title: Human hepatocytes support the hypertrophic but not the hyperplastic response to the murine nongenotoxic hepatocarcinogen sodium phenobarbital in an in vivo study using a chimeric mouse with humanized liver [Mouse Liver Experiments]

status: Public on Aug 29 2014

city: Osaka

first: Kayo

last: Sumida

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

department: Environmental Health Science Laboratory

institute: Sumitomo Chemical Co., Ltd.

summary: High doses of sodium phenobarbital (NaPB), a constitutive androstane receptor (CAR) activator, have been shown to produce hepatocellular tumors in rodents by a mitogenic mode of action (MOA) involving CAR activation. The effect of 1 week dietary treatment with NaPB on liver weight and histopathology, hepatic CYP2B enzyme activity and CYP2B/3A mRNA expression, replicative DNA synthesis and  selected genes related to cell proliferation and functional transcriptomic and metabolomic analyses was studied in male CD-1 mice, Wistar Hannover (WH) rats and chimeric mice with human hepatocytes. The treatment of chimeric mice with 1000-1500 ppm NaPB resulted in plasma levels around 3-5 fold higher than those observed in human subjects given therapeutic doses of NaPB. NaPB produced dose-dependent increases in hepatic CYP2B activity and CYP2B/3A mRNA levels in all animal models. Integrated functional metabolomic and transcriptomic analyses demonstrated the responses to NaPB in human liver were clearly different from those in rodents. While NaPB produced a dose-dependent increase in hepatocyte replicative DNA synthesis in CD-1 mice and WH rats, no increase in replicative DNA synthesis was observed in human hepatocyte-originated areas of chimeric mice. In addition, treatment with NaPB had no effect on Ki-67, PCNA, GADD45β, and MDM2 mRNA expression in chimeric mice, whereas significant increases were observed in CD-1 mice and/or WH rats. Thus, while NaPB could activate CAR in rodent and human hepatocytes, NaPB did not increase replicative DNA synthesis in human hepatocytes of chimeric mice, whereas it was mitogenic to rat and mouse hepatocytes. As human hepatocytes are refractory to the mitogenic effects of NaPB, the MOA for NaPB-induced rodent liver tumor formation is thus not relevant for humans.

overall_design: Male CD-1 mice were fed diets containing 0 (control) or 2500 ppm NaPB for 7 days. Liver samples were used for gene expression analysis.

first: Tomoya

last: Yamada

first: Yu

last: Okuda

first: Masahiko

last: Kushida

first: Hayato

last: Takeuchi

first: Hirohisa

last: Nagahori

first: Takako

last: Fukuda

first: Brian

last: Lake

first: Samuel

last: Cohen

first: Satoshi

last: Kawamura


title: Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients

status: Public on Jun 15 2014

city: Barcelona

first: Jelena

last: Raspopovic

address: Calle Dr.Aiguader 88

department: Systems Biology

country: Spain

institute: CRG

summary: The goal of this microarray analysis was to see which genes are differentially expressed between Sox9-EGFP positive cells and Sox9-EGFP negative cells in E11.5 mouse limb bud autopods of the reporter Sox9-EGFP knock-in mouse(Nakamura et al 2011). This was done in order to gain insight of the genes that could contribute to the specification of the digits (Sox9 positive cells).

overall_design: Mesenchymal cells were extracted from the mouse  (Sox9EGFP knock-in, Nakamura et al . 2011) embryo forelimb autopod at stage E11.5. Sox9EGFP-positive cells were FACS-sorted from Sox9EGFP-negative cells . Each FACS-sorted sample was made from several forelimb autopods (approximately  n=10). Three replicates were used for each group of Sox9EGFP-positive cells and Sox9EGFP-negative cells. Extraction of total RNA, labeling and hybridization to the microarray were performed using attached protocols. We identified the genes that were differentially expressed between the two groups.

first: James

last: Sharpe


title: Gene expression of Bone marrow-derived macrophages isolated in ERR-alpha knock-out mice

status: Public on Jun 17 2014

city: Daejeon

first: Jae-Min

last: Yuk

address: Jung-Gu Munhwa dong

department: Department of Microbiology

country: South Korea

institute: College of Medicine, Chungnam National University

summary: We investigated the molecular mechanisms by which ERRα negatively regulates TLR-signaling pathways. To examine this, we performed global gene expression analysis of ERRα+/+ and ERRα-/- BMDMs after LPS stimulation. Microarray analysis revealed that several genes encoding various TLR-negative regulators were downregulated in LPS-stimulated ERRα-/- BMDMs, when compared with ERRα+/+ BMDMs

overall_design: Bone marrow-derived macrophages were isolated in 6~8 week old male C57BL6 mice and then divided into 4 groups 1) Solvent control-treated ERRα+/+ BMDM  2) LPS-treated ERRα+/+ BMDM 3) Solvent control-treated ERRα-/- BMDM 4) LPS-treated ERRα-/- BMDM

first: Eun-Kyeong

last: Jo


title: A crucial role of the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification [array]

status: Public on Jun 12 2014

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

summary: Mammalian development is regulated by the interplay of tissue-specific and ubiquitously expressed transcription factors, such as Sp1. Sp1 knock-out mice die in utero with multiple phenotypic aberrations, but the underlying molecular mechanism of this differentiation failure has been elusive. Here we used conditional knock-out mice as well as the differentiation of mouse ES cells as a model to address this issue. To this end we examined differentiation potential, global gene expression patterns and Sp1 target regions in Sp1 wild-type and deficient cells representing different stages of hematopoiesis. Sp1-/- cells progress through most embryonic stages of blood cell development but cannot complete terminal differentiation. For most Sp1 target and non-target genes, gene expression is unaffected by Sp1 inactivation. However, Cdx and multiple Hox genes are stage-specific targets of Sp1 and are down-regulated at an early stage. As a consequence, expression of genes involved in hematopoietic specification are progressively deregulated, highlighting the regulatory hierarchy of hematopoietic specification. Our work demonstrates that the early absence of active Sp1 sets a cascade in motion that culminates in a failure of terminal hematopoietic differentiation and emphasizes the role of ubiquitously expressed transcription factors for tissue-specific gene regulation.

overall_design: Microarray expression data, 16 arrays with 2 independent biological replicates (8 arrays wildtype and 8 arrays knock out) obtained from differentiation of ES cells to study the transcription factor Sp1 activity at early stages of early hematopoietic specification.

first: Jane

last: Gilmour

middle: A

first: Ulrike

last: Jaegle

first: Divine

last: Kulu

first: Harmen

last: van de Werken

first: Deborah

last: Clarke

first: David

middle: R

last: Westhead

first: Sjaak

last: Philipsen

first: Constanze

last: Bonifer


title: Expression data from Control or ShSuz12 rat Intestinal epithelial cells IEC-6

status: Public on Aug 02 2014

city: Sherbrooke

first: Martin

last: Lessard

state: Qc

address: 2000 College

department: Sherbrooke Research Centre

country: Canada

institute: Agriculture and AgriFood Canada

summary: Polycomb-group proteins form multimeric protein complexes involved in transcriptional silencing. The Polycomb Repressive complex 2 (PRC2) contains the Suppressor of Zeste-12 protein (Suz12) and the histone methyltransferase Enhancer of Zeste protein-2 (Ezh2). This complex, catalyzing the di- and tri-methylation of histone H3 lysine 27, is essential for embryonic development and stem cell renewal. However, the role of Polycomb-group protein complexes in the control of the intestinal epithelial cell (IEC) phenotype is not known. We investigated the impact of Suz 12 depletion on gene expression in IEC-6 cells.

overall_design: Multiple shRNA lentiviral constructs were tested in IEC-6 cells for their ability to down-regulate Suz12 expression (MISSION shRNA lentiviral transduction particles, Sigma–Aldrich Canada, Oakville, ON). Forty percent confluent cells were infected in medium supplemented with 4 mg/ml polybrene (Sigma–Aldrich Canada) for 6 h. Two days after infection, cell populations were selected with 2 mg/ml puromycin (Sigma–Aldrich Canada). The clone TRCN0000038728 was selected: the shRNA against Suz12 (GCTGACAATCAAATGAATCAT) is conserved in rat (accession number FM084383), murine (accession number NM_199196) and human (accession number NM_015355.2) Suz12 sequences. Efficiency of infection was estimated at 25%. Control or ShSuz12 IEC-6 cell total RNAs were isolated with the Rneasy kit (Qiagen, Mississauga, ON, Canada), according to the manufacturer’s instructions. RNA samples from three independent experiments were used for microarray analysis.

first: Naomie

last: Turgeon

first: Mylene

last: Blais

first: Jean-François

last: Delabre


title: The role of Ch25h in the macrophage response to poly(I:C) (bone-marrow-derived macrophages)

status: Public on Jun 20 2014

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

country: USA

institute: Seattle Children's Research Institute

summary:
Cross-talk between sterol regulatory pathways and inflammatory pathways has been demonstrated to play an important role in the response to viral infections.  25-Hydroxycholesterol (25HC) is an oxysterol that plays multiple roles in lipid biosynthesis and immunity, and has recently been shown to have anti-viral activity.  Surprisingly, we found that deletion of Ch25h, the gene encoding the enzyme responsible for 25HC production, is protective in a mouse model of influenza infection as a result of decreased inflammatory-induced pathology.  Anti-viral responses involve complex gene regulatory circuits with multiple feedback loops and we demonstrated that 25HC acts as an amplifier of TLR3 signaling in macrophages and airway epithelial cells.
We determined that 25HC amplifies TLR3 signaling, at least in part, by mediating the up-regulation and recruitment of the AP1 components Fos and Jun to the promoters of a subset of TLR3 responsive genes.   Thus, our study demonstrates for the first time that in addition to its direct anti-viral role, 25HC also regulates transcriptional responses and acts as an amplifier of TLR3-induced inflammation via AP1.

overall_design: 24 RNA samples from murine bone-marrow-derived macrophages were analyzed using Agilent microarrays. Macrophages from C57BL/6 and Ch25h-/- mice were analyzed after mock stimulation or stimulation with 6ug/mL poly(I:C) or for 6 or 18 hours. For each condition, three biological replicates (macrophages derived from independent mice) were analyzed.

first: Elizabeth

middle: S

last: Gold

first: Alan

last: Aderem


title: The organoid generated from murine small intestine: mCherry-positive vs. mCherry-negative

status: Public on Jul 16 2014

city: Bunkyo-ku

first: Kiichiro

last: Tsuchiya

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University

summary:
The organoids heterogenously expressed mCherry by the lentivirus transduction were dissociated into single cells. A single mCherry- positive and -negative cell were collected and grown up to the organoids, respectivery.
The difference of the gene expression profile between  mCherry- positive and -negative organoids was assessd by maicroarray.

overall_design: mCherry- positive vs. -negative organoids

first: Nobukatsu

last: Horita


title: Gene expression analysis in  macrophages stimulated 18 h with Adiponectin

status: Public on Jul 03 2014

city: Madrid

first: Susana

last: Alemany

state: Madrid

address: Arturo DUperier 4

institute: Instituto de Investigaciones Biomédicas ALberto Sols

summary: Bone marrow derived macrophages (BMDM) generated from c57bl/6j mice bone marrow cells were stimulated for 18 h with 12 microgram/ml  adiponectin, RNA from non-stimulated or 18 h adiponectin-stimulated BMDM subjected to a agilent microarray analysis

overall_design: Three  different non-stimulated  and 3 different  18 h adiponectin (12 microgram/ml) RNA samples were subjected to a micrrorray analysis

first: Carlos

last: Sanz

first: Margarita

last: Fernandez


title: The Chronic Gavage Toxicity/Carcinogenicity Study of Indole-3-Carbinol (I3C) in Harlan Sprague-Dawley Rats (G823524-B), CAS No 700-06-1

status: Public on Jul 17 2014

city: Research Triangle Park

first: Michael

last: Wyde

state: NC

address: 111 T.W. Alexander Drive

institute: National Institute of Environmental Health Sciences

summary: Indole-3-carbinol is used as a dietary supplement and has potential use as a therapeutic agent for the prevention of various types of cancer. While substantial evidence exists that indole-3-carbinol can reduce the risk of cancers induced by several known carcinogens when administered to animals, indole-3-carbinol can also function as an initiator and tumor promoter in certain models. The carcinogenic potential of indole-3-carbinol has not been studied in a 2-year bioassay. The objective of the microarray study was to evaluate the transcriptional changes in liver from rats exposed to 0 or 300 mg/kg indole-3-carbinol. At 3 months, livers were analyzed from female Harlan Sprague Dawley rats in the 2-year gavage study of indole-3-carbinol.

overall_design: Female rats were administered 300 mg indole-3-carbinol/kg body weight in corn oil by gavage, 5 days per week in a 2 year toxicology study of indole-3-carbinol.   Gene expression studies were performed on rat liver with samples hybridized to whole rat genome RG230_2.0 rat GeneChip arrays (Affymetrix, CA).


title: Expression data of rat insulinoma cells induced with ER stress +/- IRE1 inhibitor treatment

city: Toronto

first: Allen

last: Volchuk

address: 101 College st

institute: University of Toronto

summary:
The Akita mutation (C96Y) in the insulin gene results in early onset diabetes in both humans and mice. Expression of the mutant proinsulin (C96Y) causes endoplasmic reticulum (ER) stress in pancreatic -cells and consequently the cell activates the unfolded protein response (UPR). Since the proinsulin is terminally misfolded however, the ER stress is irremediable and chronic activation of the UPR eventually activates apoptosis in the cell population.
We used microarray gene expression arrays to analyze the IRE1-dependent activation of genes in response to misfolded proinsulin expression in an inducible mutant proinsulin (C96Y) insulinoma cell line by inhibiting the IRE1 endoribonucleas activity with a specific inhibitor, 4u8c.

overall_design: Insulinoma cells with doxycycline inducible C96Y-proinsulin expression were either untreated, treated with doxycycline alone or treated with dox and 4u8c.  This was done with two biological replicates.

first: Liling

last: Zhang

first: Courtney

last: Nosak

first: Pietro

last: Sollazzo

first: Tanya

last: Odisho


title: Liver differentially expressed genes between microsomic and control inbred mice at birth

status: Public on Jun 04 2014

city: Utrecht

first: Alberto

last: Miranda Bedate

address: Yalelaan 104

country: Netherlands

institute: Universiteit Utrecht

summary: To understand the processes involved in the natural development of microsomic imbred mice, a whole genome microarray expression profiling of mouse liver was performed.

overall_design: Total RNA of liver from C57BL/6J microsomic mice of both sexes were extracted and compared with total RNA of liver from normal (control) mice of both sexes.

first: Ángela

middle: P

last: López-Cardona

first: Ricardo

last: Laguna-Barraza

first: Alexandra

last: Calle

first: Irene

last: López-Vidriero

first: Belén

last: Pintado

first: Alfonso

last: Gutiérrez-Adán


title: Gene Expression Profiling for Plk2 -/- mammary gland

status: Public on May 20 2014

city: Houston

first: Elizabeth

last: Villegas

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary:
Identify gene expression changes in the absence of Plk2
Disruptions in polarity and mitotic spindle orientation contribute to the progression and evolution of tumorigenesis. However, little is known about the molecular mechanisms regulating these processes in vivo. Here we demonstrate that Polo-like kinase 2 (Plk2) regulates mitotic spindle orientation in the mammary gland and is a putative tumor suppressor. Plk2 is highly expressed in the mammary gland and is required for proper mammary gland development. Loss of Plk2 leads to increased mammary epithelial cell proliferation and ductal hyperbranching. Additionally a novel role for Plk2 in regulating the orientation of the mitotic spindle and maintaining proper cell polarity in the ductal epithelium was discovered. In support of a tumor suppressor function for Plk2, loss of Plk2 increased the formation of lesions in multiparous glands. Collectively, these results demonstrate a novel role for Plk2 in regulating mammary gland development and as a tumor suppressor in mammary tumorigenesis. Disruptions in polarity and mitotic spindle orientation contribute to the progression and evolution of tumorigenesis. However, little is known about the molecular mechanisms regulating these processes in vivo. Here we demonstrate that Polo-like kinase 2 (Plk2) regulates mitotic spindle orientation in the mammary gland and is a putative tumor suppressor. Plk2 is highly expressed in the mammary gland and is required for proper mammary gland development. Loss of Plk2 leads to increased mammary epithelial cell proliferation and ductal hyperbranching. Additionally a novel role for Plk2 in regulating the orientation of the mitotic spindle and maintaining proper cell polarity in the ductal epithelium was discovered. In support of a tumor suppressor function for Plk2, loss of Plk2 increased the formation of lesions in multiparous glands. Collectively, these results demonstrate a novel role for Plk2 in regulating mammary gland development and as a tumor suppressor in mammary tumorigenesis.

overall_design: Comparison between Plk2 +/+ (n=3) and Plk2 -/- (n=3) mouse mammary epithelial cells

first: Jeffrey

middle: M

last: Rosen


title: Cryptorchidism in the orl rat is associated with muscle patterning defects in the fetal gubernaculum and altered hormonal signaling

status: Public on Jul 02 2014

city: Wilmington

first: Julia

middle: S.

last: Barthold

state: DE

address: 1600 Rockland Road

department: Urology

institute: Nemours/AI duPont Hospital for Children

summary: This study was designed to provide additional insight into testicular hormone production and responsiveness in the orl strain and complement ongoing efforts to characterize the genetic basis of cryptorchidism in this isolated rat colony.

overall_design:
Gubernacula were harvested from Long Evans and ORL rat embryos at gestational day 17 and 19.  RNA was purified from litter-based organ pools.  26 RNA samples were processed and hybridized to GeneChips.

Please note that a mix-up of the samples gubernaculum-GD19-a and -b appears to have occurred as data from these samples clustered with the opposite strain than expected in hierarchical  clustering analysis. Thus the strain information was annotated as 'unknown'.

first: Alan

last: Robbins

first: Yanping

last: Wang

first: Joan

last: Pugarelli

first: Abigail

last: Mateson

first: Ravinder

last: Anand-Ivell

first: Richard

last: Ivell

first: Suzanne

last: McCahan

first: Robert

middle: E

last: Akins Jr


title: The role of Ch25h in the macrophage response to poly(I:C)

first: Aderem

last: Lab

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

overall_design: Refer to individual Series


title: Gut microbiome metabolites alter genomic networks in PC12 cells relevant to autism spectrum diorders

status: Public on Jun 02 2014

city: Valhalla

first: Bistra

last: Nankova

state: NY

address: 95 Grassland Rd

institute: New York Medical College

summary: Alterations in the composition of the gut microbiome have an emerging role in brain function and behaviour. We have porposed that short chain fatty acids (SCFA) including propionate and butyrate which are present in the diet and are fermantation products of many gastrointestinal bacteria are contributing environmental factors in autism spectrum disorders (ASD). Here we used the microarray technology to compare global changes in gene expression profiles following exposure of PC12 cells to structurally related SCFA propionate and butyrate each in two different concentrations. Large number of affected genes, common for both SCFA were identified, including genetic networks and GO processes implicated in ASD.

overall_design: PC12 cells were exposed to propionate or butyrate. RNA was isolated from each experimental group (n=6, pooled samples) and subjected to genome-wide expression profiling using Affymetrix microarrays to reveal dose- and SCFA-specific changes in gene expression and specific molecular pathways or processes affected as compared to vehicle treated controls.

middle: B

first: Raj

last: Agarwal

first: Derrick

middle: F

last: MacFabe

first: Edmund

last: LaGamma


title: Mechanisms of protection of a novel murine cytomegalovirus vaccine vector against Mycobacterium tuberculosis

status: Public on May 13 2014

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

institute: University of  Oxford

summary: To identify the gene signature induced by MCMV that modulates innate immune function

overall_design: Microarray comparison of gene expression in the lungs of 4 individual naive and 4 eMCMV infected mice two weeks after infection.

first: Peter

middle: C

last: Beverley

first: Zsolt

last: Ruzsics

first: Ariann

last: Hey

first: Claire

last: Hutchings

first: Simone

last: Boos

first: Beatrice

last: Bolinger

first: Emanuele

last: Marchi

first: Geraldine

last: O'Hara

first: Paul

last: Klenerman

first: Ulrich

middle: H

last: Koszinowski

first: Elma

middle: Z

last: Tchilian


title: Gene expression at skin wound sites of WT and FoxO1+/- mice

status: Public on Jun 01 2014

city: Nagasaki

first: Ryoichi

last: Mori

address: 1-12-4 Sakamoto

department: School of Biomedical Sciences

institute: Nagasaki University

summary: In order to determine molecular mechanisms of faster skin wound healing under decreasing FoxO1 protein expression, we performed microarray analysis on 3 days skin wounded samples from FoxO1+/- and WT mice.

overall_design: Skin wound-induced gene expression in WT and FoxO1+/- mice were measured on 3 days after injury. Three independent experiments were performed at each mouse.


title: The role of Ch25h in the macrophage response to poly(I:C) (Let1a)

first: Aderem

last: Lab

overall_design: 14 RNA samples from murine Let1a cells (immortalized airway epithelial cells) were analyzed using Agilent microarrays. Cells from C57BL/6 and Ch25h-/- mice were analyzed after mock stimulation or stimulation with 6ug/mL poly(I:C) or 5μM 25-Hydroxycholesterol for 6 or 18 hours. For each condition, two biological replicates were analyzed.

first: Elizabeth

last: Gold

first: Alan

last: Aderem


title: Microarray analysis of the testis from the aromatase overexpression transgenic and WT mice

status: Public on Apr 18 2014

city: Beijing

first: Wanpeng

last: Yu

address: Yuanmingyuan West Road No.2

country: China

institute: China Agricultrual University

summary: To futher find the gene expression due to the aromatase overexpression in the mouse testis,we have employ whole genome microarray expression profiling as a discovery platform to identify genes compared to the wild type mice. The testes were taken from 5 month old aromatase overexpression  mice and  WT mice as control.

overall_design: We investigated  genes that were significantly upregulated or downregulated in AROM+ mouse testis compared with WT testis. Two groups: 1) total RNA from three 5 month old  AROM+ overexpression transgenic mice testes were collected and processed for microarray;2) total RNA from three 5 month old WT mice testes as control.

first: Xiangdong

last: Li


title: Biological events associated with 99mTcO4--mediated thyroid stunning effect

status: Public on Apr 22 2014

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Rationale: Auger electrons bear a low energy (0-10 keV) which is deposited in a very small volume (a few nm3) around the site of emission. From a radio-toxicological point of view, the effects of Auger electrons on normal tissues are largely unknown, understudied and generally assumed negligible. In this context, the discovery that the Auger electron emitter 99mTc can induce stunning on primary thyrocytes in vitro, at low doses, is intriguing. Extrapolated in vivo, this observation suggests that, a radioisotope as commonly used in nuclear medicine as 99mTc may significantly influence thyroid biology. The aim of the present study was to evaluate the absorbed dose of 99mTc pertechnetate (99mTcO4−) required to induce thyroid stunning in vivo and to analyse the biological events associated/concomitant with this effect.    Methods: SPECT/CT imaging of thyroid uptake of 99mTcO4− was used to demonstrate stunning effect in mice and quantitative analysis of the images was used for dosimetric calculations. The biological effects associated with this phenomenon were evaluated by Western blotting, quantitative RT-PCR, histology, immuno-histochmistry and global gene expression pattern analysis.    Results: Auger electrons-mediated thyroid stunning can be observed in vivo, in mouse thyroid. The threshold of the absorbed dose to the thyroid required to obtain a significant stunning effect is in the range of 20 Gy. This effect is associated with a reduction in the levels of functional Na/I symporter (NIS) protein without any significant cell death. It is reversible within days. At the cellular level, a decrease in NIS mRNA, the activation of the p53 pathway and the generation of double-strand DNA breaks can be observed.     Conclusion: Auger electrons emitted by 99mTc can induce thyroid stunning in vivo, in mice but the thyroid needs to be exposed to a dose of at least 20 Gy, a dose unlikely to be encountered in the clinical practice. Nevertheless, this report represents, to our knowledge, the first example of a significant action of Auger electrons on a normal tissue, in vivo and provides a unique experimental set-up to understand the fine molecular mechanisms involved in the biological effects of Auger electrons.

overall_design: One color design, corresponding to 2 conditions performed on 4 mice: TcO4- (Tc)-treated versus Control (Ct) mice for a total of 8 samples.

first: G

last: Vassaux

first: B

last: Mari

first: P

last: Barbry

first: K


title: Integration of toxicological end points with molecular measurements in a 28-day rat repeated dose inhalation study with cigarette smoke provides mechanistic understanding of smoke impact

status: Public on May 15 2014

city: Neuchatel

first: Sam

last: Ansari

state: Neuchatel

address: Quai Jeanrenaud 5

department: Research & Development

country: Switzerland

institute: Philip Morris Products SA

summary:
Demonstration of reduced biological effects with a prototypic modified risk tobacco product.
Towards a systems toxicology-based risk assessment, we investigated molecular perturbations accompanying histopathological changes in a 28-day rat inhalation study combining transcriptomics with classical histopathology, and demonstrated reduced biological activity of a prototypic modified risk tobacco product (pMRTP) in comparison to the reference research cigarette 3R4F.
Rats were exposed to filtered air or to three concentrations of mainstream smoke (MS) from 3R4F, or to a high concentration of MS from a pMRTP.
Histopathology revealed dose-dependent changes for 3R4F: irritative stress-related in nasal and bronchial epithelium and inflammation-related in the lung parenchyma. For pMRTP, significant changes were seen in the nasal epithelium only.
Transcriptomics data were obtained from nasal and bronchial epithelium and lung parenchyma. Dose-dependent gene expression changes were seen for 3R4F with much smaller changes for pMRTP. A computational-modeling approach that is based on causal models of tissue-specific biological networks identified cell stress, inflammation, cell proliferation, and senescence as the most perturbed molecular mechanisms. These perturbations correlated with the histopathological observations. Only weak perturbations were observed for the pMRTP.
In conclusion, a correlative evaluation of classical histopathology together with gene expression?based computational network models may facilitate a systems toxicology-based risk assessment as shown for a pMRTP.

overall_design: SD-rats were exposed for 28 days to filtered air (sham), or to a low, medium, or high concentration of mainstream (MS) cigarette smoke (CS) from the Reference cigarette 3R4F in addition to MS CS from a prototypic modified risk tobacco product (pMRTP) at the same nicotine concentration as the high 3R4F group, i.e., 23 ug nicotine/l. Each treatment group contains 5 biological replicates. 3 different tissue types were dissected: nasal cavity respiratory epithelium, lung parenchyma and lung bronchi. Tissues were processed and hybridized on Affymetrix Rat230_2 chips.

first: Ulrike

last: Kogel

first: Walter

middle: K

last: Schlage

first: Florian

last: Martin

first: Yang

last: Xiang

first: Patrice

last: Leroy

first: Patrick

last: Vanscheeuwijck

first: Stephan

last: Gebel

first: Ansgar

last: Buettner

first: Christoph

last: Wyss

first: Marco

last: Esposito

first: Julia

last: Hoeng

first: Manuel

last: Peitsch


title: Cross-species gene expression analysis of species-specific differences in preclinical assessment of pharmaceutical compounds (rat)

status: Public on Apr 30 2014

city: Nottingham

first: John

last: Okyere

address: BioCity Nottingham

institute: CrossGen Limited

summary: Significant qualitative and quantitative differences exist between humans and the animal models used in research. However, significant quantitative and qualitative differences exist between humans and the animal models used in research. This is as a result of genetic variation between human and the laboratory animal. Therefore the development of a system that would allow the assessment of all molecular differences between species after drug exposure would have a significant impact on drug evaluation for toxicity and efficacy. Here we describe a cross-species microarray methodology that identifies and selects orthologous probes after cross-species sequence comparison to develop an orthologous cross-species gene expression analysis tool. The assumptions made by the use of this orthologous gene expression strategy for cross-species extrapolation is that; conserved changes in gene expression equate to conserved pharmacodynamic endpoints. This assumption is supported by the fact that evolution and selection have maintained the structure and function of many biochemical pathways over time, resulting in the conservation of many important processes.  We demonstrate this difference using a cross-species methodology by investigating species specific differences of the peroxisome proliferator activator receptor (PPAR) alpha in rat and human.

overall_design: Rat primary hypatocytes were treated with 30µ, 100µ EMD and 0.1% DMSO as vehicle control. All samples were incubated at 24hr and 72hr intervals before RNA extrations and hybridization onto Affymetrix Rat microarrays.

first: J

last: Oppon

first: D

last: Dzidzienyo

first: L

last: Sharma

first: G

last: Ball


title: The effect of type-I interferon signaling directly on CD8+ T cells following LCMV infection in the presence or absence of NK cells.

status: Public on May 07 2014

city: Zurich

first: Annette

last: Oxenius

address: Vladimir-Prelog-weg 1-5/10

department: Microbiology

institute: ETH Zurich

summary: To understand the effect of type-I IFN signaling directly on CD8+ T cells following an LCMV infection we compared the overall gene expression of WT and Ifnar1-/- T cells following an LCMV infection.

overall_design: WT and Ifnar1-/- P14 cells were sorted from infected mice (day 3) that were depleted of NK cells or left untreated. Each sample and condition (WT or IFNAR) was performed in triplicates

first: Josh

last: Crouse


title: Deregulated expression of cytoskeleton related genes in the spinal cord and sciatic nerve of presymptomatic SOD1G93A Amyotrophic Lateral Sclerosis mouse model

city: Sao Paulo

first: Jessica

middle: Ruivo

last: Maximino

state: SP

address: Av. Dr. Arnaldo, 455

department: Neurology

country: Brazil

institute: University of Sao Paulo (FMUSP)

summary: Early molecular events related to cytoskeleton are poorly described in Amyotrophic Lateral Sclerosis (ALS), especially in the Schwann cell (SC), which offers strong trophic support to motor neurons. DAVID tool identified cytoskeleton-related genes by employing the Cellular Component of Gene Ontology (CCO) in a large gene profiling of lumbar spinal cord and sciatic nerve of presymptomatic SOD1G93A mice. One and five CCO terms related to cytoskeleton were described from the spinal cord deregulated genes of 40 days (actin cytoskeleton) and 80 days (microtubule cytoskeleton, cytoskeleton part, actin cytoskeleton, neurofilament cytoskeleton and cytoskeleton) old transgene mice, respectively. Also, four terms were depicted from the deregulated genes of sciatic nerve of 60 days old transgenes (actin cytoskeleton, cytoskeleton part, microtubule cytoskeleton and cytoskeleton). Kif1b was the unique gene that appeared deregulated in more than one studied region or presymptomatic age. The expression of Kif1b (qPCR) elevated in the lumbar spinal cord (40 days old) and decreased in the sciatic nerve (60 days old) of presymptomatic ALS mice, results that were in line to microarray findings. Upregulation (24.8 fold) of Kif1b was seen in laser microdissected enriched immunolabeled motor neurons from the spinal cord of 40 days old presymptomatic SOD1G93A mice. Furthermore, Kif1b was downregulated in the sciatic nerve Schwann cells of presymptomatic ALS mice (60 days old) that were enriched by means of cell microdissection (6.35 fold), cell sorting (3.53 fold) and primary culture (2.70 fold) technologies. The gene regulation of cytoskeleton molecules is an important occurrence in motor neurons and Schwann cells in presymptomatic stages of ALS and may be relevant in the dying back mechanisms of neuronal death. Differential regulation of Kif1b in the spinal cord and sciatic nerve cells emerged as key event in ALS.

overall_design: Sciatic nerve from SOD1G93A and Non transgenic controls from 60 days were used in the experiments. 4 biological replicates were used. A reference sample, comprised by RNA from different neonatal organs (heart, liver, kidney) were used in the hybridations

first: Gabriela

last: de Oliveira

first: Chrystian

middle: J

last: Alves

first: Gerson

last: Chadi


title: Microarray Analysis of Microcystin-LR

status: Public on Jul 25 2014

first: Nigel

last: Walker

summary: Microcystins are produced by the cyanobacteria, most commonly Microcystis aerµginosa. Upon ingestion, toxic microcystins are actively absorbed by fish, birds and mammals where they are primarily liver toxins.

overall_design: Groups of 4-6 rats were exposed to 0, 1, 10, 50 or 100 µg/kg microcystin-LR for 0.5, 1, 3 or 6 hours and gene expression analysis performed on liver with samples hybridized to whole rat genome RG230_2.0 GeneChip arrays (Affymetrix, CA).


title: Effect of ingested whey protein hydrolysate on gene expression profiles compared to an identical composition of amino acid mixture in rat skeletal muscle

status: Public on Apr 15 2014

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: We have previously showed that whey protein hydrolysate (WPH) causes a greater increase in muscle protein synthesis than an identical composition of amino acids mixture does. The present study was conducted to investigate a comparative effect of WPH on gene expression. Male Sprague-Dawley rats subjected to a 2-h swimming exercise were administered either a carbohydrate-amino acid diet or a carbohydrate-WPH diet immediately after exercise. One hour after exercise, epitrochlearis muscle mRNA was sampled and subjected to DNA microarray analysis. As a result, ingestion of WPH altered 189 genes in considering the false discovery rate. Among the upregulated genes, 8 Gene Ontology (GO) terms were enriched, which included key elements in muscle repair after exercise such as Cd24, Ccl2, Ccl7 and Cxcl1. On the other hand, 9 GO terms were enriched in the gene sets downregulated by ingestion of WPH and these GO terms fell into 2 clusters, ‘regulation of ATPase activity’, and ‘immune response’.  Furthermore, we found that WPH activate the 2 upstream proteins, extracellular signal-regulated kinase 1/2 (ERK1/2) and hypoxia-inducible factor-1α (HIF-1α), which may act as key factors for regulation of gene expression. These results suggest that ingestion of WPH, compared to an identical composition of amino acid mixture, induces greater changes in the after-exercise gene expression profile via activation of the proteins, ERK1/2 and HIF-1α.

overall_design: Male Sprague-Dawley rats (5-week-old) with body weights of approximately 150 g each (CLEA Japan, Inc., Tokyo, Japan) were used in this study. Rats were maintained at 23 ± 2oC, with lights on from 8:00 to 20:00 and off from 20:00 to 8:00. Rats had free access to food (protein 23.6%, fat 5.3%, carbohydrate 54.4%, ash 6.1%, fiber 2.9%, moisture 7.7%, MF, Oriental Yeast Co., Ltd., Osaka, Japan) and water. After 2- or 3-day acclimation, the rats were pre-trained to swimming exercise for 3 days. One day before the experiment, they were fed 5 g of a restricted diet (MF, Oriental Yeast Co., Ltd., Osaka, Japan). On the day of the experiment, rats swam for 2 hours, with 4 rats swimming simultaneously in a barrel filled with water to a depth of 50 cm, allowing an average surface area of 400 cm2 for each animal. The water temperature was maintained at a constant of 35°C. Immediately following exercise, rats were given one of two isoenergetic test solutions by gavage. These solutions contained 44 kJ in a four-test dose that represented about 15% of daily energy needs and included either a mixed meal containing carbohydrate and amino acid mixture (AAM) or a mixed meal containing carbohydrate and whey protein hydrolysate (WPH; Meiji Co., Ltd., Japan). This study was approved by the Animal Committee of Food Science Research Lab., Meiji Co., Ltd., with the animals receiving care according to the guidelines laid down by this committee.

first: Atsushi

last: Kanda

first: Tomoko

last: Ishijima

first: Fumika

last: Shinozaki

first: Kyosuke

last: Nakayama

first: Tomoyuki

last: Fukasawa

first: Keiko

last: Abe

last: Kawahata

first: Shuji

last: Ikegami


title: ATF3 is a novel regulator of mouse neutrophil migration.

status: Public on Apr 05 2014

city: Cincinnati

first: Christopher

last: Karp

state: OH

address: 3333 Burnet Ave

department: Molecular Immunology

institute: Cincinnati Children's Hospital Medical Center

summary: Expression of the activating transcription factor 3 (ATF3) gene is induced by Toll-like receptor (TLR) signaling. In turn, ATF3 protein inhibits the expression of various TLR-driven pro-inflammatory genes. Given its counter-regulatory role in diverse innate immune responses, we defined the effects of ATF3 on neutrophilic airway inflammation in mice. ATF3 deletion was associated with increased lipopolysaccharide (LPS)-driven airway epithelia production of CXCL1, but not CXCL2, findings concordant with a consensus ATF3-binding site identified solely in the Cxcl1 promoter. Unexpectedly, ATF3-deficient mice did not exhibit increased airway neutrophilia after LPS challenge. Bone marrow chimeras revealed a specific reduction in ATF3-/- neutrophil recruitment to wild type lungs. In vitro, ATF3-/- neutrophils exhibited a profound chemotaxis defect. Global gene expression analysis identified ablated Tiam2 expression in ATF3-/- neutrophils. TIAM2 regulates cellular motility by activating Rac1-mediated focal adhesion disassembly. Notably, ATF3-/- and ATF3-sufficient TIAM2 knockdown neutrophils, both lacking TIAM2, exhibited increased focal complex area, along with excessive CD11b-mediated F-actin polymerization. Together, our data describe a dichotomous role for ATF3-mediated regulation of neutrophilic responses: inhibition of neutrophil chemokine production, but promotion of neutrophil chemotaxis.

overall_design: Ly6G+ neutrophils were purified by magnetic beads from WT or ATF3 KO bone marrow and RNA was immediately isolated for global gene expression using microarrays.

middle: L

first: Nicholas

middle: D

last: Boespflug


title: Scgb1a1, Lpo and Gbp2 is Characteristically Expressed in Rat Peri-Implant Epithelium.

status: Public on Apr 08 2014

city: Chiyoda-ku

first: Hodaka

last: Sasaki

address: 2-9-18, Kandamisaki-cho

department: Dept. of Oral and Maxillofacial Implantology

institute: Tokyo Dental College

summary: The peri-implant epithelium plays an important role in the prevention against initial stage of inflammation. In order to minimize the risk of peri-implantitis, it is necessary to understand the biological characteristics of the peri-implant epithelium. The aim of this study was to investigate the characteristic gene expression profile of peri-implant epithelium as compared to junctional epithelium using laser microdissection and microarray analysis.

overall_design: Left upper first molars of 4 week-old rat were extracted, and titanium alloy implants were placed. Four weeks after surgery, samples were harvested by laser microdissection, and total RNA samples were isolated. Comprehensive analyses of genes expressed in the junctional epithelium and peri-implant epithelium were performed using microarray analysis. Confirmation of the differential expression of selected genes was performed by quantitative real-time polymerase chain reaction and immunohistochemistry.

first: G

last: Mori

first: H

first: Y

last: Makabe

first: M

last: Yoshinari

last: Yajima


title: Comparison of the gene expression profiles between MEF, MEF treated with n-Butylenephthalide (BP) 10 and 40ug/ml.

status: Public on Mar 31 2014

city: Taichung

first: Shih-Ping

last: Liu

address: No.6, Hsueh-Shih Road

country: Taiwan

institute: China medical university

summary: The microarray analysis was used for comparing the gene expression profiles between MEF, MEF treated with n-Butylenephthalide (BP) 10 and 40ug/ml.

overall_design: The total RNA extracted from MEF, MEF treated with n-Butylenephthalide (BP) 10 and 40ug/ml was used for the microarray analysis to compare the gene expression profiles.


title: Expression data from liver of young and old rats fed on different dietary fat sources, namely virgin olive, sunflower or fish oils

status: Public on Mar 26 2014

city: ARMILLA

first: PATRICIA

last: PEREZ

state: GRANADA

address: AVDA DEL CONOCIMIENTO S/N

department: INYTA

institute: CIBM

summary:
Since the liver is the central organ of metabolism, changes in diet have a great impact on this organ and overall on health with aging. It is well known that dietary fat source strongly influences many parameters of the hepatic mitochondria. These changes includes modification of lipid composition of mitochondrial membrane, affecting the mtETC functions, oxidative stress and mtDNA alterations.
We used microarrays to detail the changes in gene expression provides by feeding lifelong on different dietary fat sources, and identified distinct classes of up and down-regulated genes during aging under different dietary conditions.

overall_design: Rats were fed lifelong on a normolipidic diet (4% w/w) with virgin olive, sunflower or fish oil as dietary fat source. At 6 and 24 months, animals were killed and liver were removed for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain changes in gene expression due to both aging and dietary conditions. There were 6 experimental groups (virgin olive oil at 6 months, sunflower oil at 6 months, fish oil at 6 months, virgin olive oil at 24 months, sunflower oil at 24 months and fish oil at 24 months. 3 animals were studied of each experimental group, so a total of 18 samples were analyzed.

first: P

last: Perez-Lopez

first: J

last: Quiles


title: Gene regulation in denervated hairy skin of the adult rat

city: Louisville

first: Jeffrey

last: Petruska

state: KY

address: 511 S. Floyd St.

department: Department of Anatomical Sciences and Neurobiology

institute: University of Louisville

summary: This study aimed to quantify the regulation of transcripts in the hairy skin of the back of adult rats in the condition of loss of sensory and autonomic (sympathetic) innervation (i.e., denervated). Denervated skin has reduced wound healing capacity, reduced proliferation of epidermal progenitor cells, and also expresses factors that regulate ingrowth of sensory and sympathetic axons from neighboring regions of innervated skin. It was expected that this quantification f transcript regulation would offer insight into the general and specific mechanisms that may contribute to these important biological processes.

overall_design: All animals were adult (200-250g) Sprague-Dawley female rats. Three conditions were examined. Groups were naïve (n=6), 7-day denervated skin (n=5), and 14-day (n=5) denervated skin. Denervation preparations: Full-thickness incision along long-axis of the body 1cm to right of midline (to avoid injuring skin to be sampled). Incision was centered rostro-caudally on the T13 (thoracic 13) costo-vertebral angle so as to allow access to the T9-L2 (lumbar 2) cutaneous nerves. Skin was reflected to the left and the left T9, T10, L1, and L2 dorsal and lateral cutaneous nerves were isolated, ligated with 7-0 monofilament suture close to their exit from the body wall, and transected. Approximately 5mm of the distal portion of the nerve was resected. The T11 nerves were left unperturbed and were not isolated from the surrounding fascia. This generated two strips of skin that were devoid of sensory and autonomic innervation (those strips served by the T9 and T10 nerves, and by the L1 and L2 nerves). Between these denervated strips of skin was a strip of skin that retained the sensory and autonomic axons supplied by T11 nerves. The denervated zones were identified by mapping the cutaneous trunk muscle (CTM) reflex (see Petruska-JC et al. (2013) Journal of Comparative Neurology; Diamond-J et al., (1992) J Neuroscience), and the border marked with pen and remarked every few days. The samples were taken from the rostral (T9/10) denervated zone. Samples from naive animals (no denervation) were taken from the same region, using the dorsal cutaneous nerves as registration landmarks. Animals displayed no signs of overgrooming of the denervated skin. Because the CTM inserts onto the dermis of this region of skin, samples necessarily include both skin and underlying CTM (which is innervated from another source so was not denervated in the experiment).

first: Lawrence

last: Moon

first: Benjamin

last: Harrison

first: Robert

last: Flight

first: Eric

last: Rouchka

first: Mary

last: Bartlett Bunge

first: Lorne

last: Mendell


title: Induction of regulatory M2 macrophage-like immunosuppressive cells from mouse ES cells that contribute to prolong allogeneic immune rejection

status: Public on Mar 28 2014

city: Sapporo

first: Ken-ichiro

last: Seino

state: Hokkaido

address: Kitaku, Kita 15 Nishi 7

institute: Hokkaido Univ.

summary: A promise of cell replacement therapy using pluripotent stem cells (PSCs) such as embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) as donor source has been increased. However, particularly when ESCs were used, immune suppression should be required because the donor-recipient combination would be allogeneic. In this study, we examined a concept that some immunosuppressive cells could be induced from PSCs and those cells could prevent allogeneic immune rejection of the PSCs-based transplantation. In fact, we successfully induced immunosuppressive cells that resemble M2 macrophages in terms of cell surface molecule and gene expressions. They efficiently suppressed allogeneic T cell proliferative responses, at least partly, in nitric oxide dependent manner. We applied these cells to in vivoallogeneic transplantation and found that they substantially prolonged ESCs-derived graft survival. These results open a new insight for development of a practical immune-regulatory strategy in cell replacement therapy using PSCs.

overall_design: Difference of the gene expression between ESdSC and ESdDC was analyzed. Two independent experiment were performed.

first: Hiroya

last: Kudo

first: Haruka

last: Wada


title: Gene expression analysis of prefrontal cortex in mice exposed to chronic mild stress

status: Public on Feb 28 2014

city: Nichinomiya

first: Kyosuke

last: Yamanishi

state: Hyogo

address: 1-1, Mukogawa

department: Neuropsychiatry

institute: Hyogo College of Medicine

summary: Major depressive disorder (MDD) is a common disorder and is responsible for considerable disability in global functioning, anorexia, and severer medical comorbidity. Recently, some reports showed the relationship between MDD and the metabolic disorders such as diabetes. We examined gene expression profiles in the mice prefrontal cortex using genome-wide microarray technology, and determined gene expression profiles with and without chronic mild stress(CMS) for 4 weeks which was often used to make models of depression. To analyze the candidate genes involved in not only depression but dysfunction of physiological homeostasis like diabetes, we campared the gene expression levels between with and without CMS, then we isolated 494 genes showing a more than 2-fold increase or a less than 1/2-fold decrease, in addition, we chose the isolated genes transcriptional products of both samples were confirmed clearly.

overall_design: The prefrontal cortex of C57Bl/6 N sea mice with and without CMS. We mixed tatal RNA from 7 mice prefrontal cortex per each.

first: Nobutaka

last: Doe

first: Hisato

last: Matsunaga


title: Nkx6.1 β-cell expansion pathway

status: Public on Feb 18 2014

city: Durham

first: Larry

middle: Gene

last: Moss

address: 4321 Medical Park Drive S200

department: Duke Molecular Physiology Institute

institute: Duke University School of Medicine

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

overall_design: Refer to individual Series


title: Genes affected by SFRP5 overexpression in LSK cells and CLP

status: Public on Mar 20 2014

city: Suita

first: Takafumi

last: Yokota

state: Osaka

address: 2-2 Yamadaoka

department: Hematology & Oncology

institute: Osaka University

summary: To understand  gene expression signatures between wild-type and SFRP5-overexpressing cells

overall_design: To examine genes regulated by SFRP5 expression, sets of microarrays were conducted with Lin- c-kitHi Sca-1+ cells and Lin- c-kitLo Sca-1Lo IL7Rα+ CLP-enriched cells derived from adult bone marrow of SFRP5-transgenic mice or their WT littermates.


title: Nkx6.1 regulates islet β-cell proliferation via Nr4a1 and Nr4a3 nuclear receptors

summary: Loss of functional β-cell mass is a hallmark of Type 1 and Type 2 diabetes, and methods for restoring these cells are needed. We have previously reported that overexpression of the homeodomain transcription factor Nkx6.1 in rat pancreatic islets induces β-cell proliferation and enhances glucose-stimulated insulin secretion, but the pathway by which Nkx6.1 activates β-cell expansion has not been defined. Here we demonstrate that Nkx6.1 induces expression of the Nr4a1 and Nr4a3 orphan nuclear receptors, and that these factors are both necessary and sufficient for Nkx6.1-mediated β-cell proliferation. Consistent with this finding, global knockout of Nr4a1 results in a decrease in β-cell area in neonatal and young mice. Overexpression of Nkx6.1 and the Nr4a receptors results in increased expression of key cell cycle inducers E2F1 and cyclin E1. Furthermore, Nkx6.1 and Nr4a receptors induce components of the anaphase-promoting complex, including Ube2c, resulting in degradation of the cell cycle inhibitor p21CIP1. These studies identify a new bipartite pathway for activation of β-cell proliferation, suggesting several new targets for expansion of functional β-cell mass.

overall_design: We set up a microarray using primary rat islets that were left untreated or transduced with adenoviruses overexpressing βgal or Nkx6.1 for 48 h.

last: Tessem

first: L

middle: G

last: Chao

first: M

last: Arlotto

first: D

last: Lu

middle: V

last: Jensen

first: S

last: Stephens

first: P

last: Tontonoz

first: H

last: Hohmeier

first: C

last: Newgard


title: Transcription factor GATA1 is dispensable for mast cell differentiation in adult mice

status: Public on Mar 02 2014

city: Takasaki

first: Kinuko

last: Ohneda

state: Gunma

address: 60 Nakaorui machi

institute: Takasaki Univ Health Welfare

summary: The zinc finger transcription factor GATA1 plays an essential role for differentiation in several hematopoietic cell lineages including erythroid cells, megakaryocytes and eosinophils. Although some studies demonstrated that GATA1 is also required for mast cell differentiation, the effect of complete ablation of GATA1 in mast cell differentiation has not been examined. Here, by using tamoxifen-inducible conditional Gata1 knockout mice, we show that the role of GATA1 in mast cell differentiation is less than previously anticipated in adult mice. Although systemic administration of tamoxifen resulted in complete ablation of GATA1 protein in bone marrow and spleen, cell number and distribution of peripheral tissue mast cells in Gata1-null mice were comparable to those in wild type mice. Bone marrow cells derived from Gata1-null mice differentiated into mast cells that express both c-Kit and IgE receptor α subunit. Finally, we show a line of evidence that GATA1 and GATA2 cooperatively regulate the expression of several mast cell-specific genes by chromatin immunoprecipitation assays and quantitative RT-PCR analyses. These results indicate that GATA1 is dispensable for differentiation and maintenance of mast cells in postnatal hematopoiesis and the loss of GATA1 function is likely compensated by GATA2.

overall_design: Murine bone marrow-derived mast cells from C57BL/6 mice were transfected with of control or GATA1 siRNA (200 pmol). Two samples were analyzed. Sample1 (ctrsi-mix) is prepared from cells transfected with control siRNA. Sample2 (G1si-mix) is prepared from cells transfected with GATA1 siRNA. For each siRNA treatment, two replicate samples prepared from different animals were pooled and used for the analysis.

first: Shinya

last: Ohomori


title: Nr4a1 and Nr4a3 upregulate cell cycle genes upregulated in the Nkx6.1 β-cell proliferation pathway

summary: Loss of functional β-cell mass is a hallmark of Type 1 and Type 2 diabetes, and methods for restoring these cells are needed. Nkx6.1 induces β-cell proliferation, but the pathway by which Nkx6.1 activates β-cell expansion has not been defined. Here we demonstrate that Nkx6.1 induces expression of the Nr4a1 and Nr4a3 orphan nuclear receptors, and that these factors are both necessary and sufficient for Nkx6.1-mediated β-cell proliferation. Overexpression of the Nr4a receptors results in increased expression of key cell cycle inducers E2F1 and cyclin E1. Furthermore, Nr4a receptors induce components of the anaphase-promoting complex, including Ube2c.

overall_design: We set up a microarray using primary rat islets that were left untreated or transduced with adenoviruses overexpressing GFP, Nr4a1 or Nr4a3 for 48 h.

first: J

middle: S


title: Alternatively activated macrophages derived from monocytes and tissue macrophages are phenotypically and functionally distinct

status: Public on Feb 05 2014

city: Saint Louis

first: Mei San

last: Tang

state: MO

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

institute: Washington University in St Louis

summary: Macrophages adopt an alternatively activated phenotype (AAM) when activated by IL-4. While these AAMs can be derived from local proliferation of resident tissue macrophages or recruited inflammatory monocytes, it is not known whether these different AAMs are phenotypically and functionally distinct. Using microarray analysis of gene expression, we demonstrated that while both monocyte- and tissue-derived AAM expressed high levels of Arg1, Chi3l3 and Retnla, only monocyte-derived AAM upregulated Raldh2 and PD-L2. The distinction between monocyte- and tissue-derived macrophages can, therefore, be made using different phenotypic markers.

overall_design: Gene expression profiling analysis with whole genome microarray of tissue-derived and monocyte-derived macrophages, induced using IL-4c and/or 4% thioglycollate.

first: Uma

middle: M

last: Gundra

first: Natasha

last: Girgis

first: Dominik

last: Ruckerl

first: Stephen

last: Jenkins

first: Lauren

middle: N

last: Ward

first: Zachary

last: Kurtz

first: Kirsten

last: Wiens

first: Upal

last: Basu-Roy

first: Alka

last: Mansukhani

first: Judith

last: Allen

first: P'ng

last: Loke


title: Gene expression profile in visceral-pancreatic adipose tissue from control rats fed a standard chow diet and obese rats fed a high-caloric cafeteria diet for 30 days.

status: Public on Feb 15 2014

city: Barcelona

first: Susana

last: Kalko

state: BARCELONA

address: c/Rosello 153

department: Bioinformatics Platform

institute: IDIBAPS

summary:
Changes in the secretion profile of visceral-pancreatic white adipose tissue due to diet-induced obesity are partially responsible for increased beta cell replication, suggesting that a crosstalk between pWAT and beta cells may play a role in regulating beta cell plasticity. The molecular mechanisms underlying this cross-talk are still not fully understood.
The aim of this study was to integrate transcriptomic, proteomic and metabolomic data to unravel the cross-talk between adipose tissue and pancreatic islets during evolution of obesity.

overall_design: Adipose tissue from control lean and obese rats were obtained. RNA was extracted and processed for further hybridization on Affymetrix microarrays (GeneChip Rat Genome 230 2.0 (Affymetrix, Santa Clara, CA)).

first: Rita

last: Malpique


title: Impact of the peripancreatic adipose tissue on beta-cell adaptation to obesity: an integrated, multi-platform analysis


title: Gene expression profile in pancreatic islets from control rats fed a standard chow diet and obese rats fed a high-caloric cafeteria diet for 30 days.

summary:
Changes in the secretion profile of visceral-pancreatic white adipose tissue (pWAT) due to diet-induced obesity are partially responsible for increased beta cell replication, suggesting that a crosstalk between pWAT and beta cells may play a role in regulating beta cell plasticity. The molecular mechanisms underlying this cross-talk are still not fully understood.
The aim of this study was to integrate transcriptomic, proteomic and metabolomic data to unravel the cross-talk between adipose tissue and pancreatic islets during evolution of obesity.

overall_design: Pancreatic islets from control lean and cafeteria diet fed obese rats were obtained. RNA was extracted and processed for further hybridization on Affymetrix microarrays (GeneChip Rat Genome 230 2.0 (Affymetrix, Santa Clara, CA)).


title: shRNA Screening Identifies JMJD1C as being required for Leukemia Maintenance (Agilent)

status: Public on Jan 23 2014

city: Copenhagen

first: Kristian

last: Helin

address: Ole Maaløes vej 5

department: BRIC

country: Denmark

institute: Copenhagen University

summary: We used a mouse model of human AML induced by the MLL-AF9 fusion oncogene, and an epigenetic shRNA library to screen for novel potential drug targets. One of the best candidate drug targets identified in these screens was Jmjd1c. Depletion of Jmjd1c impairs growth and colony formation of mouse MLL-AF9 cells in vitro, as well as establishment of leukemia after transplantation. Depletion of JMJD1C impairs expansion and colony formation of human leukemic cell lines, with the strongest effect observed in the MLL-rearranged ALL cell line, SEM. In both mouse and human leukemic cells, the growth defect upon JMJD1C depletion appears to be primarily due to increased apoptosis, which implicates JMJD1C as a potential therapeutic target in leukemia.

overall_design: To assess the effect of JMJD1C depletion on transcription, we compared the transcriptome of shJMJD1C- and shScr-transduced mouse MLL-AF9 transformed cells 48h after infection. A total of 451 transcripts were detected as changing between the two conditions (FDR<0.25)

first: K


title: Altered Gene Expression Profile in Ovarian Follicle in Rats Treated with Indomethacin and RU486

status: Public on Feb 01 2014

city: Osaka

first: Kenjiro

last: Tsubota

address: 1-6, Kashima 2-chome

institute: Astellas Pharma

summary: It is well-known that indomethacin (the cyclooxygenase 1 & 2 inhibitor) and RU486 (or mifepristone, the progesterone receptor antagonist) block follicular rupture in rats. To characterize genetic alterations in unruptured follicles, gene expression profiles in ovarian follicle were analyzed in indomethacin- and RU486-treated female Sprague-Dawley rats. Ovaries are collected at 22:00 on the proestrus day and 10:00 on the following estrus day after a single dose of indomethacin and RU486. Histopathologically, changes depicting responses to LH surge were observed in ovaries, uteri and vagina. Total RNA was extracted from pre-ovulatory follicles or unruptured follicles collected by laser microdissection and analyzed by GeneChip. Among genes showing statistically significant changes compared to control groups, following changes were considered relevant to induction of unruptured follicles. In indomethacin-treated rats, Wnt4 was down-regulated, suggesting effect on tissue integrity and steroid genesis. In RU486-treated rats, Adamts1, Adamts9, Edn2, Ednra, Lyve1, Plat, and Pparg were down-regulated. These changes suggest effects on proteolysis for extracellular matrix or surrounding tissue (Adamts1 & 9, and Plat), constriction of smooth muscle surrounding follicles (Edn2, Ednra, and Pparg), follicular fluid (Lyve1), and angiogenesis (Pparg). Down-regulation of angiogenesis related genes (Angpt2, Hmox1, and Vegfa) was observed in both treatment groups. Here, we clarify genetic alterations induced by the inhibition of cyclooxygenase or progesterone receptor.

overall_design:
Animals were singly administered orally 4mg/kg of Indomethacin (IM) at 16:00 or 100 mg/kg of RU486 (RU) at 10:00 on the proestrus day, and sacrificed by exsanguination under anesthesia at 22:00 on the proestrus day, and 10:00 on the following estrus day. Three animals were contained per each treatment group at each timing. Pre-ovulatory follicle (PeF) and unruptured follicles (UF) were laser-microdissected from ovaries collected on the proestrus day, and the estrus day, respectively. From untreated animals, PeF and post-ovulatory follicle (PoF) were also laser-microdissected from the ovaries collected on the proestrus day, and the estrus day, respectively, as the control group.
The ovaries were removed and embedded in OCT (Tissue-Tek, Sakura Finetek, Torrance, CA), frozen in dry-ice-cold isopentan, and stored at -70 °C until used. Frozen sections (8 micro meter thick) were mounted on the membrane slides (MMI, Glatteburg, Zurich, Switzerland), and stained with HistogeneTM LCM frozen section staining kit (Arcturus Engineering, Mountain View, CA). Then, 15 follicles in each phase were retrieved by Laser Micro Dissection system (LMD, CellCut Plus®, MMI). The collected follicle sections were lysed by the buffer RLT in the collection tube supplied in RNeasy Micro Kit (Qiagen, Hilden, Germany), and total RNA was extracted according to manufacturer's instructions.

first: Masayuki

last: Kanki


title: A network pharmacology study of Chinese Medicine QSYQ to reveal its underlying multi-compound, multi-target, multi-pathway mode of action

status: Public on Jan 17 2014

city: Hangzhou

first: Xiaohui

last: Fan

state: Zhejiang

address: Yuhangtang 866

institute: Zhejiang Univ.

summary:
Chinese medicine is a complex system guided by traditional Chinese medicine (TCM) theories, which has proven to be especially effective in treating chronic and complex diseases. However, the underlying modes of action (MOA) are not always systematically investigated. Herein, a systematic study was designed to elucidate the multi-compound, multi-target and multi-pathway MOA of a Chinese medicine ,QSYQ, on myocardial infarction.
Male Sprague Dawley rat model of myocardial infarction were administered QSYQ intragastrically for 7 days while the control group was not treated. The differentially expressed genes (DEGs) were identified from myocardial infarction rat model treated with QSYQ, followed by constructing a cardiovascular disease (CVD)-related multilevel compound-target-pathway network connecting main compounds to those DEGs supported by literature evidences and the pathways that are functionally enriched.

overall_design:
Three conditions were compared with three replicates each:
(1) sham, i.e. without left anterior descending coronary artery (LAD) ligation; (2) model, with LAD ligation; (3) QSYQ, with LAD ligation and treated with QSYQ intragastrically for 7 days, the dosage was 105.6 mg/kg once a day. Rats were sacrificed after 7 days of i.g. administration under 10% chloral hydrate anesthesia (300mg/kg). Three tissue samples on the border between infarct and non-infarct area were dissected from left ventricles of each group. The tissue samples were stored at -80℃ refrigerator. Total RNA was extracted using TRIZol Reagent (Invitrogen) and purified using RNeasy Mini kit (QIAGEN), following manufacturers’ protocols. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and electrophoresis in 2% (w/v) agarose gels. Only RNA with RNA integrity numbers (RINs) greater than 7.0 and 28SrRNA/18S rRNA ratio greater than 0.7 was used for microarray analyses. Whole genome microarray analysis was performed using Affymetrix rat Genome 230 2.0 chips.

first: Xiang

last: Li

first: Yi

last: Wang

first: Yiyu

last: Cheng


title: Association of Cellular and Molecular Responses in the Rat Mammary Gland to 17beta-Estradiol with Susceptibility to Mammary Cancer

city: Madison

first: James

last: Shull

state: WI

address: 1400 University Avenue

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin-Madison

summary: We are using ACI and BN rats, which differ markedly in their susceptibility to 17beta-Estradiol (E2)-induced mammary cancer, to identify genetic variants and environmental factors that determine mammary cancer susceptibility.  The objective of this study was to characterize the cellular and molecular responses to E2 in the mammary glands of ACI and BN rats to identify qualitative and quantitative phenotypes that associate with and/or may confer differences in susceptibility to mammary cancer.  Female ACI and BN rats were treated with E2 for 1, 3 or 12 weeks and cell proliferation, apoptosis, differentiation and gene expression were evaluated.  The luminal epithelium of ACI rats exhibited a rapid and sustained proliferative response to E2.  By contrast, the proliferative response exhibited by the mammary epithelium of BN rats was restrained and transitory.  Moreover, the epithelium of BN rats appeared to undergo differentiation in response to E2, as evidenced by production of milk proteins as well as luminal ectasia and associated changes in the extracellular matrix (ECM).  Marked differences in expression of genes that encode proteins with well-defined roles in mammary gland development (Pgr, Wnt4, Tnfsf11, Prlr, Stat5a, Areg, Gata3), differentiation and milk production (Lcn2, Spp1), regulation of extracellular environment (Mmp7, Mmp9), and cell-cell or cell-ECM interactions (Cd44, Cd24, Cd52) were observed.  We propose that these cellular and molecular phenotypes are heritable and may underlie, at least in part, the differences in mammary cancer susceptibility exhibited by ACI and BN rats.

overall_design: Two groups of 17beta-estradiol treated female rats were compared. Five ACI and five BN rats were treated with 17beta-estradiol for 12 weeks. Total RNA was isolated from the mammary glands of these animals, labeled, and hybridized to Affymetrix Rat Genome 230 2.0 Arrays (Affymetrix Inc.). Significantly differentially expressed genes were found between these groups.

first: L

last: Ding

first: C

last: Warren

first: J


title: Identification of genes involved in cell death induced by sodium fluoride in rat oral epithelial cells

status: Public on Jan 09 2014

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
Although an appropriate range of fluoride is thought to be safe and effective, excessive fluoride intake results in toxic effects in either hard tissues of teeth and skeleton or soft tissues of kidney, lung and brain. It is also well known that fluoride at a millimolar range elicits the complex cellular responses such as enzyme activity, signal transduction and apoptosis in many kinds of cells. However, its toxic effects are still unclear.
In this study, to identify genes involved in cell death induced by sodium fluoride (NaF) in rat oral epithelial ROE2 cells, global-scale gene expression analysis was carried out using a GeneChip® system.

overall_design: NaF (2 mM) significantly induced apoptosis accompaning chromatin condensation and caspase-3 activation. Total RNA samples were prepared from the NaF-treated cells, and quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was monitored by an Affymetrix GeneChip® system with a Rat Genome 230 2.0  array. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Tatsuya

last: Yunoki


title: Geriatric muscle stem cells switch reversible quiescence into senescence (Set 4; Bmi1-deficient)

status: Public on Dec 31 2013

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

institute: UPF

summary: Regeneration of skeletal muscle depends on a population of adult stem cells (satellite cells) that remain quiescent throughout life. Satellite cell regenerative functions decline in geriatric satellite cells, compared to old cells are incapable of maintaining their normal quiescent state in muscle homeostatic conditions, and this irreversibly affects their intrinsic regenerative and self-renewal capacities. In geriatric mice, resting satellite cells lose reversible quiescence by switching to an irreversible pre-senescence state, caused by derepression of p16INK4a. Young Bmi1-deficient satellite cells shares similar features.

overall_design: We analyzed the global changes in gene expression occurring within muscle stem cells (satellite cells) in homeostatic conditions during physiological aging.  Pure satellite cell populations from dissociated skeletal muscle from WT and Bmi1-deficient mice were isolated using a well-established flow cytometry protocol gating on integrin a7(+)/CD34(+) (positive selection) and Lin- (CD31, CD45, CD11b, Sca1) (negative selection).

first: Pura

last: Munoz-Canoves


title: Geriatric muscle stem cells switch reversible quiescence into senescence (Set 3; Adult vs. Young)

summary: Regeneration of skeletal muscle depends on a population of adult stem cells (satellite cells) that remain quiescent throughout life. Satellite cell regenerative functions decline with aging. We report that geriatric satellite cells, compared to old and adult cells, are incapable of maintaining their normal quiescent state in muscle homeostatic conditions, and this irreversibly affects their intrinsic regenerative and self-renewal capacities.

overall_design: We analyzed the global changes in gene expression occurring within muscle stem cells (satellite cells) in homeostatic conditions during physiological aging.  Pure satellite cell populations from dissociated skeletal muscle from Young (2-3 months) and Adult (6 months)  mice were isolated using a well-established flow cytometry protocol gating on integrin a7(+)/CD34(+) (positive selection) and Lin- (CD31, CD45, CD11b, Sca1) (negative selection).


title: Transcriptoma analysis of B splenocytes of 3'RR-deficient mice and wt mice

status: Public on Jan 15 2014

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: The IgH 3' regulatory region (3'RR) controls class switch recombination and somatic hypermutation in mice. Similar numbers of B cells are found in spleen of 3'RR-deficient mice and wt mice. We compare their transcriptoma in order to find differences in their maturation status.

overall_design: B splenocytes from four wt mice and four 3'RR-deficient mice are investigated. Splenic B cells are purified with anti-B220-coupled beads.

first: Y

last: Denizot

first: P

last: Barbry

last: LEBRIGAND


title: SMC5/6 facilitates joint molecule resolution and stepwise loss of cohesin to promote meiotic chromosome segregation

status: Public on Dec 27 2013

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

type: Genome binding/occupancy profiling by array

summary: During meiosis, Structural Maintenance of Chromosome (SMC) complexes underpin two fundamental features of meiosis: homologous recombination and chromosome segregation. While meiotic functions of the cohesin and condensin complexes have been delineated, the role of the third SMC complex, Smc5/6, remains enigmatic. Diminished Smc5/6 function causes severe defects in nuclear division, but the underlying causes of these defects remain unclear. Here we identify specific, essential meiotic functions for the Smc5/6 complex in homologous recombination and regulation of cohesin. We show that Smc5/6 is enriched at centromeres and cohesin-association sites where it regulates sister-chromatid cohesion and the timely removal of cohesin from chromosomal arms, respectively.  Smc5/6 also localizes to recombination hotspots, where it promotes normal formation and resolution of joint-molecule intermediates. Furthermore, we find that Smc5/6 specifically promotes resolution of joint molecules via the XPF-family endonuclease, Mus81-Mms4Eme1. We propose that Smc5/6 acts as a chaperone for ‘mitotic’-like recombination processes during meiosis.

overall_design: ChIP-chip was used to compare Smc5 localization in wild-type and spo11 strains

first: Alice

last: Copsey

first: Shangming

last: Tang

first: Philip

middle: W

last: Jordan

first: Hannah

last: Blitzblau

first: Sonya

last: Newcombe

first: Nils

last: Lambacher

first: Andrew

last: Chan

first: Louise

last: Newnham

first: Zhaobo

first: Alex

last: Herbert

first: Prakash

last: Arumugam

first: Neil

last: Hunter

first: Eva

last: Hoffmann


title: Geriatric muscle stem cells switch reversible quiescence into senescence

first: Eusebio

last: Perdiguero

summary: Regeneration of skeletal muscle depends on a population of adult stem cells (satellite cells) that remain quiescent throughout life. Satellite cell regenerative functions decline with aging and in progeric conditions. Here we show that geriatric satellite cells, compared to old cells, are incapable of maintaining their normal quiescent state in muscle homeostatic conditions, and this irreversibly affects their intrinsic regenerative and self-renewal capacities.

overall_design: Refer to individual Series

first: Pura

last: Munoz-Canoves


title: Zrf1 is required to establish and maintain neural progenitor identity (mRNA array)

status: Public on Dec 21 2013

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

institute: Centre for Genomic Regulation

summary: Our work aims  to characterize the role of Zrf1 in the generation and maintenance of neural progenitor cells (NPCs)

overall_design: Gene expression profile of shCtrl and shZrf1 cells during generation of RGC-like NPC from ESC at day 6 of neural induction. Cells were grown according to this protocol: Bibel et al, Nat Prot., 2007

first: Luigi

last: Aloia


title: Expression data from Sar1 isoform overexpressing rat hepatoma cell lines

status: Public on Dec 16 2013

city: London

first: Carol

last: Shoulders

address: Charterhouse Square

department: Centre for Endocrinology

institute: QMUL

summary:
The endoplasmic reticulum (ER) is the site of secretory lipoprotein production and de novo cholesterol synthesis, yet little is known about how these activities are coordinated with each other, or with the activity of the COPII machinery, which transports ER cargo to the Golgi. The Sar1B component of this machinery is mutated in Chylomicron Retention Disorder, establishing that this Sar1 isoform secures delivery of dietary lipids into the circulation.
We used microarrays to investigate the effect of overexpression of Sar1 isoforms and a constitutively active mutant form of Sar1B, Sar1B:H79G, on global gene expression in rat hepatoma cell line, McArdle RH7777 and identified a strong down-regulation of cholesterol biosynthetic gene mRNA expression in the Sar1B:H79G-, but not the wild-type Sar1A- or Sar1B-overexpressing cell lines.

overall_design: RNA was extracted from cell cultures of control McArdle RH7777, and transgenic lines overexpressing human Sar1-isoforms: one for Sar1A, two for Sar1B and two expressing a constitutively active mutant form of Sar1B, Sar1B:H79G, that cannot complete GTP hydrolysis, and hybridized on Affymetrix GeneChip Rat Genome 230 2.0 arrays.

first: Bethan

last: Jones


title: Behaviorally activated mRNA expression profiles produce signatures of learning and enhanced inhibition in aged rats with preserved memory

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

institute: Johns Hopkins Univ. School of Medicine

summary: Aging is often associated with cognitive decline, but many elderly individuals maintain a high level of function throughout life. Here we studied outbred rats, which also exhibit individual differences across a spectrum of outcomes that includes both preserved and impaired spatial memory. Previous work in this model identified the CA3 subfield of the hippocampus as a region critically affected by age and integral to differing cognitive outcomes. Earlier microarray profiling revealed distinct gene expression profiles in the CA3 region, under basal conditions, for aged rats with intact memory and those with impairment. Because prominent age-related deficits within the CA3 occur during neural encoding of new information, here we used microarray analysis to gain a broad perspective of the aged CA3 transcriptome under activated conditions. Behaviorally induced CA3 expression profiles differentiated aged rats with intact memory from those with impaired memory. In the activated profile, we observed substantial numbers of genes (greater than 1000) exhibiting increased expression in aged unimpaired rats relative to aged impaired, including many involved in synaptic plasticity and memory mechanisms. This unimpaired aged profile also overlapped significantly with a learning induced gene profile previously acquired in young adults. Alongside the increased transcripts common to both young learning and aged rats with preserved memory, many transcripts behaviorally-activated in the current study had previously been identified as repressed in the aged unimpaired phenotype in basal expression. A further distinct feature of the activated profile of aged rats with intact memory is the increased expression of an ensemble of genes involved in inhibitory synapse function, which could control the phenotype of neural hyperexcitability found in the CA3 region of aged impaired rats. These data support the conclusion that aged subjects with preserved memory recruit adaptive mechanisms to retain tight control over excitability under both basal and activated conditions.

overall_design: RNA profiles from cognitively unimpaired and impaired aged rats were compared under 2 conditions: spatial learning task and a non-spatial learning task.

first: Rebecca

middle: P

last: Haberman

first: Ming-Teng

last: Koh

first: Michela

last: Gallagher


title: Expression data from rat androgenetic embryonic stem cells

status: Public on Dec 15 2013

city: Beijing

first: Wei

last: Li

address: Beichen West Road

department: State key lab of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
The rat androgenetic embryonic stem cells (RahES cells) have only 21 chromosomes. However, they express pluripotency markers, differentiate into three germ layer cells as well as contribute to the germline as the normal diploid rat ES cells. Moreover, the RahES cells can produce fertile rats after intracytoplasmic injection into oocytes, thus are capable to transmit genetic modifications to offspring.
We used microarrays to detail the global gene expression profile of RahES cells and identified distinct classes of up-regulated and down-regulated genes compared with the expression of normal diploid rat ES cells.

overall_design: Two different RahES cell lines, one diploid rat ES cell line and round sperm cells were selected for RNA extraction and hybridization on Affymetrix Chip.


title: Transcriptional profiling of retinal progenitors, exposed to endothelial cells or EGF

status: Public on Dec 14 2013

city: Omaha

first: Iqbal

last: Ahmad

state: Nebraska

address: 985840 Nebraska Medical Center

department: Ophthalmology and Visual Sciences

institute: University of Nebraska Medical Center

summary:
Retinal histogenesis occurs over an extended period, which necessitates retinal progenitors to self-renew to sustain the temporal generation of diverse cell types.
Embryonic day 18 retinal cells showed self-renewal properties such as clonal propagation without compromising multipotentiality when grown in the presence of endothelial cell conditioned medium and not EGF alone.

overall_design: Timed pregnant Sprague Dawley (Embryonic day 18) rats were obtained from Charles River Laboratories. Embryos were harvested and enucleated. Retinae were dissected out and dissociated by trypsin-EDTA followed by manual trituration. The retinal cells  obtained from 10 embryos were cultured  in the presence of EGF (condition1) or EGF and Endothelial cell conditioned medium (condition 2) to obtain neurospheres. To get biological replicate for both conditions, another batch of embryos were pooled and subjected to neurosphere formation. Total RNA was extracted from both conditions using Qiagen RNeasy mini kit following manufacturer's protocol. The RNA was subjected to microarray analysis using Affymetrix Rat 230 2.0 platform  by UNMC microarray Core facility. RMA analysis was performed using Genepattern software. Log2 transformed values of each condition was used to obtain fold change of specific genes.

first: Sowmya

last: Parameswaran


title: Gene expression profiles in the spinal cord below the lesion level and influence of treadmill locomotor training

status: Public on Nov 27 2013

city: Suwon

first: Hae young

last: Shin

address: Wonchoen dong

department: Brain disease research center

institute: Hae young Shin

summary: Traumatic spinal cord injury (SCI) often leads to loss of locomotor function. Neuroplasticity of spinal circuitry underlies some functional recovery and therefore represents a therapeutic target to improve locomotor function following SCI. However, the cellular and molecular mechanisms mediating neuroplasticity below the lesion level are not fully understood. The present study performed a gene expression profiling in the rat lumbar spinal cord at 1 and 3 weeks after contusive SCI at T9. The below-level gene expression profiles were compared with those of animals that were subjected to treadmill locomotor training.

overall_design: Rat lumbar spinal cords were taken for the microarray analysis at 1 and 3 weeks after contusive spinal cord injury at the T9 level. Another group of rats received treadmill locomotor training for 3 weeks, and theirs spinal cords were harvested for the microarray. The changes in gene expression after spinal cord injury were analyzed at the two time points. The influence of treadmill locomotor training was evaluated by comparing gene expression profiles between animals with or without treadmill training.

first: Hae

middle: Y

first: Hyosil

last: Kim

first: Min

last: Kwon

first: Dong

last: Hwang

first: KiYoung

last: Lee

first: Byung


title: Transcriptional profiling of macrophage plasticity following recovery from Lipopolysaccharide (LPS) tolerance

status: Public on Dec 06 2013

city: Cork

first: Christine

middle: Elizabeth

last: O'Carroll

address: University College Cork

department: Biochemistry

country: Ireland

institute: Alimentary Pharmabiotic Centre, University College Cork

summary: To investigate the plasticity of Lipolysaccharide (LPS) tolerance, we employed microarray profiling to analyse the gene expression profile in macrophage. Four macrophage populations were induced; Untreated macrophages (Control group), Acute response to LPS (LPS activation group), LPS tolerance (T – Tolerant group) and recovered (R = recovered macrophage group) Using transcriptional analysis we demonstrate that recovery from LPS tolerance (R – Recovery), as defined by cytokine gene expression, is associated with a global change in the transcriptional profile of macrophage. This data confirms that LPS tolerance is a transient state which results in induction of novel hybrid macrophage activation state with a unique transcriptional signature.

overall_design: Bone marrow derived macrophages were polarised into three activation states; Acute response to LPS (A), LPS tolerant (T) and recovered (R). Gene expression was measured at 4 hours post stimulation with LPS. Three independent experiments were performed to measure gene expression changes between each macrophage group.

first: Ruiadhrí

last: Carmody

first: Ailís

last: Fagan


title: Expression signatures in heart tissues of mice simulating posttraumatic stress disorder (PTSD)

status: Public on Dec 04 2013

city: Seattle

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

type:
Expression profiling by array
Non-coding RNA profiling by array

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae


title: Gene expression signatures in heart tissues of mice simulating posttraumatic stress disorder (PTSD) [Study2]

summary: Using a PTSD mouse model, we investigated the longitudinal transcriptomic changes in heart tissues after the exposure to stress through intimidation

overall_design: We designed our time-course study (Study II) with three experimental conditions where we varied the length of time that subservient mice were exposed to aggressor mice with the same length of rest time after the exposure (1day).  The conditions included were 1day-exposure (T1R1), 2day-exposure (T2R1) and 3day-exposure (T3R1).

first: Kai

last: Wang

first: Inyoul

first: Rasha

last: Hammamieh

first: David

last: Baxter

first: Kelsey

last: Scherler

first: Alton

last: Etheridge

first: Yue

last: Yuan

first: Sara

last: McClarty

first: Alena

last: Kulchenko

first: Aarti

last: Gautam

first: Seid

last: Muhie

first: Nabarun

last: Chakraborty

first: Marti

last: Jett

last: Galas

first: Leroy

last: Hood


title: Exposure to Cobalt Causes Transcriptomic and Proteomic Changes in Two Rat Liver Derived Cell Lines

status: Public on Dec 01 2013

city: Fort Detrick

first: Matthew

last: Permenter

address: 568 Doughten Dr

institute: US Army Center for Environmental Health Research

summary: Cobalt is a transition group metal present in trace amounts in the human diet, but in larger doses it can be acutely toxic or cause adverse health effects in chronic, long term exposures. Its use in many industrial processes and alloys worldwide presents opportunities for occupational exposures, as well as exposures to military personnel. While the toxic effects of cobalt have been widely studied, the exact mechanisms of toxicity remain unclear. In order to further elucidate these mechanisms and identify potential biomarkers of exposure or effect, we exposed two rat liver-derived cell lines, H4-II-E-C3 and MH1C1, to two concentrations of cobalt chloride. We examined changes in gene expression using DNA microarrays in both cell lines and examined changes in cytoplasmic protein abundance in MH1C1 cells using mass spectrometry. We chose to closely examine differentially expressed genes and proteins changing in abundance in both cells lines in order to remove cell line specific effects. We identified enriched pathways, networks, and biological functions using commercial bioinformatic tools and manual annotation.  Many of the genes, proteins, and pathways modulated by exposure to cobalt appear to be due to an induction of a hypoxic-like response and oxidative stress. Genes that may be differentially expressed due to a hypoxic-like response are involved in Hif-1α signaling, glycolysis, gluconeogenesis, and other energy metabolism related processes. Gene expression changes linked to oxidative stress are also known to be involved in the NRF2-mediated response, protein degradation, and glutathione production. Using microarray and mass spectrometry analysis, we were able to identify modulated genes and proteins, further elucidate the mechanisms of toxicity of cobalt, and identify biomarkers of exposure and effect in vitro, providing targets for focused in vitro studies.

overall_design: H4-II-E-C3 and MH1C1 cells were treated with two doses of CoCl2 for 24 h in serum free DMEM. For each condition, we ran four biological replicates, with each replicate having its own untreated control. Therefore, this study contains 24 samples.

first: William

middle: E

last: Dennis

first: Thomas

last: Sutto

middle: A

last: Jackson

first: John

last: Lewis

first: Jonathan

last: Stallings


title: Genome-Wide Gene Expression Profiling of Spinal Cord Injury in Rat

status: Public on Nov 15 2013

city: Toronto

first: Mahmood

last: Chamankhah

state: Ontario

address: 399 Bathurst Street

institute: University Health Network

summary: The aneurysm clip impact-compression model of spinal cord injury (SCI) in animals mimics the primary mechanism of SCI in human, i.e. acute impact and persisting compression; and its histo-pathological and behavioural outcomes are extensively similar to the human SCI. In order to understand the distinct molecular events underlying this injury model, an analysis of global gene expression of the acute, subacute and chronic stages of a moderate to severe injury to the rat spinal cord was conducted using a microarray gene chip approach.

overall_design: Rat thoracic spinal cord (T7) was injured using aneurysm clip impact-compression injury model and the epicenter area of injured spinal cord was isolated for RNA extraction and processing and hybridization on Affymetrix GeneChip arrays.

first: Eftekhar

last: Eftekharpour

first: Soheila

last: Karimi-Abdolrezaee

first: Paul

middle: C

last: Boutros

first: Michael

last: Fehlings


title: The transcriptomic response of rat hepatic stellate cells to endotoxin: implications for hepatic inflammation and immune regulation

status: Public on Oct 31 2013

city: Pittsburgh

first: Stephen

middle: Alan Kenneth

last: Harvey

state: PA

address: 203 Lothrop St

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

summary: Located in the perisinusoidal space of Disse, hepatic stellate cells (HSCs) communicate with all other liver cell types by physical association and / or by producing cytokines and chemokines. In liver disease and folllowing liver transplantation, elevated levels of endotoxin (bacterial lipopolysaccharide: LPS) stimulate HSCs to produce increased amounts of cytokines and chemokines. Transcriptomic analysis of cultured HSCs stimulated with LPS yields a survey of expression changes which potentially modulate the hepatic inflammatory and immune responses.

overall_design:
In two independent experiments, rat HSCs were cultured with or without 10 ng/ml LPS for 1h and 24h, then harvested for microarray analysis (i.e., 8 samples).
In the first of these experiments, cells also were also harvested after 3, 6 and 12 hours of LPS treatment, for a total of 11 samples.

first: Anil

last: Dangi

first: Ashish

last: Tandon

first: Chandrashekhar

middle: R

last: Gandhi


title: Gene expression signatures in heart tissues of mice simulating posttraumatic stress disorder (PTSD) [Study1]

first: Ji-Hoon

last: Cho

overall_design: We designed our initial study (Study I) with four experimental conditions where we varied the length of time that subservient mice were exposed to aggressor mice and the length of rest time after the exposure.  The conditions included were short exposure-short rest (T5R1-T indicates the number of days of trauma exposure; R indicates the number of days of rest after exposure), short exposure-long rest (T5R10), long exposure-short rest (T10R1) and long exposure-long rest (T10R42)

first: Kai

last: Wang

first: Inyoul

last: Lee

first: Rasha

last: Hammamieh

first: David

last: Baxter

first: Kelsey

last: Scherler

first: Alton

last: Etheridge

first: Yue

last: Yuan

first: Sara

last: McClarty

first: Alena

last: Kulchenko

first: Aarti

last: Gautam

first: Seid

last: Muhie

first: Nabarun

last: Chakraborty

last: Jett

middle: J

last: Galas


title: Identifying an Apical Ectodermal Ridge (AER) signature in embryonic day 11.5 mouse forelimb.

city: Barcelona

first: William

last: Keyes

address: Carrer del Dr. Aiguader, 88

department: Gene Regulation, Stem Cells and Cancer

institute: Centre for Genomic Regulation (CRG)

summary: The apical ectodermal ridge (AER) is a transient ectodermal population of cells that defines the dorso-ventral border of the developing limb bud. It functions as a major signaling centre that, through the secretion of various growth factors including FGF8, instructs the growth and patterning of the developing limb. We have identified that the AER expresses markers of cellular senescence and wanted to examine if there was any overlap with oncogene-induced senescence, an adult form of senescence induced in premalignant lesions. To achieve this, we microdissected the AER from embryonic day 11.5 mouse embryos. In addition, we collected the surface ectoderm from the proximal limb bud, that was not senescent and profiled both populations, to identify those genes that are enriched in the AER

overall_design: The AER was microdissected from embryonic day 11.5 mouse forelimb. Surface ectoderm from the posterior limb was used as a comparative control. Samples from 2-3 mice were pooled for each replicate, for 3-4 replicates.

first: Bill

first: Mekayla

last: Storer


title: Geriatric muscle stem cells switch reversible quiescence into senescence (Set 2; Old/Geriatric vs. Young and SAMR1 vs. SAMP8)

first: Eusebio

last: Perdiguero

summary: Regeneration of skeletal muscle depends on a population of adult stem cells (satellite cells) that remain quiescent throughout life. Satellite cell regenerative functions decline with aging and in progeric conditions. Here we report that geriatric satellite cells, compared to old cells, are incapable of maintaining their normal quiescent state in muscle homeostatic conditions, and this irreversibly affects their intrinsic regenerative and self-renewal capacities.

overall_design: We analyzed the global changes in gene expression occurring within muscle stem cells (satellite cells) in homeostatic conditions during physiological aging and progeria.  Pure satellite cell populations from dissociated skeletal muscle from Young (2-3 months), Old (22-24 months), Geriatric (28-30 months), SAMR1 and SAMP8 mice were isolated using a well-established flow cytometry protocol gating on integrin a7(+)/CD34(+) (positive selection) and Lin- (CD31, CD45, CD11b, Sca1) (negative selection).

first: Pura

last: Munoz-Canoves


title: The gene expression analysis of the spinal cord and skeletal muscle of SBMA (Spinal Bulbar Muscular Atrophy) model mice with or without pioglitazone (PG) treatment

status: Public on Oct 29 2013

city: Nagoya

first: Madoka

last: Iida

state: Aichi

address: 65 Tsurumai-cho Showa-ku

department: Neurology department

institute: Nagoya University

summary:
To identify the gene expression changes by administering PG to SBMA model mice, we prepared total RNA samples from the spinal cords and skeletal muscles of transgenic mice carrying a full-length human AR with 97 CAGs (AR-97Q) that were treated with or without PG. We used AR-97Q (Line #7-8) male mice because they show progressive muscular atrophy and weakness as well as SBMA-like pathology such as the accumulation of the pathogenic androgen receptor in the nucleus of motor neurons.
Using microarray analysis, we identified the genes with significantly altered expression of AR-97Q mice by PG treatment.

overall_design: For non-treated and PG-treated groups, we examined the male mice at 13 weeks of age. RNA from the total spinal cord and skeletal muscle was isolated from three mice of each group.

first: Masahisa

last: Katsuno

first: Gen

last: Sobue