: OA was surgically induced in 5 rats by anterior cruciate ligament transection and partial medial meniscectomy. Sham surgery was performed in 5 additional animals, which were used as controls. Both groups underwent 4 weeks of forced mobilization, 3 times per week. RNA was extracted directly from articular chondrocytes in the OA (operated), contralateral, and sham-operated knees. Affymetrix GeneChip expression arrays were used to assess genome-wide changes in gene expression. Expression patterns of selected dysregulated genes, including Col2a1, Mmp13, Adamts5, Ctsc, Ptges, and Cxcr4, were validated by real-time polymerase chain reaction, immunofluorescence, or immunohistochemistry 2, 4, and 8 weeks after surgery. RESULTS: After normalization, comparison of OA and sham-operated samples showed 1,619 differentially expressed probe sets with changes in their levels of expression >/=1.5-fold, 722 with changes >/=2-fold, 135 with changes >/=4-fold, and 20 with changes of 8-fold. Dysregulated genes known to be involved in human OA included Mmp13, Adamts5, and Ptgs2, among others. Several dysregulated genes (e.g., Reln, Phex, and Ltbp2) had been identified in our earlier microarray study of hypertrophic chondrocyte differentiation. Other genes involved in cytokine and chemokine signaling, including Cxcr4 and Ccl2, were identified. Changes in gene expression were also observed in the contralateral knee, validating the sham operation as the appropriate control. CONCLUSION: Our results demonstrate that the animal model mimics gene expression changes seen in human OA, supporting the relevance of newly identified genes and pathways to early human OA. We propose new avenues for OA pathogenesis research and potential targets for novel OA treatments, including cathepsins and cytokine, chemokine, and growth factor signaling pathways, in addition to factors controlling the progression of chondrocyte differentiation.
Keywords: disease state analysis

overall_design: OA was surgically induced in 5 rats by anterior cruciate ligament transection and partial medial meniscectomy. Sham surgery was performed in 5 additional animals, which were used as controls. Both groups underwent 4 weeks of forced mobilization, 3 times per week. RNA was extracted directly from articular chondrocytes in the OA (operated), contralateral, and sham-operated knees, 28 days post-surgery. Affymetrix GeneChip expression arrays were used to assess genome-wide changes in gene expression.

first: Vasek

last: Pitelka

first: Jim

last: Henry

first: Frank

last: Beier


title: Puberty and Diabetes in the Kidney

status: Public on Sep 30 2007

city: Omaha

first: Pascale

middle: Hammond

last: Lane

state: NE

address: 982169 Nebraska Medical Center

department: Pediatrics

institute: University of Nebraska

summary:
Puberty unmasks or accelerates nephropathies, including the nephropathy of diabetes mellitus (DM). A number of cellular systems implicated in the kidney disease of DM interweave, forming an interdependent functional web. We performed focused microarray analysis to test the hypothesis that one or more genes in the transforming growth factor beta (TGF-β) signaling system would be differentially regulated in male rats depending on the age of onset of DM.
Keywords: Age-Disease State Interaction Analysis

overall_design: Male rat littermates began the 6-week-protocol at 4 or 14 weeks of age with injection of streptozocin, 65 mg/kg iv, or equal volume of vehicle. 3 days later insulin palmitate or palmitate vehicle pellets were implanted once hyperglycemia was confirmed. Rats received ad lib food and water for 6 weeks and maintained blood glucose levels 350-350 mg/dl in diabetic groups. Kidneys were removed under isoflurane anesthesia. The cortex was rapidly dissected from the medulla and snap-frozen. Cortex was stored at -80 until all rats had completed the protocol. RNA was isolated from renal cortex and the transcriptome analyzed using gene chips with more than 30,000 transcripts. Age-specific effects of DM were demonstrated for 1,760 transcripts. Analysis then focused on 89 genes involved in the TGF-β signaling pathway.

first: William

last: Langer

first: Kay

last: Devish

first: Pamela

last: Carmines

middle: H


title: Gene expression in kidney from Lewis and Dahl(S) rat

status: Public on May 09 2007

first: Kazuaki

last: Kajimoto

address: 5-7-1 Fujishirodai

department: Department of Epidemiology

summary:
Male Dahl salt sensitive and Lewis rats (n=3 each) were fed an 8% NaCl diet starting at 5 weeks of age for 8 weeks.  Total RNA was isolated with TRIzol reagent from DS and LEW kidneys and was subjected to microarray analysis.
Keywords: animals with different genetic background comparison

overall_design: Male Dahl salt sensitive and Lewis rats (n=3 each) were fed an 8% NaCl diet starting at 5 weeks of age for 8 weeks.  Total RNA was isolated with TRIzol reagent from DS and LEW kidneys and was subjected to microarray analysis. The resulting data were analyzed with GeneChip Operating Software ver1.4.  Three independent experiments comparing expressions between salt-loaded Dahl salt sensitive and salt-loaded Lewis rats were performed.

first: Toshiki

last: Sumiya

first: Tomohiro

last: Okuda

first: Naoharu

last: Iwai


title: Gene profiling of the heart myocardium after a single dose administration of Isoproterenol hydrochloride

status: Public on Jun 02 2007

city: Nutley

first: Charu

last: Kanwal

state: NJ

address: 340 Kingsland Street

department: RIGG

institute: Hoffman-La Roche

summary:
Gene expression was evaluated in the myocardium of male Wistar rats after a single sc administration of 0.5 mg of isoproterenol, a β-adrenergic agonist that causes acute tachycardia with subsequent myocardial necrosis. Histology of the heart, clinical chemistry and hematology were evaluated at 9 time-points (0.5 hr to 14 d post-injection). Myocardial gene expression was evaluated at 4 time-points (1 hr to 3 d). Contraction bands and loss of cross striation were identified on phosphotungstic acid-hematoxylin-stained sections 0.5 hr post-dosing. Plasma troponin I elevation was detected at 0.5 hr, peaked at 3 hr, and returned to baseline values at 3 d post-dosing. Interleukin 6 (Il6) expression spiked at 1-3 hr and was followed by a short-lived time-dependant dysregulation of its downstream targets. Concurrently and consistent with the kinetics of the histologic findings, many pathways indicative of necrosis/apoptosis (p38 MAPK signaling, NF-kB signaling) and adaptation to hypertension (PPAR signaling) were over-represented at 3 hr. The 1 d and 3 d time-points indicated an adaptative response, with down-regulation of the fatty acid metabolism pathway, up-regulation of the fetal gene program, and superimposed inflammation and repair at 3 d. These results suggest early involvement of Il6 in isoproterenol-induced myocardial necrosis and emphasize the value of early time-points in transcriptomic studies
Keywords: time course study of Isoproternol hydrochloride

overall_design: Myocardial gene expression was evaluated at 4 time-points: 1 hour, 3 hours, 24 hours and 48 hours for doses of 0mg and 0.5 mg Isoproternol.

first: Igor

last: Mikaelian


title: Granulosa cell gene expression associated with oocyte developmental competence

status: Public on May 11 2007

city: Ottawa

first: Benjamin

last: Tsang

address: 725 Parkdale Avenue

institute: Ottawa Health Research Institute

summary:
Gene expression profiles of granulosa cells from rat ovarian follicles by Affymetrix rat whole genome array showed that twelve genes were up-regulated, while one gene down-regulated more than 1.5 folds in the normal developmental competence group compared with those in the poor developmental competence group. Gene ontology classification showed that the up-regulated genes included lysyl oxidase and nerve growth factor receptor associated protein 1, which are important in the regulation of protein-lysine 6-oxidase activity, and in apoptosis induction, respectively. The down-regulated genes included glycoprotein-4-beta galactosyltransferase 2, which is involved in the regulation of extracellular matrix organization and biogenesis.
Keywords: Dose response

overall_design: Immature rats were injected with eCG and 24h thereafter with anti-eCG antibody to induce follicular atresia or with pre-immune serum to stimulate follicle development. A high percentage (30-50%, normal developmental competence, NDC) of oocytes from eCG/pre-immune serum group developed to term after embryo transfer compared to those from eCG/anti-eCG (0%, poor developmental competence, PDC). Gene expression profiles of granulosa cells from the above oocyte-collected follicles were assessed by Affymetrix rat whole genome array.

first: Jin-Yi

last: Jiang


title: Gene Expression Changes in the Rat Nasal Epithelium Following Formaldehyde Exposure

status: Public on Apr 23 2007

first: Russell

middle: Scott

last: Thomas

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

summary:
Formaldehyde, an important industrial chemical, is used for multiple commercial purposes throughout the industrialized world.  This simple, one carbon aldehyde is a natural metabolite formed in cells throughput the body.  However, it is also a rodent nasal carcinogen, when inhaled by rats every day for two-years at irritant concentrations.  High tumor incidences occur at concentration of 10 ppm and above; no tumors are observed at concentrations below 6.0 ppm.  The US Environmental Protection Agency (US EPA) is now (2007) conducting a risk assessment to try to evaluate possible cancer risks for much lower levels of human exposure.  Sensitive methods are needed to evaluate tissue responses below those concentrations that are clearly irritant or carcinogenic.  This microarray study was undertaken to evaluate the mode of action for nasal responses to inhaled formaldehyde in Fisher 344 rats over a range of exposure concentrations.  The range of concentrations used spanned those at which virtually no tissue responses were observed (0.7 ppm) to those that represent the highest concentration in the cancer studies (15 ppm) that produced nasal tumors in half the exposed group of rats.  The study identified doses at which there were no statistically significant changes in gene expression; intermediate doses with changes in a small number of genes not easily grouped by function; and then concentrations where changes were consistent with irritation and cell stress responses.
Keywords: time course, dose response, gene expression

overall_design: Eight week old male F344/NCrl rats were exposed to formaldehyde through either instillation or inhalation. For animals exposed via instillation, 40 ul per nostril of 400 mM formaldehyde was instilled intranasally.  Vehicle control animals were instilled with 40 ul per nostril of distilled water.  All animals exposed via instillation were sacrificed 6 hours post-exposure.  For animals exposed via inhalation, whole-body exposures were performed at doses of 0, 0.7, 2, 6, and 15 ppm (6 hours per day, 5 days per week).  Inhalation animals were sacrified at 6 hours, 24 hours, 5 days, and 19 days following initiation of exposure except for the 15 ppm concentration which was sacrificed at only the 6 hour time point.  Following sacrifice, tissue from the Level II region of the nose was dissected and digested with a mixture of proteases to remove the epithelial cells.  The epithelial cells scquired from this section of the nose consisted primarily of transitional epithelium with some respiratory epithelium.  Microarray analysis was performed on the epithelial cells.

first: Melvin

middle: E

last: Andersen

first: Edilberto

last: Bermudez

first: Linda

last: Pluta

first: Longlong

last: Yang

first: Harvey

last: Clewell


title: Normal gene expression in male and female Sprague-Dawley rat nasal respiratory and olfactory epithelium

status: Public on May 01 2007

city: Greensboro

first: Elizabeth

middle: Sherman

last: Roberts

address: 3200 Northline Ave, Suite 300

institute: Novartis Animal Health US

summary:
The nasal epithelium is an important target site for chemically-induced toxicity and carcinogenicity.  Human epidemiological investigations and experimental laboratory animal studies show that the nasal olfactory epithelium is selectively damaged by inhalation exposure to several chemicals, including vinyl acetate and hydrogen sulfide.  The reason for the relative sensitivity of the nasal olfactory epithelium is not known.  To better understand and predict the response of the nasal epithelium to inhaled xenobiotics, gene expression profiles from naїve male and female Sprague-Dawley rats were constructed.  Epithelial cells were manually collected from the nasal septum, naso- and maxillo-turbinates, and ethmoid turbinates of 9 male and 9 female rats.  Gene expression analysis was performed using the Affymetrix Rat Genome 430 2.0 microarray.  Gene ontology enrichment analysis identified several functional categories including xenobiotic metabolism, cell cycle, apoptosis, and ion channel/transport with significantly different expression between tissue types. Surprisingly, there were few gender differences in gene expression. This baseline data will contribute to our understanding of the normal physiology and selectivity of the nasal epithelial cells’ response to inhaled environmental toxicants.
Keywords: Comparative

first: Nicole

middle: V

last: Soucy

first: Anna

last: Bonner

first: Todd

last: Page

first: David

last: Dorman


title: Olanzapine vs. Saline rat pfc

status: Public on Apr 10 2007

city: Minneapolis

first: S.

middle: Hossein

last: Fatemi

state: MN

address: 420 Delaware St SE, MMC 392

department: Department of Psychiatry, Division of Neuroscience Research

institute: University of Minnesota

summary:
Male Sprague-Dawley albino rats (Charles River) initially weighting approximately 200 grams were randomly assigned to one of the following:  1) olanzapine (2 mg/kg/day, I.P.) (N=20) or 2) Saline (N=20) and administered olanzapine or saline for 21 days.
Frontal cortex (N=4/group) was dissected and homogenized for microarray, QPCR and western blotting following previous methods (Fatemi et al. 2003; Brooks et al. 2003).
RNA isolation, cDNA preparation, microarray hybridization and QPCR followed previous methods (Brooks et al. 2003).

Keywords = olanzapine
Keywords = frontal cortex
Keywords: repeat sample

first: S

first: Teri

last: Reutiman

first: Christopher

last: Bell

first: Lisa

last: Nos

first: Peter

last: Fried

first: Timothy

middle: D

last: Folsom

first: Anne

last: Snow

first: Andrew

middle: I

last: Brooks

last: Pearce


title: Expression data from Rat lungs

status: Public on Feb 15 2007

first: Ankit

last: Desai

summary:
We sought to confirm the genetic influence in the development of Ventilation-Associated Lung Injury (VALI) and, in the process, identify potential candidate genes involved in the disease by integrating differential gene expression profiling on rat lungs to a traditional strain survey analysis of the parental rat strains, VALI-sensitive Brown Norway rats versus VALI-resistant Dahl Salt Sensitive rats, comparing control (under room air ventilation) versus under high tidal volume (HTV) ventilation.
We used microarrays to detail the global programme of gene expression underlying VALI susceptibility and identified distinct classes of up-regulated and down-regulated genes during this process.
Keywords: strain-condition analysis

overall_design: Rat lungs (Right lungs) from both sets of parents under the two conditions (control vs. HTV ventilation) were isolated for RNA extraction and hybridization on Affymetrix microarrays.

first: Nonas

last: Stephanie

first: Moreno

last: Liliana

first: Desai

last: Ankit


title: Mutant SOD1 rats (lobsi-affy-rat-194438)

status: Public on Apr 11 2007

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Missense mutations in the gene for the ubiquitously expressed superoxide dismutase-1 (SOD1) are one of the causes of familial amyotrophic lateral sclerosis (ALS), the most common adult onset motor neuron disease in humans killing selectively large motor neurons. Mice and rats overexpressing mutant SOD1 develop an adult onset neurodegenerative disease with hindlimb-paralysis and subsequent death similar to the human condition. In order to analyze the effects of mutant SOD1 expression onto the most affected cell-type in ALS, a small subpopulation of spinal cord cells, we propose to use laser microdissection to isolate mouse lumbar motor neurons and to assess the changes onto the mRNA expression profile using Affymetrix GeneChips compared to control animals. While two studies applying a genomic approach on the ALS mouse models used the entire spinal cord, contributions of changes to motor neurons were masked by the inflammatory effects of mutant SOD1 and the much larger population of non-motor neuronal cells. What is therefore needed is a cell-type specific expression profile that could reveal dysregulations in the transcriptome of the affected motor neurons.
In order to find and analyze disease relevant gene expression profile changes in the mutant vs. the wildtype overexpressing SOD1 mice, we propose to use two different mutant SOD1 lines. Both lines develop the same ALS-like motor neuron disease, however, line 1 (with a G37R mutation) retains the full activity of the SOD1 enzyme while line 2 (with a G85R mutation) has almost no SOD1 enzymatic activity. We believe that by using these two most extreme variants of ALS-inducing mutant SOD1 forms, candidate genes that will be similarly dysregulated in both mutant lines will have great potential to be a disease relevant hit. We will collect from both mutant SOD1 mouse lines lumbar motor neurons from three presymptomatic timepoints, equally distributed during their adult life and before obvious hindlimb-weakness or paralysis signs and compare them to two control lines, negative littermates and wildtype SOD1 overexpressing mice. Furthermore, to determine if their are already mutant SOD1-induced changes since the formation of the affected cells, we will also isolate embryonic spinal cord motor neurons and compare them between mutant SOD1 and wildtype SOD1 overexpressing animals.
Both, mice deleted in wildtype SOD1 and mice overexpressing mutant human SOD1 clearly established that the toxic property of mutant SOD1 is based upon a gain-of-toxic function phenomenon rather than a loss-of-function effect, since the SOD1 knock-out mice are overall normal. Furthermore, mice overexpressing wildtype SOD1 are healthy and serve as ideal control animals. Therefore, one of the most important question in ALS is to determine what slowly acting mechanism, or build-up of toxic products is responsible for ultimately killing more than 50-70% of the large lumbar spinal cord motor neurons. We hypothezise that the toxic property of mutant SOD1 must already induce changes onto the transcriptome of the most at-risk cell-type, the large lumbar spinal cord motor neuron, very early on in the presymptomatic phase of the disease course, when the animal is still without any paralysis signs and moving normally around the cage.
We will choose 3 timepoints before phenotypic disease-onset that is at 22 weeks for the SOD1G37R line (L42) and at 11 months for the SOD1G85R line (L148). The timepoints are 8, 15 and 18 weeks for SOD1G37R line and 4, 7.5 and 9 months for the SOD1G85R line all compared to age-matched control animals (wildtype SOD1 overexpressing mice (L76) for the SOD1G37R line (high mutant SOD1 levels) and negative littermates for the SOD1G85R line (low mutant SOD1 levels)). Using the Leica lasermicrodissection system on fresh frozen spinal cord sections, we process a single spinal cord sample in 3 days resulting in approximately 4000 ventral horn motor neurons collected from 150 consecutive 20 um sections of the most affected lumbar spinal cord region (L4-L6). To visualize the motor neurons, we have established a fast Nissel-staining protocol that is optimized for speed to preserve the integrity of the RNA. Before lasermicrodissection slides containing 5 spinal cord sections are dessicated for 1 hour and samples are collected directly into RNA-preserving lysis-buffer. Using Stratagene's NanoPrep RNA-extraction columns a yield of around 150 ng of total RNA was obtained (Ribogreen-quantification), that is enough for both the 2-round linear RNA amplification and for future candidate confirmation studies using real-time PCR analysis. We are using the Affymetrix Two-Cycle 3'-Amplification Kit, starting with 100 ng of total RNA and will hybridize on Affymetrix Mouse 430 2.0 GeneChips. Embryonic motor neurons are isolated from e14 mutant SOD1G93A overexpressing rat embryos and compared to wildtype SOD1 overexpressing embryos using a metrazimide gradient followed by a p75-antibody purification in combination with magnetic beads. Cells from one litter of embryos were directly collected into lysis-buffer, yielding at least 200-500 ng of total RNA, enough for one Rat 230 2.0 GeneChip (2-round amplification using 100 ng total RNA).
Keywords: time-course

first: Christian

last: Lobsiger


title: Expression data from cerivastatin-treated rat skeletal muscle

status: Public on Mar 05 2007

city: Ann Arbor

first: Jennifer

middle: L

last: Seachrist

state: MI

address: 2800 Plymouth Road

department: Safety Sciences

institute: Pfizer Inc

summary:
Adverse effects of statins include skeletal muscle toxicity; Type II glycolytic fibers are more senstive to statin damage; exercise exacerbates statin muscle degeneration. We used a well-characterized rat model of statin-induced muscle degeneration, at which 1.0 mg/kg/day (high dose) cerivastatin produces mild to moderate histological degeneration.
We used microarrays to detail the global programme of gene expression underlying cerivastatin effects on rat gastrocnemius and soleus muscles, as well as the effect of cerivastatin combined with treadmill exercise. We identified distinct classes of up- and down-regulated genes during this process.
Keywords: dose response; exercise effect

overall_design: We treated female SD rats with vehicle or 3 doses of cerivastatin (0.1, 0.5, 1.0 mg/kg/day) for 14 days, plus or minus 5 days/week of exercise on treadmills (20 min/day at 20 m/min). Gastrocnemius and soleus muscle samples were harvested for RNA extraction and hybridization on Affymetrix microarrays. A total of 12 samples were analyzed with 3-4 biological replicates per sample. Our goals were to determine 1) the effect of cerivastatin; 2) the effect of exercise combined with cerivastatin; 3) an explanation for the muscle fiber type sensitivity to statins. Since all doses of cerivastatin had no effect on soleus muscle (PubMed ID: 16141437), we analysed samples from soleus from control and high dose groups only.

first: Ping

last: Jiang

first: Michael

middle: T

last: Leininger

first: Steven

middle: J

last: Madore

first: Charles

last: Rothwell


title: Hippocampus response to ketone bodies (maalo-affy-rat-387180)

status: Public on Mar 20 2007

summary:
Diets characterized by increased blood levels of ketone bodies can protect the brain against a variety of acute and chronic neurological diseases. Moreover, ketone bodies are neuroprotective in many in vitro models of neurological injury. The underlying mechanisms remain unknown however. Recently, we have shown that ketone bodies do not only decrease neuronal injury and death but also protect long-term potentiation in acute hippocampal slices exposed to oxidative stress in the form of exogenous hydrogen peroxide. Elucidating the mechanisms behind the effects of ketone bodies on neuronal survival and function will undoubtedly lead to the development of novel neuroprotective treatments.
Our aim is to determine acute changes in gene expression of CA1 pyramidal neurons exposed to various duration of the ketone bodies acetoacetate and beta-hydroxybutyrate.
CA1 hippocampal pyramidal neurons exposed to oxidative stress do not display any long-term potention following burst stimulation of Schaffer collaterals. Incubation with the ketone bodies acetoacetate and beta-hydroxybutyrate for at least 20 min prior to hydrogen peroxide application restores long-term potentiation to control levels. We hypothesize that the neuroprotective effects of ketone bodies are mediated by changes in gene expression.
Acute hippocampal slices (400 microns in thickness) were obtained from 4 week-old rats and exposed to acetoacetate and beta-hydroxybutyrate (1 mM each) for 1 h and 6 h.  A control group was incubated in artificial cerebrospinal fluid only. After treatment, the hippocampal slices were used immediately for RNA isolation. Isolated RNA was sent for analysis. Each sample sent for analysis included tissue from 7 separate animals. Hybridization to an Affymetrix array is being performed 3 times for each experimental condition.
Keywords: dose response

first: Jong

last: Rho


title: Expression data from ischemia and reperfusion events in NRVMs using Coverslip Hypoxia

status: Public on Jan 11 2007

city: Westminster

first: Kelly

last: Pitts

state: CO

department: Molecular Pharmacology

institute: Gilead Sciences

summary:
NRVMs were subjected to varying durations of ischemia or ischemia+reperfusion using coverslip hypoxia.  Expression profiling was used to identify genes that are differentially regulated in either event.
We used microarrays to detail the global program of gene expression underlying ischemia and reperfusion using Coverslip Hypoxia and identified distinct classes of genes regulated during these processes.
Keywords: time course

overall_design: RNA was extracted from NRVMs subjected to varying durations of ischemia or ischemia+reperfusion and hybridized to rat genome Affymetrix arrays.


title: A Multi- Kinase Inhibitor Modulates Pulmonary Hypertension in a Rodent Model 1

status: Public on Jun 15 2007

middle: A

summary:
Pulmonary hypertension (PH) and cancer pathophysiology share common signal transduction pathways leading to abnormal endothelial and smooth muscle cell interactions and angioproliferative vasculopathy. Sorafenib (Sor) a drug in clinical trials for cancer treatment, is an inhibitor of multiple kinases important in angiogenesis (Raf-1 kinase, VEGFR-2, VEGFR-3, PDGFR-beta). In this study, we assessed the efficacy of Sor as a potential therapy for PH, and hypothesized that Sor prevents the development of both a conventional and an augmented rodent model of PH.  We performed studies in Dahl Salt-Sensitive rats (SS) exposed to hypoxia alone and in combination with the VEGFR-2 inhibitor, SU5416, known to induce a well-characterized augmented PH  phenotype. Rats were, thus, divided into 5 groups: normoxia/vehicle (Norm), hypoxia/vehicle (H), hypoxia/ SU5416 (H-SU), hypoxia/Sorafenib (H-Sor) and hypoxia/ SU5416/ Sorafenib (H-SU-Sor). Except for the Norm group, all rats were maintained in a hypoxia chamber with a FiO2 of 10%. Rats received a single injection of SU5416 on Day 1 (20 mg/kg) and Sor solution was administered daily by gavage (2.5mg/kg). After 3.5 weeks, all rats were assessed by open chest catheterizations for pulmonary vascular and right ventricular pressures. Lung and heart tissue were harvested for histological and microarray analyses. Our results showed H-SU rats developed severe PH with changes in hemodynamic and histologic parameters when compared to Norm controls while rats exposed to H alone only displayed mildly elevated pressures compared with Norm. There was no significant change in pressures in the H-Sor or H-SU-Sor compared to Norm. Histopathology demonstrated a dramatic prevention of the PH phenotype in the H-SU-Sor rats with no significant remodeling compared with H-SU rats. Expression profiling data from H (n=4) and H-SU (n=3) rat lungs were compared to Norm (n=4) using normalization in R and SAM (δ>.639,) (minimum fold change >1.4). With false discovery rates (FDR) of 6.5% in hypoxia and 1.6% in H-SU, 1019 and 465 genes, respectively, were differentially-regulated compared to Norm. In addition, 38 genes were differentially expressed between H-SU and H-SU-Sor (n=4, FDR 6.7%) revealing  a molecular signature with potentially novel target genes of Sor. Five differentially expressed genes (Tgfbeta3, C1qg, Nexn, Frzb, and Plaur) were examined by real-time RT-PCR and three were further validated by immunohistochemistry confirming the regulation on protein level. Based on the known pathways of hypoxic-induced PH and Sor, we further utilized immunohistochemistry to show the up-regulation of mediators of the MAPK cascade in the H and H-SU models of PH with subsequent, down-regulation by Sor. We therefore present Sor as a novel treatment for the development of severe PH and theorize that the MAPK cascade is a canonical pathway involved both in the development of PH and in the attenuation by Sor.
Keywords: Drug Effect

first: Liliana

last: Moreno-Vinasco

first: Patrick

last: Singleton

first: Sam

last: Lee

first: Yves

last: Lussier

first: Mardi

last: Gomberg-Maitland

last: Maitland

first: Alyna

last: Hussein

first: Ye

last: Liu

first: Keith

last: Collins

first: Saad

last: Sammani

first: Roberto

last: Lang

first: Joe

last: Garcia


title: Gene expression and cell cycle arrest in a rat keratinocyte cell line exposed to 56 Fe Ions

status: Public on Nov 16 2006

city: Tuxedo Park

first: Ronghe

last: Zhang

address: 57 Old Forge Rd

department: Environmental Medicine

institute: New York University School of Medicine

summary:
The purpose of the present work was to examine gene expression patterns in a rat keratinocyte line exposed to a 56Fe ion beam
Keywords: Dose response

overall_design: The cells were exposed to 1.01 geV/nucleon 56Fe ions generated by the NASA Space Radiation Laboratory facility. Data from Affymetrix rat microarrays (RAT 230_2) were processed by BRB ArrayTools 3.3.0 software, and the Gene Ontogeny (GO) database was utilized to categorize significantly responding genes.

first: Feng

last: Wu

first: Fred

last: Burns


title: Expression data from Normal (control) and Diabetic animals LV heart tissue (At 16wks)

status: Public on Oct 31 2006

city: Auckland

first: Sarah

last: Glyn-Jones

address: 3A Symonds St

department: School of Biological Sciences

country: New Zealand

institute: University of Auckland

summary:
Analysis of gene expression changes in the LV of a rodent heart that occur with uncontrolled diabetes
We used microarrays to detail the global changes that occur in gene expression in the LV of the heart as a result of STZ-induced diabetes.
Keywords: single time point, comparison control animal v. diabetic animal

overall_design: Male wistars were anaesthetised (Halothane 2-5%) and randomly received a tail vein injection of either saline or STZ 60mg/kg. Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study. Animal weight and blood glucose were recorded weekly. After 16wks the whole heart was excised from the animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C.RNA from 7 animals from each of the two groups was hybridised to an Affymetrix Rat Genome 230 2.0 Genechip and the resulting changes in gene expression were analysed.

first: Liam

last: Williams

first: Anthony

last: Phillips


title: Expression data for an eQTL experiment in rat eye

status: Public on Aug 31 2006

city: Iowa City

first: Bartley

middle: Joseph

last: Brown

state: IA

institute: The University of Iowa

summary:
We used expression quantitative trait locus mapping in the laboratory rat (Rattus norvegicus) to gain a broad perspective of gene regulation in the mammalian eye and to identify genetic variation relevant to human eye disease. Of >31,000 gene probes represented on an Affymetrix expression microarray, 18,976 exhibited sufficient signal for reliable analysis and at least 2-fold variation in expression among 120 F2 rats generated from an SR/JrHsd x SHRSP intercross. Genome-wide linkage analysis with 399 genetic markers revealed significant linkage with at least one marker for 1,300 probes (alpha = 0.001; estimated empirical false discovery rate = 2%). Both contiguous and noncontiguous loci were found to be important in regulating mammalian eye gene expression. We investigated one locus of each type in greater detail and identified putative transcription-altering variations in both cases. We found an inserted cREL binding sequence in the 5' flanking sequence of the Abca4 gene associated with an increased expression level of that gene, and we found a mutation of the gene encoding thyroid hormone receptor beta 2 associated with a decreased expression level of the gene encoding short-wave sensitive opsin (Opn1sw). In addition to these positional studies, we performed a pairwise analysis of gene expression to identify genes that are regulated in a coordinated manner and used this approach to validate two previously undescribed genes involved in the human disease Bardet-Biedl syndrome. These data and analytic approaches can be used to facilitate the discovery of additional genes and regulatory elements involved in human eye disease.
Keywords: eQTL, F2 cross

overall_design: mRNA from whole eye tissue was used to assay gene expression level. Samples were acquired from 120 F2 rats generated from an SR/JrHsd x SHRSP intercross. Each sample was run individually, according to standard Affymetrix protocols, without replicates.

first: Todd

last: Scheetz

first: Kwang-youn

last: Kim

first: Ruth

last: Swiderski

first: Alisdar

middle: R

last: Philp

first: Terry

last: Braun

first: Kevin

last: Knudtson

first: Anne

last: Dorrance

first: Gerald

middle: F

last: DiBona

first: Jian

last: Huang

first: Thomas

last: Casavant

first: Val

middle: C

last: Sheffield

first: Edwin

last: Stone


title: Exogenous Glucosamine Globally Protects Chondrocytes from the Arthritogenic Effects of IL-1beta

status: Public on Oct 30 2006

city: gainesville

first: jean noel

last: gouze

state: FL

address: 1600 SW archer rd

department: orthopaedics

institute: university of florida

summary:
Glucosamine proved to be a potent, broad-spectrum inhibitor of IL-1beta. Of the 2,813 genes whose transcription was altered by IL-1beta stimulation (p<0.0001), glucosamine significantly blocked the response in 2,055 (~73%). Glucosamine fully protected the chondrocytes from IL-1-induced expression of inflammatory cytokines, chemokines and growth factors as well as proteins involved in PGE2 and NO synthesis. It also blocked the IL-1-induced expression of matrix specific proteases such as MMPs -3,-9,-10,-12 and ADAMTS-1.
Keywords: treatment response

overall_design: Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions. Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2. Experiments were subsequently performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then divided into 4 treatment groups to evaluate the effects of glucosamine and IL-1 on global transcription patterns.To the culture medium in half of the flasks, glucosamine, HCl  was added to a final concentration of 20 mM. Six hours later, IL-1beta was added at 10 ng/ml to 5 of the flasks receiving glucosamine and to 5 of the untreated flasks. Fourteen hours post IL-1beta stimulation,  total RNA was isolated individually from the respective cultures and microarray experiments processed.

first: Jean-noel

last: Gouze

first: Elvire

first: Mick

middle: P

last: Popp

first: Marsha

last: Bush

first: E

last: Dacanay

first: Jesse

last: Kay

first: Padraic

last: Levings

first: Kunal

last: Patel

first: Jeet-Paul

middle: S

last: Saran

first: Rachel

last: Watson

first: Steven

last: Ghivizzani


title: Expression data from Rat liver 48 hours after treated with different toxic compounds.

status: Public on Aug 12 2006

city: Lundtofte

first: Jeppe

middle: Skytte

last: Spicker

address: Building 208

department: CBS

country: Denmark

institute: Danish University of Technology

summary:
Rat has been treated with different compounds with the purpose of investigating toxicological mechanisms. But toxic and non-toxic compounds has been administered. 3 toxic (ANIT, DMN, NMF) 3 non-tox (Caerulein, dinitrophenol(DNP), Rosiglitazone) in 5-plicates (30 arrays in all) and 9 untreated (control), 39 samples in all.
The array data was used to identify genes with biomarker potential for detecting toxic properties of compounds.
Keywords: other

overall_design: Rats was treated with different compounds and RNA from liver was extracyed after 48 hours. Microarrays (GeneChip Rat230 version 2) was run on the RNA


title: Expression data from female SD rats with access to lifelong exercise

status: Public on Jul 01 2006

city: Oxford

first: Natalie

last: Schweitzer

state: OH

institute: Miami University

summary:
Gene expression and phenotypic consequences of laboratory housing in rats.
Disease related-phenotypes and associated gene expressions of sedentary animals (living solely in a standard cage) were compared with animals that had access to twice-weekly one-hour physical activity in a large box (PA) and with those that had access to voluntary running wheel exercise (EX).
Keywords: exercise dose reponse, sedentary, twice weekly physical activity, daily exercise

overall_design: The left ventricle of 16 month female Sprague-Dawley rats was used for RNA extraction and hybridization on Affymetrix GeneChip Rat Genome 230 2.0 Arrays. Twelve animals from each treatment group (SED, PA, and EX) were used for microarray analysis (4 animals pooled per GeneChip).

first: Helaine

middle: M

last: Alessio

first: Ann

middle: E

last: Hagerman

middle: B


title: Astrocytes in response to activation of EGFR

status: Public on Jul 12 2006

city: St. Louis

first: Bin

last: Liu

state: MO

address: 660 S. Euclid

department: Ophthalmology

institute: Washington University

summary:
Primary cultures of astrocytes from rat optic nerve heads were treated with EGFR ligand, EGF. Two cell lines from two different rat donors were used. The sister cell cultures were set as control and EGF treated groups.
Keywords: rat optic nerve head astrocytes

overall_design:
experiment #1: compared control astrocyte cultures to sister cultures treated with EGF for 4 hours.
experiment #2: compared control astrocyte cultures to sister cultures treated with EGF for 12 hours

first: Arthur

middle: H

last: Neufeld


title: Expression data from rat lung alveolar development

status: Public on Apr 12 2007

city: Créteil

first: Jacques

last: Bourbon

address: 8 rue du Général Sarrail

department: Faculté de Médecine

country: France

institute: Université de Paris 12

summary:
Lung alveolarization is a complex process that involves interactions between several cell types and leads to considerable increase in gas-exchange surface area. The step designated secondary septation includes elastogenesis from interstitial fibroblasts.
We used microarrays to detail the global programme of fibroblast gene expression that underly secondary septation, and identified numerous genes that undergo signficant changes in expression
Keywords: Time course

overall_design: Rat lung fibroblats were extemporaneously isolated at successive stages of postnatal development that flank the septation period for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates from three different litters were prepared for each time point.

first: Olivier

last: Boucherat


title: Expression profile of syngeneic (sTX) and allogeneic kidney (aTX) transplantation compared to control (ctr) kidneys

status: Public on Apr 01 2007

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

institute: University Hospital Halle (Saale)

summary:
Microarray analyses provide a powerful approach to identify gene expression alterations following kidney transplantation. However, the heterogeneity of human kidney transplant specimens and the variation in sample preparation precludes conclusions regarding the underlying mechanisms of the observed alterations. We used a well defined experimental rat kidney transplantation model with consistent transplant and sample preparation procedures to analyze genome wide changes in gene expression after syngeneic (sTX) and allogeneic transplantation (aTX) four days after transplantation. Both interventions were associated with dramatic changes in gene expression. Genes and Pathways related to immune response were extremely up regulated after aTX. Several of the up regulated genes have been described by other groups and we are able to proof this in one study. But several genes are reported for the first time to be up regulated in expression after renal aTX. The function of these genes in acute rejection process has to be evaluated. On the other hand the up regulation of regulatory or protective genes indicates that regulatory mechanism are activated after aTX trying to down regulate the immune response or protect the tissue against the immune system. The study is capable to serve as a representative study in aTX mediated gene expression by covering the known transcriptional changes reported by other groups and identification of novel markers and pathways. Further analysis of the duplicated datasets by other groups can help for a better understanding of the mechanisms mediated by acute rejection and thereby increase the therapeutic threatment.
Keywords: gene expression changes due to acute rejection

overall_design: Male Lewis–Brown-Norway (LBN) and Lewis (LEW) rats were used in the present study. All recipients were bilaterally nephrectomized immediately before donor kidney TX. In brief, the left kidney including ureter, renal artery, a piece of aorta and renal vein was transplanted into the recipient. For the allogeneic TX (aTX) model, kidneys of LBN-rats (n=5) were transplanted into LEW-rats and for the syngeneic TX (sTX) model kidneys from LBN-rats (n=5) were transplanted into LBN-rats. The LBN-into-Lewis model leads to marked histological changes typical for acute transplant rejection. The second kidney of the LBN-donors (n=5) served as controls.

first: Martin

last: Eisenacher


title: Adjudin-induced germ cell loss from adult rat testes

status: Public on Jul 07 2006

city: New York

first: Weiliang

last: Xia

address: 1230 York Avenue

institute: Population Council

summary:
This is a study to explore the transcriptional changes after Adjudin treatment in adult rat testes at three time points (control, 8 hour and 4 day). Adjudin, [1-(2,4-dichlorobenzyl)-1H-indazole-3-carbohydrazide], is a potential male contraceptive that targets the Sertoli-germ cell interface and causes germ cell depletion from the seminiferous epithelium. Adjudin has been proved to be a useful model to study the mechanisms that regulate junction restructuring in the testis.
Keywords: Sertoli-germ cell adhesion regulation using an Adjudin model

overall_design: Sprague-Dawley rats treated with a single dose of Adjudin at 50 mg/kg b.w. by gavage and terminated after 8 hours (n=2) and 4 days (n=3). Testes from Adjudin-treated rats and untreated (control, n=3) rats were harvested and total RNA were prepared.  Standard Affymetrix genechip procedures were followed for the subsequent experiments. Data were analysed in MAS 5.0 and GeneSpring 7.2.

first: Dolores

middle: D

last: Mruk

first: Will

last: Lee

first: Yan

last: Cheng


title: Comparison of three populations of OECs

status: Public on May 25 2006

city: Madrid

first: Erika

last: Pastrana

state: Madrid

address: Cantoblanco

department: Universidad Autonoma de Madrid

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

summary:
Comparison of three populations of OECs derived from the ONL of rats. The three populations were cultured employing the same culture medium but were maintained in vitro for a different amount of time (number of population doublings or PDs). OEC Ep cells were maintained for less than one week in vitro (less than 3 PDs); OEC Lp were maintained for over a year (more than 50 PDs) and TEG3 OEC cell line has been serially passed in culture for long-periods of time after genetic immortalization.
Keywords: OEC cells, adaptation to long-term culture, genetic immortalization

overall_design:
RNA sample preparation and experimental design. Total RNA was isolated with TRIZOL (Invitrogen, Gibco-BRL) from primary OEC cultures (OEC Ep and Lp) and the OEC cell line (TEG3). Cultured cells were harvested at confluency with a rubber scrapper, resuspended in the TRIZOL reagent and processed following the manufacturers’ instructions. Two RNA pools were obtained from each OEC population (OEC Ep, OEC Lp and TEG3 cells). Each RNA pool was purified from three individual cultures (three 100mm dishes) and in the case of OEC Ep, each culture was derived from one rat. The total RNA was resuspended in DEPC (Sigma) water and stored at -70ºC prior to use. Total RNA concentration and purity were determined using Agilent2100 Bioanalizer.

Microarray analysis. Total RNA pools were cleaned using Rneasy Kit from Qiagen. Biotinylated cRNA probes were generated from each RNA pool, fragmented, and applied to two different sets of Rat Genome Affymetrix GeneChip U34A Array. Affymetrix software (Microarray Suite version 5.0) was used to filter inaccurately represented probe sets.

first: Javier

last: Diaz-Nido

first: Maria

last: Moreno-Flores

first: Francisco

last: Wandosell

first: Jesus

last: Avila


title: Thompson-5R01NS040338-02

status: Public on Jun 09 2006

first: Winnie

last: Liang

summary:
Epilepsy is a chronic disorder characterized by recurring seizures, and results from excessive, synchronized discharge in populations of cells. Epilepsy affects 1% of the population and results from a variety of CNS insults. Traumatic physical brain injury causes 4% of cases. Posttraumatic epilepsy (PTE) is characterized by a delay of weeks to years between the trauma and the first seizures. Proper prophylactic intervention during this incubation time might prevent PTE. Many PTE patients are resistant to anticonvulsant medications and suffer from negative side effects. Better knowledge of the cell biology underlying injury-induced epileptogenesis should lead to better therapeutic strategies for interrupting the events occurring between the injury and the development of epilepsy. The aim of my experiments is to identify cellular factors underlying PTE using an in vitro model system to study two key aspects of brain injury in isolation: deafferentation and axonal transection.
My aim is to perform a non-biased comparison of the expression of genes in area CA1, and separately in area CA3, in unlesioned cultures and in cultures lesioned 1, 3 and 7 days earlier. Changes in gene expression due to neuronal denervation will be apparent in area CA1, whereas changes in expression due to axonal transection will be apparent in area CA3. In performing these experiments, I hope to gain insight into the molecular underpinnings of the electrophysiological and immunocytochemical effects that we have already detected, as well as to generate new hypotheses that we can test further using our own expertise and techniques.
We use cultured slices of rat hippocampus to study the effects of brain injury. Our model is to lesion the Schaffer collateral projection pathway between areas CA1 and CA3, producing a selective injury of the axons of CA3 cells and selective denervation of CA1 cells. Our preliminary electrophysiological and immunocytochemical data indicate that axonal sprouting is triggered in area CA3 and that the dendritic excitability is increased in CA1 pyramidal cells. Both effects occur only after about 7 days, suggesting they are mediated by changes in gene expression. My hypothesis is that the expression of numerous genes changes after Schaffer collateral transection. I predict that neurotrophins and their receptors change in area CA3 to trigger axonal sprouting, along with genes for proteins mediated axonal extension, and that changes in the expression of genes for glutamate receptors and voltage-dependent ion channels occur in area CA1 to account for their increased excitability.
Hippocampal slice cultures prepared from male Sprague-Dawley rats at PN day 6. Slices will be maintained in vitro for 14 days in serum-containing medium. Cultures will then be examined and unhealthy cultures discarded. Remaining sister cultures will be divided into two groups: cultures to be lesioned and cultures remaining unlesioned. Lesioned cultures will have a sterile transection of the Schaffer collateral pathway using a razor blade shard. All cultures then returned to the incubator. At various times , cultures will be removed from the incubator. Individual cultures will be soaked in RNAlater buffer(Ambion), and a razor blade shard will be used to subdissect the CA3 and CA1 segments. Segments are sucked up with a sterile pipette-tip containing RNAlater buffer and transferred into a sterile tube. Total RNA will be prepared by homogenization in TRIzol reagent (GibcoBRL) and precipitation in isopropyl alcohol. Rneasy Kit (Qiagen) will further isolate RNA. Spectrographic analysis of RNA prepared indicates 260nm:280nm ratios above 1.6, and insignificant amounts of either degraded RNA or DNA contaminants detected on a 2% denaturing gel. We have found that it is necessary to pool 15 CA3 or CA1 segments to obtain 5+ ug of total RNA. Total RNA samples will be sent to the consortium for additional quality control, labeling, hybridizations using the Affymetrix Neuro U34 chip, scanning, and preliminary analyses. The gene array data will then be compared in several pairwise manners (lesion vs. age matched control and region vs. region, for each time point), as well as time sequence comparisons for gene expression in each region.
Keywords: time-course

first: Scott

last: Thompson


title: wilso-affy-rat-132990

status: Public on May 02 2006

summary:
Hypoxic-ischemic (HI) injury in the developing brain is a common cause of disability in children, and there are no effective treatments at this time.  Exposure to sublethal hypoxic conditions (hypoxic preconditioning) 24 hours prior to hypoxic-ischemic insult is protective in the developing rat model.  We have observed protective effects on brain histopathology and on long-term sensory-motor behavioral tasks.  Changes in gene expression are thought to underlie this protective effect.  By comparing gene expression in rats subjected to hypoxic preconditioning or sham conditioning at several time points from 0 to 24 hrs after preconditioning, we should gain insight into the mechanisms underlying these neuroprotective effects and may identify targets for therapeutic intervention.
The aim of this study is to determine the effect of hypoxic preconditioning on global gene expression, and, in littermates, to examine the effect of hypoxic preconditioning 24 h prior to hypoxic-ischemic insult on brain histopathology.
We hypothesize that changes in gene expression underlie the protective effect of hypoxic preconditioning against subsequent hypoxic-ischemic insult.
Gene expression will be examined in two groups, 1) preconditioned and 2) sham controls, at 4 time points.  On postnatal day 6, preconditioned animals are exposed to normothermic hypoxia for 3 hrs (8.0% oxygen, 36 degrees C), and sham animals are simultaneouosly exposed to normoxia at 36 degrees C. Animals are then returned to their dams until euthanized at 4 time points (0h, 2h, 8h, and 24h later).  Five brains/group/timepoint will be used, with an equal number of males and females in each group.  Brains are removed and dissected on ice.  Cerebral cortex is dissected from both hemispheres and rapidly frozen on dry ice.  Total RNA is isolated using the QIAGEN RNeasy Protect Maxi Kit.  Littermates of these animals will be exposed to hypoxic preconditioning or sham preconditioning and subjected to hypoxic-ischemic injury 24 h later.  These animals are euthanized at postnatal day 14 for histopathologic evaluation of injury.
Keywords: time-course

first: Mary-Ann

last: Wilson


title: sabba-affy-rat-212007

summary:
Stress leads to important adaptive physiological responses including release of catecholamine from the adrenal medulla. Repeated or prolonged stess increses the propensity for many disorders including cardiovascular disease and neuropsychiatric disorders. The susceptibility to stress is determined by a number of factors including prior experience with stress. It has been found that while there is adaptation to prolonged  cold stres; it leads to sensitization when cold stressed animals are exposed to a different (novel) stressor. Our study aims to determine the mechanis of this adaptatio and sensitization.
We will determine teh gene expression patterns in rat adrenal medulla in response to severa times of cold stress. We will also determine the changes in gene expresion with single immobilization stress in adrenal medulla of rat with an dwithout preexposure to cold stress to investigate the mechanism of sensitizatio in cold adapted animals.
We hypothesize that during the course of cold stess there are alterations in gene expression of several neurotransmitter related genes and transcription factors. In expression of several trascription factors, such as Fra-2 which lead to an exaggerated response to teh novel stresor.
Rats were exposed to cold stress (4 degree C) for 1, 7, or 28 days. A parallel group was kept at room temperature (unstressed). Unstressed or rats preexposed to 28 days cold were immobilized for 2 hrs and killed by decapitation. The adrenal medullae, separatedly from right and left side, have been dissected and individually frozen at - 70 degree C. We will pool samples from 4 rats per treatment to control for variability.
Keywords: dose response

first: Esther

last: Sabban


title: Thrivikraman-5P50MH058922-050002

status: Public on Jun 06 2006

summary:
It is suggested that the stress induced activation of the HPA axis and associated increases in plasma ACTH and glucocorticoids (corticosterone, B in the rat) are contributing factors in the development of many psychopathologies.  However, the circadian fluctuation of the HPA axis activity (characterized by a zenith in the plasma ACTH and B, before the beginning of the active awake state and the nadir during the inactive sleeping period) occurs throughout the life and is important for normal physiological and behavioral functioning. A blunting or enhancement of this rhythm through changes in the trough or in the peak is a characteristic feature of many pathological states. At the CNS level, the circadian fluctuation of the HPA axis activity is associated with changes in the expression profile of structural, functional, and immediate early genes. However, little is known about the specific role of B in the modulation of the circadian pattern of gene regulation in the CNS.
Thus, during the circadian cycle B is a major factor, which could influence the expression profile of a large family of genes. Accordingly, the microarray technology, because of its characteristic feature that facilitates the identification of the expression profiles of a wide range of genes simultaneously, is an ideal technique. Because the B status of animals can be easily manipulated by adrenalectomy (ADX) surgery with or without B replacement, this model will be used in these studies. Thus, the proposed studies are intended to characterize, by the use of the microarray technique, the effects of the B milieu on diurnal gene expression profiles in selected rat brain regions strongly influenced by: a.) B status: amygdala, hippocampus, hypothalamus, and septum; and  b.)  Circadian Activity: dorsal raphe, frontal Cortex and locus coeruleus.
The gradient of the B response during the circadian cycle implies that at the beginning of the sleep cycle MR are predominantly occupied while at the end of the sleep cycle, both MR and GR are occupied. Thus, we propose that differing ratios of activation of these nuclear receptors could differentially modulate gene expression and impart temporal characteristics in the expression profile of a large family of genes. Furthermore, we propose that these effects may be region specific, reflecting regional differences in GR and MR distribution, B uptake, and neural activity. B may exert these circadian effects on regional gene expression profiles either directly or indirectly via interneurons. However, little is known about the circadian effect of B on gene expression profiles in different brain regions. Such knowledge is important to identify the specific role of B in circadian differences in CNS function and, potentially, the development of psychopathologies.
After arrival at the facility the rats (male Long Evans) will be maintained on 12:12 h LD cycle ('lights-on" at 0700 h) with food and water ad libitum. One week after, they will undergo bilateral ADX under survival anesthetics (day-0).  The study will include three groups (n=10); (a) ADX: rats with no adrenals, (b) pADX: ADX rats with subcutaneous 40 percent B pellet (fused cholesterol and B), and (c) SHAM: rats undergoing flank incisions without the removal of the adrenals. After surgery, rats will be housed individually. The ADX rats will receive 0.5 percent saline in addition to regular tap water. On post-surgical day-7, 15 rats (five/group) will be sacrificed by decapitation 2h after 'lights-on", and the remaining 15, 2h after "lights-off". The brains will be removed immediately, frozen on dry ice, and stored at -80 C. The trunk blood will be collected with EDTA and plasma frozen for ACTH and B RIA. The brains from rats with confirmed ADX will be used for free hand dissection of brain regions: frontal cortex, septum, hypothalamus, amygdala, hippocampus, dorsal raphe, and locus coeruleus. Tissue will be stored at -80 C. Total RNA will be extracted from individual brain regions using Qiagen RNeasy Lipid Tissue kit. Initial evaluation of quality and quantity of the RNA will be done by the absorbance method. Frozen samples containing 0.5 ul total RNA or higher will be sent to the NINDS-NIMH Microarray Consortium in dry ice for evaluation of the integrity of 28S and 18S RNA on an Agilent Bioanalyzer. If the integrity of RNA is not good, the experiment will be repeated and new RNA samples will be provided. Replicates of each brain region with 28S/18S ratio of 1.7 and higher will be selected for assay using Affymetrix Rat U34A array. The RNA samples from one region from all the brains will be processed together. A total of 84 chips may be utilized in these studies, however the final number will depend upon integrity of the total RNA.
Keywords: other

first: K.

middle: V

last: Thrivikraman


title: Clenbuterol, X-ray and Tempol treatments on Contusion Rat model

city: valhalla

first: koko

middle: murakami

last: midelfort

address: grasslands reservation

department: anatomy and cell biology

institute: new york medical college

summary:
Gene expression analysis after the treatments for functional recovery after contusion injury which are mediated by glutathione
Keywords: treatment

overall_design:
24 hours after contusion and treatments
Groups include normal, laminectomy, contusion and treatments on contused rats (clenbuterol, X-ray, tempol, BSO and tempol/BSO)

last: murakami

first: xialing

last: wen

first: nengtai

last: ouyang

first: kaoru

last: sato

first: joseph

middle: d

last: etlinger

first: richard

middle: j

last: zeman


title: mRNA expression in rat proximal femoral growthplate after mid-shaft fracture

status: Public on Mar 31 2006

city: Charlotte

first: Ralph

middle: A.

last: Meyer

state: NC

department: Orthopaedic Research Laboratory

institute: Carolinas Medical Center

summary:
Mid-shaft fracture stimulates bone lengthening by increasing linear growth at the growthplate.  This project studied changes in mRNA in the proximal growthplate after a mid-shaft fracture in a rat model.
Keywords: time course, fracture, growthplate, rat

overall_design: Study of rat proximal femoral growthplate after mid-shaft fracture in 4 week old Sprague-Dawley female rats.  RNA from two rats were pooled for each sample.  Proximal femoral growthplate was studied from the fractured femora and the intact contralateral femora.

middle: A

first: Martha

first: Steven

last: Frick

first: Nomaan

last: Ashraf


title: Diethylstilbestrol effects on rat anterior pituitary gland

city: Madison

first: James

last: Shull

state: WI

address: 1400 University Avenue

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin-Madison

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

overall_design: Refer to individual Series