title: Transcriptional Biomarkers to Predict Female Mouse Liver Tumors in Rodent Cancer Bioassays - A 26 Chemical Set

first: Russell

middle: Scott

last: Thomas

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

summary: Two-year rodent bioassays play a central role in evaluating both the carcinogenic potential of a chemical and generating quantitative information on the dose-response behavior for chemical risk assessments. The bioassays involved are expensive and time-consuming, requiring nearly lifetime exposures (two years) in mice and rats and costing $2 to $4 million per chemical. Since there are approximately 80,000 chemicals registered for commercial use in the United States and 2,000 more are added each year, applying animal bioassays to all chemicals of concern is clearly impossible. To efficiently and economically identify carcinogens prior to widespread use and human exposure, alternatives to the two-year rodent bioassay must be developed. In this study, animals were exposed for 13 weeks to 10 chemicals that were positive for liver tumors in the two-year rodent bioassay, 14 chemicals that were negative for liver tumors, and two chemicals that produced an equivocal response. Matched vehicle control groups were run concurrently with each chemical treatment.  Gene expression analysis was performed on the livers of the animals to assess the potential for identifying gene expression biomarkers and signaling pathways that can predict tumor formation in a two-year bioassay following a 13 week exposure.

overall_design: Five-week-old female B6C3F1 mice were exposed for 13 weeks to 26 chemicals. The chemical and dose information are provided with the individual sample annotations. With each chemical treatment, a matched vehicle control group was run concurrently with the exposure. A subset of five chemicals, methylene chloride, naphthalene, 1,2,3-trichloropropane, propylene glycol mono-t-butyl ether, and 1,4-dichlorobenzene, were performed in a five-point dose response with matched control groups. The concentrations for these exposures overlapped those in the original cancer bioassay. Gavage exposures were administered 5 days per week and feed exposures were provided 7 days per week. For inhalation exposures, mice were exposed 6 hr per day, 5 days per week. After 13 weeks, animals were euthanized and livers were collected. The right, caudate and median liver lobes were minced together and used for microarray analysis.  Microarray analysis was performed on the livers of three to five mice per treatment group.

middle: S


title: KDM7 is a dual demethylase for histone H3 lysines 9 and 27 and functions in brain development

status: Public on Mar 01 2010

city: Fukuoka

first: Yuichi

last: Tsukada

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu university

summary: The roles of histone demethylase KDM7 in gene expression were analyzed by gene expression profiling experiments with the mouse neuroblastoma cell line Neuro2A.

overall_design:
In order to examine the effect of KDM7 in gene expression, we generated stable KDM7 knockdown cell lines in the mouse neuroblastoma cell line Neuro2A. Total RNAs were extracted from 5 cell lines and analyzed for gene expression profiles using the Affymetrix platform.

Cell lines:
Parental cells: Neuro2A (N2A)
empty vector: Neuro2A transfected with empty vector
EGFP KD: Neuro2A transfected with vector for EGFP knock down
KDM7 KD1: Neuro2A transfected with vector 1 for KDM7 knock down
KDM7 KD2: Neuro2A transfected with vector 2 for KDM7 knock down

first: Yu-ichi


title: Expression data from side population subfraction hematopoietic stem cells

city: Houston

first: Grant

middle: Anthony

last: Challen

state: TX

address: 1 Baylor Plaza

department: Center For Cell And Gene Therapy

country: USA

institute: Baylor College of Medicine

summary:
The traditional view of hematopoiesis has been that all the cells of the peripheral blood are the progeny of a unitary homogeneous pool of hematopoietic stem cells (HSCs).  Recent evidence suggests that the hematopoietic system is actually maintained by a consortium of HSC subtypes with distinct functional characteristics.  We show here that myeloid-biased HSCs (My-HSCs) and lymphoid-biased (Ly-HSCs) can be purified according to their capacity for Hoechst dye efflux in combination with canonical HSC markers.
We used microarray expression profiling to determine the transcriptional profiles of myeloid-biased lower-SP HSCs and lymphoid-biased upper-SP HSCs

overall_design: Three biological replicates were analyzed for each HSC subpopulation.  Lower-SP and upper-SP HSCs were purified from three pools of mice on separate days.  HSCs were further purified with the addition of canonical HSC makers; Sca-1+ c-Kit+ Lineage-

middle: A

first: Nathan

middle: C

last: Boles

first: Stuart

middle: M

last: Chambers

first: Margaret

last: Goodell


title: Genome-wide comparison between IL-17 and combined TNF-alpha/ IL-17 induced genes in primary murine hepatocytes

city: Freiburg

first: Irmgard

last: Merfort

state: BW

address: Stefan-Meier-Str. 19

department: Department of Pharmaceutical Biology and Biotechnology

country: Germany

institute: University of Freiburg - Institute of Pharmaceutical Science

summary:
Cytokines such as TNF-alpha and IL-1beta are known for their contribution to inflammatory processes in liver . In contrast, the cytokine IL-17 has not yet been assigned a role in liver diseases. IL-17 can cooperate with TNF-alpha to induce a synergistic response on several target genes in different cell lines, but no data exist for primary hepatocytes. To enhance our knowledge on the impact of IL-17 alone and combined with TNF-alpha in primary murine hepatocytes a comprehensive microarray study was designed. IL-1beta was included as this cytokine is suggested to act in a similar manner as the combination of TNF-alpha and IL-17, especially with respect to its role in mRNA stabilization. Results: The present microarray analysis demonstrates that primary murine hepatocytes responded to IL-17 stimulation by upregulation of chemokines and genes, which are functionally responsible to increase and sustain inflammation. Cxcl2, Nfkbiz and Zc3h12a were strongly induced, whereas the majority of the genes were only very moderately upregulated.
Promoter analysis revealed involvement of NF-kappaB in the activation of many genes. Combined stimulation of  TNF-alpha/IL-17 resulted in enhanced induction of gene expression, but significantly synergistic effects could be applied only to a few genes, such as Nfkbiz, Cxcl2, Zc3h12 and Steap4. Comparison of the gene expression profile obtained after stimulation of TNF-alpha/IL-17 versus IL-1 proposed a IL-1beta-like effect of the latter cytokine combination. Moreover, evidence was provided that modulation of mRNA stability may be a major mechanism by which IL-17 regulates gene expression in primary hepatocytes. This assumption was exemplarily proven for Nfkbiz mRNA for the first time in hepatocytes. Our studies also suggest that RNA stability can partially be correlated to the existence of AU rich elements, but further mechanisms like the RNase-activity of the upregulated Zc3h12a have to be considered. Conclusions: Our microarray analysis gives new insights in IL-17 induced gene expression in primary hepatocytes highlighting the crosstalk with the NF-kappaB signalling pathway. Gene expression profile suggests IL-17 a role in sustaining liver inflammatory processes most likely by RNA stabilization. Altogether, our results provide evidence that IL-17 alone and in concert with TNF-alpha may play a role in inflammatory liver diseases.

overall_design: Primary murine hepatocytes of three animals stimulated for 1 or 4h by TNF-alpha, IL-1beta, IL-17 or TNF-alpha followed by IL-17 were used for microarray analysis.

first: Titus

last: Sparna

first: Julia

last: Retéy

first: Kathrin

last: Schmich

first: Ute

last: Albrecht

first: Katrin

last: Naumann

first: Sabine

last: MacNelly

first: Fritz

last: von Weizsäcker

first: Norbert

last: Gretz

first: Hans-Peter

last: Fischer

first: Jens

last: Timmer

first: Johannes

last: Bode


title: Expression data from lung of septic PPTA knockout mouse

status: Public on Mar 04 2010

city: Singapore

first: Akhil

last: Hegde

address: Centre for life Sciences,#03-06, 28 Medical Drive

department: Pharmacology

country: Singapore

institute: National University of Singapore

summary: In this study, we have explored microarray-based differential gene expression profile in mouse lung tissue 8 h after inducing polymicrobial sepsis and the effect of preprotachykinin-A (PPTA) gene deletion. A range of genes differentially expressed (> 2-fold) in microarray analysis was assessed, PPTA-knockout septic mice with their respective sham controls.

overall_design:
We used microarrays to detail the global gene expression underlying sepsis in mice lacking the gene for substance P and identified distinct classes of up-regulated genes during this process.
Lung samples from wild-type or PPTA-knockout mice were selected at 8 h after cecal ligation and puncture (CLP) or sham surgery for RNA extraction and hybridization to Affymetrix microarrays. Triplicates were performed for each condition.

first: Madhav

last: Bhatia


title: Foxa2 programs Th2-cell mediated innate immunity in the developing lung.

status: Public on Feb 25 2010

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Deletion of the gene encoding Foxa2, a winged helix transcription factor selectively expressed in respiratory epithelial cells, caused spontaneous pulmonary eosinophilic inflammation and goblet cell metaplasia.  Loss of Foxa2 induced the recruitment and activation of myeloid dendritic cells (mDCs) and Th2 cells in the lung, and was associated with the increased production of T helper 2 (Th2) cytokines and chemokines.  mRNA microarray analysis demonstrated that deletion of Foxa2 induced the expression of a number of mRNAs regulating pulmonary dendritic cell activation, Th2 mediated inflammation, and goblet cell differentiation.  The spontaneous pulmonary inflammation and goblet cell metaplasia caused by loss of Foxa2 was inhibited by treatment of newborn Foxa2∆/∆ mice with monoclonal IL-4Ralpha antibody.  Expression of Foxa2 in non-ciliated secretory cells (Clara cells) in vivo inhibited goblet cell differentiation induced by pulmonary allergen exposure.  The respiratory epithelium plays a central role in the regulation of Th2-mediated inflammation and innate immunity in the developing lung in a process regulated by Foxa2.

overall_design: To investigate the role of Foxa2 and its downstream targets associated with the Th2 inflammation and goblet cell hyperplasia, RNAs were isolated from the lungs of Foxa2-/- and control littermates at PN15.  Lung cRNA was hybridized to the murine genome MOE430 V2 chips.

first: Gang

last: Chen

first: Huajing

last: Wan

first: Fengming

last: Luo

first: Liqian

last: Zhang

first: Ian

last: Lewkowich

first: Marsha

last: Wills-Karp

first: Jeffrey

last: Whitsett


title: Gene Expression of ApoE Null and ApoE Null/RAGE Diabetic and Non-diabetic Mice

city: New York

first: Ann

middle: Marie

last: Schmidt

state: NY

department: Department of Surgery

institute: Columbia University

summary:
The multi-ligand Receptor for AGE (RAGE) contributes to atherosclerosis in apolipoprotein (ApoE) null mice in both the non-diabetic and diabetic states. Previous studies using soluble RAGE, the extracellular ligand-binding domain of RAGE, or homozygous RAGE null mice showed that blockade or deletion of RAGE resulted in marked reduction in atherosclerotic lesion area and complexity compared to control animals. In parallel, significant down-regulation of inflammatory mediators and matrix metalloproteinases was evident in ApoE null mice aortas devoid of RAGE compared to those of ApoE null RAGE-expressing mice. Although these findings suggested that RAGE triggered pro-atherogenic mechanisms via regulation of inflammatory gene expression, these studies did not reveal the broader pathways by which RAGE contributed to atherosclerosis in ApoE null mice.
Therefore, we performed Affymetrix gene expression arrays on aortas of non-diabetic and diabetic ApoE null mice expressing RAGE or devoid of RAGE at nine weeks of age, as this reflected a time point at which frank atherosclerotic lesions were not yet present, but, that we would be able to identify the genes likely involved in diabetes- and RAGE-dependent atherogenesis. The comparisons were as follows: 1. diabetic ApoE null relative to non-diabetic ApoE null; 2. non-diabetic ApoE null / RAGE null relative to non-diabetic ApoE null; 3. diabetic ApoE null / RAGE null relative to non-diabetic ApoE null /  RAGE null; and 4. diabetic ApoE null / RAGE  null relative to diabetic ApoE null aorta.
 Our data reveal that there is very little overlap of the genes which are differentially expressed both in the onset of diabetes in ApoE null mice, and in the effect of RAGE deletion in diabetic ApoE null mice. We next performed a Pathway-Express analysis to determine the pathways that were most associated with the onset of diabetes in ApoE null mice and the effect of RAGE gene deletion in diabetic ApoE null mice. Rigorous statistical analysis was undertaken and revealed that the transforming growth factor-β pathway (tgf-β) and focal adhesion pathways might be expected to play a significant role in both the mechanism by which diabetes facilitates the formation of atherosclerotic plaques in ApoE null mice, and the mechanism by which deletion of RAGE ameliorates this effect. We focused on three genes of the tgf-β family which were found to be up-regulated in diabetic vs. non-diabetic ApoE null aorta, and which were reduced by deletion of RAGE. These included: thrombospondin1 (Thbs1), transforming growth factor-β2 (tgf-β2) and rho-associated kinase (ROCK1). Real-time quantitative polymerase chain reaction and Western blotting experiments were performed, as well as ROCK1 activity assays in mouse aorta, and validated the findings of the Affymetrix gene array. Further, confocal microscopy revealed that a principal cell type in the ApoE null aorta expressing these factors was the vascular smooth muscle cell. Our data suggest the novel finding that the observed reduction of accelerated atherosclerosis in diabetic ApoE null / RAGE null vs. diabetic ApoE null mice occurs, all or in part, through the ROCK1 branch of the TGF-β pathway. We have inferred a detailed mechanism for this process.
Taken together, these data suggest that suppression of ROCK1 activity in the atherosclerosis-vulnerable vessel wall, especially in diabetes, but in non-diabetes as well, may underlie the beneficial effects of RAGE antagonism and genetic deletion in murine models. These findings highlight logical and novel targets for therapeutic intervention in cardiovascular disease and diabetes.

overall_design:
1. diabetic ApoE null relative to non-diabetic ApoE null; 2. non-diabetic ApoE null / RAGE null relative to non-diabetic ApoE null; 3. diabetic ApoE null / RAGE null relative to non-diabetic ApoE null /  RAGE null; and 4. diabetic ApoE null / RAGE  null relative to diabetic ApoE null aorta.

There were 4 mice in each group initially. However there are only 3 non-diabetic ApoE null /  RAGE null mice  in the final experimental sample in group 3 due to a failure to generate cRNA from that sample. All samples were normalized to remove chip-dependent regularities using the RMA method. Chips and controls at each combination of  genotype and disease sate were normalized together. The statistical significance of  differential expression was calculated using the empirical Bayesian LIMMA (LInear Model for MicroArrays) method  A cut-off B>0 was used for the statistical significance of gene expression.

first: De-xiu

last: Bu

first: Vivek

last: Rai

first: Xiaoping

last: Shen

first: Rosa

last: Rosario

last: Lu

first: Shi-Fang

last: Yan

first: Richard

last: Friedman

first: Ann-Marie


title: Subtle variations in Pten dose determine cancer susceptibility: Gene expression profiling of a Ptenhy/+ mouse model

status: Public on Feb 15 2010

city: Cambridge

first: Jiangwen

state: MA

address: 7 Divinity Ave

department: FAS Center for Systems Biology

institute: Harvard University

summary:
Subtle variations in Pten dose determine cancer susceptibility: Gene expression profiling for MEF cells from a Ptenhy/+ mouse model.
We have analyzed the survival and tumor spectrum in a population of Pten ‘hypermorphic’ mice (Ptenhy/+), which express approximately 80% of total Pten protein. Notably, the Ptenhy/+ developed a spectrum of tumors of variable latencies, with breast tumors occurring at the highest penetrance. Surprisingly, all breast tumors analyzed retain two intact copies of Pten, and maintain Pten protein levels above that observed in heterozygosity. Importantly, subtle down-regulation of Pten was found to alter the expression profile of genes involved in cell proliferation. Taken together, our findings support the notion that initiation of tumorigenesis can occur in the absence of genetic hits, thereby questioning the uniqueness of a saltatory model for cancer susceptibility.
In order to understand whether subtle variations in Pten level may affect pathways involved in tumorigenesis, we analyzed the genome-wide expression profile of Ptenhy/+ mouse embryonic fibroblasts (MEFs).

overall_design: In the Ptenhy/+ mouse model, mice are born with approximately 80% of total Pten protein and are viable and normally fertile. To decrease the expression level of Pten below homozygosity, we targeted intron 3 of Pten with a neomycin (Neo) cassette, under the control of the strong CMV promoter, thereby taking advantage of transcriptional interference. Next, we intercrossed Pten hy/+ mice with Pten+/- mice to generate cohorts of hypomorphic littermate mice with decreasing levels of Pten expression as follows: Ptenwt > Ptenhy/+ > Pten+/- >Ptenhy/- mice littermates. To preserve a constant 129/C57BL/6 mixed genetic background, we have crossed Pten hy/+ mice with Pten +/- for more than seven generations prior to analysis.  As expected, Ptenhy/+ mouse embryonic fibroblasts (MEFs) display a level of Pten protein below Ptenwt and above Pten+/- .

first: Andrea

last: Alimonti

first: Arkaitz

last: Carracedo

first: John

middle: G

last: Clohessy

first: Pier

middle: P

last: Pandolfi


title: Arx acts as a key selector gene of the ventral telencephalon mainly through its repression transcriptional activity

status: Public on Feb 26 2010

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: The homeobox containing gene Arx is expressed during ventral telencephalon development and it is required for correct GABAergic interneuron tangential migration from the ganglionic eminences to the olfactory bulbs, cerebral cortex and striatum. Its human ortholog is associated with a variety of neurological clinical manifestations whose syntoms are compatible with a loss of cortical interneurons and altered basal ganglia related-activities in humans. Herein, we reported the identification by global expression profiling of a group of genes whose expression is consistently altered in Arx mutant ganglionic eminences. Following analysis revealed the striking ectopic expression in the ganglionic eminences of a number of genes normally not, or only marginally, expressed in the ventral telencephalon. Among them, we functionally analyzed Ebf3, whose ectopic expression in ventral telencephalon is preventingneuronal tangential migration. Further, we showed that Arx is sufficient to repress Ebf3 endogenous expression and that its silencing in Arx mutant tissue might marginally rescue tangential cell movements. Together, these data provide an initial analysis of the molecular pathways regulated by Arx and how their networking might regulate those specific cellular processes during telencephalon development strongly altered by loss of Arx.

overall_design: Three timed-pregnant Arx heterozygous dams crossed with C57Bl/6 males were sacrificed at E14.5, the embryos harvested and placed into cold PBS. After brain isolarion, meninges and olfactory bulbs were removed, and the ventral telencephalon separated from the overlying cerebral cortex. The same procedure was repeated for 5 wt and 5 Arx mutant embryos.

first: Gaia

last: Colasante

first: Alessandro

last: Sessa

first: Stefania

last: Crispi

first: Patrick

last: Collombat

first: Vania

last: Broccoli


title: LKR13-Kras-WT1-KO

city: Stanford

last: Sweet-Cordero

state: CA

address: CCSR-1215B, 269 Campus Dr

department: Pediatrics

institute: Stanford University

summary:
K-ras is one of the most frequently mutated human oncogenes.  However, activation of K-ras can lead to either senescence or proliferation in primary cells.  The precise mechanism governing these distinct outcomes remains unclear.  Here we describe a novel loss-of-function screen to assess the role of specific genes identified as potential key regulators of K-ras driven oncogenesis.  Using this approach, we identify the transcription factor Wt1 as an inhibitor of senescence in primary cells expressing oncogenic K-ras.  Deletion or suppression of Wt1 expression leads to senescence of primary cells expressing oncogenic K-ras under the control of the native promotor and at physiological levels, but had no effect on cells expressing wild-type K-ras.  Furthermore, loss of Wt1 in lung cancer cell lines that harbor mutant K-ras leads to apoptosis.  Taken together, these observations reveal a novel role for Wt1 as a key regulator of the complex genetic network required for the oncogenic effect of the small GTPase K-ras.

We compare the expression profiles of K-ras mutant mouse cell line (LKR13) upon shRNA knockdown of K-ras itself or Wt1. The study provides insights into the transcriptional role of Wt1 in the context of oncogenic K-ras.

overall_design: LKR13 cells were infected with plko.1s vectors carrying one of two shRNAs against K-ras or Wt1.  Control cells were infected with an shRNA against GFP.  48 hours after infection, cells were selected with puromycin for 3 days.  RNA was isolated using Trizol 7 days after infection.  RNA was further prepared by passage over an RNeasy column.  cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara). Microarray data was normalized with Expression Console software (Affymetrix, Santa Clara), using RMA algorithms.


title: MEF-mKras-WT1

summary:
K-ras is one of the most frequently mutated human oncogenes.  Activation of K-ras can lead to either senescence or proliferation in primary cells. The precise mechanism governing these distinct outcomes remains unclear. Here we utilized a loss-of-function screen to assess the role of specific genes identified as potential key regulators of K-ras driven oncogenesis. Using this approach, we identify the transcription factor Wt1 as an inhibitor of senescence in primary cells expressing oncogenic K-ras.  Deletion or suppression of Wt1 expression leads to senescence of primary cells expressing oncogenic K-ras under the control of the native promotor at physiological levels, but has no effect on cells expressing wild-type K-ras.  Wt1 contributes to K-ras driven lung tumorigenesis in vivo and loss of Wt1 is specifically deleterious to human lung cancer cell lines that are dependent on oncogenic K-ras.  Taken together, these observations reveal a novel role for Wt1 as a key regulator of the complex genetic network required for the oncogenic effect of the small GTPase K-ras.

We compare the expression profiles of Wild type, K-ras mutant, Wt1-null, and double K-ras mutant/Wt1-null mouse embryonic fibroblasts (MEFs). The study provides insights into the transcriptional role of Wt1 in the context of oncogenic K-ras.

overall_design: MEFs were infected with adenoviral Cre to activate K-ras (6 samples), knockout Wt1 (5 samples), both activate K-ras and knockout Wt1 (7 samples). As a control, MEFs were infected with adenoviral GFP (5 samples).  RNA was isolated using Trizol 7 days after infection. RNA was further prepared by passage over an RNeasy column. cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer's instructions (Affymetrix, Santa Clara). Microarray data was normalized with Expression Console software (Affymetrix, Santa Clara) using RMA algorithms.


title: Estrogen regulation and physiopathologic significance of alternative promoters in breast cancer

status: Public on Feb 17 2010

city: ORSAY

first: Martin

last: Dutertre

address: Rue Henri Becquerel

country: France

institute: INSERM

summary: Alternative promoters (APs) occur in >30% protein-coding genes and contribute to proteome diversity. However, large-scale analyses of AP regulation are lacking, and little is known about their potential physiopathologic significance. To better understand the transcriptomic impact of estrogens, which play a major role in breast cancer, we analyzed gene and AP regulation by estradiol in MCF7 cells using pan-genomic exon arrays. We thereby identified novel estrogen-regulated genes, and determined the regulation of AP-encoded transcripts in 150 regulated genes. In <30% cases, APs were regulated in a similar manner by estradiol, while in >70% cases, they were regulated differentially. The patterns of AP regulation correlated with the patterns of estrogen receptor (ERα) and CCCTC-binding factor (CTCF) binding sites at regulated gene loci. Interestingly, among genes with differentially regulated APs, we identified cases where estradiol regulated APs in an opposite manner, sometimes without affecting global gene expression levels. This promoter switch was mediated by the DDX5/DDX17 family of ERα coregulators. Finally, genes with differentially regulated promoters were preferentially involved in specific processes (e.g., cell structure and motility, and cell cycle). We show in particular that isoforms encoded by the NET1 gene APs, which are inversely regulated by estradiol, play distinct roles in cell adhesion and cell cycle regulation, and that their expression is differentially associated with prognosis in ER+ breast cancer. Altogether, this study identifies the patterns of AP regulation in estrogen-regulated genes, demonstrates the contribution of AP-encoded isoforms to the estradiol-regulated transcriptome, as well as their physiopathologic significance in breast cancer.

overall_design: 16 samples of MCF7 cells exposed to different treatments were analyzed: 4 x control_6 hours; 4 x estradiol_6 hours; 4 x control_24 hours;  4 x estradiol_24 hours.

first: Lise

last: Gratadou

first: Etienne

last: Dardenne

first: Sophie

last: Germann

first: Samaan

last: Samaan

first: Rosette

last: Liderau

first: Keltouma

last: Driouch

first: Pierre

last: de la Grange

first: Didier

last: Auboeuf


title: The Apcmin mouse has altered hematopoietic stem cell function and provides a model for MPD/MDS

status: Public on Feb 16 2010

first: Fatima

last: Al-Shahrour

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

summary: Apc, a negative regulator of the canonical Wnt signaling pathway, is a bona-fide tumor suppressor whose loss of function results in intestinal polyposis. APC is located in a commonly deleted region on human chromosome 5q, associated with myelodysplastic syndrome (MDS) suggesting that haploinsufficiency of APC contributes to the MDS phenotype. Analysis of the hematopoietic system of mice with the Apcmin allele that results in a premature stop codon and loss of function, showed no abnormality in steady state hematopoiesis. Bone marrow derived from Apcmin mice showed enhanced repopulation potential, indicating of a cell intrinsic gain of function in the long-term hematopoietic stem cell (HSC) population. However, Apcmin bone marrow was unable to repopulate secondary recipients due to loss of the quiescent HSC population. Apcmin mice developed a myelodysplastic/ myeloproliferative phenotype. Our data indicate that Wnt activation through haploinsufficiency of Apc causes insidious loss of HSC function that is only evident in serial transplantation strategies. These data provide a cautionary note for HSC expansion strategies through Wnt pathway activation, provide evidence that cell extrinsic factors can contribute to the development of myeloid disease and indicate that loss of function of APC may contribute to the phenotype observed in patients with MDS and del(5q).

overall_design: LKS+ cells were isolated from Apcmin or WT mice using high-speed multiparameter flow cytometry. At least 2x104 cells per mouse were isolated with confirmed purity in excess of 90%. The cells were treated with RLT lysis buffer (Qiagen) containing beta-mercaptoethanol to stabilize RNA. RNA was extracted using Qiagen RNeasy Micro Kit according to manufacturers instruction. The RNA was amplified using a linear amplification protocol (Nugen Ovation V2 amplification system). cDNA was fragmented and biotinylated before hybridization onto Affymetrix mouse genome 430 2.0 Array chips

first: Steven

middle: W

last: Lane

first: Stephen

last: Sykes

first: Sebastian

last: Shterental

first: Mahnaz

last: Paktinat

first: Cristina

middle: L

last: Celso

first: Jonathan

last: Jesneck

first: Benjamin

last: Ebert

first: David

last: Williams

first: D

last: Gilliland


title: Expression data from different stages of hematopoietic cells development

status: Public on Feb 13 2010

city: Toronto

first: Sasan

last: Zandi

state: Ontario

address: 101 college St

country: Canada

institute: UHN

summary:
18 different population of cells in different developmental stages in hematopoietic hierarchy have been purifyed by FACS analyses from wild type C57Bl6 mice and subjected to Micrroarray Affymetrix mouse 430.2 platform
We used microarrays to compare global expression pattern in different hematopoietic cell populations to reconstruct the whole hierarchy of hematopoietic tree based on gene profiling

Keywords: Hematopoietic Development

overall_design: For analysis of progenitor populations, RNA was extracted from 2000 purified adult BM cells using RNAeasy microkit. RNA was labeled and amplified by dual amplification and hybridized to Affymetrix micro array u480A, according to AffymetrixTM GeneChip Expression Analysis Technical Manual. Probe level expression values were calculated using RMA

first: Mikael

last: Sigvardsson

first: Robert

last: Mansson

last: Bryder


title: Non-targeted effects of low dose ionizing radiation act via TGFβ to promote mammary carcinogenesis

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

summary:
It is widely believed that the carcinogenic action of ionizing radiation is due to targeted DNA damage and resulting mutations, but there is also substantial evidence that non-targeted radiation effects alter epithelial phenotype and the stromal microenvironment.  Activation of transforming growth factor β1 (TGFβ) is a non-targeted radiation effect that mediates cell fate decisions following DNA damage and regulates microenvironment composition; it could either suppress or promote cancer.  We asked if such non-targeted radiation effects contribute to carcinogenesis by using a novel radiation chimera model.  Unirradiated Trp53 null mammary epithelium was transplanted to the mammary stroma, previously divested of endogenous epithelia, of mice previously exposed to a single low (10 -100 cGy) radiation dose.   By 300 days, 100% of transplants in irradiated hosts at either 10 or 100 cGy had developed Trp53 null breast carcinomas compared to 54% in unirradiated hosts.  Tumor growth rate was also increased by high, but not low, dose host irradiation.  In contrast, irradiation of Tgfb1 heterozygote mice prior to transplantation failed to decrease tumor latency, or increase growth rate at any dose. Host irradiation significantly reduced the latency of invasive ductal carcinoma compared to spindle cell carcinoma.  However, irradiation of either host genotype significantly increased the frequency of estrogen receptor negative tumors.  These data demonstrate two concepts critical to understanding radiation risks. First, non-targeted radiation effects can significantly promote the frequency and alter the features of epithelial cancer.  Second, radiation-induced TGFβ activity is a key mechanism of tumor promotion.

Keywords: Differential gene expression after low dose irradiation

overall_design:
[Samples GSM455405-GSM455421]: Two genotypes: TGBbeta1 heterozygote and wildtype mouse mammary glands.  Two time points post-10cGy-irradiation per genotype (1 week, 4 weeks); control time point was 1 week post-sham-irradiation.  Two or three replicates per time point.

[Samples GSM691226-GSM691263, GSM691272-GSM691281] = Differential gene expression of syngeneic murine p53null tumors from irradiated hosts in the BALB/c background.
Total RNA was extracted from mammary tumors derived from transplantations of non-irradiated p53null mammary fragments into irradiated hosts.  We analyzed a total of 32 p53null tumors from irradiated wild type mice: 9 from sham-irradiated hosts, and 23 from irradiated hosts.  We also analyzed 16 tumors from irradiated TGFb1 heterozygote hosts: 6 from sham-irradiated hosts, and 10 from irradiated hosts.

middle: H

last: Nguyen

first: Hellen

last: Oketch-Rabah

first: Felipe

last: Geyer

first: Jorge

last: Reis-Filho

first: Shraddha

last: Ravani

first: Jin-Hua

last: Mao

last: Zavadil

middle: J

last: Jerry

first: Daniel

last: Medina

first: Sandra

last: Haslam

first: Mary

last: Barcellos-Hoff


title: B bifidum actively changes the gene expression profile induced by L acidophilus in murine dendritic cells

city: Kongens Lyngby

first: Simon

last: Rasmussen

address: Kemitorvet, Building 208

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

summary: Dendritic cells (DC) play a pivotal regulatory role in activation of the innate as well as the adaptive part of the immune system by responding to environmental microorganisms. We have previously shown that some lactobacilli strains induce a strong production of the pro-inflammatory and Th1 polarizing cytokine IL-12 in DC. Contrary, bifidobacteria do not induce IL-12, but are able to inhibit the IL-12 production induced by lactobacilli. In the present study, genome wide microarrays were used to investigate the maturation and gene expression pattern murine bone marrow derived DC stimulated with Lactobacillus acidophilus NCFM and Bifidobacterium bifidum Z9. L. acidophilus NCFM strongly induced expression of interferon (IFN)-β, multiple virus defence genes, and cytokine and chemokine genes related to both the adaptive and the innate immune response. Contrary, B. bifidum Z9 mostly up-regulated genes encoding cytokines and chemokines related to the innate immune response. Moreover, B. bifidum Z9 inhibited the expression of the genes initiating the adaptive immune response induced by L. acidophilus NCFM and had an additive effect on genes of the innate immune response and some Th2 skewing genes. The gene encoding Jun dimerization protein 2 (JDP2), a key regulator in cell signalling, was one of the few genes only induced by B. bifidum Z9. Blocking of the JNK1/2 pathway completely inhibited the gene expression of Ifn-β. We suggest that B. bifidum Z9 employs an active mechanism to inhibit induction of genes in DC triggering the adaptive immune system and that JPD2 is involved in the regulatory mechanism.

overall_design: In the experiment saline control, Lactobacillus acidophilus NCFM, Bifidobacterium bifidum Z9 or both bacteria were were added to murine dendritic cells and stimulated for 10 hours. Experiments were run in triplicates and analyzed in a Two-way ANOVA design.

first: Gudrun

last: Weiss

first: Lisbeth

middle: F

last: Nielsen

first: Hanne

last: Jarmer

first: Birgit

middle: N

last: Frøkiær


title: The Gene Expression Analysis in E12.5 Mouse Hearts with GATA4-FOG2 Interaction Loss

status: Public on Feb 18 2010

city: Hanover

first: Sergei

last: Tevosian

state: NH

address: 7400 Hinman Box

department: Genetics

institute: Dartmouth Medical School

summary: In order to identify the targets of GATA4-FOG2 action in mammalian heart development we performed Affymetrix microarray comparisons of gene expression in normal and mutant at embryonic (E) day E12.5 hearts.  We compared RNA samples from both Fog2-null and Gata4ki/ki mutant E12.5 hearts to the wild-type control E12.5 hearts. We reasoned that as the phenotypes of the Fog2 knockout and Gata4ki/ki mutation (a V217G mutation that specifically cripples the interaction between GATA4 and FOG proteins) are similar, we should expect to identify a similar set of differentially expressed genes in both experiments. As an additional control, we expected to find the Fog2 gene expression absent in the mutant (null) Fog2 cardiac sample, but not Gata4ki/ki sample.

overall_design: We have analyzed 6 RNA samples total (3 from control hearts, 2 from FOG2 null hearts and 1 from GATA4ki hearts)

first: Nikolay

last: Manuylov

first: Fatima

middle: O

last: Smagulova


title: Single-cell gene expression data from Bergmann glial cells of mouse cerebellum

status: Public on Feb 12 2010

city: Boston

first: Gabriel

last: Corfas

address: 300 Longwood Avenue

department: Neurobiology Program

institute: Children's Hospital Boston

summary:
Bergmann glial cells of the vertebrate cerebellum play essential roles in the development and maintenance of cerebellar structure and function.  During development, Bergmann glia provide structural support to the expanding cerebellar anlage and also serve as guides for migrating neurons (granule cells).  As the cerebellum matures, Bergmann glia become important in dendritic arborization, synapse maintenance and synaptic function.  The molecular mechanisms underlying these diverse and important functions of Bergmann glia remain largely unknown.
We used microarray analysis to examine global gene expression in individual Bergmann glial cells derived at P6 (a time of extensive neuronal migration and cerebellar growth) and at P30 (when cerebellar development is complete and Bergmann glia play important roles at synapses).

overall_design: After gentle dissociation of cerebellar tissue derived from mice expressing GFP under the GFAP gene promoter (GFAP-GFP mice) (Zhuo, L., et al., 1997, Developmental biology), single GFP-positive Bergmann glial cells were aspirated into microcapillary tubes.  Amplified cDNAs were prepared from single cells using RT-PCR and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 expression arrays (one array per cell).  Five P6 cells and five P30 cells were used to generate the data presented in this study.

first: Samir

last: Koirala


title: Transcriptional Networks in Mouse Trophoblast Stem Cell Self-Renewal

status: Public on Feb 09 2010

city: Rockland

first: Benjamin

last: Kidder

address: 1 Technology Place

department: Reproductive Health

institute: EMD Serono Research Institute

type: Genome binding/occupancy profiling by genome tiling array

summary: Trophoblast stem cells (TS cells), derived from the trophectoderm (TE) of blastocysts, require transcription factors (TFs) and external signals (Fgf4, Activin/Nodal/Tgfb) for self-renewal.  While many reports have focused on TF networks that regulate embryonic stem cell (ES cell) self-renewal and pluripotency, little is know about TF networks that regulate self-renewal in TS cells.  To further understand transcriptional networks in TS cells we used chromatin immunopreciptiation and DNA microarray analysis (ChIP-chip) to investigate targets of TFs Ap-2g (Tcfap2c), Eomes, Ets2, and Gata3, and a chromatin remodeling factor, Brg1 (Smarca4).  We then evaluated the transcriptional states of target genes using transcriptome analysis and genome-wide analysis of histone H3 acetylation (AcH3).  Our results describe previously unknown transcriptional networks in TS cells, including TF occupancy of genes involved in ES cell self-renewal and pluripotency, co-occupancy of multiple TFs at target genes, and transcriptional regulatory circuitry within the 5 factors.  Through genome-wide mapping and global expression analysis of 5 TF target genes, our data provide a comprehensive analysis of transcriptional networks that regulate TS cell self-renewal.

overall_design:
RNA was harvested at 7 time points from TS cells cultured without Fgf4 over two weeks for transcriptome analysis.  RNA was collected from undifferentiated TS cells at T=0hr, and differentiated TS cells cultured without Fgf4 for 24-hrs, 48-hrs, 72-hrs, 6 days, 10 days, and 14 days.

Mouse TS cells were ChIPed with antibodies specific to Ap-2g (Tcfap2c), Brg1 (Smarca4), Eomes, Ets2, and Gata3 vs. Input DNA from TS cells


title: Gene profiling within the orexin-producing neurons

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

summary:
Narcolepsy is a sleep disorder characterized by excessive daytime sleepiness and attacks of muscle atonia triggered by strong emotions (cataplexy). The best biological marker of narcolepsy is orexin deficiency with dramatic loss in hypothalamic orexin-producing neurons. Together with a tight HLA and T-cell receptor alpha(5) association, narcolepsy is believed to be autoimmune although all attempts to prove it have failed.To characterize orexin specific peptides we produced a transgenic mouse model to access to the orexin neurons transcription profile. We generated BAC-based transgenic mice by replacing the orexin coding sequence by a flag-tagged poly(A) binding protein (Pabp1) cDNA sequence. The basis of this construct is to take advantage of the ability of Pabp1 to bind to the poly(A) tails of mRNAs in vivo. Thus mRNAs from orexin cells are expected to be enriched by cross-linking them to the flag-tagged PABP and then co-immunoprecipitating this complex with a specific anti-flag monoclonal antibody.

Keywords: cell type comparison

overall_design: Comparison between immunoprecipitated (IP) mRNA (n=9) and whole brain (WB) RNA (n=9) from BAC-based transgenic mice

first: Cvetkovic

last: Vesna

first: Bayer

last: Laurence

first: Dorsaz

last: Stéphane

first: Maret

last: Stéphanie

first: Pradervand

last: Sylvain

first: Muhlethaler

last: Michel

first: Tafti

last: Mehdi


title: Gene Expression Data from Prefrontal Cortex and Nucleus Accumbens from Inbred Strains of Mice

status: Public on Feb 03 2010

city: Chapel Hill

first: Samantha

middle: Katherine

last: Segall

state: NC

address: 120 Mason Farm Road

institute: UNC- Chapel Hill

summary: Catechol-O-methyltransferase (COMT) is an ubiquitously expressed enzyme that maintains basic biologic functions by inactivating catechol substrates. In humans, polymorphic variance at the COMT locus has been associated with modulation of pain sensitivity (Andersen & Skorpen, 2009) and risk for developing psychiatric disorders (Harrison & Tunbridge, 2008). A functional haplotype associated with increased pain sensitivity was shown to result in decreased COMT activity by altering mRNA secondary structure-dependent protein translation (Nackley et al., 2006). However, the exact mechanisms whereby COMT modulates pain sensitivity and behavior remain unclear and can be further studied in animal models. We have pursued a genome-wide approach to examining gene expression in multiple brain regions in inbred strains of mice and have discovered that Comt1 is differentially expressed.  This expression difference was validated with qPCR.  A B2-B4 Short Interspersed Element (SINE) was inserted in the 3'UTR of Comt1 in 14 strains that also shared a common haplotype. Experiments using mammalian expression vectors of full-length cDNA clones with and without the SINE element demonstrate that strains with the SINE haplotype (+SINE) have greater Comt1 enzymatic activity. +SINE mice also exhibit behavioral differences in anxiety assays and decreased pain sensitivity. These results suggest that a haplotype, defined by a 3'UTR B2-B4 SINE element, regulates Comt1 expression and mouse behavior.

overall_design:
Brain region samples were isolated from male and female mice of 29 strains (n = 3), 129S1/SvImJ, A/J, AKR/J, BALB/cByJ, BTBR T+ tf/J, BUB/BnJ , C3H/HeJ, C57BL/6J, C57BR/cdJ, C58/J, CBA/J, CE/J,  DBA/2J, FVB/NJ, I/LnJ, KK/HIJ, MA/MyJ, MRL/MpJ, NOD/LtJ, NON/LtJ, NZO/HILTJ, NZW/LacJ, P/J, PL/J, RIIIS/J, SJL/J, SM/J, SWR/J, and WSB/EiJ. Eight to ten week old male and female mice of each strain were purchased from the Jackson Laboratory (Bar Harbor, ME, USA).  The mice were habituated for one week prior to tissue collection. Mice were sacrificed by cervical dislocation without anesthesia to avoid gene expression differences in response to anesthetic. All dissections were conducted between the hours of 9:00AM to 11:30AM. Prefrontal cortex and nucleus accumbens were dissected as follows. Immediately following euthanasia, mice were decapitated and the whole brain was removed from the skull.  The brain was then transferred, ventral side up, to an ice-cold brain matrix with 0.5mm spacing (505C Braintree Scientific).  A single razor blade was placed into the first space on the brain matrix and the rostral surface of the brain was placed in the matrix and touching this blade.  Thin, double-edged razor blades were placed in the twelve most anterior spaces.  Following removal from the matrix, the 0.5 mm brain slices were placed flat onto an ice-cold dissection stage and specific regions dissected using anatomical landmarks as described below.  The prefrontal cortex was taken from the slice corresponding to approximately 2.5 mm to 2.0 mm anterior to Bregma.  To do so, a V-shaped wedge was made just medial to the corpus callosum with the apex terminating at about the lateral ventricle (viewed from the caudal side of the slice).  Nucleus accumbens was taken from the adjacent slice approximately 2.0mm to 1.5mm anterior to Bregma.   To isolate nucleus accumbens, 1mm punches were taken just ventromedial to the anterior commissure.
All of the array data in this Series are from male mice.


title: C-peptide and/or transforming growth factor beta 1 effect on human proximal tubular cell line

status: Public on Feb 11 2010

city: Leicester

first: Nigel

middle: John

last: Brunskill

state: Leics

address: University Road

department: Infection Immunity and Inflammation

country: United Kingdom

institute: University of Leicester

summary:
Microarray analysis reveals up-regulation of retinoic acid and hepatocyte growth factor related signaling pathways by pro-insulin C-peptide in kidney proximal tubular cells: Antagonism of the pro-fibrotic effects of TGF-b1
Novel signaling roles for C-peptide have recently been discovered with evidence that it can ameliorate complications of type 1 diabetes.  Here we sought to identify new pathways regulated by C-peptide of relevance to the pathophysiology of diabetic nephropathy.  Microarray analysis was performed to identify genes regulated by either C-peptide and/or transforming growth factor beta 1 (TGF-β1) in a human proximal tubular cell line, HK-2.  Expression of retinoic acid receptor β (RARβ), hepatcoyte growth factor (HGF), cellular retinoic acid binding protein II (CRABPII), vimentin, E-cadherin, Snail and β-catenin was assessed by immunoblotting.  The cellular localisation of vimentin and β-catenin was determined by immunocytochemistry.  Changes in cell morphology were assessed by phase contrast microscopy.  Gene expression profiling demonstrated differential expression of 953 and 1,458 genes after C-peptide exposure for 18h or 48h respectively.  From these, members of the anti-fibrotic retinoic acid (RA) and HGF signaling pathways were selected.  Immunoblotting demonstrated that C-peptide increased RARβ, CRABPII and HGF.  We confirmed a role for RA in reversal of TGF-β1-induced changes associated with epithelial-mesenchymal transition (EMT), including expression changes in Snail, E-cadherin, vimetin and redistribution of β-catenin.  Importantly, these TGF-β1-induced changes were inhibited by C-peptide.  Further, effects of TGF-β1 on Snail and E-cadherin expression were blocked by HGF and inhibitory effects of C-peptide were removed by blockade of HGF activity.  This study identifies a novel role for HGF as an effector of C-peptide, possibly via an RA signaling pathway, highlighting C-peptide as a potential therapy for diabetic nephropathy.

overall_design: For microarray analyses, all treatments were performed in triplicate to yield 18 flasks, and RNA from each flask hybridized to a separate chip to give an n of 3 for each of 6 treatments.  Flasks were subjected to identical media changes and cells cultured for identical periods in media without supplements.  In all experiments, cells were serum-starved overnight before agonist addition.  Treatments were initiated such that 18h and 48h incubation periods ended coincidentally and all RNA was prepared at this point.

first: Claire

middle: E

last: Hills

first: Gary

middle: B

last: Willars


title: The Transcriptome of Nrf2-Deficient Mice in Cigarette Smoke-Induced Emphysematous Changes

status: Public on Feb 06 2010

city: Koeln

first: Stephan

last: Gebel

address: Fuggerstr. 3

institute: Philip Morris Research Laboratories

summary: Cigarette smoke (CS) imposes a strong oxidative burden on exposed tissues resulting in a severely disturbed oxidant/antioxidant balance, which in the context of chronic exposure is assumed to be a key contributor to CS-related diseases. Because of its emerging central role in orchestrating the general cellular antioxidant response, the pathway leading to the activation of the transcription factor Nrf2 has received mounting attention over the past decade in investigations aimed at elucidating CS-induced patho-physiological mechanisms. To comprehensively characterize the impact of Nrf2 in acute and sub-chronic smoking scenarios, Nrf2 knock-out mice and their wildtype ICR littermates were exposed to either ambient air (sham exposure) or to one of three doses of CS for up to 5 months with two post-exposure endpoints of 1 and 13 days. The lungs of the mice were monitored for transcriptomic changes on a genome-wide level.

overall_design: 110 samples from 28 different groups are analyzed. For each group there are 4 replicates, besides two groups with only 3 replicates. Group parameteres are: genotype (WT, KN), treatment (sham, smoke), dosage of smoke treatment (low, medium, high), time of smoke treatment (1 day, 2 month, 5 month, 5 month + 1 day recovery, 5 month + 13 days recovery)

first: Thomas

last: Mueller

first: Svenja

last: Diehl

first: Jutta

last: Schüller

first: Masayuki

last: Yamamoto


title: Polycomb-like 2 associates with PRC2 and is required for mouse embryonic stem cell

status: Public on Feb 05 2010

first: William

last: Stanford

address: 164 College St

department: IBBME

institute: University of Toronto

summary: Polycomb group (PcG) proteins are highly conserved epigenetic transcriptional repressors important for the control of numerous developmental gene expression programs and have recently been implicated in the modulation of embryonic stem cell (ESC) identity. We identified the PcG protein PCL2 (polycomb-like 2) in a genome-wide screen for novel regulators of self-renewal and pluripotency and predicted that it would play an important role in mouse ESC fate determination. Using multiple biochemical strategies, we provide evidence that PCL2 is a novel Polycomb Repressive Complex 2 (PRC2)-associated protein in mouse ESCs. Knockdown of Pcl2 in ESCs resulted in heightened self-renewal characteristics, defects in differentiation and altered patterns of histone methylation. Through integration of global gene expression and promoter occupancy analyses of both PCL2 and PRC2 components EZH2 and SUZ12, we have predicted PCL2 target genes and formulated regulatory networks describing the role of PCL2 both in modulating transcription of ESC self-renewal genes in undifferentiated ESCs as well as developmental regulators during early commitment and differentiation.

overall_design: Cells were stably expressing Pcl2 shRNA or shRNA mismatch control sequences. Hybridizations of three biological replicates for both the control and Pcl2 shRNA clone were performed.

first: Emily

last: Walker

first: Wing

middle: Y

last: Chang

first: Julie

last: Hunkapiller

first: Gerard

last: Cagney

first: Kamal

last: Garcha

first: Joseph

last: Torchia

first: Nevan

last: Krogan

first: Jeremy

last: Reiter


title: Differential gene expression in stellate sympathetic ganglia after cardiac pressure overload

city: Freiburg

first: Ralf

last: Gilsbach

address: Albertstr. 25

institute: Institute of Pharmacology

summary: Transcriptom analysis of stellate sympathetic ganglia after 8 weeks of cardiac pressure overload caused by transverse aortic constriction.

overall_design: Comparative transcriptome analysis was determined using the GeneChip Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA, USA). Six microarrays from stellate sympathetic ganglia of mice were performed 8 weeks after transverse aortic constriction or sham operation.

first: Lutz

last: Hein

first: Tomi

last: Ivacevic


title: Identification of genes characteristic of committed preadipocyte fibroblasts

status: Public on Feb 01 2010

first: Rana

middle: K

last: Gupta

address: 44 Binney Street CLSB 11119

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: In order to identify the molecular mechanisms controlling preadipocyte commitment we derived new sublines of Swiss 3T3 fibroblasts with varying potential for adipogenesis.  Swiss 2, Swiss 8, Swiss 9, and Swiss 19 differentiate into fat cells while Swiss 3, Swiss 5, and Swiss 22 have a lower propensity to differentiate into fat cells.  The overall goal was to identify genes whose expression in the fibroblast state correlates with the ultimate potential of the cells to undergo adipogenesis

overall_design: 4 preadipose fibroblast cell lines (Swiss 2, Swiss 8, Swiss 9, and Swiss 19 in triplicate or duplicate) were compared to 3 non-adipogenic fibroblast cell lines (Swiss 3, Swiss 5, Swiss 22 in triplicate)

first: Bruce

last: Spiegelman


title: Microarray analysis of CA-AhR transgenic mice

city: Pittsburgh

first: Jung Hoon

last: Lee

state: PA

address: 3501 Terrace St.

department: Pharmaceutical Sciences

institute: Univeristy of Pittsburgh

summary:
We have generated transgenic mice expressing constitutively activated aryl hydrocarbon receptor (CA-AhR) to examine the biological consequences of AhR activation..
We used microarrays  to identify genes that are regulated by AhR.

overall_design: Livers or intestines from three female mice were pooled at 5-6 week-old for RNA extraction and hybridization on Affymetrix Mouse Genome 430 2.0 Array.

first: Wen

last: Xie

first: Jung


title: Expression data for melanoma short-term cultures and cell lines

first: Michael

last: Berger

department: Cancer Program

institute: The Broad Instititute

summary: We profiled the gene expression levels from 8 melanoma short-term cultures and 1 melanoma cell line in order to compare to expression level estimates obtained by RNA-seq.

overall_design: Melanoma short-term cultures and cell lines were propagated in vitro, and total RNA was extracted for microarray hybridization and sequencing.  The 9 Samples report the microarray hybridization results.

first: Levi

middle: A

last: Garraway


title: Differentiation time course of trophoblast stem cells

first: Brian

middle: Joseph

last: Cox

address: 1 King's College Circle, Rm 3360

department: Physiology

summary:
To characterized the changes in gene expression during the differentiation of TS cells. TS cells can be derived from two time point during embryogenesis, cell lines tested were from each of these time points.

Keywords: time course

overall_design: TS cells derived from either E3.5 or E6.5 embryos were differentiated over 6 days by withdrawal of FGF4 and feeder conditioned medium. Cell were sampled every 24 hrs and assayed by microarray.

first: Amy

last: Ralston

first: Janet

last: Rossant


title: Gata3 acts alongside Cdx2 to promote trophoblast gene expression downstream of Tead4 during mouse development

summary:
The first lineage decisions during mouse development lead to establishment of embryonic and extraembryonic tissues. The transcription factor Cdx2 plays a central role by repressing pluripotency genes, such as Oct4 and promoting trophoblast fate at the blastocyst stage. Here we show that the transcription factor Gata3 is coexpressed with Cdx2 in the blastocyst and that overexpression of Gata3 in embryonic stem cells is sufficient to induce expression of trophoblast genes. Gata3 expression in the blastocyst does not depend on Cdx2, nor do Gata3 overexpressing cell lines require Cdx2 for expression of a subset of trophoblast genes. In the embryo, expression of Gata3, like Cdx2, depends on Tead4, and expression of both factors becomes restricted to nascent trophoblast by an Oct4-independent mechanism. These observations place Tead4 at the top of a trophoblast hierarchy, with Gata3 and Cdx2 acting downstream to induce expression of common and independent targets in this lineage.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Expression of Cdx2 or Gata3 in R1 mouse embryonic stem cells

summary:
To identify whether Cdx2 or Gata3 can activate trophoblast specific gene expression when expressed in R1 ES cells. To assess the dependency of Gata3 activity on Cdx2, Gata3 was also expressed in Cdx2-null ES cells.

Keywords: gene expression

overall_design: a fusion construct of either Cdx2 or Gata3 and the tamoxifen responsive estrogen receptor ligand binding domain was expressed in R1 ES cells. Cell were induced with tamoxifen for 6 days to activate the transcription factor and cultured under trophoblast stem cell conditions


title: Striatum of Huntington's disease model mice

status: Public on Jan 31 2010

city: Vancouver

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

institute: University of British Columbia

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

overall_design: Refer to individual Series


title: Striatum of Huntington's disease model mice [Affymetrix data]

summary: Evaluation of transcriptional changes in the striatum may be an effective approach to understanding the natural history of changes in expression contributing to the pathogenesis of Huntington disease (HD). We have performed genome-wide expression profiling of the YAC128 transgenic mouse model of HD at 12 and 24 months of age using two platforms in parallel; Affymetrix and Illumina. We performed gene expression profiling on the same striatal mRNA across both platforms.

overall_design: Transgenic mice expressing human HD huntingtin with 120 CAG repeats (YAC128) and wildtype littermates were used for the described experiments. The mice were group housed in polystyrene cages under a normal light-dark cycle (6 am to 8 pm) in a clean facility and with free access to water and standard rodent chow. All experiments were performed in accordance with the University of British Columbia animal care committee. Striatal tissue was collected from 12 and 24 month old YAC128 mice and wildtype littermates.

first: Kristina

last: Becanovic


title: Analyses of cyclin D1 function using a "genetic-proteomic" approach

status: Public on Jan 29 2010

first: Frederic

middle: Emile

last: Bienvenu

address: 1 Jimmy Fund Way

type: Genome binding/occupancy profiling by array

summary:
We examined the transcriptional function of cyclin D1 in mouse development using two approaches. First, we queried association of cyclin D1 with the genome of E14.5 mouse embryos using ChIP-on-chip approach.  We observed binding of cyclin D1 to several promoter regions.  Second, we compared gene expression profiles between wild-type and cyclin D1-null retinas. We observed several transcripts with altered levels in cyclin D1-null organs.

This SuperSeries is composed of the SubSeries listed below.


title: Expression data from mouse liver infected with Ft LVS (without or with LPS pretreatment)

city: blacksburg

first: Saroj

last: Mohapatra

state: VA

address: washington Street

department: VBI

institute: Virginia Tech

summary:
Background: It has been shown previously that administration of Francisella tularensis (Ft) LVS lipopolysaccharide (LPS) protects mice against subsequent challenge with Ft LVS and blunts the pro-inflammatory cytokine response.
Methods: To investigate further the molecular mechanisms that underlie Ft LVS LPS-mediated protection, we profiled global hepatic gene expression following Ft LVS LPS or saline pretreatment and subsequent Ft LVS challenge using Affymetrix arrays.
Results: A large number of genes (> 3000) were differentially expressed at 48 hours post-infection. The degree of modulation of inflammatory genes by infection was clearly attenuated by LPS-pretreatment in the surviving mice. However, LPS alone had a subtle but significant effect on the gene expression profile of the uninfected mice. By employing gene set enrichment analysis, we discovered significant up-regulation of peroxisome proliferator activated receptors (PPARs) and their target genes in LPS-treated liver.
Conclusions: We hypothesize that the LPS-induced blunting of pro-inflammatory response in mouse is, in part, mediated by PPARs (alpha and gamma).

overall_design: Two groups of 9 mice each were used for this experiment. 48 hours prior to Ft LVS challenge, mice were injected i.p. with either 100 ng of Ft LVS LPS or an equivalent volume of saline. On the day of challenge, 3 saline- and 3 Ft LVS LPS-pretreated animals were sacrificed (uninfected controls), while all remaining mice were challenged  i.p. with ~4-5 X 105 Ft LVS.  Ft LVS-challenged mice were sacrificed (in groups of 3) at 24 and 48 hours post-infection.

first: Leah

last: Cole

first: Clive

last: Evans

first: Bruno

last: Sobral

first: Josep

last: Bassaganya-Riera

first: Raquel

last: Hontecillas

first: Stefanie

last: Vogel

first: Oswald

middle: R

last: Crasta


title: S1P lyase deficiency disrupts lipid homeostasis in liver

status: Public on Jan 28 2010

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: The cleavage of sphingoid base phosphates by sphingosine-1-phosphate (S1P) lyase to produce phosphoethanolamine and a fatty aldehyde is the final degradative step in the sphingolipid metabolic pathway. We have studied mice with an inactive S1P lyase gene and have found that, in addition to the expected increase of sphingoid base phosphates, other sphingolipids (including sphingosine, ceramide, and sphingomyelin) were substantially elevated in the serum and /or liver of these mice. This latter increase is consistent with a reutilization of the sphingosine backbone for sphingolipid synthesis due to its inability to exit the sphingolipid metabolic pathway. Furthermore, the S1P lyase deficiency resulted in changes in the levels of serum and liver lipids not directly within the sphingolipid pathway, including phospholipids, triacyglycerol, diacylglycerol, and cholesterol. Even though lipids in serum and lipid storage were elevated in liver, adiposity was reduced in the S1P lyase-deficient mice. Microarray analysis of lipid metabolism genes in liver showed that the S1P lyase deficiency caused widespread changes in their expression pattern. These results demonstrate that S1P lyase is a key regulator of the levels of multiple sphingolipid substrates and reveal functional links between the sphingolipid metabolic pathway and other lipid metabolic pathways that may be mediated by shared lipid substrates and changes in gene expression programs. The disturbance of lipid homeostasis by altered sphingolipid levels may be relevant to metabolic diseases.

overall_design: RNA samples from liver for three sphingosine-1-phosphate lyase knock-out and three WT mice.

first: Meryem

last: Bektas

first: Maria

last: Allende

first: Bridgin

last: Lee

first: Oksana

last: Gavrilova

first: Marcelo

last: Amar

first: Alan

middle: T

last: Remaley

first: Julie

middle: D

last: Saba

first: Richard

last: Proia


title: Gene expression change in cyclin D1 -/- retinas in comparison to wildtype.

first: Frederic

last: Bienvenu

summary: Cyclin D1 belongs to the core cell cycle machinery1, and it is frequently overexpressed in human cancers2.  The full repertoire of cyclin D1 functions in normal development and in cancer cells is currently unknown. To address this question, here we introduce a novel approach that allows one to determine the set of cyclin D1-interacting proteins  (D1 “interactome”) and cyclin D1-bound genomic fragments (D1 “cistrome”) in essentially any mouse organ, at any point of development or at any stage of cancer progression.   Using this approach, we detected several novel tissue-specific interactors of cyclin D1.  A significant number of these partners represent proteins involved in transcription.  We show, using genome-wide location analysis3, that cyclin D1 occupies promoters of a very large number of genes in the developing mouse, where it binds in close proximity to transcription start sites.  Bioinformatics analyses of cyclin D1-bound genomic segments in the developing embryo revealed DNA recognition sequences for several transcription factors.  By querying SAGE libraries4, promoter CpG content5 and gene expression profiles of cyclin D1-null organs, we demonstrate that cyclin D1 binds promoters of highly expressed genes, and that it functions to activate or to repress gene expression in vivo.  Analyses of cyclin D1 transcriptional targets reveal that cyclin D1 contributes to cell proliferation by upregulating genes required for S-phase entry and progression.  Hence, cyclin D1 plays a broad transcriptional regulatory function in vivo during normal mouse development.

overall_design: We wished to determine whether cyclin D1 functioned to positively or negatively regulate transcription of the target genes (identified by chip-on-chip) in vivo.  To address this question, we asked how expression of cyclin D1-bound genes changes when cyclin D1 has been knocked-out.  We dissected retinas from eyes of cyclin D1-/- or wild-type neonates, isolated RNA and hybridized it onto Affymetrix expression arrays.


title: Gene expression analyses of C/EBPb knockout in stem/progenitor cell populations

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
CCAAT/enhancer binding protein beta (C/EBPb) is a member of a family of highly conserved transcription factors that regulates numerous genes involved in proliferation and differentiation in a variety of tissues.  C/EBPb is deregulated in human breast cancer and germline deletion of this gene results in multiple defects in mammary gland development.  We hypothesized that C/EBPb regulates mammary stem cell self-renewal, maintenance and/or differentiation through the regulation of multiple target genes that coordinate mammary gland development.  Utilizing both a germline knockout mouse model and a conditional knockout strategy, we demonstrated that mammosphere formation was significantly decreased in C/EBPb-deficient mammary epithelial cells (MECs).  The ability of C/EBPb-deleted MECs to regenerate the mammary gland in vivo was severely impaired when transplanted at limiting dilution.  Furthermore, serial transplantation of C/EBPb-null mammary tissue resulted in decreased outgrowth potential when compared to wildtype, and an early senescence phenotype.  Flow cytometric analysis revealed that C/EBPb-null MECs contain a lower frequency of repopulating stem cells accompanied by an increase in committed, differentiated luminal cells as compared to wildtype. Microarray analysis of stem/progenitor cell populations was performed and revealed an alteration in cell fate specification in C/EBPb-null glands, exemplified by the aberrant expression of basal markers in the luminal cell compartment.  Collectively, our studies demonstrate that C/EBPb is a critical regulator of mammary stem cell differentiation, and an important determinant of luminal cell fate specification.

Keywords: multiple group comparison

overall_design: To identify potential signaling pathways regulated by C/EBPb in stem/progenitor cells, microarray analysis was performed on two stem/progenitor cell subpopulations.  For this analysis, subpopulations defined by LIN-CD24+CD29hi and LIN-CD24hiCD29lo were FACS sorted from wildtype and germline C/EBPb-/- glands, and RNA was isolated from each group.

first: Heather

last: LaMarca

first: Jeff

last: Rosen


title: Microarray Experiments for mice lacking or with  the Stat5a and 5b genes in blood cells that were treated w/o CMP

status: Public on Feb 02 2010

summary: GM-CSF controls the development of granulocytes but little is known about the contribution of the downstream mediating transcription factor STAT5A/B.  To elucidate this pathway, we generated mice lacking the Stat5a and 5b genes in blood cells.  Peripheral neutrophils were decreased and administration of 5-FU and GM-CSF failed to induce granulopoiesis in Stat5a/b-mutant mice. CMPs were isolated and cultured with GM-CSF.

first: Akiko

last: Kimura

first: Lothar

last: Hennighausen


title: Transcriptome of the Nxnl1-/- mouse retina

status: Public on Jan 24 2010

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

institute: IGBMC

summary:
Rod-derived Cone Viability Factor (RdCVF, alias nxnl1) is a retina-specific protein identified for its therapeutic potential in supporting cone survival during retinal degeneration.
A nxnl1 knockout mouse model was created and the transcriptome used to demonstrate that the retina is compromised by the absence of nxnl1.

Keywords: genetic modification, transcription-profile, retina

overall_design: In total 9 samples were analyzed, they represent three different genotypes (wt/wt, ko/wt, ko/ko) that were tested in triplicate each.

first: Therese

last: Cronin

first: Irene

last: Lee-Rivera

first: Bernd

last: Kinzel

first: Emanuelle

last: Clerin

first: Olivier

last: Poch

first: Jose-Alain

last: Sahel

first: Thierry

last: Leveillard


title: Prolonged IL-2R alpha expression on virus-specific CD8+ T cells favors terminal effector differentiation in vivo

status: Public on Jan 21 2010

city: Atlanta

first: Vandana

last: Kalia

state: GA

address: 1510 Clifton Road

department: Microbiology and Immunology

institute: Emory University

summary: CD25, the high affinity interleukin-2 (IL-2) receptor alpha-chain, is rapidly upregulated by antigen-specific CD8+ T cells after T cell receptor stimulation. We demonstrated that during an acute viral infection, CD25 expression was dynamic, and a subset of virus-specific CD8+ T cells sustained CD25 expression longer than the rest. Examination of the in vivo fate of effector CD8+ T cells exhibiting differential responsiveness to IL-2 revealed that CD25lo cells, which were relatively less sensitive to IL-2, preferentially upregulated CD127 and CD62L and gave rise to the functional long-lived memory pool. In contrast, CD25hi cells that accumulate enhanced IL-2 signals, proliferated more rapidly, were prone to apoptosis, exhibited a more pronounced effector phenotype, and appeared to be terminally differentiated. Sustained IL-2 receptor signaling resulted in increased CD8+ T cell proliferation, higher granzyme B expression and exaggerated contraction after antigen clearance. These data support the hypothesis that prolonged IL-2 signals during priming promote terminal effector differentiation of CD8+ T cells.

overall_design: An important question in memory development is understanding the differences between effector CD8 T cells that die versus effector cells that survive and give rise to memory cells. In this study we have performed genomic profiling of terminal effectors and memory precursors as defined by CD25 heterogeneity, towards better understanding the generation of these subsets. The two effector subsets were FACS purified based on the amount of cell surface CD25 expression into CD25lo and CD25hi subsets during the early expansion phase (Days 3-4 post-infection) and analyzed for their gene expression profiles (by genome-wide microarray analyses).

first: Surojit

last: Sarkar


title: Effect of c-Myb deficiency on pre-selection DP thymocytes

status: Public on Jan 22 2010

city: Charlottesville

first: Timothy

middle: P

last: Bender

address: 345 Crispell Dr

department: Microbiology

institute: University of Virginia

summary:
Comparing the mRNA expression profiles of c-Myb deficient and c-Myb sufficient Tcra-/- DP thymocytes.
Results provide insight into the role of c-Myb in the regulation of survival and differentiation during the pre-selection DP stage where c-Myb expression is abundant during T cell development.

overall_design: DP thymocytes were purified from four c-Myb deficient and four c-Myb sufficient mice over magnetic columns.  RNA from each biological replicate was individually hybridized onto a total of eight MOE430 2.0 Chips.

first: Joan

last: Yuan


title: Human Negative Elongation Factor Activates Transcription and Regulates Alternative Transcription Initiation

status: Public on Jan 20 2010

first: Jianlong

last: Sun

address: 1 Blackfan Street

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: The human Negative Elongation Factor (NELF) is a four-subunit protein complex that inhibits the movement of RNA polymerase II (RNAPII) at an early elongation stage in vitro.  NELF-mediated stalling of RNAPII also attenuates transcription of a number of inducible genes in human cells.  To obtain a genome-wide understanding of human NELF-mediated transcriptional regulation in vivo, we carried out an exon-array study in T47D breast cancer cells with transient siRNA knockdown of individual NELF subunits.  Upon depletion of NELF-A, -C, or -E, the vast majority of NELF-regulated genes were down-regulated.  Many of the down-regulated genes encode proteins that play key roles in cell cycle progression. Consequently, NELF knockdown resulted in significant reduction in DNA synthesis and cell proliferation.  Chromatin immunoprecipitation showed that NELF knockdown led to dissociation of RNAPII from the promoter-proximal region of the cell cycle-regulating genes.  This was accompanied by decreased histone modifications associated with active transcription initiation (H3K9Ac) and elongation (H3K36Me3), as well as reduced recruitment of the general transcription factor TFIIB and increased overall histone occupancy at a subset of the down-regulated promoters.  Lastly, our study indicates that NELF regulates alternative transcription initiation of Basigin gene (BSG) by differentially influencing RNAPII density at the two neighboring exons at the 5’ end of the gene.  Taken together, our data suggest a diverse transcriptional consequence of NELF-mediated RNAPII pausing in the human genome.

overall_design:
Gene expression analysis of RNA samples from NELF-depleted T47D breast cancer cell line.
We analyzed gene expression of T47D cells transfected with siRNAs for control and each of the four NELF subunits by exon array.  Each knockdown condition contains three technical repeats.  Differentially expressed genes and exons between knockdown of the individual NELF subunits and the control are analyzed by the Arrayassist software from Stratagene.  The commonly affected genes and exons among all four NELF subunits knockdown samples are chosen for further studies.

first: Rong

last: Li


title: Gene Expression in the Blood of Parkinson's Disease Patients

status: Public on Feb 04 2010

city: Miami

first: Lina

last: Shehadeh

state: FL

department: Medicine

institute: University of Miami

summary: Peripheral blood was collected from 18 Parkinson's Disease (PD) patients and 12 healthy controls (Ctrls). Total RNA was isolated and hybridized onto Affymetrix Exon_ST1 arrays to find in PDs versus controls: 1) genes that are differentiallly expressed and 2) genes with differential exonic expression (alternative splicing).

overall_design: 17 PD samples vs 11 Control samples

first: Spyros

last: Papapetropoulos


title: CHF1/Hey2 Promotes Physiological Hypertrophy in response to Pressure Overload

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: We have previously found that overexpression of CHF1/Hey2 in the myocardium prevents the development of phenylephrine-induced hypertrophy. To determine the role of CHF1/Hey2 in pressure overload hypertrophy, we performed ascending aortic banding on wild type and transgenic mice overexpressing CHF1/Hey2 in the myocardium. We found that both wild type and transgenic mice developed increased ventricular weight to body weight ratios one week after aortic banding. Wild type mice also developed decreased fractional shortening after one week when compared to preoperative echocardiograms and sham operated controls. Transgenic mice, in comparison, demonstrated preserved fractional shortening. Histological examination of explanted heart tissue demonstrated extensive fibrosis in wild type hearts, but minimal fibrosis in transgenic hearts. TUNEL staining demonstrated increased apoptosis in the wild type hearts but not in the transgenic hearts. Exposure of cultured neonatal myocytes from wild type and transgenic animals to hydrogen peroxide, a potent inducer of apoptosis, demonstrated increased apoptosis in the wild type cells. Gene Set Analysis of microarray data from wild type and transgenic hearts one week after banding revealed suppression and activation of multiple pathways involving apoptosis, cell signaling and biosynthesis. These findings demonstrate that CHF1/Hey2 promotes physiological over pathological hypertrophy in pressure overload through suppression of apoptosis and global regulation of multiple transcriptional pathways.

overall_design: Ascending aortic banding on four wild type and four transgenic mice were compared

first: Richard

last: Beyer

first: Man

last: Yu

first: Yonggang

last: Liu

first: Fan

last: Xiang

first: Yuxin

first: Darragh

last: Cullen

first: Ronglih

last: Liao

first: Theodor

last: Bammler

first: Michael

last: Chin


title: Telmisartan Improves Insulin Resistance with Modulating Adipose Tissue Macrophage Polarization in High Fat-fed Mice

status: Public on Jan 23 2010

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary: Diet-induced obesity is reported to induce a phenotypic switch in adipose tissue macrophages from an antiinflammatory M2 state to a proinflammatory M1 state.   Telmisartan, an angiotensin II type 1 receptor antagonist and a peroxisome proliferator-activated receptor-gamma (PPAR-gamma) agonist, reportedly has beneficial effects on insulin sensitivity.  We studied the effects of telmisartan on the adipose tissue macrophage phenotype in high fat-fed mice.  Telmisartan was administered for 5 weeks to high fat-fed C57BL/6 mice.  Insulin sensitivity, macrophage infiltration, and the gene expressions of M1 and M2 markers in epididymal fat tissues were examined.  Insulin- or a glucose-tolerance test showed that telmisartan treatment improved insulin resistance, decreasing the body weight gain, visceral fat weight and adipocyte size without affecting the amount of food intake.  Telmisartan treatment reduced the number of CD11c-positive cells and crown-like structures.  Telmisartan reduced the mRNA expressions of M1 macrophage markers, such as TNF-alpha and IL-6, and increased the expression of M2 markers, such as IL-10 and Mgl2.  The reduction of M1 macrophage markers, as well as the increased gene expression of M2 markers especially IL-10, is a possible mechanism for the improvement of insulin sensitivity by telmisartan.

overall_design: Six-week-old male C57BL/6J mice were purchased from CLEA Japan.  The mice were fed a chow that contained 10% of its calories from fat (control) or a high-fat diet (HFD) that contained 30% of its calories from fat for 24 weeks.  The high fat-fed mice were randomized to 3 groups.  Either telmisartan (~3 mg/kg/day) in drinking water (HFD+Tel), candesartan (~3 mg/kg/day) in drinking water (HFD+Can), or a HFD without any drugs (HFD) was administered for the next 5 weeks.  Two mice were treated per group. Epididymal adipose tissues were rapidly removed from each mouse.  Gene expression in epididymal fat tissue was analyzed using a GeneChip® system with the Mouse Genome 430 2.0 Array, which was spotted with 45,101 probe sets (Affymetrix, Santa Clara, CA, USA).  Sample preparation for the array hybridization was performed according to the manufacturer’s instructions.  In short, 5 μg of total RNA was used to synthesize double-stranded cDNA using the GeneChip® Expression 3′-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix).  Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3′-Amplification Reagents for IVT Labeling (Affymetrix).  After fragmentation, the biotinylated cRNA was hybridized to arrays at 45 °C for 16 h.  The arrays were washed, stained with streptavidin-phycoerythrin, and scanned using a probe array scanner.  The scanned chip was analyzed using the GeneChip Analysis Suite software (Affymetrix).  Hybridization intensity data were converted into a presence/absence call for each gene, and changes in gene expression between experiments were detected by a comparison analysis.  Data was shown as the fold change relative to the expression level of normal chow-fed mice.

first: Shiho

last: Fujisaka

first: Isao

last: Usui

first: Ichiro

last: Takasaki

first: Kazuyuki

last: Tobe


title: Gene expression profiles of P7 bladder epithelium compartments isolated from Upk1b mice. (GUDMAP Series ID: 34)

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary: The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing genitourinary tract The central thesis is straightforward. The combination of microdissected tissues and FACS sorted cells plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here delineates the gene expression profiles of the epithelial compartments of the P7 mouse bladder.

overall_design: At postnatal day 7 mice were euthanized by CO2 asphyxiation and the bladders were removed and cut at the bladder neck. The bladder was cut into rings and treated with 1 mg/ml trypsin in Tyrode's solution for 30 minutes at 37 °C. The layers were separated by gentle microdissection and the epithelial layer was further digested in a mixture of Blendzymes 1 & 4 at 37 °C until a single cell suspension was obtained.  The samples were placed in RLT and stored at -80 °C.RNA was prepared and the Epicentre 2-round amplification scheme described under the Lessard Group Protocols on the GUDMAP pages were performed. The Affymetrix GeneChip Mouse Genome 430 2.0 Array was used to interrogate the amplified RNA.

last: Lessard

first: Alfor

last: Lewis


title: Luteolin has anti-inflammatory and neurotrophic effects on microglia

status: Public on Jan 19 2010

city: Regensburg

first: Thomas

last: Langmann

address: Franz-Josef-Strauss-Allee 11

department: University of Regensburg

institute: Institute of Human Genetics

summary:
Our aim was to identify genes that were differentially expressed in microglia stimulated with Lipopolysaccharide, Luteolin, or both.
Affymetrix microarrays were used to analyze RNA samples

overall_design: RNA from control BV-2 cells, and cells treated for 24h with LPS, Luteolin, or LPS+Luteolin was analyzed with Affymetrix GeneChip Mouse Genome 430 2.0 Arrays. Biological triplicates were analyzed for each condition

first: Konstantin

last: Dirscherl


title: Role of Bmi1 in Shh-mediated shift in gene expression levels

city: London

first: Tatiana

last: Subkhankulova

address: 4 Newark Street

department: Neuroscience

institute: Queen Mary University London

summary: We investigated the role of Bmi1 in Shh-mediated shift in gene expression levels

overall_design:
Primary cerebellar granule cell precursors (GCPs) cultures were prepared from P7 Bmi-1-/- or wild type mice as described before {Messer, 1977 #810}.  Cells were grown in Dulbecco MEM high Glucose, supplemented with 10% FCS glutamine, 20 mM KCl and penicillin–streptomycin for 24 hours. Shh (R&D Systems) if appropriate was added for 24 hours to give at final concentration of 3 mg/ml.

We performed 3 biological replicates for both WT and Bmi-1-/- cultures, and 2 biological replicates for both WT and Bmi-1-/- cultures, treated with Shh.

Total RNA was isolated using RNeasy Mini Kit (Qiagen) and reverse-transcribed into double-stranded cDNA with One-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA) and labelled biotin. Biotin-labeled cRNA samples were fragmented randomly to 35–200 bp and hybridized  to GeneChip® Mouse Genome 430 2.0. An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.

first: Olga

last: Shakhova

first: Silvia

last: Marino


title: Genome wide analysis of L1mAb treated SKOV3ip tumors in vivo

status: Public on Jan 15 2010

city: Heidelberg

first: Silke

last: Wolterink

address: INF 580

department: Translationale Immunologie

institute: DKFZ Heidelberg

summary: Recent work has indentified L1-CAM as a novel marker for human carcinoma progression. Functionally, L1-CAM promotes tumor cell invasion and motility, augments tumor growth in nude mice and facilitates experimental tumor metastasis. These functional features qualify L1 as an interesting target molecule for tumor therapy. Here we generated a series of novel mAbs to the L1-CAM ectodomain. Among the novel mAbs, L1-9.3 was selected and its therapeutic potential was analyzed in various isotype variants in a model of SKOV3ip cells growing intraperitoneally in CD1 nude mice. Therapy with the IgG2a variant efficiently prolonged survival and reduced tumor burden. This was accompanied by an increased infiltration of F4/80 positive monocytic cells. Expression profiling of tumor derived mRNA revealed that L1-9.3-IgG2a therapy induced altered expression of cellular genes associated with apoptosis and tumor growth. Our results establish that L1 mAb therapy acts via immunological and non-immunological effector mechanism to block tumor growth.

overall_design: Total RNA obtained from SKOV3ip tumors isolated from L1 9.3/IgG2a or control treated Balb/c nude mice

first: Peter

last: Altevogt


title: Expression data from murine hearts exposed to ischemic preconditioning comparing A2BAR null and wildtype BL6/C57 mice

status: Public on Jan 14 2010

city: Denver

first: Tobias

last: Eckle

state: CO

address: 12700 E 19th Avenue

department: Anesthesiology

institute: UC Denver

summary:
Genetically targeted mice with deficiency for the A2BAR show increased susceptibility to acute myocardial ischemia and are not protected by IP, a powerful strategy for cardioprotection, where short and repeated episodes of ischemia and reperfusion prior to myocardial infarction result in attenuation of infarct size.
The purpose of this study was to identify genes that are potentially under the control of the cardiac A2B adenosine receptor

overall_design: Untreated wildtype and A2BAR-/- mice were compared to wildtype and A2BAR-/- mice with IP treatment following a 2 hours reperfusion period

last: Walter


title: Expression data from B6C3F1 mice treated with 2-butoxyethanol and reduced oxygen

status: Public on Jan 11 2010

city: groton

first: Petra

last: Koza-Taylor

state: CT

address: Eastern Point Road

institute: Pfizer

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

overall_design: Refer to individual Series


title: Expression data from mouse bone marrow derived macrophages

first: Laurel

last: Lenz

address: 1400 Jackson St

institute: National Jewish Health

summary: Macrophages phagocytose bacteria. Certain pathogenic bacteria access and replicate within the cytosol of infected macrophages and induce changes in macrophage gene expression by triggering of innate immune receptors and/or the effects of bacterial virulence factors. We used microarray analysis to identify changes in macrophage gene expression following infection with Listeria monocytogenes.

overall_design:
Macrophages were cultured from bone marrow of female C57BL/6 mice using 10% L-cell conditioned media and mock infected (3 chips) or infected with log phase L. monocytogenes (2 chips). Samples were harvested for RNA isolation at 10 h after infection.

Supplementary file below reports Genesifter-processed data: mean ("P" only) signal intensities and SEM for the MOCK and LM_INF groups.


title: Expression data from B6C3F1 mice treated with baclofen

status: Public on Jan 12 2010

summary: Mice were treated with either 100mg/kg baclofen or 0.5% methylcellulose alone by oral gavage for 1 or 5 days.

overall_design: Mice were sacrificed by cervical dislocation after either a single dose (1day) or 5 daily doses (5 days) of either baclofen or 0.5% methylcellulose two hours after the last dose. The bone marrow from the right humerus, a portion of the left lateral liver lobe and half a cross-section of the spleen were harvested and the RNA was isolated from these tissues using standard Qiagen reagents. Standard Affymetrix protocols were used for GeneChip probe preparations. 59 arrays.

first: William

last: Ladd


title: Mad2-induced chromosome instability leads to lung tumor relapse after oncogene withdrawal

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: Inhibition of an initiating oncogene often leads to extensive tumor cell death, a phenomenon known as oncogene addiction. This has led to the search for compounds that specifically target and inhibit oncogenes as anti-cancer agents. Whether chromosomal instability (CIN) generated as a result of deregulation of the mitotic checkpoint pathway, a frequent characteristic of solid tumors, has any effect on oncogene addiction, however, has not been explored systematically. We show here that induction of chromosome instability by overexpression of the mitotic checkpoint gene Mad2 does not affect the regression of Kras driven lung tumors upon Kras inhibition. However, tumors that experience transient Mad2 overexpression and consequent chromosome instability recur at dramatically elevated rates. The recurrent tumors are highly aneuploid and have varied activation of pro-proliferative pathways. Thus, early CIN may be responsible for tumor relapse after seemingly effective anti-cancer treatments.

overall_design: Lung tumor tissue from TI-K (CCSP-rtTA;TRE-KrasV12), TI-KM (CCSP-rtTA; TRE-KrasV12; TRE-Mad2), recurrence (TI-KM) or normal lung tissue (CCSP-rtTA) was subjected to RNA extraction and individual samples hybridized to array platform MOE430A 2.0 Affymetrix.

first: Rocio

last: Sotillo

first: Juan-Manuel

last: Schvartzman

first: Nick

last: Socci

first: Robert

last: Benezra


title: Expression data from B6C3F1 mice treated with 2-butoxyethanol

summary: Mice were dosed  with 2-BE (900mg/kg) or vehicle by oral gavage and sacrificied either after 4 hours of a single dose or after 7 days of daily dosing.

overall_design: Mice were euthanased by cervical dislocation under ketamine / acepromazine (100 mg/kg / 5 mg/kg, I.P) anesthesia. The bone marrow from the right humerus, a portion of the left lateral liver lobe and half a cross-section of the spleen were harvested and the RNA was isolated from these tissues using standard Qiagen reagents. Standard Affymetrix protocols were used for GeneChip probe preparations. 44 arrays.


title: Expression data from B6C3F1 mice treated with reduced oxygen

summary: Mice received decreasing oxygen concentrations from 21% to 6% O2 for ~ 30 minutes. Then, the mice remained an additional 120 minutes at 6% O2, control mice were placed insimilarchambers but recieved normal (21%) oxygen.

overall_design: Mice were euthanased by cervical dislocation under ketamine / acepromazine (100 mg/kg / 5 mg/kg, I.P) anesthesia. The bone marrow from the right humerus, a portion of the left lateral liver lobe and half a cross-section of the spleen were harvested and the RNA was isolated from these tissues using standard Qiagen reagents. Standard Affymetrix protocols were used for GeneChip probe preparations. 39 arrays.


title: Expression Data from Bone Marrow Progenitor-Derived Adipocytes, White Adipocytes and Brown Adipocytes.

status: Public on Jan 08 2010

city: Aurora

first: Dwight

last: Klemm

address: 12700 East 19th Ave., Mail Stop B-133

department: Cardiovascular Pulmonary Research

institute: University of Colorado Denver

summary:
We have identified a population of adipocytes in fat tissue that arise from bone marrow-derived progenitor cells.
We used microarrays to compare the global gene expression patterns of the bone marrow progenitor-derived adipocytes as well as conventional white and brown adipocytes to evaluate the relationship between these adipocyte subpopulations.

overall_design: Gonadal fat tissue (for white adipocytes) and intrascapular fat tissue (for brown adipocytes) was digested with collagenase and adipocytes were recovered by centrifugation/flotation.  Bone marrow derived adipocytes were isolated from the adipocyte fraction of gonadal fat tissue from mice receiving bone marrow tranplants from donors expressing either green fluorescent protein (GFP) or beta-galactosidase (LacZ) by flow cytometry.

middle: J


title: Gene profiling of quiescent and activated skeletal muscle satellite cells by an in vivo approach

status: Public on Jan 04 2010

city: paris

first: didier

last: montarras

address: 25, rue du dr. Roux

department: developmental biology

institute: institut pasteur

summary:
The satellite cell of skeletal muscle provides a paradigm for quiescent and activated tissue stem cell states. We have carried out transcriptome analyses by comparing satellite cells from adult skeletal muscles, where they are mainly quiescent, with cells from growing muscles, regenerating (mdx) muscles, or with cells in culture, where they are activated. Our study gives new insights into the satellite cell biology during activation and in respect with its niche.
We used microarrays to study the global programme of gene expression underlying adult satellite cell quiescence compared to activation states and to identify distinct classes of up-regulated genes in these two different states

overall_design: Skeletal muscle satellite cells were isolated by flow cytrometry using the GFP fluorescence marker from Pax3GFP/+ mice skeletal muscle. The transcriptome of quiescent satellite cells from adult Pax3GFP/+ muscle was compared to the transcriptome of activated satellite cells obtained from three different samples: 1) regenerating Pax3GFP/+:mdx/mdx muscle (Ad.mdx) , 2) growing 1 week old Pax3GFP/+ muscle (1wk), and 3) adult Pax3GFP/+ cells after 3 days in culture (Ad.cult).

first: Giorgia

last: Pallafacchina

first: Didier

last: Montarras

first: Béatrice

last: Regnault

first: Margaret

last: Buckingham


title: Interactions between developing B-lymphocytes and stromal cells reveal complex interactions and two-way communication

status: Public on Jan 05 2010

city: Toronto

first: Sasan

last: Zandi

address: 101 college St

institute: UHN

summary:
Full title: Genomics based analysis of interactions between developing B-lymphocytes and stromal cells reveal complex interactions and two-way communication

In order to identify extra cellular signals that promote B lymphocyte development we created a database with approximately 400 receptor ligand pairs and software matching gene expression data from two cell populations to obtain information about possible communication pathways. Using this database and gene expression data from NIH3T3 cells (unable to support B cell development) and OP-9 cells (strongly supportive of B cell development) and data from pro-B and pre-B cells as well as mature peripheral B-lineage cells, we were able to identify a set of potential stage and stromal cell restricted communication pathways. Functional analysis of some of these potential ways of communication allowed us to identify BMP-4 as a potent stimulator of B-cell development in vitro. Further, the analysis suggested that there existed possibilities for progenitor B cells to send signals to the stroma. The functional consequences of this were investigated by co-culture experiments revealing that the co-incubation of stromal cells with pro-B cells altered both the morphology and the gene expression pattern in the stromal cells.

overall_design: OP9 Stromal cells has been cultured with and without primary PreB cells drived from LSK cells in culture or PreB cell lines 230-238. OP9 cells has been isolated by FACS and microarray performed to study the effect of PreB cells on OP9's at the level of RNA expression. The results have been compared with 3T3 and MC3T3 cells.

first: Jenny

last: Zetterblad

first: Hong

last: Qian

last: Mansson

first: Anna

last: Lagergren

first: Frida

last: Hansson

first: Nils

last: Paulsson

first: David

last: Bryder

first: Mikael

last: Sigvardsson