title: Impact of dietary fatty acids on gene expression of liver-specific knockout of cytochrome P450 reductase

status: Public on Oct 09 2010

city: Lincoln

first: Concetta

middle: Christine

last: DiRusso

state: NE

department: Nutrtion and Health Science

institute: University of Nebraska

summary: In the present study, we explored the hypothesis that the fatty liver phenotype and associated gene expression changes associated with the specific deletion of the POR gene in adult mouse liver could be abrogated by supplementation of the mouse diet with the very long chain highly unsaturated fatty acids, arachidonic acid (C20:4ω6), eicosapentaenoic acid (C20:5ω3) and docosahexaenoic acid (C22:6ω3).  We expected the fatty liver phenotype would not be reduced by the polyunsaturated fatty acids linoleic (C18:2ω6) or linolenic acid (C18:3ω3), since these accumulated in the fatty livers of LivPORKO animals.  This proved to be the case.  However, we also made two surprising observations.  First, control animals fed a diet enriched in PUFA had fatty livers and gene expression profiles similar to animals fed a lard diet, which was deficient in both PUFA and HUFA.   Second, while a diet enriched in HUFA did result in reduced steatosis in livers of the LivPOKO animals, fat accumulation was still elevated relative to controls.  Array analyses indicated most differences in gene expression were related to fatty acid metabolism and could explain differences in fat accumulation in LivPORKO livers with dietary treatment.

overall_design: Generation of the founder line with hepatic ablation of POR is described in Wu, et al. ((2003) Genesis 36, 177-181).  Male test animals used in this study had the genotype Alb-Cre+/-/POR-lox+/+ and were called LivPORKOs. For each series of experiments, mice were placed on one of three synthetic diets upon weaning. Siblings of the same genotype were randomized between dietary groups. Upon weaning (four weeks after birth) male mice of each genotype were placed on one of the test diets for eight weeks. Synthetic diets used base diet AIN-93G and contained 18.7% protein, 64.7% carbohydrate, 5% fiber, 6% fat, 0.025% cholesterol, 0.008% sodium cholate, and 3.97 kcal per gram.  The added fats were as follows: 6% lard (lard diet); 6% canola oil (canola diet); or 3.27% ARASCO oil (Martek Biosciences Corp.) and 2.73% menhadin oil (fish/fungal diet). After 8 weeks on the test diets (12 weeks of age) the animals were fasted for four hours prior to sacrifice. Liver samples were placed in mRNAlater® for mRNA analysis and immediately frozen and stored at -80°C. To reduce variability between arrays, three RNA samples from individual mice of the same genotype/diet group were pooled using equivalent RNA amounts for each animal.  Three microarrays on three pools were done per genotype/diet.  The quality of RNA was analyzed using an Agilent 2100 Bioanalyzer.  Three micrograms of RNA was reverse transcribed to make cDNA.  Hybridization of cDNA, washing, and scanning of the Affymetrix GeneChip Mouse Genome 430 2.0 (containing 45,101 probe sets representing over 34,000 mouse genes) was performed according to standard Affymetrix protocol.

first: Whitney

last: Sealls


title: Expression profiles of villus and crypt layers of large intestine from C57Bl/6, Apc1638N+/-, and p21-/-  mice.

status: Public on Oct 06 2010

city: Bronx

first: Georgia

last: Corner

state: NY

address: 111 East 210th Street

department: Oncology

country: USA

institute: Albert Einstein Comprehensive Cancer Center

summary:
Expression profiles obtained from the villus and crypt layers of murine large intestine can elucidate the process of differentiation undergone by epithelial cells as they migrate from the undifferentiated bottom of the crypt to the villus tip before being shed into the intestinal lumen.  This series includes profiles from wild type mice, as well as mice harboring mutations in genes (APC and p21) which play key roles in the differentiation process.
We used microarrays to characterize gene expression profiles at the base of the crypt and at the villus tip of the lumenal layer of the large intestine in order to better understand the process of differentiation and eventual shedding undergone by cells of the large intestinal epithelium.

overall_design: Four wild type, four APC1638+/- and four p21-/- mice were sacrified and the large intestines dissected out.  Cells from the villus tip and from the bottom of the crypt were isolated from the lumenal face of the each large intestine using the Weiser method of sequential elution.  RNA was extracted from each eluted sample and used to hybridize to Affymetrix 3' expression arrays.

first: Leonard

last: Augenlicht

first: Donghai

last: Wang


title: Role of sex chromosome complement in autosomal gene expression

status: Public on Oct 02 2010

city: London

first: Patrick

middle: JEC

last: Wijchers

address: Imperial College London, Hammersmith Campus, Du Cane Road

department: Gene Control Mechanisms and Disease Group

country: United Kingdom

institute: MRC Clinical Sciences Centre

summary: It has generally been assumed that most differences between males and females are due to developmental and hormonal differences between the sexes. Here we investigate the contribution of sex chromosomal complement to such sexual dimorphisms. These genome-wide transcription profiling showed that the expression of hundreds of autosomal genes was sensitive to sex chromosome complement, rather than gender. The existence of such differences between males and females holds important implications for understanding sexual dimorphisms in physiology and disease hitherto attributed solely to gender or hormonal effects.

overall_design: Thymic total RNA was isolated from 7-8 week old mice, with 3 biological replicates for each of four genotypes with different sex chromosome complements

first: Richard

last: Festenstein


title: Diosgenin supplementation effect on liver

status: Public on Oct 08 2010

city: Shizuoka

first: Noriyuki

last: Miyoshi

country: Japan

institute: University of Shizuoka

summary: Expression profile of liver of ICR mice (13-week old) treated with control diet (CRF-1) or CRF-1 containing 500 ppm diosgenin for 4 weeks.

overall_design: Nine-week old ICR mice were fed with a basal diet (CRF-1) or that containing 500 ppm diosgenin for 4 weeks ad libitum (n = 3 in each group). Food intake and body weight were measured on a weekly basis for the duration of the study.

first: Hiroshi

last: Ohshima


title: Hepatic xenobiotic metabolizing enzyme gene expression through the life stages of the mouse

status: Public on Oct 01 2010

city: RTP

first: Hongzu

last: Ren

state: NC

address: 109 TW Alexander Dr

institute: US Environmental Protection Agency

summary:
Using full-genome arrays, the expression of all XMEs was examined during fetal (gestation day (GD) 19), neonatal (postnatal day (PND) 7), prepubescent (PND30), middle age (12 mon), and old age (18 and 24 mon) in the C57Bl6/J mouse liver and compared to young adults.  Fetal and neonatal life stages had a dramatic effect on XME expression compared to the relatively minor effects of old age. At all life stages except PND30 down-regulated genes outnumbered up-regulated genes.  The altered XMEs included those in all of the major metabolic phases including phase I (alcohol and aldehyde dehydrogenase and Cyp genes), phase II (aldo-keto reductase, glutathione-S-transferases, sulfotransferases and UDP-glucuronosyl transferases) and phase III (transporters). We have generated a comprehensive catalog of XME hepatic gene changes through the life stages of the mouse that can be used to predict chemicals and chemical classes different life stages are more sensitive to. Some CEL files used in this study have been submitted through GSE21224.

Keywords: gene expression/microarray

overall_design: We characterized gene expression changes in the developing mouse liver at gestational days (GD) 19), neonatal (postnatal day (PND) 7), prepubescent (PND30), middle age (12 mon), and old age (18 and 24 mon) in the C57Bl6/J mouse liver using full-genome microarrays and compared these changes to that in the adult liver.. We also compared results to GD19, PND32, and PND67 C3H mice.  Total RNA was isolated from liver samples and gene expression analyzed using Affymetrix Mouse 430 2.0 GeneChips.  Data from 28 samples, four mice in each of the age groups for C57BL/6 and C3H, were analyzed.

first: Janice

middle: S

last: Lee

first: William

middle: O

last: Ward

first: Jie

last: Liu

first: Beena

last: Vallanat

first: Don

middle: A

last: Delker

first: J

middle: C

last: Corton


title: Reverse myocardial remodeling by aortic bending debanding in mice

status: Public on Sep 30 2010

city: Oslo

first: Johannes

middle: L

last: Bjørnstad

address: Kirkeveien 166

department: Dept. of Cardiothoracic Surgery

country: Norway

institute: Oslo University Hospital Ulleval

summary:
The objective of this study was to identify alterations in gene expression during reverse myocardial remodeling in a mouse model of reversible pressure overload.
Mice were subjected to 4 weeks of aortic banding (AB) or sham procedure (sAB), banding and subsequent debanding (DB3), or sham procedure and subsequent debanding (sDB3), with saccrifice 3 days after debanding.

overall_design: Microarray screening was performed in 3 mice from each group. Sham was used as control, and we used an ANOVA model for each gene programmed in R-script to identify the effect of debanding.

first: Ståle

last: Nygård


title: Expression data from mouse adult fibroblasts with  Rb deletion and/or p53DD expression exposed to cisplatin (CDDP)

city: Philadelphia

first: Erik

last: Knudsen

state: PA

address: 233 S 10th St

department: Cancer Biology

institute: Kimmel Cancer Center

summary:
The RB and p53 tumor suppressor pathways regulate the transcription of genes involved in cell cycle progression, DNA replication, DNA repair, and apoptosis. These tumor suppressors are critical modulators of the response to genotoxic damage and both pathways are frequently inactivated in human cancers.
We used microarrays to monitor gene expression patterns upon exposure to cisplatin treatment in fibroblasts harboring loss/inactivation of RB and/or p53.

overall_design: We generated mouse adult fibroblasts harboring loss/inactivation of RB and/or p53 and subjected these cell populations to cisplatin treatment for 24 hours. Treated cell populations were allowed to recover from cisplatin exposure, generating a recurred cell popuation. Untreated and recurred cell populations were then subjected to RNA extraction and hybridization on Affymetrix microarrays.

first: Kathleen

last: McClendon

first: Jeffry

last: Dean

first: Adam

last: Ertel


title: Transcriptional ontogeny of the developing liver

summary:
We characterized gene expression changes in the developing mouse liver at gestational days (GD) 11.5, 12.5, 13.5, 14.5, 16.5, and 19.5 and in the neonate (postnatal day (PND) 7 and 30) using full-genome microarrays and compared these changes to that in the adult liver. The fetal liver, and to a lesser extent the neonatal liver, exhibited dramatic differences in gene expression compared to adults. Canonical pathway analysis of the fetal liver signature demonstrated increases in functions important in cell replication and DNA fidelity whereas most metabolic pathways of intermediary metabolism were suppressed. Comparison of the dataset to a number of previously published datasets revealed 1) a striking similarity between the fetal liver and that of the pancreas in both mice and humans, 2) a nucleated erythrocyte signature in the fetus and 3) suppression of most xenobiotic metabolism genes throughout development, except a number of transporters associated with expression in hematopoietic cells.

Keywords: gene expression/microarray

overall_design: We characterized gene expression changes in the developing mouse liver at gestational days (GD) 19 and in the neonate (postnatal day (PND) 7 and 30) using full-genome microarrays and compared these changes to that in the adult liver. Total RNA was isolated from liver samples and gene expression analyzed using Affymetrix Mouse 430 2.0 GeneChips. Data from 16 samples, with four mice in each of the four age groups, were analyzed.

first: Geremy

last: Knapp

first: Barbara

last: Abbott

first: Seth

middle: J

last: Karp


title: In vitro carcinogenicity testing with Balb/c 3T3 Cells treated with various chemical carcinogens

city: Hannover

first: Astrid

last: Rohrbeck

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Department of Toxicology

country: Germany

institute: Medizinische Hochschule Hannover

summary: Background: Information on the carcinogenic potential of chemicals is only availably for High Production Volume products. There is however, a pressing need for alternative methods allowing for the chronic toxicity of substances, including carcinogenicity, to be detected earlier and more reliably. Here we applied advanced genomics to a cellular transformation assay to identify gene signatures useful for the prediction of risk for carcinogenicity.  Methods: Genome wide gene expression analysis and qRT-PCR were applied to untransformed and transformed Balb/c 3T3 cells that exposed to 2, 4-diaminotoluene (DAT), benzo(a)pyrene (BaP), 2-Acetylaminoflourene (AAF) and 3-methycholanthrene (MCA) for 24h and 120h, at different concentrations, respectively. Furthermore, various bioinformatics tools were used to identify gene signatures predicting for the carcinogenic risk.  Results: Bioinformatics analysis revealed distinct datasets for the individual chemicals tested while the number of significantly regulated genes increased with ascending treatment concentration of the cell cultures. Filtering of the data revealed a common gene signature that comprised of 13 genes whose regulation in cancer tissue has already been established. Strikingly, this gene signature was already identified prior to cell transformation therefore confirming the predictive power of this gene signature in identifying carcinogenic risks of chemicals. Comparison of fold changes determined by microarray analysis and qRT-PCR were in good agreement.   Conclusion: Our data describes selective and commonly regulated carcinogenic pathways   observed in an easy to use in vitro carcinogenicity assay. Here we defined a set of genes which can serve as a simply assay to predict the risk for carcinogenicity by use of an alternative in vitro testing strategy.

overall_design: Balb/c 3T3 cells were seeded at 200 cells in each 60 x 15 mm culture dish with 4 ml M10F, using six culture dishes for every treatment. When cells reached a confluence of 60-65%, the culture medium was removed and replaced with fresh medium containing all tested chemicals at a specific concentration and two time points (24 and 120h).   First we treated the cells both 24h and 120h with concentrations reported in the literature (0.5µM BaP, 50µM DAT, 25µM AAF and 2µM MCA). In a second approach IC20 concentrations were investigated for each chemical at both time points. The concentrations determined for IC20 ranged from 1.5 µM BaP to 700 µM DAT for 24h of treatment, and from 0.1 µM BaP or MCA to 10µM AAF for 120h of treatment. Balb/c 3T3 cells treated with 0.75% DMSO alone were kept as controls. Each experiment was run in triplicate.

first: Jürgen

last: Borlak

first: Rafaella

last: Corvi

first: Gabriela

last: Salinas

first: Kerstin

last: Maaser

first: Susan

last: Salovaara

first: Jens

last: Linge


title: Profiling gene expression in 32Dcl3 cells following Xbp1 retrovirus vector transfection

city: Tokyo

first: Morito

last: Kurata

address: bunkyo-ku yusima1-5-45

department: Comprehensive Patho.

institute: Tokyo Med. & Dent. univ.

summary: The significant changes of hematopoietic cells induced by Xbp1S expression indicate that there is global alteration in gene expression. UPR induces transcription of Xbp1, and phosphorylation of the ER transmembrane kinase IRE1 initiates UPR-mediated mRNA splicing of Xbp1, resulting in the production of Xbp1S, an active form of a basic leucine zipper transcription factor. In the present study, Xbp1S retrovirus vector infected 32cl3 cells show cell cycle arrest and myeloid differentiation. Xbp1S may modulate important genes of differentiation and the cell cycle.

overall_design: RNA samples extracted from 32Dcl3 cells with pMIG (empty vector), pMY-Xbp1U (unspliced form) and pMY-Xbp1S (spliced form) retroviral vector transfected cells were subjected to expression profiling using the Affymetrix GeneChip microarray system.

first: Takuro

last: Nakamura


title: Identification of angiotensin II-responsive genes in the kidney

city: Durham

first: Natalia

last: Makhanova

address: 106 Research Drive

department: Nephrology

institute: Duke University

summary: In order to characterize gene expression networks linked to AT1 angiotensin receptors in the kidney, we carried out genome-wide transcriptional analysis of  RNA from kidneys of wild-type (WT) and AT1A receptor-deficient mice (KOs) at baseline and after 2 days of angiotensin II infusion (1 ug/kg/min), using Affymetrix GeneChip Mouse Genome 430 2.0 Arrays. At baseline, 405 genes were differentially expressed (>1.5X) between WT and KO kidneys. Of these, more than 80% were up-regulated in the KO group including genes involved in inflammation, oxidative stress, and cell proliferation. After 2 days of angiotensin II infusion in WT mice, expression of ~805 genes was altered (18% up-regulated, 82% repressed). Genes in metabolism and ion transport pathways were up-regulated while there was attenuated expression of protective genes against oxidative stress including glutathione synthetase and mitochondrial SOD2. Angiotensin II infusion has little effect on blood pressure in KOs.  Nonetheless, expression of more than 250 genes was altered in kidneys from KO mice during angiotensin II infusion; 14% were up-regulated, while 86% were repressed including genes involved in immune responses, angiogenesis, and glutathione metabolism.  Between WT and KO kidneys during angiotensin II infusion, 728 genes were differentially expressed; 10% were increased and 90% were decreased in the WT group.  Differentially regulated pathways included those involved in ion transport, immune responses, metabolism, apoptosis, cell proliferation, and oxidative stress. This genome-wide assessment should facilitate identification of critical distal pathways linked to blood pressure regulation.

overall_design: To define gene expression patterns in kidney triggered by of activation AT1 receptors, we used genome-wide transcriptional analysis of RNA from kidneys of wild-type and AT1A receptor-deficient mice at baseline and after 2 days of angiotensin II infusion (1 ug/kg/min), using Affymetrix GeneChip Mouse Genome 430 2.0 Arrays. All of the experiments were conducted with male mice  2.5 months old and included 3 mice per experimental group. Synthesis of cRNA, hybridization and scanning of chips were conducted by Duke University microarray core facility (Duke University, Durham, NC).

first: Steven

middle: D

last: Crowley

first: Robert

last: Griffiths

first: Thomas

middle: M

last: Coffman


title: Acute Lymphocytic Leukemia versus associated xenografts

status: Public on Oct 18 2010

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

summary: Leukemic cells from either peripheral blood or bone marrow were obtained from 6 patients with acute lymphocytic leukemia.  These cells were used to generate mouse xenografts and a comparison was made between those two sample sources.

overall_design: Six pairs of human leukemia and associated xenografts are compared.

first: Sebastien

last: Morisot

first: Alan

last: Wayne

first: Paul

last: Meltzer

first: Curt

middle: I

last: Civin

first: Patrick

last: Brown


title: Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes

city: Davis

first: Seth

middle: Eric

last: Frietze

state: CA

address: 451 Health Sciences Dr. GBSF 4617A

department: Genome Center

institute: UC Davis

summary: Background: The orphan nuclear receptor TR4 (human testicular receptor 4 or NR2C2) plays a pivotal role in a variety of biological and metabolic processes. With no known ligand and few known target genes, the mode of TR4 function was unclear. Results: We report the first genome-wide identification and characterization of TR4 in vivo binding. Using chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq), we identified TR4 binding sites in 4 different human cell types and found that the majority of target genes were shared among different cells. TR4 target genes are involved in fundamental biological processes such as RNA metabolism and protein translation. In addition, we found that a subset of TR4 target genes exerts cell-type specific functions.  Analysis of the TR4 binding sites revealed that less than 30% of the peaks from any of the cell types contained the DR1 motif previously derived from in vitro studies, suggesting that TR4 may be recruited to the genome via interaction with other proteins.  A bioinformatics analysis of the TR4 binding sites predicted a cis regulatory module involving TR4 and ETS transcription factors. To test this prediction, we performed ChIP-seq for the ETS factor ELK4 and found that 30% of TR4 binding sites were also bound by ELK4.  Motif analysis of the sites bound by both factors revealed a lack of the DR1 element, suggesting that TR4 binding at a subset of sites is facilitated through the ETS transcription factor ELK4. Further studies will be required to investigate the functional interdependence of these two factors. Conclusions: Our data suggest that TR4 plays a pivotal role in fundamental biological processes across different cell types. In addition, the identification of cell type specific TR4 binding sites enables future studies of the pathways underlying TR4 action and its possible role in metabolic diseases.

overall_design: This is one part of the study that involved the examination of HepG2 gene expression. Biological triplicate Illumina Sentrex bead arrays.

first: Henriette

last: O'Geen

first: Peggy

last: Farnham


title: Persistence of effector memory Th1 cells is regulated by the homeobox only protein Group1 Hopx-/-, Group2 Hopx+/-, Group3 Hopx+/+

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: Hopx appears to be needed for persistence of Th1 effector memory cells. IFN-gamma-producing Th cells are significantly reduced in Hopx-deficient mice compared to Hopx-expressing littermates and Hopx-deficient Th1 cells show a defective persistence upon adoptive transfer. Moreover, Hopx protects Th1 cells from Fas-mediated cell death in vitro. To further dissect the role of Hopx and to identify target genes of Hopx, we have performed transcriptome analysis to compare gene expression in Hopx-deficient versus Hopx-competent Th1 cells. In agreement with the role of Hopx in supporting survival of Th1 effector memory cells, anti-apoptotic cells were up-regulated and pro-apoptotic genes were down-regulated in Hopx-competent compared to Hopx-deficient Th1 cells.

overall_design: Gene expression profiles of Hopx-/- versus Hopx+/- and Hopx+/+ Th1 cells, respectively. Naïve Th cells were isolated from Hopx+/+, Hopx+/- and Hopx-/- OT2 mice and activated in vitro with their cognate antigen (OVA) under Th1 polarizing conditions. On day 6, viable cells were repeatedly activated. On day 12, viable cells were harvested and compared using Affymetrix 430A Version 2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: Hopx-/-, Group2: Hopx+/-, Group3: Hopx+/+. Lists of differentially regulated genes were created using High Performance Chip Data Analysis (HPCDA) with Bioretis database (http://www.bioretis-analysis.de). Worldwide data sharing is possible via Bioretis, please ask the authors.

first: Inka

last: Albrecht

first: Uwe

last: Niesner

first: Marko

last: Janke

first: Astrid

last: Menning

first: Christoph

last: Loddenkemper

first: Anja

last: Kühl

first: Inga

last: Lepenies

first: Maria

middle: H

last: Lexberg

first: Kerstin

last: Westendorf

first: Kristyna

last: Hradilkova

first: Joachim

middle: R

last: Grün

first: Alf

last: Hamann

first: Jonathan

last: Epstein

first: Hyun-Dong

last: Chang

first: Koji

last: Tokoyoda

first: Andreas

last: Radbruch


title: Molecular Events Initiating B Cell Fate Specification

city: Rochester

first: Kay

last: Medina

state: MN

address: 200 1st Street SW

department: Immunology

institute: Mayo Clinic

summary:
Functional genomics comparison of EBFko, Pax5ko, and RAG2ko cell lines.
Identify gene signatures associated with specfication and commitment to the B cell fate.

overall_design: Cultured cells harvested and for RNA extraction and hybridization to Affymetrix 430 2.0 Arrays.


title: TGF-β1 Accelerates Dendritic Cell Differentiation from Common Dendritic Cell Progenitors (CDPs) and Directs Subset Specification Towards Conventional Dendritic Cells

status: Public on Oct 04 2010

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary: Dendritic cells (DCs) in lymphoid tissue comprise conventional DCs (cDCs) and plasmacytoid DCs (pDCs) that develop from common DC progenitors (CDPs). CDPs are Flt3+c-kitintM-CSFR+ and reside in bone marrow. Here we describe a two-step culture system that recapitulates DC development from c-kithiFlt3-/lo multipotent progenitors (MPPs) into CDPs and further into cDC and pDC subsets. MPPs and CDPs are amplified in vitro with Flt3 ligand, stem cell factor, hyper-IL-6 and insulin- like growth factor-1. The four-factor cocktail readily induces self-renewal of MPPs and their progression into CDPs and has no self-renewal activity on CDPs. The amplified CDPs respond to all known DC poietins and generate all lymphoid tissue DCs in vivo and in vitro. Additionally, in vitro CDPs recapitulate the cell surface marker and gene expression profile of in vivo CDPs and possess a DC-primed transcription profile. Transforming growth factor-β1 (TGF-β1) impacts on CDPs and directs their differentiation towards cDCs. Genome-wide gene expression profiling of TGF-β1-induced genes identified transcription factors, such as interferon regulatory factor-4 (IRF-4) and RelB, that are implicated as instructive factors for cDC subset specification. TGF-β1 also induced the transcription factor inhibitor of differentiation/DNA binding 2 (Id2) that suppresses pDC development. Thus, TGF-β1 directs CDP differentiation into cDC by inducing both cDC instructive factors and pDC inhibitory factors.

overall_design:
20 samples in total.

Multipotent progenitor
- MPP_1
- MPP_2
Common dendritic cell progenitor
- CDP_1
- CDP_2
Plasmacytoid dendritic cell
- pDC_1
- pDC_2
Conventional dendritic cell
- cDC_1
- cDC_2
In vivo common dendritic cell progenitor
- In vivo CDP_1
- In vivo CDP_2

Untreated common dendritic cell progenitor (CDP)
- CDP_0h_1
- CDP_0h_2
TGF-beta1 treated (4 hours) CDP
- CDP_4h_1
- CDP_4h_2
TGF-beta1 treated (8 hours) CDP
- CDP_8h_1
- CDP_8h_2
TGF-beta1 treated (12 hours) CDP
- CDP_12h_1
- CDP_12h_2
TGF-beta1 treated (24 hours) CDP
- CDP_24h_1
- CDP_24h_2

first: Piritta

last: Felker

first: Kristin

last: Sere

first: Qiong

last: Lin

first: Christiane

last: Becker

first: Mihail

last: Hristov

first: Thomas

last: Hieronymus


title: Medulloblastoma tumors derived from Ptch+/-p53-/- transgenic mouse allografted in nude mice

status: Public on Sep 29 2010

city: Cambridge

first: Michael

last: Morrissey

state: MA

address: 250 Massachusetts Ave

institute: Novartis Institutes for Biomedical Research

summary: Nude mice were allografted with medulloblastoma tumors derived from Ptch+/-p53-/- transgenic mouse and treated with vehicle or NVP-LDE225.

overall_design: RNA was prepared from tumours from vehicle or NVP-LDE225 treated nude mice allografted with medulloblastoma tumors derived from Ptch+/-p53-/- transgenic mouse and hybridized on the Affymetrix Mouse Genome 430A 2.0 RNA expression microarray.

first: Silvia

last: Buonamici


title: Medulloblastoma tumors derived from Ptch+/-HIC+/- transgenic mouse allografted in nude mice

summary: Nude mice were allografted with medulloblastoma tumors derived from Ptch+/-HIC+/- transgenic mouse and treated with vehicle or NVP-LDE225.

overall_design: RNA was prepared from tumours from vehicle or NVP-LDE225 treated nude mice allografted with medulloblastoma tumors derived from Ptch+/-HIC+/- transgenic mouse and hybridized on the Affymetrix Mouse Genome 430A 2.0 RNA expression microarray.


title: Targeting resistance to Smoothened antagonists by inhibiting the PI3K pathway

first: John

middle: E

last: Monahan

department: Oncology Translational Research

institute: Novartis

type: Genome variation profiling by genome tiling array

summary: Mutations in Hedgehog (Hh) pathway genes, leading to constitutive  activation of Smoothened (Smo), occur in sporadic medulloblastoma, the most common brain cancer in children. Antagonists of Smo induce tumor regression in mouse models of medulloblastoma and hold great promise for targeted therapy for this tumor. However, acquired resistance has emerged as one of the major challenges of targeted cancer therapy. Here, we describe novel mechanisms of acquired resistance to Smo antagonists in medulloblastoma. NVP-LDE225, a potent and selective Smo antagonist, inhibits Hh signaling and induces tumor regressions in allograft models of medulloblastoma that are driven by mutations of Patched (Ptch), a tumor suppressor in the Hh pathway. However, after long-term treatment, evidence of acquired resistance was observed. Genome-wide profiling of resistant tumors revealed distinct mechanisms to evade the inhibitory effects of Smo antagonists. Chromosomal amplification of Gli2, a downstream effector of Hh signaling, reactivated Hh signaling and restored tumor growth. Analysis of pathway gene-expression signatures selectively deregulated in resistant tumors identified increased phosphoinosite-3-kinase (PI3K) signaling as another potential resistance mechanism. Probing the functional relevance of increased PI3K signaling, we showed that the combination of NVP-LDE225 with the dual PI3K/mTOR inhibitor NVP-BEZ235 markedly delayed the development of resistance. Our findings have important clinical implications for future treatment strategies in medulloblastoma.

overall_design:
mRNA profiling: RNA was prepared from tumours from vehicle or NVP-LDE225 treated nude mice allografted with medulloblastoma tumors derived from Ptch+/-p53-/- transgenic mouse and hybridized on Affymetrix Mouse Genome 430 2.0 RNA expression array. The dosage terminology (BID & QD) reflects the dosing schedule, where BID = twice a day, QD = once a day.
aCGH: DNA was prepared from tumors from vehicle or NVP-LDE225 treated nude mice allografted with medulloblastoma tumors derived from Ptch+/-p53-/- transgenic mouse and hybridized on Agilent mouse CGH 244K Array.


title: UC San Diego_Friedmann_Kang_Human fibroblast knockdown

status: Public on Sep 25 2010

city: La Jolla

first: Tae Hyuk

last: Kang

address: 9500 Gilman Drive # 0634

department: Pediatrics

institute: University of California, San Diego

summary: To characterize mechanisms responsible for the CNS dopamine deficiency and the resulting neuropathology caused by deficiency of the housekeeping purine salvage function hypoxanthine guanine phospho- ribosyltransferase (HPRT) in the Lesch Nyhan Disease (LND), we have used microarray-based methods of global gene expression together with quantitative PCR and Western blot analysis to identify dysregulation of genes and aberrant cellular processes in human fibroblasts and in SH-SY5Y neuroblastoma cells made HPRT-deficient by transduction with a retrovirus stably expressing an shRNA targeted against HPRT. Analysis of the microarray expression data by Gene ontology (GO) and Gene Set Enrichment Analysis (GSEA) as well as by GeneSpring GX10 and Panther Classification System reveal that HPRT deficiency is accompanied by aberrations in a variety of pathways known to regulate neurogenesis or to be implicated in neurodegenerative disease, including the canonical Wnt/β-catenin and the Alzheimer’s disease/presenilin signaling pathways. Dysregulation of the Wnt/β-catenin pathway is confirmed by Western blot demonstration of cytosolic sequestration of β-catenin during in vitro differentiation of the SH-SY5Y cells toward the neuronal phenotype. We also demonstrate that two key transcription factor genes known to be regulated by Wnt signaling and to be vital for the generation and function of dopaminergic neurons; i.e., Lmx1a and Engrailed 1, are down-regulated in the HPRT knockdown SH-SY5Y cells. In addition to the Wnt signaling aberration, we found that expression of presenilin-1 shows a severely disturbed expression in HPRT-deficient cells, reflected by marked instability of the 23kDa C-terminal fragment of presenilin-1 in knockdown cells.  Western blot analysis of primary cultures of two LND patients with 2.5% and 0% residual HPRT activity also shows dysregulated b-catenin and presenilin-1 expression, including elevated levels of cytosolic phospho-catenin and, in one of the two patient cells, failure of nuclear transport. Similarly, the presenilin-1 processing defect was most clearly demonstrated by markedly increased levels of both the N-terminal and C-terminal presenilin-1 fragments in the human cell line with no detectable residual enzyme activity but less marked over-expression in the cell with 2.5% residual enzyme activity. These demonstrations of dysregulated Wnt and presenilin-1 signaling and impaired expression of transcription factors necessary for dopaminergic development reveal broad pleitropic neuro-regulatory defects played by HPRT and suggest new directions for investigating mechanisms of aberrant neurogenesis and neuropathology in LND and potential new targets for restoration of effective signaling in this neuro-developmental defect.

overall_design: For microarray analysis, RNAs from triplicate independent cultures of vector-infected HPRT knockdown and control fibroblasts were prepared separately, pooled and used to prepare cRNA and finally subjected to microarray transcriptional analysis in triplicate. The integrity of total RNA from HPRT knockdown and control cells was confirmed by bioanalyzer (Agilent Technologies, Santa Clara, CA). The quality of total RNA samples from HPRT knockdown and control cells was assessed by 2100 bioanalyzer before application to microarray analysis. We determined that the RNA integrity number (RIN), (maximal degradation = 1; maximal molecular integrity = 10) was 10 for both the normal and knockdown cells (data not shown), indicating that isolated RNA samples were of sufficiently high quality to permit subsequent preparation of cDNA for microarray analysis. Microarray transcriptional analysis was performed in triplicate using the HumanWG-6 v3.0 Expression BeadChip system (Illumina, San Diego, CA). All reagents were obtained from HumanWG-6 v.3 Expression BeadChip Kit (Illumina) and all experimental processes were carried out according to manufacturer’s instruction (Illumina). After scanning of hybridized BeadChip, quantitation of slide images were performed using Illumina’s BeadArray software and the raw data were normalized by Loess normalization method, and then the normalized raw data in BeadStudio was exported to GeneSpring GX 10.0.2 (Agilent, Santa Clara, CA). For identification of genes significantly altered in knockdown cell compared with the control normal gene set, total detected entities were filtered by signal intensity value (upper cut-off 100th and lower cut-off 20th percentile) and error (coefficient of variation: CV < 50.0 percent) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, t-test unpaired (p < 0.05) was applied and all significant changes above 2-fold were selected. Signals were selected if they were above microarray background (detection p-value < 0.05) in either all six experiments or in at least three knockdown or control experiments. Analysis of GO, GSEA and signaling pathway was carried out using GeneSpring GX 10.0.2 (Agilent) and the PANTHER Classification System (http://www.pantherdb.org/). In the analysis of signaling pathways using GeneSpring GX 10.0.2 (Agilent), a total of 140 cellular pathways were identified. For GSEA analysis, we used the false discovery rate (FDR) of <0.4 and p ≤ 0.1.

first: Tae-Hyuk

first: Theodore

last: Friedmann


title: Lubiprostone effects on small intestinal gene expression in wild type and Cftr-null mice

status: Public on Sep 20 2010

city: Kansas City

first: Robert

last: De Lisle

state: KS

address: 3901 Rainbow Blvd

department: Anatomy & Cell Biology

institute: Univ Kansas Med Ctr

summary:
Background: Cystic fibrosis (CF) is caused by mutations in the CFTR gene that impair function of this cAMP-regulated Cl- channel. In the small intestine, loss of CFTR function creates a dehydrated, acidic luminal environment which is believed to cause an accumulation of mucus, a phenotype characteristic of CF. CF mice have an innate immune response and impaired intestinal transit as well. We investigated whether lubiprostone, which activates the CLC2 Cl- channel, would improve the CF intestinal phenotype.
Methods: Cftrtm1UNC (CF) and wildtype (WT) littermate mice on the C57BL/6 background were used. Lubiprostone (10ug/kg-day) was administered by gavage for two weeks. Mucus accumulation was estimated from crypt lumen widths in Carnoy's-fixed, PAS/AB stained sections. Luminal bacterial load was measured by qPCR for the bacterial 16S gene. Gastric emptying and small intestinal transit were assessed by gavage of rhodamine dextran. Gene expression was evaluated by Affymetrix Mouse430 2.0 microarray.
Results: Crypt width in control CF mice was 700% that of WT mice (P<0.001). Lubiprostone did not affect WT crypt width but, unexpectedly, increased CF crypt width 22% (P=0.001). Lubiprostone increased bacterial load in WT mice to 490% of WT control levels (P=0.008). Conversely, lubiprostone decreased bacterial overgrowth in CF mice by 60% (P=0.005). Lubiprostone significantly increased gastric emptying at 20 min postgavage in both WT (P<0.001; control=57±3%, treated=81±4%) and CF mice (P<0.001; control=48±4%, treated=75±5%). After lubiprostone small intestinal transit was significantly enhanced in WT mice (P=0.024) but the effect was not significant in CF mice (P=0.377). Among other innate immune markers, expression of mast cell genes was elevated ~20-fold in the control CF intestine and lubiprostone decreased expression to WT control levels.
Conclusions: These results indicate that lubiprostone has some benefits for the CF intestinal phenotype, especially on bacterial overgrowth and the innate immune response. The unexpected observation of increased mucus accumulation in the crypts of lubiprostone-treated CF mice suggests the possibility that lubiprostone increases mucus secretion.

overall_design: For each group (control wild type n=10, lubiprostone-treated wild type n=7, control Cftr null n=10 , and lubiprostone-treated cftr null n=8), total RNA was extracted from the entire small intestine and equal amounts were pooled for analysis.

first: Lauren

last: Meldi


title: IL-35-mediated induction of a potent regulatory T cell population.

status: Public on Sep 18 2010

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Regulatory T cells (Tregs) play a critical role in the maintenance of immunological self-tolerance.  Naïve human or murine T cell treatment with the inhibitory cytokine IL35 induces a regulatory population, termed iTR35, that mediates suppression via IL35, but not IL10 or TGFβ, neither express nor require Foxp3, are strongly suppressive in five in vivo models, and exhibit in vivo stability.  Treg-mediated suppression induces iTR35 generation in an IL35- and IL10-dependent manner in vitro, and in inflammatory conditions in vivo in Trichuris-infected intestines and within the tumor microenvironment, where they appear to contribute to the regulatory milieu.  iTR35 may constitute a key mediator of infectious tolerance and may contribute to Treg-mediated tumor progression, and ex vivo-generated iTR35 may possess therapeutic utility.

overall_design: Five IL35-treated samples, in parallel with 5 control-treated samples, were compared to 3 Treg and 3 Tconv cell samples.

middle: W

last: Collison

first: Creg

last: Workman


title: Fz1Fz2 double knock out mouse palate microarray (E13.5)

status: Public on Sep 22 2010

city: Baltimore

first: Huimin

last: Yu

address: 725 N Wolfe Street, PCTB 805

department: Molecular Biology and Genetics

institute: Johns Hopkins School of Medicine

summary: The closure of an open anatomical structure by the directed growth and fusion of two tissue masses is a recurrent theme in mammalian embryology, and this process plays an integral role in the development of the palate, ventricular septum, neural tube, urethra, diaphragm, and eye.  In mice, targeted mutations of the genes encoding frizzled1 (Fz1) and frizzled2 (Fz2) show that these highly homologous integral membrane receptors play an essential and partially redundant role in closure of the palate and ventricular septum, and in the correct positioning of the cardiac outflow tract.  When combined with a mutant allele of the planar cell polarity (PCP) gene Vangl2 (Vangl2Lp), Fz1 and/or Fz2 mutations also cause defects in neural tube closure and mis-orientation of inner ear sensory hair cells.  These observations indicate that frizzled signaling is involved in diverse tissue closure processes, defects in which account for some of the most common congenital anomalies in humans.

overall_design:
Microdissect E13.5 palates from Fz1-/-;Fz2+/+ and Fz1-/-;Fz2-/- embryos and compare transcript abundances by hybridization to Affymetrix 430 2.0 gene chips

Supplementary file below reports fold change data.


title: A20 Role in Liver regeneration

city: Boston

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

summary: Genome wide transcriptional profiling on liver mRNA retrieved from recombinant adenovirus A20 (rAd.A20) and rAd.bgalactosidase transduced livers, before and 24 hours after 78% extended liver resection. Overexpression of the NF-kB inhibitory protein A20 improves recovery of liver function and mass following extended liver resection and severe liver ischemia reperfusion injury in mice. In this project, we explored effects of A20 using transcriptional profiling on liver mRNA retrieved from recombinant adenovirus A20 (rAd.A20) and rAd.bgalactosidase transduced livers, before and 24 hours after 78% extended liver resection.

overall_design: A20 or beta-galactosidase gene expression in the mouse liver was achieved by penile vein injection of 1x109 pfu of rAd. in 100uL of normal saline, which results in optimal transgene expression 5 days after injection in 30% to 40% of hepatocytes (Longo et al, 2005). Extended (78%) LR, consisting of resection of the lateral, medial, left, and right lobes, was performed 5 days following rAd. administration in 8-week old BALB/c mice weighing 25 to 30 grams (Taconic, Germantown, NY), as described (Longo et al, 2005). RNA was extracted from the resected portion of the liver (before samples) and from the remnant liver 24 hours after resection (after samples). RNA from three animals was pooled per microarray and 2 microarrays per group were performed.

first: Scott

last: Damrauer

first: Peter

last: Studer

first: Cleide

middle: G

last: da Silva

middle: K

last: Ferran


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

overall_design: Refer to individual Series


title: Unexpected Role for the B cell-specific Src Family Kinase Blk in the Development of IL-17-Producing gamma/delta T Cells

status: Public on Sep 23 2010

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: The Ag receptors on alpha/beta and gamma/delta T cells differ not only in the nature of the ligands that they recognize but also in their signaling potential. We hypothesized that the differences in alpha/beta - and gamma/delta TCR signal transduction were due to differences in the intracellular signaling pathways coupled to these two TCRs. To investigate this, we employed transcriptional profiling to identify genes encoding signaling molecules that are differentially expressed in mature alpha/beta and gamma/delta T cell populations. Unexpectedly, we found that B lymphoid kinase (Blk), a Src family kinase expressed primarily in B cells, is expressed in gamma/delta T cells but not in alpha/beta T cells. Analysis of Blk-deficient mice revealed that Blk is required for the development of IL-17-producing gamma/delta T cells. Furthermore, Blk is expressed in lymphoid precursors and, in this capacity, plays a role in regulating thymus cellularity during ontogeny.

overall_design: Naive alpha/beta and gamma/delta T cells isolated from mouse lymph nodes and purified by negative selection were compared using MOE430 2.0 GeneChip.

first: Renee

last: Laird

first: Karen

last: Laky

first: Sandra

last: Hayes


title: Adult epidermal Notch activity induces dermal accumulation of stromal cells

status: Public on Sep 15 2010

first: Carrie

last: Ambler

state: Durham

address: South Road

department: School of Biological and Biomedical Sciences

institute: Durham University

summary:
K14NICDER transgenic and wildtype littermate mice were treated with 4OHT for 14 days to activate the transgene
Epidermis and dermis preparations from Transgenic and Wild type mice plus whole skin

overall_design: We sought to compare gene expression patterns in K14NICDER transgenic epidermis and dermis to wild type controls

first: Fiona

last: Watt


title: Differential roles of Sall4 isoforms in ES cell pluripotency: expression

status: Public on Sep 13 2010

first: Sridhar

last: Rao

address: 1 Blackfan Circle

department: Pediatric Oncology

institute: Dana Farber Cancer Institute and Children's Hospital, Boston

summary: Murine embryonic stem cells (ESCs) are defined by continuous self-renewal and pluripotency. A diverse repertoire of protein isoforms arising from alternative splicing are expressed in ES cells without defined biological roles. Sall4, a transcription factor essential for pluripotency, exists as two isoforms  (Sall4a and Sall4b). By genome-wide location analysis, we have determined that Sall4b, and not Sall4a, binds preferentially to highly expressed loci in ES cells. Sall4a and Sall4b binding sites are distinguished by both epigenetic marks at target loci and their clustering with binding sites of other pluripotency factors.  When ESCs expressing a single isoform of Sall4 are generated, Sall4b alone could maintain the pluripotent state, although it could not completely suppress all differentiation markers. Sall4a and Sall4b collaborate in maintenance of the pluripotent state, but play distinct roles.  Our work is novel in establishing such isoform-specific differences in ES cells.

overall_design: Cells infected with an empty lentivirus (Wt) are compared with cells missing both isoforms of Sall4 (WT+shRNA) or a single isoform (Sall4aIMM+shRNA or Sall4bIMM+shRNA).  ES cells expressing a single isoform of Sall4 (either Sall4a or Sall4b) were generated by using a lentivirally based shRNA (Open Biosystems TRC0000097821) that depleted both endogenous isoforms and then adding back a single isoform cDNA that was immune to the shRNA. Transcriptome analysis was performed 48 hrs after infection to identify changes in gene expression at various loci when only a single isoform of Sall4 was present.

first: Stuart

last: Orkin


title: Overexpression of Hoxd4 transcription factor alters transcriptional profiles in mouse chondrocytes at E18.5

status: Public on Oct 15 2010

city: Baton Rouge

first: Claudia

last: Kappen

state: LA

address: 6400 Perkins Road

department: Developmental Biology

institute: Pennington Biomedical Research Center

summary: Homeobox genes of the Hox class are required for proper patterning of skeletal elements and play a role in cartilage differentiation. In transgenic mice with overexpression of Hoxd4 during cartilage development, we observed severe defects, namely physical instability of cartilage, accumulation of immature chondrocytes, and decreased maturation to hypertrophy. To define the molecular basis underlying these defects, we performed gene expression profiling using the Affymetrix microarray platform.

overall_design: Embryos were dissected from four different mouse litters at E18.5. Embryos from each litter were grouped according their genotype: TA=control; TR=transgenic.

last: Kruger


title: Expression data from wild-type and PPARalpha-null mice exposed to perfluorooctane sulfonate (PFOS)

city: Research Triangle Park

first: Mitchell

middle: B

last: Rosen

department: Reproductive Toxicology

institute: U.S. EPA

summary: Perfluorooctane sulfonate (PFOS) is a perfluoroalkyl acid (PFAA) and a persistent environmental contaminant found in the tissues of humans and wildlife.  Although blood levels of PFOS have begun to decline, health concerns remain because of the long half-life of PFOS in humans. Like other PFAAs, such as perfluorooctanoic acid (PFOA), PFOS is an activator of peroxisome proliferator-activated receptor-alpha (PPARα) and exhibits hepatocarcinogenic potential in rodents.  PFOS is also a developmental toxicant in rodents where, unlike PFOA, it’s mode of action is independent of PPARα.  Wild-type (WT) and PPARα-null (Null) mice were dosed with 0, 3, or 10 mg/kg/day PFOS for 7 days.  Animals were euthanized, livers weighed, and liver samples collected for histology and preparation of total RNA.  Gene profiling was conducted using Affymetrix 430_2 microarrays.  In WT mice, PFOS induced changes that were characteristic of PPARα transactivation including regulation of genes associated with lipid metabolism, peroxisome biogenesis, proteasome activation, and inflammation.  PPARα-independent changes were indicated in both WT and Null mice by altered expression of genes related to lipid metabolism, inflammation, and xenobiotic metabolism.  Such results are similar to prior studies done with PFOA and are consistent with modest activation of the constitutive androstane receptor (CAR) and possibly PPARγ and/or PPARβ/δ.  Unique treatment-related effects were also found in Null mice including altered expression of genes associated with ribosome biogenesis, oxidative phosphorylation and cholesterol biosynthesis. Of interest was up-regulation of Cyp7a1, a gene which is under the control of various transcription regulators.  Hence, in addition to its ability to modestly activate PPARα, PFOS induces a variety of “off-target” effects as well.

overall_design: PPARalpha-null and wild-type male mice at 6-9 months of age were dosed by gavage for 7 consecutive days with either 0, 3, or 10 mg/kg PFOS (potassium salt) in 0.5% Tween 20.   Five biological replicates consisting of individual animals were included in each dosage group.  Data were compared to results previously published by our group for PFOA and Wy-14,643, a commonly used agonist of PPARalpha (Rosen et al., Toxicol Pathol. 36:592-607, 2008; GSE9796)

first: Judith

last: Schmid

first: J

last: Corton

first: Robert

last: Zehr

first: Kaberi

middle: P

last: Das

first: Barbara

last: Abbott

first: Christopher

last: Lau


title: Differential roles of Sall4 isoforms in ES cell pluripotency

type: Genome binding/occupancy profiling by genome tiling array


title: Expression profiling of 3T3-L1 adipogenesis

first: Tarjei

middle: S

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

summary: 3T3-L1 pre-adipocyte cells were grown to confluence and induced to differentiate in adipogeneic media.

overall_design: Two technical replicates from four time points relative to induction of adipogenesis (day 0)

first: Zhao

last: Xu

first: Jeffery

last: Gimble

first: Eric

last: Lander

first: Evan


title: Stimulatory effect of Echinacea purpurea extract on trafficking activity in mouse dendritic cells

city: Taipei

first: Ning-Sun

last: Yang

state: Taiwan

address: No.128 Sec.2, Academia Rd.

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

summary: To seek scientific evidence supporting therapeutic use of Echinacea, the transcriptomic effects of Echinacea purpurea extract on mouse bone marrow-derived dendritic cells (BMDCs) were analyzed using primary cultures. Affymetrix DNA microarray and bioinformatics analyses of genes differentially expressed in DCs treated with [BF/S+L/Ep] for 4 or 12 h revealed that the majority of responsive genes were related to cell adhesion or motility (Cdh10, Itga6, Cdh1, Gja1 and Mmp8), or were chemokines (Cxcl2, Cxcl7) or signaling molecules (Nrxn1, Pkce and Acss1).

overall_design: BMDCs from mice were treated with [BF/S+L/Ep] or DMSO for 4 h or 12 h in duplicates.

first: Shu-Yi

last: Yin

first: Wen-Hsin

last: Wang


title: Assessing Statistical Significance in Microarray Experiments Using the Distance Between Microarrays

first: Wenzhong Xiao

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

summary:
We propose a method to compare the location and variability of gene ex-pression between two groups of microarrays using a permutation test based on the pairwise distance between microarrays. The microarrays could be samples from distinct clinical or biological populations or microarrays prepared at two different levels of an experimental factor. For these tests the entire microarray or some pre-specifed subset of genes, not the individual gene, is the unit of analysis. We apply this method to compare results from two dfferent protocols for preparing labeled targets for microarray hybridization and their subsequent gene expression analysis.
Keywords: Comparative genomic expression

overall_design: Overall design - Splenocytes were extracted from six sham mice and six trauma-hemorrhagic mice. Total RNA was prepared from individual mice and labeled as targets by two different methods for analysis on Affymentrix MOE 430 2+chips.

first: Douglas

last: Hayden

first: Bernard

last: Brownstein

first: Peter

last: Lazar

first: David

last: Schoenfeld


title: Expression data from SSEA1+  differentiated murine embryonic stem cells

status: Public on Sep 11 2010

city: Los Angeles

first: Anne

last: Lindgren

address: 621 Charles E Young Dr S

department: MCDB

institute: UCLA

summary:
SSEA1+ cells sorted from mouse embryonic stem cells differentiated for 4 days in 10uM Retinoic acid do not form teratomas when transplated into SCID mice while Pten-/- cells do.
We used microarrays to identify genes and pathways besides Pten that could explain this difference in tumorigenicity.

Keywords: wild type vs Pten-/-

overall_design: Wild type and Pten mutant SSEA1 positive differentiated cells were compared as the wild type cells were non-tumorigenic upon transplant to SCID mice and the Pten-/- cells were tumorigenic.

first: Amander

middle: T

last: Clark


title: Gene expression in germinal center light zone, dark zone, and naïve B cells

status: Public on Sep 07 2010

first: Gabriel

last: Victora

address: 9 Cambridge Center

institute: Whitehead Institute

summary:
Microarrays of gene expression in mouse germinal center B cells photoactivated in the light zone or dark zone, and of naïve cells for comparison.
We used microarray data to identify genes differentially expressed by B cells in the light and dark zones of the germinal center.

overall_design: Light and dark zone cells were photoactivated in day 7 germinal centers and sorted by flow cytometry. Naïve splenic B cells(IgD+CD19+) were sorted for comparison.

first: Michel

middle: C

last: Nussenzweig


title: GENE EXPRESSION ALTERATIONS IN ADULT UTP14b (jsd) MICE BY CONDITIONAL KNOCKOUT OF ANDROGEN RECEPTOR IN SERTOLI CELLS

status: Public on Sep 06 2010

city: Houston

first: JoAnne

last: Richards

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Spermatogenesis is dependent primarily on testosterone action on the Sertoli cells.  Although the identification of testosterone-regulated target genes in Sertoli cells has been approached using microarray analysis to compare gene expression in mice with androgen receptor (AR) elimination in the Sertoli cells (SCARKO) and wild type mice, the analysis has been complicated by alteration of germ cell composition of the testis when pubertal or adult mice were used and differences in Sertoli-cell gene expression from those in adult when prepubertal mice were used.  Since the testicular cell components of adult jsd (Utp14bjsd ,juvenile spermatogonial depletion) mice and SCARKO-jsd mice are essentially identical, consisting of only type A spermatogonia and somatic cells, comparisons of gene expression profiles between jsd and SCARKO-jsd testes would identify AR regulated genes in adult Sertoli cells, with minimum effects of cell number changes.  Microarray analysis identified 161 genes as downregulated and 202 genes as upregulated in the SCARKO-jsd mice compared to jsd mice.  Some of the genes identified in the previous studies, including Rhox5, Drd4, and Fhod3, were also AR-regulated in the jsd testes but others, such as proteases and components of junctional complexes, were not androgen regulated in our model.  Surprisingly, a set of germ-cell-specific genes preferentially expressed in differentiated spermatogonia and meiotic cells, including Meig1, Sycp3, and Ddx4, were all upregulated about 2-fold in SCARKO-jsd testes, demonstrating that, although there was no significant differentiation to spermatocytes in SCARKO-jsd mice, AR-regulated genes in Sertoli cells are involved in the regulation of spermatogonial differentiation.  Further gene ontogeny analysis revealed possible sets of genes whose expression changes may be involved in the disruption of Sertoli cell organization in SCARKO-jsd testes.

overall_design: Comparisons of gene expression profiles between the testis of jsd mice (n=3) and SCARKO-jsd mice (n=3).

first: Wei

last: Zhou

first: Gensheng

first: Chris

last: Small

first: Zhilin

last: Liu

first: Connie

last: Weng

first: Lizhong

first: Michael

last: Griswold

first: Marvin

middle: L

last: Meistrich


title: Lewis lung carcinoma cells and TDAG8 overexpression

city: Tokyo

first: Satoshi

last: Ishii

address: 7-3-1 Hongo, Bunkyo

department: Department of Biochem. & Mol. Biol.

institute: The University of Tokyo

summary: We observed the effects of TDAG8-overexpression in Lewis lung carcinoma (LLC) cells on the gene expression pattern.

overall_design: TDAG8-overexpressing or vector-transfected control LLC cells (5 × e5 in 200 µL of HBSS) were injected into the lateral tail veins of 6–8-week-old C57BL/6 mice. Lungs were removed on day 19 post-injection, and total RNA was extracted.

first: Yuichro

last: Ihara

first: Takao

last: Shimizu


title: Gene expression in epithelial and non-epithelial cells of renal origin

first: Kai

middle: Martin

last: Schmidt-Ott

address: Robert-Roessle-Str. 10

department: Differentiation and Regeneration of Kidney Epithelia

institute: Max-Delbrueck Center for Molecular Medicine

summary: We aimed to define epithelial-specific genes in the kidney. In the developing mouse kidney at E12.5 epithelial cells are restricted to the ureteric bud, while mesenchymal cells surrounding the ureteric bud are non-epithelial. The mouse renal epithelial cell line mIMCD-3 was used to represent kidney epithelia in vitro. Gene expression was analyzed using Affymetrix microarrays in ureteric bud stalks, ureteric bud tips, and mIMCD-3 cells and compared to metanephric mesenchyme.

overall_design: Affymetrix Mouse Genome 430 2.0 microarrays from mouse E12.5 ureteric bud tips, ureteric bus stalks, and metanephric mesenchymes had previously been published (GEO deposition: GDS1583) (Schmidt-Ott, K. M., Yang, J., Chen, X., Wang, H., Paragas, N., Mori, K., Li, J. Y., Lu, B., Costantini, F., Schiffer, M. et al. (2005). Novel regulators of kidney development from the tips of the ureteric bud. J Am Soc Nephrol 16, 1993-2002.). We added a new microarray analysis from a subclone of mIMCD-3 cells and recalculated expression values in the complete dataset by robust multichip analysis.

first: K

first: J

last: Barasch

last: Walentin

first: M

last: Werth


title: Ikaros deficient mouse thymic lymphomas

status: Public on Sep 03 2010

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

country: France

institute: IGBMC

summary: This dataset comprises expression profiles from 3 thymic lymphomas from Ikaros deficient mice (IkL/L model, see Dumortier et al, Mol. Cell. Biol. 26, 209-220, 2006 for a description of the tumor model) and 3 thymic lymphomas from IkL/L mice that harbor a mutation of the Notch1 gene (deletion of floxed sequences comprising the promoter and exon 1 with the CD4-Cre transgene). The results from this experimpent is that the expression of Notch target genes was unexpectedly not altered in the tumors with the Notch1 deletion. This result is explained by the activation of a cryptic 3' Notch1 promoter in the deleted tumors, which leads to constitutive Notch1 activation. These results are described in the following publication: R Jeannet, J Mastio, B Macias-Garcia, A Oravecz, T Ashworth, AS Geimer-Lelay, B Jost, S Le Gras, J Ghysdael, T Gridley, T Honjo, F Radtke, J Aster, S Chan and P Kastner. Oncogenic activation of the Notch1 gene in mouse T-cell leukemia by deletion of its promoter. Blood, in press (2010)

overall_design: Primary thymic tumors from 3 IkL/L Notch1+/+ CD4-Cre+ mice (aged 18-20 weeks) were compared to similar tumors from 3 IkL/L Notch1f/f CD4-Cre+ mice (aged 8-10 weeks).

first: Philippe

last: Kastner


title: Expression data from mouse wild-type and Dnmt1-/-Dnmt3a-/-Dnmt3b-/- embryonic stem(ES) cells and nuclear transfer-trophoblastic stem(ntTS) cells, and wild-type trophoblastic stem(TS) cells, primitive endoderm cells, and extra-embryonic endoderm(XEN) cells

city: Kobe

first: Morito

last: Sakaue

state: Hyogo

address: 2-2-3 Minatojimaminamimachi, Chuoku

department: CDB

institute: RIKEN

summary: To investigate the role of DNA methylation in early embryogenesis, we created Dnmt1-/-Dnmt3a-/-Dnmt3b-/- triple knockout (TKO) embryos by the nuclear transfer (NT) technique using TKO ES cells as the nucleus donor, and found that the TKO NT embryos could develop into blastocysts. From the TKO NT blastocysts, we successfully established trophoblastic stem cells (ntTS cells), and these TKO ntTS cells could self-renew and contribute to the placenta in vivo. Expression profile analysis using microarray revealed that, although many genes were aberrantly expressed, the fundamental gene expression patterns of stem cells were retained in these TKO ntTS cells.

overall_design: To investigate the properties of the TKO ntTS cells from their expression profiles, we compared the microarray data from the TKO ntTS cells with data from wild-type (WT) ntTS cells and other cell types that represent the three blastocyst-derived lineages: the epiblast (EPI), trophectoderm (TE), and primitive endoderm (PE). WT and TKO ES cells were used as EPI, TS cells derived from wild-type blastocysts were used as TE, and extra-embryonic endoderm (XEN) cells derived from wild-type blastocysts were used as PE. We also treated WT ES cells with Gata4 to induce parietal endoderm cells as PE. The total RNA was extracted from these cell lines, and microarray data were obtained using mouse expression microarrays.

first: Hiroshi

last: Ohta

first: Yuichi

last: Kumaki

first: Masaki

last: Okano


title: Foxo1/3-deficient Treg cells

city: New York

first: Weiming

last: Ouyang

institute: MSKCC

summary: Identification of Foxos target genes in Treg cells. Foxo1and Foxo3 are transcription factors of Foxo family. CD4+Foxp3+ Treg cells isolated from wild-type and Foxo1/3-deficient mice were analyzed by global gene expression profiling. Results indicate Foxos regulate expression of a subset of Treg cell signature genes and genes in control of T cell homeostasis, signaling and metabolism.

overall_design: 2 sets wild-type and Foxo1/3-deficient CD4+Foxp3+ Treg cells

middle: O

last: Li

first: W


title: Expression profiles of laser dissected colon tumor samples of wild-type mice and vil-Cre-Bcl9-/-/Bcl9l-/- mice

status: Public on Sep 01 2010

city: Lausanne

first: Michel

last: Aguet

address: Rue du Bugnon 25

department: Life Sciences

country: Switzerland

institute: EPFL/ISREC

summary: To investigate the impact of ablating Bcl9/Bcl9l on tumorigenesis, 6-8- week-old mice were exposed first to a single dose dimethylhydrazine (DMH, 44 mg/kg body weight), which is metabolized in the liver to carcinogenic azoxymethane (AOM), followed by 7 days oral administration of 2 % dextrane sulfate sodium (DSS) in the drinking water. This regimen results in the emergence of dysplastic adenomas, which progress to differentiated adenocarcinomas that are morphologically similar to human colorectal adenocarcinomas and typically harbor β-catenin stabilizing mutations of GSK3ß phosphorylation sites. Accordingly, these tumors present hallmarks of active Wnt signaling such as accumulation of nuclear β-catenin and expression of Wnt target genes.

overall_design: Total RNA of laser dissected samples from five different tumors each of two wild-type mice and three vil-Cre-Bcl9-/-/Bcl9l-/- mice was collected and resulting amplified cDNA hybridized to Affymetrix Mouse Genome 430 2.0 arrays. Samples are labeled as follows: Genotype_TumorID_MouseID_UniqueID.

last: Deka

first: N

last: Wiedemann

first: P

last: Anderle

first: F

last: Murphy-Seiler

last: Bultinck

first: JC

last: Stehle

first: S

last: André

last: Vilain

first: O

last: Zilian

last: Robine

last: Delorenzi

last: Basler


title: Enhanced Pathogenicity of Th17 cells Generated in the Absence of Transforming Growth Factor-β Signaling

status: Public on Aug 31 2010

city: Bethesda

first: Lai

last: Wei

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

summary: CD4+ T cells that selectively produce interleukin (IL)-17, are critical for host defense and autoimmunity1-4. Crucial for T helper17 (Th17) cells in vivo5,6, IL-23 has been thought to be incapable of driving initial differentiation. Rather, IL-6 and transforming growth factor (TGF)-β1 have been argued to be the factors responsible for initiating specification7-10. Herein, we show that Th17 differentiation occurs in the absence of TGF-β signaling. Neither IL-6 nor IL-23 alone efficiently generated Th17 cells; however, these cytokines in combination with IL-1β effectively induced IL-17 production in naïve precursors, independently of TGF-β. Epigenetic modification of the Il17a/Il17f and Rorc promoters proceeded without TGF-β1, allowing the generation of cells that co-expressed Rorγt and T-bet.           T-bet+Rorγt+ Th17 cells are generated in vivo during experimental allergic encephalomyelitis (EAE), and adoptively transferred Th17 cells generated with IL-23 in the absence of TGF-β1 were more pathogenic in this experimental disease. These data suggest a new model for Th17 differentiation. Consistent with genetic data linking the IL23R with autoimmunity, our findings re-emphasize the role of IL-23 and therefore have important implications for the development of new therapies.

overall_design: Mouse T helper 17 cell differentiation with or without TGFB

first: Kamran

last: Ghoreschi

first: Arian

last: Laurence

first: Xiang-Ping

last: Yang

first: Cristina

middle: M

last: Tato

first: Mandy

middle: J

last: McGeachy

first: Joanne

last: Konkel

first: Haydeé

last: Ramos

first: Todd

last: Davidson

first: Nicolas

last: Bouladoux

first: John

last: Grainger

first: Qian

last: Chen

first: Yuka

last: Kanno

first: Wendy

last: Watford

first: Hong-Wei

last: Sun

first: Gérard

last: Eberl

first: Ethan

last: Shevach

first: Yasmine

last: Belkaid

first: Daniel

last: Cua

first: Wanjun

last: O’Shea


title: Expression analysis of stimulated macrophages from CEBPB-knockout, CEBPE-knockout, and CEBPB/CEBPE double-knockout mice

status: Public on Sep 02 2010

city: Münster

first: Nils

last: Thoennissen

address: Albert-Schweitzer-Str. 33

department: Hematology Oncology

institute: University Hospital of Münster

summary:
The CCAAT/enhancer-binding proteins (CEBPs) are transcription factors involved in hematopoietic cell development and induction of several inflammatory mediators. Here, we generated CEBP-beta (CEBPB) and CEBP-epsilon (CEBPE) double-knockout (bbee) mice and compared their phenotypes to those of single-deficient (bbEE and BBee) and wild-type (BBEE) mice.
The bbee mice were highly susceptible to fatal infections and died within 2-3 months. Morphologically, their neutrophils were blocked at the myelocytes/metamyelocytes stage, and clonogenic assays of bone marrow cells indicated a significant decrease in the number of myeloid colonies of the bbee mice. In addition, the proportion of hematopoietic progenitor cells [Lin(-)Sca1(+)c-Kit(+)] in the bone marrow of the bbee mice was significantly increased, reflecting the defective differentiation of the myeloid compartment. Furthermore, microarray expression analysis of lipopolysaccharide (LPS)- and interferon-gamma (IFN-gamma)-activated bone marrow-derived macrophages from bbee compared to single knockout mice revealed decreased expression of essential immune response-related genes and networks, including some direct CEBP targets such as Marco and Clec4e. Overall, the phenotype of the bbee mice is distinct from either the bbEE or BBee mice, demonstrating that both transcription factors are crucial for the maturation of neutrophils and macrophages, as well as the innate immune system, and can at least in part compensate for each other in the single knockout mice.

overall_design: To rule out the regulatory influence of both CEBPB and CEBPE on macrophage-related genes, expression analysis of bone marrow-derived macrophages was performed. Macrophages were derived from murine bone marrow with the use of murine M-CSF. The macrophages were stimulated with both LPS (100 ng) and IFN-gamma (100 ng) for 24h, and RNA was extracted for array analysis. Overall, RNA was extracted from stimulated macrophages of one WT mouse, one CEBPB-KO mouse, one CEBPE-KO mouse and one double-KO mouse.


title: Genomics of medulloblastoma identifies four distinct molecular variants

status: Public on Sep 14 2010

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

summary: Recent genomic approaches have suggested the existence of multiple distinct subtypes of medulloblastoma.  We studied a large cohort of medulloblastomas to determine how many subgroups of the disease exist, how they differ, and the extent of overlap between subgroups.  We determined gene expression profiles and DNA copy number aberrations for 103 primary medulloblastomas.  Bioinformatic tools were used for class discovery of medulloblastoma subgroups based on the most informative genes in the dataset.  Immunohistochemistry for subgroup-specific ‘signature’ genes was used to determine subgroup affiliation for 294 non-overlapping medulloblastomas on two independent tissue microarrays (TMAs).  Multiple unsupervised analyses of transcriptional profiles identified four distinct, non-overlapping molecular variants: WNT, SHH, Group C, and Group D.  Supervised analysis of these four subgroups revealed significant subgroup-specific demographics, histology, metastatic status, and DNA copy number aberrations.  Immunohistochemistry for DKK1 (WNT), SFRP1 (SHH), NPR3 (Group C), and KCNA1 (Group D) could reliably and uniquely classify formalin fixed medulloblastomas in ~98% of cases. Group C patients (NPR3 +ve tumors) exhibited a significantly diminished progression free and overall survival irrespective of their metastatic status.  Our integrative genomics approach to a large cohort of medulloblastomas has identified four disparate subgroups with distinct demographics, clinical presentation, transcriptional profiles, genetic abnormalities, and clinical outcome.  Medulloblastomas can be reliably assigned to subgroups through immunohistochemistry, thereby making medulloblastoma sub-classification widely available.  Future research on medulloblastoma and the development of clinical trials should take into consideration these four distinct types of medulloblastoma.

overall_design: A total of 103 primary medulloblastoma specimens were profiled by Affymetrix exon array and gene-level analysis was performed.

middle: A

first: Andrey

last: Korshunov

first: Hendrik

last: Witt

first: Thomas

last: Hielscher

first: Charles

last: Eberhart

first: Stephen

last: Mack

first: Eric

last: Bouffet

first: Steven

last: Clifford

first: Cynthia

last: Hawkins

first: Pim

last: French

first: James

last: Rutka

first: Stefan

last: Pfister

first: Michael

middle: D

last: Taylor


title: Expression profiles of colon epithelial cells and tumor samples of wild-type and vil-Cre-Bcl9-/-/Bcl9l-/- mice

first: Michel

last: Aguet

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

overall_design: Refer to individual Series


title: Comparison of MBT/Pas and BALB/cByJ MEFs response after infection with Rift Valley Fever virus

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
The Rift Valley Fever (RVF) is an arthropod-borne disease present in several countries of Africa and Middle East. It is caused by RVF virus which can infect both humans and animals. In humans, it leads to various manifestations including hepatitis, encephalitis and death, while in domestic animals it usually causes miscarriage in pregnant females and it is often fatal for the newborn. Not all people or animal infected by the virus present the same disease. Some patients exhibit unapparent or moderate febrile reactions, while others develop severe symptoms. This observation suggests that host genetic factors play a role in controlling the outcome of infection. In this work, we compare the response of two different inbred strains of mice, MBT/Pas and BALB/cByJ, to infection with RVF virus. These strains exhibit different profiles of susceptibility to RVF virus infection. Indeed, MBT/Pas mice rapidly develop high viraemia and die soon after infection, while BALB/cByJ mice have a lower viraemia and die later. Interestingly, mouse embryonic fibroblasts (MEFs) obtained from MBT/Pas foetuses allows higher viral production than BALB/cByJ MEFs.

Keywords: expression profiling

overall_design: The experiment was designed to include ARN samples from MBT/Pas and BALB/cByJ MEFs infected with the Rift Valley Fever (RVF) virus, and their respective mock-infected controls; each one of those in triplicate. Therefore, we have used 12 different samples for the study, divided as follows: 3 samples of RVF virus-infected BALB/cByJ MEFs, 3 samples of mock-infected BALB/cByJ MEFs, 3 samples of RVF virus-infected MBT/Pas MEFs and 3 samples of mock-infected MBT/Pas MEFs. Each RNA was extracted from a different culture well.

first: R

first: K

last: Schughart

first: J

last: Panthier

first: T

last: Zaverucha do Valler


title: Expression profiles of EDTA-dissociated colon epithelial cells of wild-type mice and vil-Cre-Bcl9-/-/Bcl9l-/- mice.

summary: To assess potential changes in Wnt signaling more comprehensively, EDTA-dissociated colon epithelial cells from three pools of wild-type and Bcl9/Bcl9l-mutant mice were subjected to an exploratory comparative gene expression profiling.

overall_design: Total RNA of three samples of EDTA-dissociated colon epithelial cells of wild-type mice and three samples of vil-Cre-Bcl9-/-/Bcl9l-/- mice, each sample consisting of material of two or three different mice, was collected and resulting amplified cDNA hybridized to Affymetrix Mouse Genome 430 2.0 arrays. Samples are labeled as follows: Genotype_PoolID _UniqueID_NumberOfMice.

last: Deka

first: N

last: Wiedemann

first: P

last: Anderle

first: F

last: Murphy-Seiler

last: Bultinck

first: JC

last: Stehle

first: S

last: André

last: Vilain

first: O

last: Zilian

last: Robine

first: M

last: Delorenzi

last: Basler


title: JMJD2B knockdown treatment in normoxia and hypoxia

city: Oxford

first: Francesca

last: Buffa

address: The Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Estrogen receptor alpha plays a critical role in breast cancer and is a major target in endocrine therapy. HIF-1 alpha have been associated with ER alpha and predict a worse outcome. Recent studies indicate that histone demethylase JMJD2B is a HIF-1 alpha target. However, little is known about the biological functions of JMJD2B, especially in breast cancer. To elucidate the mechanism by which JMJD2B reguates gene expression in normoxia and hypoxia,  MCF-7 breast cancer cells were depleted forJMJD2B in normoxia and hypoxia. Our results provide insight into JMJD2B regulation of gene expression in breast cancer cells in normoxia and hypoxia.

overall_design: MCF7 cells were subjected to transfection with siRNA controls and two different siRNA oligos against JMJD2B for 24 hours. Cells were treated in normoxia and hypoxia for another 16 hours.

first: Jun

last: Yang

first: Dilair

last: Baban

first: Jiannis

last: Ragoussis

first: Adrian

last: Harris


title: Effect of dietary abscisic acid (ABA) supplementation on spleen transcriptome in LPS-challenged mice

city: blacksburg

first: Saroj

last: Mohapatra

state: VA

address: washington Street

department: VBI

institute: Virginia Tech

summary:
BACKGROUND: Dietary ABA-supplementation modulates immune and inflammatory responses in mouse models of chronic and infectious disease. However, the underlying mechanisms by which ABA elicits its immune modulatory effects are not well understood. This project used a systems approach in combination with functional and in vivo studies to investigate the target gene pathways modulated by ABA in the context of an inflammatory LPS challenge.
RESULTS: Dietary ABA-supplementation regulates the expression of gene pathways associated with peroxisome proliferator-activated receptor gamma (PPAR g), cAMP signaling and lipid metabolism in PPAR g-expressing mice. However, the pattern of differentially expressed genes is significantly reduced in the spleens of tissue-specific PPAR g null mice fed ABA. These differences in gene expression coincided with enhanced PPAR g-reporter activity of macrophages treated with ABA and enhanced intracellular cAMP accumulation in ABA-treated splenocytes.

overall_design: Splenocytes from wild-type (WT) and Null (epithelial and immune cell-specific PPARg knock-out) mice were sampled with or without ABA supplementation and with or without LPS stimulation.

first: Raquel

last: Hontecillas

first: Josep

last: Bassaganya-Riera


title: Genome-wide expression profiles of primary human SAECs infected with different adenovirus mutants.

status: Public on Aug 30 2010

city: La Jolla

first: Conrado

last: Soria

address: 10010 North Torrey Pines Rd

department: MCBL-O

institute: The Salk Institute for Biological Studies

summary:
Full title: Genome-wide expression profiles of primary human small airway epithelial cells (SAECs) infected with different adenovirus mutants.
Expression arrays were used to analyze global gene expression changes in SAECs infected with either mock, dE1B-55k, or d55k/dORF3 adenovirus at 36 hours post infection, as well as nutlin treatment for 12 hours.

overall_design: Two independent experiments were performed with each experimental condition done in duplicate. CEL files were imported and analyzed with Partek Analysis software.

first: Fanny

middle: E

last: Estermann

first: Kristen

last: Espantman

first: Clodagh

last: O'Shea


title: LPS-induced gene expression in mouse small intestinal epithelial cells

status: Public on Aug 29 2010

city: Hannover

first: Mathias

middle: W.

last: Hornef

address: Carl Neuberg Str. 1

department: Inst. of Medical Microbiology

institute: Hannover Medical School

summary: Intestinal epithelial cells express the lipopolysaccharide (LPS) receptor Toll-like receptor (TLR4) and are responsive to LPS stimulation. Following LPS exposure, epithelial cells, similar to myeloid cells such as macrophages, acquire a state of tolerance. Innate immune tolerance is characterized by a lack of expression of proinflammatory genes in response to repeated stimulation. Tolerant epithelial cells, however, exhibit sustained expression of a distinct set of genes encoding for proteins involved in metabolism and homeostasis. This study comparatively analyzes the gene expression profile 6 hours after LPS stimulation (acute response) versus 6 hours LPS followed by 90 hours incubation in the absence of LPS (tolerant response).

overall_design: We used microarrays to detail the global program of gene expression under unstimulated (control), LPS stimulated (6 hours), and tolerant (96 hours) conditions. Three biological replicates each from naive cells, 6 hour LPS-stimulated cells, and 6 hour LPS-stimulated plus 90 hour LPS-free medium-incubated cells were examined and compared.

first: Hornef

middle: W

last: Mathias


title: Analysis of differential gene expression in Cebpa-positive and Cebpa-negative hematopoietic stem cells using a Cebpa-Cre EYFP reporter mouse model

status: Public on Aug 26 2010

city: Rotterdam

first: Albert

last: Wölfler

address: Dr. Molewaterplein 50

department: Hematology

country: Netherlands

institute: Erasmus MC

summary:
C/EBPalpha is a transcription factor critically involved in myeloid development and indispensable for formation of granulocytes. To track the cellular fate of stem and progenitor (LSK) cells, which express C/EBPalpha, we developed a mouse model expressing Cre recombinase from the Cebpa promoter and an inducible EYFP allele. We show that Cebpa/EYFP+ cells represent a significant subset of LSK cells, which predominantly give rise to myeloid cells in steady state hematopoiesis.
C/EBPalpha induced a robust myeloid gene expression signature and downregulated E2A-induced regulators of early lymphoid development. In addition, Cebpa/EYFP+ cells comprise a fraction of early thymic progenitors (ETP) with robust myeloid potential. However, Cebpa/EYFP+ LSK and ETP cells retained the ability to develop into erythroid and T-lymphoid lineages, respectively. These findings support an instructive, but argue against a lineage restrictive role of C/EBPalpha in multipotent hematopoietic and thymic progenitors.

overall_design:
We performed global gene expression profiling of double-sorted Cebpa/EYFP+ and Cebpa/EYFP- LSK cells of pooled Cebpa Cre/wt R26 EYFP reporter mice to identify differentially regulated genes in Cebpa+ versus Cebpa- LSK cells. RNA was isolated from three biological replicates of Cebpa/EYFP+ LSK cells and two biological replicates of Cebpa/EYFP- LSK cells.
To determine if the identified genes were truly dependent on Cebpa expression, we also performed global gene expression profilling of Cebpa/EYFP+ and Cebpa/EYFP- fetal liver LSK cells of Cebpa Cre/fl R26 EYFP mice. Induction of Cebpa/Cre expression in these mice leads to Cre-mediated recombination of the floxed wt Cebpa allele resulting in a complete Cebpa knock-out. In this case, RNA was isolated from two biological replicates of either Cebpa/EYFP+ and Cebpa/EYFP- LSK cells. In addition, we included one biological replicate of Cebpa/EYFP+ and Cebpa/EYFP- fetal liver LSK cells of Cebpa Cre/wt R26 EYFP mice to determine the correlation of differentially regulated genes in bone marrow and fetal liver LSK cells.

first: Astrid

last: Danen-vanOorschot

first: Jurgen

middle: R

last: Haanstra

first: Marijke

last: Valkhof

first: Claudia

last: Bodner

first: Eric

last: Vroegindeweij

first: Paulina

last: van Strien

first: Alexandra

last: Novak

first: Tom

last: Cupedo

first: Ivo

last: Touw


title: Expression data from keratinocytes of WT and RASSF9-/- mice

status: Public on Sep 17 2010

city: Kwei-Shan

first: Chiou-Mei

last: Lee

state: Taoyuan

address: 5, Fusing St

department: Department of Medical Research and Development

institute: Chang Gung Memorial Hospital

summary:
Mice with deficient expression of RASSF9 exhibit intriguing phenotypes of skin-related pathology, including abnormal thickening of the epidermis, dysregulated proliferation of keratinocytes, and alopecia.
To delineate the underlying mechanism, we profiled gene expression in keratinocytes of RASSF9-mutant mice to identify targets whose expressions were affected by RASSF9 gene deletion.

overall_design: Primary keratinocytes from neonatal ICR mice of wildtype control (WT) or homozygous RASSF9 deletion (RASSF9-/-) were harvested for RNA extraction and hybridization on Affymetrix microarrays. For WT, a single microarray hybridization was performed. For RASSF9-/-, one hybridization was performed for each of two independent samples.

first: Lih-Chyang

last: Chen


title: Adipose tissue dysfunction signals progression of hepatic steatosis towards nonalcoholic steatohepatitis in C57Bl/6 mice

status: Public on Sep 09 2010

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary:
Objective: Nonalcoholic fatty liver disease (NAFLD) is linked to obesity and diabetes, suggesting an important role of adipose tissue in the pathogenesis of NAFLD. Here we aim to investigate the interaction between adipose tissue and liver in NAFLD, and identify potential early plasma markers that predict NASH.   Research Design and Methods: C57Bl/6 mice were chronically fed a high fat diet to induce NAFLD and compared with mice fed low fat diet. Extensive histological and phenotypical analyses coupled with a time-course study of plasma proteins using multiplex assay was performed.   Results: Mice exhibited pronounced heterogeneity in liver histological scoring, leading to classification into 4 subgroups: LF-low (LFL) responders displaying normal liver morphology, LF-high (LFH) responders showing benign hepatic steatosis, HF-low (HFL) responders displaying pre-NASH with macrovesicular lipid droplets, and HF-high (HFH) responders exhibiting overt NASH characterized by ballooning of hepatocytes, presence of Mallory bodies, and activated inflammatory cells. Compared to HFL responders, HFH mice gained weight more rapidly and exhibited adipose tissue dysfunction characterized by decreased final fat mass, enhanced macrophage infiltration and inflammation, and adipose tissue remodelling. Plasma haptoglobin, IL-1β, TIMP-1, adiponectin and leptin were significantly changed in HFH mice. Multivariate analysis indicated that in addition to leptin, plasma CRP, haptoglobin, eotaxin and MIP-1α early in the intervention were positively associated with liver triglycerides. Intermediate prognostic markers of liver triglycerides included IL-18, IL-1β, MIP-1γ and MIP-2, whereas insulin, TIMP-1, GCP-2 and MPO emerged as late markers.  Conclusions: Our data support the existence of a tight relationship between adipose tissue dysfunction and NASH pathogenesis and point to several novel potential predictive biomarkers for NASH.

Keywords: Expression profiling by array

overall_design: Male wildtype C57Bl/6 mice were fed LFD or HFD for 21 weeks. Mice were divided into 4 groups based on liver histology.

first: Caroline

last: Duval

first: Uwe

last: Thissen

first: Shohreh

last: Keshtkar

first: Bertrand

last: Accard

first: Rinke

last: Stienstra

first: Mark

last: Boekschoten

first: Tania

last: Roskams

first: Sander

last: Kersten

first: Michael

last: Müller


title: The Forkhead factor FoxQ1 influences epithelial differentiation

city: Heidelberg

first: Alexander

last: Feuerborn

state: BW

department: Department of cellular and molecular pathology

institute: DKFZ

summary: The Forkhead family of transcription factors comprises numerous members and is implicated in various cellular functions, including cell growth, apoptosis, migration and differentiation.In this study we identified the Forkhead factor FoxQ1 as increased in expression during TGF-beta1 induced changes in epithelial differentiation, suggesting functional roles of FoxQ1 for epithelial plasticity.The repression of FoxQ1 in mammary epithelial cells led to a change in cell morphology characterized by an increase in cell size, pronounced cell-cell contacts and an increased expression of several junction proteins (e.g. E-cadherin). In addition, FoxQ1 knock-down cells revealed rearrangements in the actin-cytoskeleton and slowed down cell cycle G1-phase progression.Furthermore, repression of FoxQ1 enhanced the migratory capacity of coherent mammary epithelial cells.Gene expression profiling of NM18 cells indicated that FoxQ1 is a relevant downstream mediator of TGF-beta1 induced gene expression changes. This included the differential expression of transcription factors involved in epithelial plasticity, e.g. Ets-1, Zeb1 and Zeb2.In summary, this study has elucidated the functional impact of FoxQ1 on epithelial differentiation

overall_design:
Cells treated with 200µM 4sU for 2h, biological replicate 1	:2h_co._total1,
Cells treated with 200µM 4sU for 2h, biological replicate 2	:2h_co._total2,
Cells treated with 200µM 4sU for 2h, biological replicate 3	:2h_co._total3,
Cells treated with 200µM 4sU for 2h and enriched for 4sU labelled RNA, biological replicate 1: 2h_co._enriched1,
Cells treated with 200µM 4sU for 2h and enriched for 4sU labelled RNA, biological replicate 2: 2h_co._enriched2,
Cells treated with 200µM 4sU for 2h and enriched for 4sU labelled RNA, biological replicate 3:	2h_co._enriched3,
Cells treated with 5 ng/ml TGF-b1 and 200µM 4sU for 2h, biological replicate 1	:2h_TGFbeta_total1,
Cells treated with 5 ng/ml TGF-b1 and 200µM 4sU for 2h, biological replicate 2	:2h_TGFbeta_total2,
Cells treated with 5 ng/ml TGF-b1 and 200µM 4sU for 2h, biological replicate 3	:2h_TGFbeta_total3,
Cells treated with 5 ng/ml TGF-b1 and 200µM 4sU for 2h and enriched for 4sU labelled RNA, biological replicate 1	:2h_TGFbeta_enriched1,
Cells treated with 5 ng/ml TGF-b1 and 200µM 4sU for 2h and enriched for 4sU labelled RNA, biological replicate 2	:2h_TGFbeta_enriched2,
Cells treated with 5 ng/ml TGF-b1 and 200µM 4sU for 2h and enriched for 4sU labelled RNA, biological replicate 3	:2h_TGFbeta_enriched3,

FoxQ1 dataset

Cells transfected with 25nm scrambled siRNA for 48hrs, biological replicate 1	:ns-siRNA 48hrs 1,
Cells transfected with 25nm scrambled siRNA for 48hrs, biological replicate 2	:ns-siRNA 48hrs 2,
Cells transfected with 25nm scrambled siRNA for 48hrs, biological replicate 3	:ns-siRNA 48hrs 3,
Cells transfected with 25nm scrambled siRNA for 48hrs and treated with TGF-b1 for 40hrs biological replicate 1	:ns-siRNA 48hrs TGF-b1 40hrs 1,
Cells transfected with 25nm scrambled siRNA for 48hrs and treated with TGF-b1 for 40hrs biological replicate 2	:ns-siRNA 48hrs TGF-b1 40hrs 2,
Cells transfected with 25nm scrambled siRNA for 48hrs and treated with TGF-b1 for 40hrs biological replicate 3	:ns-siRNA 48hrs TGF-b1 40hrs 3,
Cells transfected with 25nm FoxQ1 siRNA for 48hrs and treated with TGF-b1 for 40hrs biological replicate 1	:FoxQ1 siRNA 48hrs TGF-b1 40hrs 1,
Cells transfected with 25nm FoxQ1 siRNA for 48hrs and treated with TGF-b1 for 40hrs biological replicate 2	:FoxQ1 siRNA 48hrs TGF-b1 40hrs 2
Cells transfected with 25nm FoxQ1 siRNA for 48hrs and treated with TGF-b1 for 40hrs biological replicate 3	:FoxQ1 siRNA 48hrs TGF-b1 40hrs 3

last: feuerborn

first: Prashant

middle: K

last: Srivastava

first: Stefan

last: Küffer

first: William

last: Grandy

first: Tjeerd

last: Sijmonsma

first: Norbert

last: Gretz

first: Benedikt

last: Brors

first: Hermann

last: Gröne


title: A Novel Statistical Algorithm for Gene Expression Analysis Differentiates PXR-Dependent and Independent Mechanisms of Toxicity

status: Public on Aug 25 2010

city: Thousand Oaks

first: Sandra

last: Tran

address: One Amgen Center Drive

institute: Amgen

summary: The objective of the present study is to examine the potential role of the pregnane x receptor (PXR) in mice treated with an small molecule inhibitor for beta-secretase (CMP013)

overall_design: Two groups of mice, C57Bl/6 (PXR+/+) and PXR-knockout C57Bl/6NTac (PXR-/-), were administered either CMP013 or vehicle. There were five animals per treatment group for each strain. After 96 h, all animals were euthanized, and liver samples were collected for RNA. extraction.

first: M

last: Mongan

first: Robert

last: Dunn

first: Steven

last: Vonderfecht

first: Nancy

last: Everds

first: Guang

last: Chen

first: Cheng

last: Su

first: Marnie

last: Higgins-Garn

first: Yuan

first: Cynthia

last: Afshari

first: Toni

last: Williamson

first: Linda

last: Carlock

first: Christopher

last: DiPalma

first: Suzanne

last: Moss

first: Jeanine

last: Bussiere

first: Charles

last: Qualls

first: Yudong

last: He

first: Hisham

last: Hamadeh


title: Time course for bladder UCC development in UPII-SV40Tag mice

status: Public on Aug 28 2010

city: Shreveport

first: John

last: Clifford

address: 1501 Kings Hwy

department: Biochemistry

institute: LSUHSC-Shreveport

summary:
We have identified genes that are differentially expressed between the bladders of UPII-SV40Tag mice and their age-matched wild-type littermates at 3, 6, 20, and 30 weeks of age. These are ages that correspond to premalignant, carcinoma in situ, and early-stage and later stage invasive UCC, respectively
Analysis of the microarray data sets has revealed ∼1,900 unique genes differentially expressed (≥3-fold difference at one or more time points) between wild-type and UPII-SV40Tag urothelium during the time course of tumor development.

overall_design: RNA from the urothelium of duplicate UPII-SV40Tag hemizygous and age-matched wild type littermate mice was isolated at 3, 6, 20, and 30 weeks of age and gene expression profiles were obtained.

first: Randolph

last: Stone

first: Anita

last: Sabichi


title: Timecourse analysis of gene expression by murine bone marrow-generated dendritic cells following treatment with Poly I:C

city: Winston-Salem

first: Elizabeth

last: Hiltbold-Schwartz

state: NC

address: Medical Center Boulevard

department: Microbiology & Immunology

institute: Wake Forest University Baptist Medical Center

summary:
BACKGROUND: Dendritic cells (DC) play a central role in primary immune responses and become potent stimulators of the adaptive immune response after undergoing the critical process of maturation. Understanding the dynamics of DC maturation would provide key insights into this important process. Time course microarray experiments can provide unique insights into DC maturation dynamics. Replicate experiments are necessary to address the issues of experimental and biological variability. Statistical methods and averaging are often used to identify significant signals. Here a novel strategy for filtering of replicate time course microarray data, which identifies consistent signals between the replicates, is presented and applied to a DC time course microarray experiment.

RESULTS: The temporal dynamics of DC maturation were studied by stimulating DC with poly(I:C) and following gene expression at 5 time points from 1 to 24 hours. The novel filtering strategy uses standard statistical and fold change techniques, along with the consistency of replicate temporal profiles, to identify those differentially expressed genes that were consistent in two biological replicate experiments. To address the issue of cluster reproducibility a consensus clustering method, which identifies clusters of genes whose expression varies consistently between replicates, was also developed and applied. Analysis of the resulting clusters revealed many known and novel characteristics of DC maturation, such as the up-regulation of specific immune response pathways. Intriguingly, more genes were down-regulated than up-regulated. Results identify a more comprehensive program of down-regulation, including many genes involved in protein synthesis, metabolism, and housekeeping needed for maintenance of cellular integrity and metabolism.

CONCLUSIONS: The new filtering strategy emphasizes the importance of consistent and reproducible results when analyzing microarray data and utilizes consistency between replicate experiments as a criterion in both feature selection and clustering, without averaging or otherwise combining replicate data. Observation of a significant down-regulation program during DC maturation indicates that DC are preparing for cell death and provides a path to better understand the process. This new filtering strategy can be adapted for use in analyzing other large-scale time course data sets with replicates.

overall_design: DC were generated from the bone marrow of C57BL/6 mice using GM-CSF, Treated with poly I:C, and RNA was isolated at 0, 1, 3, 6, 12 and 24 hours, and subjected to microarray analysis.  Two independent replicate experiments were performed.

last: Hiltbold

first: Marlena

last: Westcott

first: Kristina

last: Brzoza-Lewis