title: Gamma-secretase inhibitors reverse glucocorticoid resistance in T-ALL

status: Public on Dec 04 2008

city: New York

first: Adolfo

last: Ferrando

address: 1130 St Nicholas Ave Irving Cancer Research Center 5-505A

department: Institute for Cancer Genetics

institute: Columbia University

summary:
Gamma-secretase inhibitors (GSIs), which block the activation of NOTCH receptors, are being tested in the treatment of T-cell acute lymphoblastic leukemia (T-ALL). Thus far, limited antileukemic cytotoxicity and severe gastrointestinal toxicity have restricted the clinical application of these targeted drugs. Here we show that combination therapy with GSIs plus glucocorticoids can improve the antileukemic effects of GSIs and reduce their gut toxicity in vivo. Inhibition of NOTCH1 signaling in glucocorticoid-resistant T-ALL restored glucocorticoid receptor auto-up-regulation and induced apoptotic cell death through induction of BIM expression. Additionally, cotreatment with glucocorticoids induced Ccnd2 upregulation in the gut which protected mice from the intestinal secretory metaplasia typically induced by loss of NOTCH signaling. These results support a role for glucocorticoids plus GSIs in the treatment of glucocorticoid-resistant T-ALL.
Keywords: drug treatment in vivo, dibenzazepine DBZ, T-ALL, glucocorticoid

overall_design: Experiments analyzing the interacition of dexamethasone and the gamma-secretase inhibitor DBZ were carried out in 6-week-old C57/Black6 female mice (Jackson Laboratory). In these studies we treated mice with vehicle (DMSO) (n=2), dexamethasone (15 mg/kg) (n=2), DBZ (10 micromol/kg) (n=2) and dexamethasone (15 mg/kg) plus DBZ (10 micromol/kg) (n=2) daily by intraperitoneal injection for 5 days. At the end of the treatment, animals were euthanized and segments of the small intestine were collected and processed for RNA extraction, histological and immunohistochemical analysis.

first: Pedro

last: Real


title: Expression profiling of activated or control 5-FU bone marrow from MLL-AF4stop knockin mice

status: Public on Nov 04 2008

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

country: Canada

institute: Bioinfo

summary:
We created a mouse model where conditional expression of physiologic levels of an Mll-AF4 fusion oncogene induces development of acute lymphoblastic (ALL) or acute myeloid leukemias (AML). Immunophenotypic and gene expression analysis of the ALL cells demonstrated bone marrow replacement with B-precursor cells which express a gene expression profile that has significant overlap with profiles in human MLL-rearranged ALL.
To examine early, pre-leukemic changes in lymphoid cells due to Mll-AF4 expression, we infected 5-FU bone marrow cells from Mll-AF4stop knocking mice with activating (Cre-GFP) or control (MIF-GFP) retrovirus ex vivo and measured expression changes after culture under lymphoid growth conditions.

Keywords: Cell type comparison

overall_design: Mll-AF4stop knock-in mice were treated with 5-FU and 5 days later their bone marrow infected ex vivo with either Cre-GFP to activate the Mll-AF4 fusion construct or with a control MIG-Cre retrovirus. GFP+ cells were sorted 2 days post-infection and cultured for 14 days under lymphoid growth conditions before total RNA was isolated for hybridization to Affymetrix expression microarrays.

middle: E


title: Activity Deprivation-Induced Transcriptional Changes in the P21 Cochlear Nucleus

status: Public on Aug 30 2008

city: Seattle

first: Julie

last: Harris

state: WA

department: Otolaryngology-HNS

country: USA

institute: University of Washington

summary: We analyzed whether cochlear removal-induced transcriptional changes in the cochlear nucleus (CN) were due to loss of electrical activity in the 8th nerve.  Pharmacological activity blockade of the auditory nerve for 24 h resulted in similar expression changes for only a subset of genes.  Thus, an additional factor not dependent on action potential-mediated signaling must also regulate transcriptional responses to deafferentation in the CN.

overall_design: TTX was infused into the cochlea unilaterally via osmotic pumps to block activity in the 8th nerve.  CN tissue was dissected out from 10-12 mice per replicate and pooled.  Three biological replicates were performed.  Gene expression was compared between the ipsilateral and contralateral CN tissue to identify genes transcriptionally regulated after activity deprivation.

middle: A

first: Edwin

middle: W

last: Rubel


title: Blastocyst Injection of Wild Type Embryonic Stem Cells Induces Global Corrections in Mdx Mice.

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: Duchenne muscular dystrophy (DMD) is an incurable neuromuscular degenerative disease, caused by a mutation in the dystrophin gene. Mdx mice recapitulate DMD features. Here we show that injection of wild-type  (WT) embryonic stem cells (ESCs) into mdx blastocysts produces mice with improved pathology. A small fraction of WT ESCs incorporates into the mdx mouse nonuniformly to upregulate protein levels of dystrophin in the skeletal muscle. The chimeric muscle shows reduced regeneration and restores dystrobrevin, a dystrophin-related protein, in areas with high and with low dystrophin content. WT ESC injection also normalizes the amount of fat, a tissue that does not express dystrophin. ESC injection without dystrophin does not prevent the appearance of phenotypes in the skeletal muscle or in the fat. Thus, dystrophin supplied by the ESCs reverses disease in mdx mice globally.

overall_design: 3-week old mdx (C57BL/10ScSn-Dmdmdx/J, Jax labs) females were superovulated and mated with mdx males (Jax labs). Blastocysts were collected at 3.5 days afer mating, injected with 15 WT or mdx R26 ES cells. Injected blastocysts were then transferred into the uteri of pseudopregnant females and allowed to develop to term. Skeletal muscle from 4 month old chimeric male mice was collected, RNA was isolated and microarray analysis were performed.

first: Diego

last: fraidenraich


title: Murine spleen B cells miR181b vs control (G4122F)

status: Public on Aug 20 2008

city: Madrid

first: Almudena

middle: R.

last: Ramiro

state: Madrid

address: Calle Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

summary:
Transcriptional profile of mouse primary spleen B cells overexpresing miR181b-GFP vectors compared to B cells overexpressing control-GFP vectors

Keywords: Genetic modification

overall_design: Two-condition experiment: B-miR181b vs. B-control. Biological replicates: 1 control, 1 miR181b. 2 independent hybridizations with dye swap.

first: A

middle: R

first: V

middle: G

last: de Yebenes


title: microRNA  expression profile of activated primary B cells and miR181b overexpressing primary B cells

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

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

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The effect of PPAR-alpha agonist on the gene expression in mice hypothalamus.

status: Public on Aug 01 2008

city: Tokushima

first: Tomoko

last: Kawai

address: 3-18-15 Kuramoto-cho

department: Institute of Health Biosciences

country: Japan

institute: The University of Tokushima Graduate School

summary:
We found that bezafibrate, PPAR-alpha agonist, increased EEG delta oscillation throughout 24 hours and decreased body temperature especially in the later half of the dark period in mice. This DNA- microarray experiment was performed due to investigate the gene expression at ZT10, when body temperature showed no difference between nomal- and bezafibrate-treated mice, and ZT22, when body temperature showed the largest difference between the groups.
Keywords: drug treatment, time course

overall_design: Both bezafibrate-treated and control mice were decapitated at each ZT10 and ZT22. Total RNA were purified from the hypothalamus of these mice. The one GSM sample of microarray analysis was resulted from equal amount of total RNA mixture of 4 mice in the same condition. Hybridizations were performed using Agilent Whole Mouse Genome oligonucleotide microarray.

first: Sachiko

last: Chikahisa

first: Kumiko

last: Tominaga

first: Kazuyoshi

last: Kitaoka

first: Katsutaka

last: Oishi

first: Noriko

last: Ishida

first: Kazuhito

last: Rokutan

first: Hiroyoshi

last: Séi


title: Gene expression profiles of sclerosing cholangitis activity in mice

city: Oslo

first: Esten

last: Nakken

address: Kirkeveien 166

department: Ulleval university Hospital

country: Norway

institute: Institute for Experimental Medical Research

summary: Background. Abcb4 (-/-) mice secrete phosphatidylcholine-deficient bile and develop sclerosing cholangitis (SC). The cholangitis involves differential hepatic transcription of genes whose products govern inflammation, activation of hepatic stellate cells and fibrosis.  This study was undertaken to test the hypothesis that several genes involved in regulation of tissue inflammation and fibrosis display transcription rates that reflect SC disease activity. Methods. Abcb4 (-/-) mice fed cholic acid (CA) display high SC activity and ursodeoxycholic acid (UDCA) fed mice display low SC activity. Differential hepatic transcription of genes was accordingly measured in abcb4 (-/-) mice maintained on CA- and UDCA-supplemented diets using cDNA microarrays. Abcb4 (+/+) mice served as controls. The differential transcription of selected genes was verified by real time polymerase chain reaction. Liver tissue pathology was quantified by histopathology scoring and immunohistochemistry to visualize bile duct cells and activated hepatic stellate cells. Results. Differential transcription of  Ccl2, Ccl20, Cxcl10, Nfκb1, Nfκb2, Tgfβ1, Tgfβ2, Sparc, Ctgf, Lgals3, Elf3, Spp1, Pdgfa, Pdgfrb, Col1a1, Col1a2 and Col4a1 genes paralleled the differing SC activities of cholic acid- and UDCA-fed abcb4 (-/-) mice. Histopathology scores and immunohistochemistry showed greatly enhanced activation of hepatic stellate cells during high SC activity due to CA feeding. Conclusion. Differential transcription of several genes relating to tissue inflammation and hepatic stellate cell activation parallels SC activity in abcb4 (-/-) mice. Data on their differential transcription may be used to gauge SC disease activity.

overall_design: To achieve different degrees of disease activity we have fed the mice with either cholic acid (CA) or ursodeoxycholic acid (UDCA) for 9 weeks to increase and decrease disease activity, respectively. Each group uses wild type mice as controls. 5 different mice (livers) in each group was harvested. In 3 hybridizations wild-type livers were marked with Cy3, in 2 hybridizations wild-type livers were marked with Cy5. In addition to these 5 hybridizations one dye swap was performed from a randomly selected liver from the 5 and wild-type marked with Cy5. Thus, a total of 6 hybridizations was used as input for data-processing in each of the two groups. No pooling was done.

first: Karl

first: Stale

last: Nygard

first: Terese

last: Haaland

first: Knut

last: Berge

first: Annlaug

last: Odegaard

middle: J

last: Labori

first: Morten

last: Raeder


title: Expression Data from wild type and E2F4 null MEFs

status: Public on Jul 11 2008

city: East Lansing

first: Eran

last: Andrechek

state: MI

address: 2120 BPS Building

department: Physiology

institute: Michigan State University

summary:
We have used primary MEFs derived from wild type and E2F4 null mice growing asynchrounously in serum to generate a signature for E2F4 pathway activation.  10 wild type and 10 E2F4 null samples were each assayed using the Affymetrics Mouse Genome 430A 2.0 array.
Keywords: Primary MEFs from wild type and E2F4 null mice

overall_design: MEFs from 3 wild type embryos on a total of 10 cultutes were grown and harvested for RNA.  MEFS from 5 E2F4 null embryos were grown on a total of 10 cultures.

first: Rachel

last: Rempel

first: Joseph

last: Nevins


title: An RNAi Screen of Chromatin Proteins Identifies Tip60-p400 as a Regulator of Embryonic Stem Cell Identity

city: Berkeley

first: Jason

middle: T

last: Huff

state: CA

address: 211 Koshland Hall

department: Plant & Microbial Biology

institute: University of California, Berkeley

type: Genome binding/occupancy profiling by genome tiling array

first: Thomas

last: Fazzio

first: Barbara

last: Panning


title: An RNAi Screen of Chromatin Proteins Identifies Tip60-p400 as a Regulator of Embryonic Stem Cell Identity, Experiment A

summary:
Proper regulation of chromatin structure is necessary for the maintenance of cell type-specific gene expression patterns. The embryonic stem cell (ESC) expression pattern governs self-renewal and pluripotency. Here, we present an RNAi screen in mouse ESCs of 1008 loci encoding chromatin proteins. We identified 68 proteins that exhibit diverse phenotypes upon knockdown (KD), including seven subunits of the Tip60-p400 complex. Phenotypic analyses revealed that Tip60-p400 is necessary to maintain characteristic features of ESCs. We show that p400 localization to the promoters of both silent and active genes is dependent upon histone H3 lysine 4 trimethylation (H3K4me3). Furthermore, the Tip60-p400 KD gene expression profile is enriched for developmental regulators and significantly overlaps with that of the transcription factor Nanog. Depletion of Nanog reduces p400 binding to target promoters without affecting H3K4me3 levels. Together, these data indicate that Tip60-p400 integrates signals from Nanog and H3K4me3 to regulate gene expression in ESCs.
Keywords: knockdown-gene expression profiling

overall_design: We identified genes encoding subunits of the Tip60-p400 complex in an RNAi screen of chromatin proteins in mouse embryonic stem cells (ESCs), which upon depletion resulted in a dramatic phenotype. To investigate the role of this complex in gene expression in ESCs, we performed expression profiling upon depletion of the catalytic subunits. We performed 4 biological replicates of p400 or Tip60 knockdown and compared them to biological replicates of control EGFP knockdown. The p400 (Ep400) experiment was performed as competitive two-color hybridizations on one 4x44K array with dye swaps and the Tip60 (Htatip) experiment was performed as single color hybridizations on two 4x44K arrays.  Note: the Tip60 KD replicate 3 was excluded from downstream analysis of differential expression, because the intensity profile was an outlier in diagnostic analyses


title: dTORC gene profiling

status: Public on Jul 04 2008

city: La Jolla

first: Biao

last: Wang

address: 10010 North Torrey Pines Road

institute: Salk Institute

summary:
In fasted mammals, glucose homeostasis is maintained through activation of the cAMP responsive CREB coactivator TORC2, which stimulates the gluconeogenic program in concert with the forkhead transcription factor FOXO1. Here we show that starvation also triggers TORC activation in Drosophila, where it maintains energy balance by promoting the expression of CREB target genes in the brain. TORC mutant flies have reduced glycogen and lipid stores, and they are sensitive to starvation as well as oxidative stress. Neuronal TORC expression rescued starvation and oxidative stress sensitivity as well as CREB target gene expression in TORC mutants. During refeeding, increases in insulin signaling inhibited TORC activity in wild type flies by stimulating the Salt Inducible Kinase 2 (SIK2)-mediated phosphorylation and subsequent degradation of TORC. Depletion of neuronal SIK2 increased TORC activity and enhanced resistance to starvation and oxidative stress in adult flies.  As disruption of insulin signaling, either by ablation of insulin-producing cells (IPCs) or by mutation of the insulin receptor adaptor gene chico, also increased TORC activity, our results illustrate the importance of an insulin-regulated pathway in brain that promotes energy balance in Drosophila.
Keywords: Fasting-induced gene expression

overall_design: Male fly heads were collected after 24h fasting, and RNA was extracted using RNAeasy kit.


title: Liver expression of Bmp6, Smad7, Id1 and Atoh8 is regulated by iron stores

status: Public on Jul 07 2008

city: Toulouse

first: Marie-Paule

last: Roth

address: Chu Purpan

country: France

institute: Inserm

summary:
Background & Aims: Although hepcidin expression was shown to be induced by the BMP signaling pathway, it is not yet known how iron regulates hepcidin and which of the BMP molecules is the endogenous regulator of iron homeostasis in vivo. We therefore assessed liver transcription profiles of mice fed an iron-deficient or an iron-enriched diet and looked for genes that were regulated similarly to hepcidin in that context.
Methods: Genome-wide liver expression profiles of mice of the B6 and D2 genetic backgrounds subjected to iron-deficient, -balanced, or -enriched diets were obtained using Agilent Whole Genome microarrays. Real-time quantitative-PCR and western-blots were used to confirm microarray results and compare gene expression variations induced by secondary iron deficiency or iron overload with those consecutive to Smad4 or Hamp1-deficiency.
Results: Among 1419 transcripts significantly modulated by the dietary iron content, four were regulated similarly to the hepcidin genes Hamp1 and Hamp2. They are coding for Bmp6, the regulator of Bmp/Smad signal transduction Smad7, the negative regulator of basic helix-loop-helix (bHLH) proteins Id1, and a protein with a bHLH domain, Atoh8. The iron overload developed by Smad4 and Hamp1-deficient mice also increased Bmp6 transcription. Body iron stores influence Smad1/5/8 phosphorylation and, as shown by analysis of mice with liver-specific disruption of Smad4, the binding partner for the receptor-activated Smads is necessary for activation of Smad7, Id1, and Atoh8 transcription by iron.
Conclusions: Liver expression of Bmp6, Smad7, Id1, and Atoh8 is regulated by body iron stores and may participate in hepcidin regulation through the Bmp/Smad pathway.
Keywords: response to dietary iron content

overall_design: Total RNA was extracted and purified using the RNeasy Lipid Tissue kit (Qiagen, Courtaboeuf, France). RNA quality was checked on RNA 6000 Nano chips using a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). RNA samples used for chip experiments all had RNA Integrity Numbers (RIN) 16 greater than 9. Agilent’s Low RNA Input Linear Amplification Kit PLUS (One-color) was used to generate fluorescent cRNA. The amplified cyanine 3-labeled cRNA samples were then purified using Qiagen’s RNeasy mini spin colums and hybridized to Agilent Whole Mouse Genome Microarrays, 4x44K. Microarray slides were washed and scanned with an Agilent Scanner, according to the standard protocol of the manufacturer. Information from probe features was extracted from microarray scan images using the Agilent Feature Extraction software v.9.5.1. All the analyses were performed using Bioconductor, an open source software for the analysis of genomic data rooted in the statistical computing environment R. Normalization between arrays was performed using the quantile method. Genes for which the background-corrected signal intensities were not greater than 2.6 standard deviations above the average background in at least 3 B6 and 3 D2 mice were assumed not to be expressed in the liver and were excluded from further analysis. The R/MAANOVA package implemented in Bioconductor was used to perform a two-way analysis of variance in which the log2-transformed expression level was considered to be a function of diet, strain, and the effects of the interaction between these two factors. Fs tests, based on the James-Stein shrinkage estimates of the error variance, were computed on a gene-by-gene basis, and p values obtained by permutation analysis. The proportion of false positives among all the genes initially identified as being differentially expressed (FDR) was assessed using the procedure described by Storey. When influence of diet on expression levels was significant, t-tests were performed to investigate specific effects of iron deficiency and iron enrichment.

first: Léon

last: Kautz

first: Delphine

last: Meynard

first: Valérie

last: Darnaud

first: Régis

last: Bouvet

first: Annabelle

last: Monnier

first: Jean

last: Mosser

first: Hélène

last: Coppin


title: Regulation of skeletal muscle gene expression by synthetic drugs and exercise

status: Public on Jun 18 2008

first: Ruth

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

summary:
Exercise training increases endurance by inducing global gene expression changes in skeletal muscles.  The extent to which the genetic effects of exercise can be mimicked by synthetic drugs is unknown.
We measured global skeletal muscle expression in sedentary and exercised mice treated with vehicle or PPARdelta ligand GW1516.  PPARdelta is a transcriptional regulator of muscle oxidative metabolism and fatigue resistance.

Keywords: Pharmacology study

overall_design: Sedentary and exercise trained C57Bl/6J mice were treated with vehicle or GW1516 for 4 weeks, followed by collection of quadriceps for gene expression analysis.

first: Vihang

last: Narkar

first: Ron

last: Evans


title: A role for mammalian Sin3 in permanent gene silencing

status: Public on Nov 06 2008

first: Brian

last: Dynlacht

department: Cancer Institute

institute: NYU Medical Center

type: Genome binding/occupancy profiling by array

summary: The multi-subunit Sin3 co-repressor complex regulates gene transcription through deacetylation of nucleosomes. However, the full range of Sin3 activities and targets is not well understood. Here, we have investigated genome-wide binding of mouse Sin3 and RBP2 as well as histone modifications and nucleosome positioning as a function of myogenic differentiation. Remarkably, we find that Sin3 complexes spread immediately downstream of the transcription start site on repressed and transcribed genes during differentiation. We show that RBP2 is part of a Sin3 complex, and on a subset of E2F4 target genes, the coordinated activity of Sin3 and RBP2 leads to deacetylation, demethylation, and repositioning of nucleosomes. Our work provides evidence for coordinated binding of Sin3, chromatin modifications, and chromatin remodeling within discrete regulatory regions, suggesting a model in which spreading of Sin3 binding is ultimately linked to permanent gene silencing on a subset of E2F4 target genes.

overall_design: Factor binding on genome-wide promoter arrays were performed at least in duplicate. Factor binding on high density tiling arrays were performed at least in triplicate. Histone modifications and nucleosome density profiles were performed at least in duplicate

first: Chris

last: van Oevelen

first: Jinhua

first: Patrik

last: Asp

first: Yuval

last: Kluger

first: Qin

last: Yan

first: William

last: Kaelin Jr

middle: D


title: Autoregulation of Th1-mediated inflammation by twist1 1st part

status: Public on May 24 2008

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

summary: The basic helix-loop-helix transcriptional repressor twist1, as an antagonist of nuclear factor κB (NF-κB)-dependent cytokine expression, is involved in the regulation of inflammation-induced immunopathology. We could show that twist1 is expressed by activated T helper (Th) 1 effector memory cells. Induction of twist1 in Th cells is dependent on NF-κB, nuclear factor of activated T cells (NFAT), and interleukin (IL)-12 signaling via signal transducer and activator of transcription (STAT) 4. Expression of twist1 is transient following T-cell receptor engagement, and increases upon repeated stimulation of Th1 cells. Imprinting for enhanced twist1 expression is characteristic of repeatedly restimulated effector memory Th cells and thus of the pathogenic memory Th cells of chronic inflammation. Th lymphocytes from the inflamed joint or gut tissue of patients with rheumatic diseases, Crohn’s disease or ulcerative colitis express high levels of twist1. Expression of twist1 in Th1 lymphocytes limits the expression of the cytokines interferon-γ, IL-2 and tumor necrosis factor-α, and ameliorates Th1-mediated immunopathology in delayed-type hypersensitivity and antigen-induced arthritis. In order to identify the effect of twist1 expression on the function of Th cells, twist1 was ectopically expressed and the transcriptome was compared to empty-virus infected control cells. In addition, this experiment allows for the identification of genes regulated by the transcription factor twist1.

overall_design: Genes differentially expressed upon ectopic twist1 overexpression. Splenic DO11.10 cells were activated in vitro with the cognate peptide ova327-339 in the presence of 1ng/ml IL-12 and 1ng/ml IL-2. On day 2 cells were infected with control virus, or twist1-encoding virus. On day 5 cells were sorted according to expression of the viral marker gene gfp. Cells were restimulated for four hours with PMA/ionomycin. The transcriptional profiles of duplicates of cultures were compared using Affymetrix Murine Genome (MG) 430A 2.0 GeneChip arrays.

first: Uwe

last: Niesner

first: Inka

last: Albrecht

first: Marko

last: Janke

first: Cornelia

last: Doebis

first: Christoph

last: Loddenkemper

first: Maria

middle: H

last: Lexberg

first: Katharina

last: Eulenburg

first: Stephan

last: Kreher

first: Juliana

last: Koeck

first: Ria

last: Baumgrass

first: Kerstin

last: Bonhagen

first: Thomas

last: Kamradt

first: Philipp

last: Enghard

first: Jens

middle: Y

last: Humrich

first: Sascha

last: Rutz

first: Ulf

last: Schulze-Topphoff

first: Orhan

last: Aktas

first: Sina

last: Bartfeld

first: Helena

last: Radbruch

first: Ahmed

middle: N

last: Hegazy

first: Max

last: Löhning

first: Daniel

middle: C

last: Baumgart

first: Rainer

last: Duchmann

first: Martin

last: Rudwaleit

last: Haeupl

first: Inna

last: Gitelman

first: Veit

last: Krenn

first: Joachim

last: Grün

first: Jochen

last: Sieper

last: Zeitz

first: Bertram

last: Wiedenmann

first: Frauke

last: Zipp

first: Alf

last: Hamann

first: Michal

last: Janitz

first: Alexander

last: Scheffold

first: Gerd

last: Burmester

first: Hyun

last: Chang

first: Andreas


title: Autoregulation of Th1-mediated inflammation by twist1

first: Pawel

last: Durek


title: PU.1 a pleiotropic regulator expressed in the first embryonic stages with a crucial function in germinal progenitors

status: Public on Jun 05 2008

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

summary:
In the adult mammalian testis, spermatogenic differentiation starts from a minute population of spermatogonial stem cells (SSCs). SSCs are generated after birth from the fetal gonocytes, themselves derived from the primordial germ cells (PGCs), which are specified during the first days after implantation. Transcriptome profiling of purified preparations evidenced the preferential accumulation in SSCs of transcripts of PU.1 (Sfpi1), a regulatory gene previously identified in hematopoietic progenitors. In situ immunolabeling and RNA determination showed a complex pattern of expression in the adult testis, first in SSCs and early spermatogonia followed by de novo expression in pachytene spermatocytes.
Spermatogenesis in a null mutant (PU.1(G/G)) was arrested at the prenatal stage, with reduced numbers of gonocytes owing to a defect in proliferation already noticeable at E12.5. Transcripts of several germinal markers, including vasa (Mvh, Ddx4), Oct4 (Pou5f1), Dazl and Taf4b, were detected, whereas stella (PGC7, Dppa3) was not. Germ cells of PU.1(G/G) newborn testes grafted in nude mice did not initiate the postnatal replicative stage, whereas grafts of their wild-type littermates underwent complete spermatogenesis. During embryonic development, PU.1 transcription was initiated as early as the blastocyst stage, with a generalized expression at E6.5 in the embryonic ectoderm. PU.1 therefore appears to play a determinant role in at least two distinct lineages and, given its wide range of expression, possibly in other stem cells.

Keywords: transcriptome profile of purified preparations of spermatogonial stem cells

overall_design: Our starting point was the establishment of a transcriptome profile of purified preparations of SSCs, on the assumption that crucial genes would appear among those expressed at elevated levels in the stem cells. Work on adult SSCs is made difficult by their small number. We previously reported an efficient procedure, in which a truncated version of the Stra8 promoter is used to express in SSCs a neutral heterologous surface protein including two domains of the human CD4 antigen (huCD4) (Giuili et al., 2002). Once fractionated by immunomagnetic sorting, the huCD4-positive fraction is homogeneous for the expression of known SSC markers and highly efficient in the colonization of a sterile recipient.

first: Virginie

last: Olive

first: Nicole

last: Wagner

first: Susan

last: Chan

first: Philippe

last: Kastner

first: Christine

last: Vannetti

first: Francois

last: Cuzin

first: Minoo

last: Rassoulzadegan


title: Dicer-null cell lines vs. wt ES cells and Dicer-null cell lines vs. Dicer-null cells overexpressing Dnmt1 or Dnmt3a/3b

status: Public on Apr 22 2008

first: Roberta

last: Benetti

address: Calle Melchor Fernandez Almagro

summary:
Dicer initiates RNA interference by generating small RNAs involved in various silencing pathways. Dicer participates in centromeric silencing, but its role in the epigenetic regulation of other chromatin domains has not been explored. Here we show that Dicer1 deficiency in Mus musculus leads to decreased DNA methylation, concomitant with increased telomere recombination and telomere elongation. These DNA-methylation defects correlate with decreased expression of Dnmt1, Dnmt3a and Dnmt3b DNA methyltransferases (Dnmts), and methylation levels can be recovered by their overexpression. We identify the retinoblastoma-like 2 protein (Rbl2) as responsible for decreased Dnmt expression in Dicer1-null cells, suggesting the existence of Dicer-dependent small RNAs that target Rbl2.
We identify the miR-290 cluster as being downregulated in Dicer1-deficient cells and show that it silences Rbl2, thereby controlling Dnmt expression. These results identify a pathway by which miR-290 directly regulates Rbl2-dependent Dnmt expression, indirectly affecting telomere-length homeostasis.
Keywords: Cell type comparison

overall_design: Two-condition experiments. 6 comparisons. One dye-swap technical replicate for all samples. 2-color platform.

first: Susana

last: Gonzalo

first: Isabel

last: Jaco

first: Purificación

last: Muñoz

last: González

first: Stefan

last: Schoeftner

first: Elizabeth

last: Murchison

first: Thomas

last: Andl

first: Taiping

last: Chenn

first: Peter

last: Klatt

first: En

last: Li

first: Manuel

last: Serrano

first: Sarah

last: Millar

first: Gregory

last: Hannon

first: Maria

last: Blasco


title: Satin mice stomach antrum

status: Public on May 01 2008

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 44 Binney St.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary:
Transcription factor Foxq1 controls mucin gene expression and granule content in mouse stomach surface mucous cells

Background and Aims: The gastric mucosa provides a stringent epithelial barrier and produces acid and enzymes that initiate digestion. In this regenerating tissue, progenitors differentiate continually into 4 principal specialized cell types, yet underlying mechanisms of differentiation are poorly understood. We identified stomach-restricted expression of the forkhead transcription factor FOXQ1.
Methods: We used a combination of genetic, histochemical, ultrastructural and molecular analysis to study gastric cell lineages with respect to FOXQ1.
Results: Within the developing and adult gastrointestinal tract, Foxq1 mRNA is restricted to the stomach, expressed prominently in foveolar (pit) cells, the abundant mucin-producing cells that line the mucosal surface, and required for their complete differentiation. Mice carrying Foxq1 coding mutations show virtual absence of mRNA and protein for the backbone of the predominant stomach mucin, MUC5AC. These observations correspond to a paucity of foveolar-cell secretory vesicles and notable loss of stomach but not intestinal mucus. Transcriptional profiling identified a surprisingly restricted set of genes with altered expression in Foxq1 mutant stomachs. MUC5AC is a highly tissue-restricted product that similarly depends on FOXQ1 in its other major site of expression, conjunctival goblet cells.
Conclusions: Taken together, these observations imply that promotion of gastric MUC5AC synthesis is a primary, cell-autonomous function of FOXQ1. This study is the first to implicate a transcription factor in terminal differentiation of foveolar cells and begins to define the requirements to assemble highly specialized organelles and cells in the gastric mucosa.
Keywords: mutant mouse stomach

overall_design: RNA from stomach antrum from 2 of each Satin, Beige, and BL6 mice were compared using microarray analysis.

first: Michael

middle: p

last: Verzi

first: Abdul

middle: h

last: Khan

first: Susumu

last: Ito

middle: a


title: Effect of starvation on the transcriptomes of the brain and liver in adult female zebrafish (Danio rerio)

status: Public on Apr 09 2008

city: Moscow

first: Robert

middle: Edward

last: Drew

state: ID

address: Life Sciences South Rm 252

department: Biological Sciences

institute: University of Idaho

summary:
We used microarray analyses in adult female zebrafish (Danio rerio) to identify metabolic pathways regulated by starvation in two key organs that 1) serve biosynthetic and energy mobilizing functions (liver) and 2) consume energy and direct behavioral responses (brain).  Starvation affected the expression of 574 transcripts in the liver, indicating an overall decrease in metabolic activity, reduced lipid metabolism, protein biosynthesis and proteolysis, and cellular respiration, and increased gluconeogenesis.  Starvation also regulated expression of many components of the Unfolded Protein Response, the first such report in a species other than yeast (Saccharomyces cerevisiae) and mice (Mus musculus).  The response of the zebrafish hepatic transcriptome to starvation was strikingly similar to that of rainbow trout (Oncorhynchus mykiss), but very different from common carp (Cyprinus carpio) and mouse.  The transcriptome of zebrafish whole brain was much less affected than the liver, with only two differentially expressed genes, both down-regulated.  Down-regulation of one of these genes, matrix metalloproteinase 9 (mmp9), suggests increased inhibition of apoptosis (neuroprotection) and decreased restructuring of the extracellular matrix in the brain of starved zebrafish.  The low level of response in the transcriptome of whole zebrafish brain agrees with observations that the brain is metabolically protected compared to the rest of the body.
Keywords: starvation study

overall_design:
Brain treatments: Starved (21 days) and Control (Fed).  Four microarrays per treatment.
Liver treatments: Starved (21 days) and Control (Fed).  Five microarrays per treatment.
Data for brain and liver were normalized and analyzed separately because variances of expression differed considerably between the tissues.

first: Kenneth

last: Rodnick

first: Matthew

last: Settles

first: Jurij

last: Wacyk

first: Erin

last: Churchill

first: Madison

middle: S

last: Powell

first: Ronald

last: Hardy

first: Gordon

middle: K

last: Murdoch

first: Rodney

last: Hill

first: Barrie

last: Robison


title: Chk2 suppresses the oncogenic potential of DNA replication-associated DNA damage

status: Public on May 15 2008

first: Agnes

last: Viale

summary:
The Mre11 complex (Mre11, Rad50, and Nbs1) and Chk2 have been implicated in the DNA damage response, an inducible process required for the suppression of malignancy.  The Mre11 complex is predominantly required for repair and checkpoint activation in S phase, while Chk2 governs apoptosis.  We examined the relationship between the Mre11 complex and Chk2 in the DNA damage response via the establishment of Nbs1∆B/∆B Chk2-/- and Mre11ATLD1/ATLD1 Chk2-/- mice.  Chk2 deficiency did not modify the checkpoint defects or chromosomal instability of Mre11 complex mutants; however, the double mutant mice exhibited synergistic defects in DNA damage-induced p53 regulation and apoptosis.  Nbs1∆B/∆B Chk2-/- and Mre11ATLD1/ATLD1 Chk2-/- mice were also predisposed to tumors.  In contrast, DNA-PKcs deficient mice, in which G1-specific chromosome breaks are present, did not exhibit synergy with Chk2-/- mutants.  These data suggest that Chk2 suppresses the oncogenic potential of DNA damage arising during S and G2 phases of the cell cycle.
Keywords: Global gene expression analysis,  response to radiation,  Nbs1∆B/∆B Chk2-/- and Mre11ATLD1/ATLD1 Chk2-/- mutant mice

overall_design: Thymocytes from Wild type (Wt), Atm-/- and Chk2-/- mice were exposed to  mock 5 Gy radiation (IR). The RNA was harvested 8 hours post treatment.

first: Travis

last: Stracker

first: John

last: Petrini


title: Sex-dependent and HNF4alpha-dependent Mouse Liver Gene Expression

status: Public on Mar 21 2008

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary:
A series of dual-channel gene expression profiles obtained using Rosetta/Agilent  Whole Mouse Genome oligonucleotide microarrays, 4 x 44K format, was used to identify sex-dependent and HNF4alpha-dependent differences in gene expression in adult mouse liver. This series is comprised of four sex-genotype combinations: adult male wild-type liver (M-WT), adult female wild-type liver (F-WT), adult male liver-specific HNF4alpha knockout liver (M-KO) and adult female liver-specific HNF4alpha knockout liver (F-KO). Four pools, each comprised of 4 randomly selected individual liver RNAs, were prepared for each sex-genotype combination. The pools were paired randomly to generate 4 separate experimental comparisons: M-WT:F-WT (first array comparison), M-WT:M-KO (second array comparison), F-WT:F-KO (third array comparison), and M-KO:F-KO (fourth array comparison). A total of 4994 HNF4alpha-dependent genes were identified, of which ~1000 fewer genes responded to the loss of HNF4alpha in female liver as compared to male liver. Moreover, 90% of the genes showing sex-specific expression in the liver were shown to lose sex specificity in HNF4alpha-deficient liver.
Keywords: genetic knockout and sex response

overall_design: An Alexa555-labeled cDNA sample is co-hybridized with an Alexa647-labeled cDNA sample. The samples are then dye-swapped and compared again on a second microarray chip. Together, these two mixed cDNA samples are considered a fluorescent reverse pair (dye swap). Similarly, a second fluorescent reverse pair is generated and the two pairs are averaged. The normalized expression ratio for each array is reported along with the two separate intensities. In this way, dye swaps were carried out for each of the four experimental comparisons. Thus, four microarrays, one for each mixed cDNA sample, were hybridized for each of the four fluorescent reverse pairs, giving a total of 16 microarrays.

first: Minita

last: Holloway

first: Gregory

last: Miles

first: Alan

middle: A

last: Dombkowski


title: Expression data from Igf-1 -/- and Igf-1+/+ mouse cochleas

status: Public on Jun 19 2008

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

summary:
Different mutations in the gene encoding humans IGF-I cause intrauterine growth retardation, postnatal growth failure, microcephaly, mental retardation, bilateral sensorineural deafness and multiple dysmorphic features. Insight into the role of IGFs in inner ear cochlear ganglion neurogenesis has come from the study of genetically modified mice. Postnatal cochlear development is severely impaired in mice Igf1-/-, which develop smaller cochlea and cochlear ganglia, an immature tectorial membrane and they display a significant decrease in the number and size of auditory neurons.
We used microarrays to define the genetic signatures of Igf-1 +/+ and Igf-1-/- mouse cochea and identify the differentially expressed genes.

Keywords: comparison between WT and KO

overall_design: Cochleae from two E18.5 were isolated from both Igf-1+/+ wild type and Igf-1-/- null mice and pooled to obtain RNA. Heterozygous male and female with a genetic background C57BL/6J were mated to obtain embryos 18.5 days post coitus (E18.5). Three independent pools were used. Cochlear tissues included the otic capsule but not vestibular tissues.

first: Hortensia

last: Sánchez-Calderón

first: Lourdes

last: Rodríguez de la Rosa

first: Jose

middle: R

last: Pichel

last: Holley

first: Isabel


title: Effect of loss of CREB and CREM on cocaine-induced gene expression in the striatum

status: Public on Apr 03 2008

city: Heidelberg

first: Jan

last: Rodriguez Parkitna

address: Im Neuenheimer Feld 581

institute: German Cancer Research Center

summary:
Ablation of the Creb1 gene in forebrain neurons was performed using the Cre/loxP system, with the recombinase expressed from the Camk2alfa promoter. Mice were crossed into the Crem KO background to prevent compensation of CREB loss by CREM overexpression.
Our goal was to analyze how loss of CREB will affect acitivity-regulated transcription induced by strong stimulation, i.e. cocaine.
Keywords: Treatment x Genotype

overall_design: Animals were injected i.p. with either 25 mg/kg cocaine or saline and sacrificed after one hour by cervical dislocation. Expression profiling was performed using total RNA isolated from the striatum.


title: NUP98/HHEX  a new oncogenic fusion with acute myeloid leukemia

status: Public on Apr 01 2008

city: Basel

first: Juerg

last: Schwaller

address: Hebelstrasse 20

department: Biomedicine

country: Switzerland

institute: Universityhospital of Basel

summary:
We have cloned and characterized a fusion gene NUP98/HHEX1 resulting from t(7;10) from a patient with acute myeloid leukemia (AML). As NUP98/HHEX acts as an aberrant transcriptional activator, putative targets were searched upon transient expression of the fusion in primary murine bone marrow cells.
Keywords: Comparative analysis of NUP98/HHEX, NUP98/HOX vs. MIG (empty virus) in primary bone marrow cells

overall_design: Murine bone marrow cells were transduced with a retrovirus (MSCV-IRES-GFP, MIG) expressing either NUP98/HHEX or NUP98/HOXA9  (or the empty vector), mRNA was isolated after 72h. Each experiment was performed in triplicates.

first: Dragana

last: Jankovic

first: Florent

last: Baty


title: Chip-chip from mouse embryonic stem (mES) cells

status: Public on May 06 2008

first: Jonghwan

last: Kim

address: 1 Blackfan circle Karp-7

institute: HMS/CHB

summary:
To understand how pluripotency is controlled, we employed a modification of standard ChIP-chip method (biotin-mediated ChIP-chip) to identify targets of nine factors, including somatic cell reprogramming factors (Oct4, Sox2, Klf4, c-Myc) and others (Nanog, Dax1, Rex1, Zpf281, and Nac1) in mouse ES cells.
We show the application of In vivo biotinylation mediated ChIP (bioChIP) to global target mapping. Our data also show that differential regulation of target genes correlates with the extent of promoter occupancy by multiple factors in maintaining stem cell pluripotency.
Keywords: Biotin-mediated Chip-chip, Antibody ChIP-chip, Mouse embryonic stem cells

overall_design: Comparison of targets of nine transcription factors in mES cells

first: Jianlin

last: Chu

first: Xiaohua

last: Shen

first: Jianlong

last: Wang

first: Stuart

last: Orkin


title: Silencing of p63 (trp63) in primary keratinocytes via siRNA oligo transfection.

status: Public on Mar 01 2008

city: Naples

first: Diego

last: di Bernardo

address: Via P Castellino 111

country: Italy

institute: Telethon Institute of Genetics and Medicine

summary:
Genome-wide identification of bona fide targets of transcription factors in mammalian cells is still a challenge. We present a novel integrated computational and experimental approach to identify direct targets of a transcription factor. This consists in measuring time-course (dynamic) gene expression profiles upon perturbation of the transcription factor under study, and in applying a novel reverse-engineering” algorithm (TSNI) to rank genes according to their probability of being direct targets. Using primary keratinocytes as a model system, we identified novel transcriptional target genes of Trp63, a crucial regulator of skin development. TSNI-predicted Trp63 target genes were validated by Trp63 knockdown and by ChIP-chip to identify Trp63-bound regions in vivo. Our study revealed that short sampling times, in the order of minutes, are needed to capture the dynamics of gene expression in mammalian cells. We show that Trp63 transiently regulates a subset of its direct targets, thus highlighting the importance of considering temporal dynamics when identifying transcriptional targets. Using this approach, we uncovered a previously unsuspected transient regulation of the AP-1 complex by Trp63, through direct regulation of a subset of AP-1 components. The integrated experimental and computational approach described here is readily applicable to other transcription factors in mammalian systems and is complementary to genome-wide identification of transcription factor binding sites.
Keywords: siRNA

overall_design: Transient transfection of primary keratinocytes with Trp63-specific small interfering RNA oligonucleotides. Cell were collected 48h after transfection.

first: Giusy

last: Gatta

first: Caterina

last: Missero


title: Mouse liver gene expression after a single acute 2h exposure to combined acoustic and restraint stress vs. control

status: Public on Jun 01 2008

city: Greifswald

first: Maren

last: Depke

address: F.-L.-Jahn-Str. 15a

department: Department of Functional Genomics

institute: Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics

summary:
Stress is a powerful modulator of neuroendocrine, behavioral and immunological functions. After 4.5 days of repeated combined acoustic and restraint stress as a murine model of chronic psychological stress severe metabolic dysregulations became detectable in female BALB/c mice. Stress-induced alterations of metabolic processes that were found in a hepatic mRNA expression profiling were verified by in vivo analyses. Repeatedly stressed mice developed a hypermetabolic syndrome with severe loss of lean body mass, hyperglycemia, dyslipidemia, increased amino acid turn-over, and acidosis. This was associated with hypercortisolism, hyperleptinemia, insulin resistance, and hypothyroidism. In contrast, after a single acute stress exposure changes in expression of metabolic genes were much less pronounced and predominantly confined to gluconeogenesis, probably indicating that metabolic disturbances might be initiated already early but will only manifest in repeatedly stressed mice .Thus, in our murine model, repeated stress caused severe metabolic dysregulations leading to a drastic reduction of the individual's energy reserves. Under such circumstances stress may further reduce the ability to cope with new stressors such as infection or cancer.
Keywords: stress response

overall_design: Two biological experiments of a single acute exposure to combined acoustic and restraint stress were performed, which consist each of an acutely stressed group and an untreated control group. Liver RNA expression profiles were analyzed using pools of 8 or 9 individual RNAs of each group.

first: Robert

last: Geffers

first: Uwe

last: Völker

first: Christine

last: Schütt

first: Cornelia

last: Kiank


title: Primary keratinocytes treated with Tamoxifen

summary:
Genome-wide identification of bona fide targets of transcription factors in mammalian cells is still a challenge. We present a novel integrated computational and experimental approach to identify direct targets of a transcription factor. This consists in measuring time-course (dynamic) gene expression profiles upon perturbation of the transcription factor under study, and in applying a novel reverse-engineering” algorithm (TSNI) to rank genes according to their probability of being direct targets. Using primary keratinocytes as a model system, we identified novel transcriptional target genes of Trp63, a crucial regulator of skin development. TSNI-predicted Trp63 target genes were validated by Trp63 knockdown and by ChIP-chip to identify Trp63-bound regions in vivo. Our study revealed that short sampling times, in the order of minutes, are needed to capture the dynamics of gene expression in mammalian cells. We show that Trp63 transiently regulates a subset of its direct targets, thus highlighting the importance of considering temporal dynamics when identifying transcriptional targets. Using this approach, we uncovered a previously unsuspected transient regulation of the AP-1 complex by Trp63, through direct regulation of a subset of AP-1 components. The integrated experimental and computational approach described here is readily applicable to other transcription factors in mammalian systems and is complementary to genome-wide identification of transcription factor binding sites.
Keywords: time course, p63, keratinocytes

overall_design: Primary keratinocytes were infected with an EMPTY retrovirus and treated with with Tamoxifen, cells were collected every 20 minutes up to 1 hours, and every hour up to 4 hours.


title: Induction of ERDNp63a via Tamoxifen in primary keratinocytes

overall_design: Primary keratinocytes were infected with a retrovirus carryng the DNp63alpha isform fused to the Estrogene receptor domain Upon induction with Tamoxifen, cells were collected every 20 minutes up to 4 hours.


title: Mouse Igf1 null publication analysis

status: Public on Jun 20 2008

first: Marta

last: Milo

first: Hortensia

last: Sánchez-Calderón

first: Lourdes

last: Rodríguez de la Rosa

first: Jose

last: Pichel

first: Matthew

last: Holley

first: Isabel

last: Varela-Nieto


title: Identification of targets of transcription factor Trp63: primary keratinocytes

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

overall_design: Refer to individual Series


title: Identification of Erythroid-Enriched Gene Expression in the Mouse Embryonic Yolk Sac using Microdissected Cells

status: Public on Jan 03 2008

city: Richmond

first: Latasha

last: Redmond

state: VA

address: 401 College Street

department: Human Genetics

institute: Virginia Commonwealth University

summary:
Primitive erythropoiesis in the mouse yolk sac is followed by definitive erythropoiesis resulting in adult erythrocytes. In comparison to definitive erythropoiesis little is known about the genes that control the embryonic erythroid program. The purpose of this study was to generate a profile of mouse embryonic yolk sac erythroid cells and identify novel regulatory genes differentially expressed in erythroid compared to non-erythroid (epithelial cells).
The identification of these genes will contribute to a greater understanding of how the primitive erythroid program is controlled. This work will have clinical implications for treating sickle cell anemia and β-thalassemia. Activating genes in adult erythroid cells that increase embryonic or fetal globin gene expression may be a therapeutic approach to treat individuals with these disorders.
Keywords: Comparison between mouse embryonic day 9.5 yolk sac microdissected primitive erythroid precursors and epithelial cells

overall_design: Embryonic day 9.5 (E9.5) yolk sacs were dissected from the embryos of timed-pregnant FVB/N mice. These tissues were frozen in OCT media and 8-micron frozen sections were obtained. Laser capture microdissection (LCM) was used to isolate primitive erythroid precursors and epithelial cells from these E9.5 yolk sac frozen sections using 2 to 4 yolk sacs from 2 different litters per biological replicate.  Paired erythroid and epithelial samples were collected from the same microscope slides. Total RNA was isolated from 4 different pairs of erythroid and epithelial samples and hybridized to Affymetrix 430 A 2.0 microarrays.

first: Catherine

middle: I

last: Dumur

first: Kellie

last: Archer

first: Jack

middle: L

last: Haar

first: Joyce

last: Lloyd


title: XX hour expression data of AM from C57Bl/6 or gp91phox-/- mice following exposure to conidia or polystyrene beads

status: Public on Dec 01 2007

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

summary:
The response of AM transcription to exposure to conidia is expected to provide information about the mechanism by which these cells prevent conidial germination and therefore invasive aspergillosis.
Keywords: timecourse comparison with mock bead and conidia

overall_design: Conidia from A. fumigatus or polystyrene beads were instilled into lungs of C57Bl/6 or gp91phox-/- mice to test the response of AM in a normal and immune compromised host to determine if different responses contributed to increased susceptibility of invasive aspergillosis. Following in vivo incubation for 0, 2, or 4 hours, AM RNA was collected and prepared for hybridization to mouse Affymetrix GeneChip arrays.

first: James

last: Burritt

first: Jean

last: Cornish

first: Brady

last: Hurtgen

first: Ross

last: Taylor

first: Nancy


title: Effect of the HF diet and Akt1-mediated muscle growth on gene expression in liver tissue.

status: Public on Nov 02 2007

first: Yasuhiro

last: Izumiya

address: 715 Albany street

department: Molecular Cardiology

institute: Boston University School of Medicine

summary:
In contrast to the well-established role of oxidative muscle fibers in regulating fatty acid oxidation and whole body metabolism, little is known that about the function of fast/glycolytic muscle fibers in these processes. Here, we generated a skeletal muscle-specific, conditional transgenic mouse expressing a constitutively-active form of Akt1. Transgene activation led to muscle hypertrophy due to the growth of type IIb muscle fibers, which was accompanied by an increase in strength. These mice were then used to assess the consequence of building fast/glycolytic muscle fibers on adiposity and metabolism. Akt1 transgene induction in obese mice resulted in reductions in body weight and fat mass, a resolution of hepatic steatosis and improved metabolic parameters. These effects were achieved independent of changes in physical activity and levels of food consumption.  Akt1-mediated skeletal muscle growth opposed the effects of high fat/sucrose diet on transcript expression patterns in the liver, and increased hepatic fatty acid oxidation and ketone body production. Our findings indicate that an increase in fast/glycolytic muscle mass can result in the regression of obesity and obesity-related metabolic disorders in part through its ability to alter fatty acid metabolism in remote tissues.
Keywords: genetic modification

overall_design: 11 samples are included in this series. 3 wild-type mice fed on a normal diet, 4 wild-type mice fed on a HF diet, and 4 Akt1 double transgenic mice fed on a HF diet. All samples are on the mixed background.

first: Teresa

last: Hopkins

first: Carl

last: Morris

first: Kaori

last: Sato

first: Ling

last: Zeng

first: Jason

last: Viereck

last: Hamilton

first: Noriyuki

last: Ouchi

first: Nathan

last: LeBrasseur

first: Kenneth

last: Walsh


title: Chronic constriction injury in cholecystokinin b receptor (Cckbr)-deficient mice

status: Public on Nov 16 2007

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

summary:
The cholecystokinin B (2) receptor knockout (Cckbr KO) protects against allodynia induced by chronic constriction injury (CCI). The mechanism of this phenomenon is unknown, but must involve persistent changes in pain modulation and/or inflammatory pathways. We performed a gene expression study in two brain areas (midbrain and medulla) after surgical induction of CCI in Cckbr KO and wild-type (wt) control mice. The patterns of gene expression differences suggest that the immune system is activated in higher brain structures following CCI in the wt mice. The strongest differences include genes related to the MAPK pathway activation and cytokine production. In Cckbr KO mice this expressional pattern was absent. In addition, we found significant elevation of the Toll-like receptor 4 (Tlr4) in the supraspinal structures of the mice with deleted Cckbr compared to wt control mice. This up-regulation is most likely induced by the deletion of Cckbr. We suggest that there is a functional deficiency in the Tlr4 pathway which disables the development of neuropathic pain in Cckbr KO mice. Indeed, real time PCR analysis detected a CCI-induced upregulation of Tlr4 and Il1b expression in the lumbar region of wt but not Cckbr KO mice. Gene expression profiling indicates that elements of the immune response are not activated in Cckbr KO mice following CCI. Our findings suggest that there may be a role for CCK in the regulation of innate immunity.
Keywords: genetic modification, neuropathic model, chronic constriction injury

overall_design: 32 chips altogether, 4 mutant mice sham-operated, 4 control mice sham-operated, 4 mutant mice CCI-operated, 4 control mice CCI-operated, midbarin and medulla samples from each animals

last: Kõks

first: Cathy

last: Fernandes

first: Kaido

last: Kurrikoff

first: Eero

last: Vasar

first: Leonard

last: Schalkwyk


title: Expression data from mouse SCN after 30-min light pulse

status: Public on Oct 31 2007

city: Kent

first: Eric

middle: M

last: Mintz

state: OH

address: Cunningham Hall

institute: Kent State University

summary:
The transmission of information about the photic environment to the circadian clock involves a complex array of neurotransmitters, receptors, and second messenger systems.  Using laser capture microscopy and microarray analysis, a population of genes rapidly induced by light in the suprachiasmatic nucleus is identified.
Keywords: comparative expression analysis

overall_design: Mice were exposed starting at 1 hour after lights off to a 30-minute light pulse.  At the end of the light pulse, mice were euthanized and the brains extracted.  Cells from the suprachiasmatic nucleus were extracted using laser capture microscopy and gene expression was quantified using Affymetrix microarrays.  Genes showing a significant increase in expression following the light pulse as compared to a sham light pulse were identified.

first: Veronica

last: Porterfield


title: Comprehensive transcriptional profiling of prion infection in mouse models reveals networks of responsive genes.

status: Public on Jan 31 2008

city: Winnipeg

first: stephanie

last: booth

address: 1015 Arlington St

institute: PHAC

summary:
Prion infection results in progressive neurodegeneration of the central nervous system invariably resulting in death.  The pathological effects of prion diseases in the brain are morphologically well defined, such as gliosis, vacuolation, and the accumulation of disease-specific protease-resistant prion protein (PrPSc).  However, the underlying molecular events that lead to the death of neurons are poorly characterised.
In this study cDNA microarrays were used to profile gene expression changes in the brains of two different strains of mice infected with three strains of mouse-adapted scrapie.  Extensive data was collected and analyzed, from which we identified a core group of 349 prion-related genes (PRGs) that consistently showed altered expression in mouse models.  Gene ontology analysis assigned many of the up-regulated genes to functional groups associated with one of the primary neuropathological features of prion diseases, astrocytosis and gliosis; protein synthesis, inflammation, cell proliferation and lipid metabolism.  Using a computational tool, Ingenuity Pathway Analysis (IPA), we were able to build networks of interacting genes from the PRG list. The regulatory cytokine TGFB1, involved in modulating the inflammatory response, was identified as the outstanding interaction partner for many of the PRGs.  The majority of genes expressed in neurons were down-regulated; a number of these were involved in regulatory pathways including synapse function, calcium signalling, long-term potentiation and ERK/MAPK signalling.  Two down-regulated genes coding for the transcription regulators, EGR1 and CREB1, were also identified as central to interacting networks of genes; these factors are often used as markers of neuronal activity and their deregulation could be key to loss of neuronal function.
These data provides a comprehensive list of genes that are consistently differentially expressed in multiple scrapie infected mouse models. Building networks of interactions between these genes provides a means to understand the complex interplay in the brain during neurodegeneration.  Resolving the key regulatory and signaling events that underlie prion pathogenesis will provide targets for the design of novel therapies and the elucidation of biomarkers.
Keywords: disease state analysis

overall_design:
C57BL/6 mice were inoculated by intracerebral infection of brain homogenate from mice clinically infected with the ME7, 79a and 22A strains of scrapie.  In addition VM mice were also inoculated with the 22A scrapie strain. Mice were sacrificed at the onset of clinical diseases as manifested by uncoordinated gait, flaccid paralysis of the hind limbs, rigidity and abolishment of the righting reflex.  Brain tissue was collected from these mice and the RNA isolated.  Mouse CNS gene expression was analysed by two-colour microarray experiments using an in house manufactured 11K mouse cDNA microarray.  RNA from individual infected mice was hybridized to each array versus pooled reference RNA from an equivalent number of age-matched, mock-infected control mice.  In total we hybridized 34 different samples to microarrays in this experiment; 8-10 individual mice from each of the four sample groups were individually processed for separate microarrays. Hierachical clustering shows that the patterns of gene expression are for the most part common to the different mouse models . We used the program EDGE to identify genes that were differentially expressed in mouse brain during clinical disease.  We used a P value cut-off of 0.05 as the criteria for selection of significantly differentially expressed genes.

A similar design was used to determine gene expression profiles from C57BL/6 mice infected with a fourth strain of scrapie, RML.  Total RNA from three mice, plus dye swaps, was hybridized to Agilent whole genome mouse arrays to validate genes identified using our manufactured BMAP arrays.

first: Stephanie

last: Booth


title: Genetic and Pharmacologic Evidence Links Oxidative Stress to Ventilator-Induced Lung Injury in Mice

status: Public on Oct 04 2007

city: Baltimore

first: Dmitry

last: Grigoryev

state: MD

institute: JHU

summary:
RATIONALE: Mechanical ventilation (MV) is an indispensable therapy for critically ill patients with acute lung injury and the adult respiratory distress syndrome. However, the mechanisms by which conventional MV induces lung injury remain unclear. OBJECTIVES: We hypothesized that disruption of the gene encoding Nrf2, a transcription factor which regulates the induction of several antioxidant enzymes, enhances susceptibility to ventilator-induced lung injury (VILI), while antioxidant supplementation attenuates such effect. METHODS: To test our hypothesis and to examine the relevance of oxidative stress in VILI, here we have assessed lung injury and inflammatory responses in Nrf2-deficient (Nrf2(-/-)) mice and wildtype (Nrf2(+/+)) animals following acute (2 h) injurious model of MV with or without administration of antioxidant. MEASUREMENTS AND MAIN RESULTS: Nrf2(-/-) mice displayed greater levels of lung alveolar and vascular permeability and inflammatory responses to MV as compared to Nrf2(+/+) mice. Nrf2-deficieny enhances the levels of several pro-inflammatory cytokines implicated in the pathogenesis of VILI. We found diminished levels of critical antioxidant enzymes and redox imbalance by MV in the lungs of Nrf2(-/-) mice; however antioxidant supplementation to Nrf2(-/-) mice remarkably attenuated VILI. When subjected to clinically relevant prolong period of MV, Nrf2(-/-) mice displayed greater levels of VILI than Nrf2(+/+) mice. Expression profiling revealed lack of induction of several VILI genes, stress response and solute carrier proteins and phosphatases in Nrf2(-/-) mice. CONCLUSIONS: Collectively, our data demonstrate for the first time a critical role for Nrf2 in VILI, which confers protection against cellular responses induced by MV by modulating oxidative stress.
Keywords: stress response; genetically modified mice

overall_design: The Nrf2 wildtype (Nrf2+/+) and Nrf2-deficient (Nrf2–/–) CD-1/ICR strains of mice were subjected to mechanical ventilation with high (HVT) amounts of tidal volumes (VT) at 30 ml/kg for 2 hours. The animals subjected to spontaneous ventilation (SpV) for 2 hours were used as controls. Lungs were immediately removed and processed for total RNA isolation using TRIzol reagent (LifeTechnologies, Grand Island, NY). The isolated RNA was applied to Murine Genome 430A GeneChip arrays (Affymetrix, Santa Clara, CA), which contain probes for detecting ~14,500 well-characterized genes and 4371 expressed sequence tags according to standard microarray protocol. Scanned output files were analyzed by using Affymetrix GeneChip Operating Software and were independently normalized to an average intensity of 500.

first: Sekhar

middle: P

last: Reddy


title: Identification of genes enriched in putative stem/progenitor cells from mouse embryonic pancreas

status: Public on Jul 11 2007

city: Kobe

first: Yuichi

last: Hori

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Surgery

institute: Kobe University School of Medicine

summary:
Identification of genes enriched in putative stem/progenitor cells (CD133highPDGFRb- cell population) from the mouse embryonic pancreas that are purified by fluorescence activated cell sorting (FACS).

Success in islet transplantation-based therapies for type 1 diabetes mellitus and an extreme shortage of pancreatic islets has motivated efforts to develop renewable sources of islet-replacement tissue. Only a few attempts have been made at prospective isolation of pancreatic stem/progenitor cells, due to the lack of specific markers and the development of cell culture method. This study demonstrates the isolation of pancreatic stem/progenitor cells from the embryonic pancreas by cell sorting. RT-PCR and microarray analysis demonstrated that pancreatic stem/progenitor cells are enriched in CD133highPDGFRb- cell population. During in vivo differentiation, these cell populations have the ability for self-renewal and multipotency, including the formation of insulin-producing cells. Since the strategy is based on the cell sorting using cell surface markers common to human and rodents, it may promote strategies to derive transplantable islet-replacement tissues from human pancreatic stem/progenitor cells.
Keywords: Cell type comparison

overall_design: A couple of total RNAs derived from the different status of PDGFRb- cells was subjected to a dual-color microarray analysis, in which the RNAs from CD133highPDGFRb- cell population was labeled with Cy3 and that of CD133negPDGFRb- cell population with Cy5 respectively.

first: Miki

last: Fukumoto

first: Yoshikaza

last: Kuroda


title: S2 cells transfected with Clk

status: Public on Jul 09 2007

city: Jerusalem

first: Sebastian

last: Kadener

address: Alexander Silberman Inst. of Life Sciences, Edmund Safra Givat Ram Campus

department: Biological Chemistry

country: Israel

institute: Hebrew University

summary:
S2 cells transfected with pAc-Clk or empty vector
Keywords: S2 cells Clk

overall_design: S2 cells transfected with pAc-Clk or empty vector. Cells were transfected and RNA collected after 48hs


title: CLKGR in S2 cells

summary:
Experiments performed in S2 cells to identify direct CLK targets
Keywords: CLK targets

overall_design: Those targets were determined using Drosophilagenome1 and Drosophila 2.0 Affymetrix CHIPS.


title: Expression data from immunized B10.BR mice

status: Public on Jun 20 2007

city: La Jolla

first: Michael

last: McHeyzer-Williams

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

summary:
Mice were immunized with PCC (pigeon cytochrome c).
Keywords: Time course

overall_design: Lymph node cells were isolated by flow cytometry at successive timepoints after immunization for RNA extraction and hybridization on Affymetrix microarrays.

first: Nicolas

last: Fazilleau

first: Louise


title: Expression data from 18h-fasted WT versus KLF15-null mice: liver and quadriceps skeletal muscle

status: Public on Apr 02 2007

first: Susan

last: Gray

address: 20 Shattuck Street

institute: Brigham and Womens Hospital

summary:
We used microarray analysis to identify differences in gene expression levels, in liver and in quadriceps skeletal muscle, between 18h (overnight) fasted WT control and Kruppel-like factor 15 (KLF15)-null mice.
Keywords: comparative expression analysis, fasted state

overall_design: Liver and skeletal muscle (quadriceps) tissues were isolated from 4-5 month old, 18h-fasted WT and KLF15-null female mice for RNA extraction and hybridization on Affymetrix microarrays.

first: Mukesh

last: Jain


title: Knock-in of Kras G12D in mouse MLP-29 cells

status: Public on Sep 17 2007

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

summary:
KRAS mutations are present at a high frequency in human cancers. The development of therapies targeting mutated KRAS requires cellular and animal preclinical models. We exploited adeno-associated virus-mediated homologous recombination to insert the KRAS G12D allele in the genome of mouse somatic cells. Heterozygous mutant cells displayed a constitutively active Kras protein, marked morphologic changes, increased proliferation and motility but were not transformed. On the contrary, mouse cells in which we overexpressed the corresponding KRAS cDNA were readily transformed. The levels of Kras activation in knock-in cells were comparable with those present in human cancer cells carrying the corresponding mutation. KRAS-mutated cells were compared with their wild-type counterparts by gene expression profiling, leading to the definition of a "mutated KRAS-KI signature" of 345 genes. This signature was capable of classifying mouse and human cancers according to their KRAS mutational status, with an accuracy similar or better than published Ras signatures. The isogenic cells that we have developed recapitulate the oncogenic activation of Kras occurring in cancer and represent new models for studying Kras-mediated transformation. Our results have implications for the identification of human tumors in which the oncogenic KRAS transcriptional response is activated and suggest new strategies to build mouse models of tumor progression.
Keywords: Genetic modification by homologous recombination in somatic cells

overall_design: Four clones have been analyzed, two controls (WT and NEO+) and two with the Kras G12D mutation inserted by homologous recombination (KI-1 and KI-2). The expression data are averages of technical replicates.

first: Claudio

last: Isella


title: Microarray analysis of monocytes recruited in the peritoneum during experimental infection with Listeria monocytogenes

status: Public on Sep 20 2007

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

summary:
The immune system cellular response to tissue damage and infection requires the recruitment of blood leukocytes to the target tissue. This process is mediated through a classical multistep mechanism which involves transient rolling on the endothelium and recognition of inflammation followed by extravasation. We show here, by direct examination of blood monocyte functions in vivo, that resident monocytes monitor the endothelium of healthy tissues through patrolling, a new mechanism which allows extravasation in the absence of rolling.Patrolling depends on the integrin LFA1 and the chemokine receptor CX3CR1, and is required for rapid tissue invasion and initiation of an early immune response by monocytes that differentiate into macrophages at the site of tissue damage and infection.
The main goal of the experiment was to compare expression levels of genes in Gr1- monocytes in the blood and after recruitment in the peritoneum during experimental infection with Listeria monocytogenes (time course analysis).
Keywords: expression profiling; time course analysis; infection response

overall_design: Six-weeks old (C57Bl6, Cx3cr1gfp/+) mice were intraperitonealy infected with a low number  (1.104) of L. monocytogenes (EGDe strain) in exponential growth phase (bacteria were grown in BHI at 108/ml, and diluted 10.000x in PBS immediately before injection). Group of three mice were euthanized, before infection (time “0”) and 2 and 8 hours after infection (time “2” and “8”). Peripheral blood cells were recovered at time “0”, and peritoneal cells were recovered at time “0”, “2h”, and “8h” by peritoneal lavage. Cells from individual mice were stained with antibodies to CD11b (PECy7), Gr1 (APC), NK1.1, B220 and CD3 (PE), and F4/80 (biotin-conjugated followed by streptavidin–pacific blue) for sorting. Gr1- monocytes were purified as NK1.1- CD3- B220- CD11b+ F4/80low Gr1-, gfphigh; Gr1+ monocytes were purified as NK1.1- CD3- B220- CD11b+ F4/80low Gr1+, gfpint; and polymorphonuclear cells were purified as NK1.1- CD3- B220- CD11b+ F4/80- Gr1high, gfp-. 1.103 cells from each mice, time point, and phenotype were purified by facs sorting according to their phenotype. Samples were kept at 4°C before and during the sort. Cells were directly sorted in the SuperAmp Lysis Buffer (Miltenyi Biotec, Bergisch Gladbach, Germany) using a FACS Aria cell-sorter (BD biosciences).

first: Cedric

last: Auffray

first: Darin

last: Fogg

first: Meriem

last: Garfa

first: Gaelle

last: Elain

first: Olivier

last: Join-Lambert

first: Samer

last: Kayal

first: Sabine

last: Sarnacki

first: Ana

last: Cumano

first: Gregoire

last: Lauvau

first: Frederic

last: Geissmann


title: Microarray expression profiling of discrete microdissected mouse inner ear tissues from E9 to E15 at half-day intervals.

status: Public on Aug 14 2007

city: Saint Louis

first: Samin

last: Sajan

state: MO

address: 4566 Scott Avenue

institute: Washington University Medical School

summary:
The inner ear in mammals is derived from a simple ectodermal thickening called the otic placode. Through a series of complex morphological changes, the placode forms the mature inner ear comprising of the auditory organ (cochlea) and the vestibular/balance organs (utricle, saccule, and three semi-circular canals). The vast majority of genes known to be involved during inner ear development have been found through mutational screens or by chance.
To identify genes that can serve as novel candidates required for inner ear development, and also candidate genes for uncloned human deafnesses, inner ear tissues from mouse embryos from E9 to E15 were microdissected and expression-profiled at half-day intervals. Also profiled was the non-inner ear mesenchymal tissue surrounding the inner ear tissue. Various patterns of gene expression were identified, and significant biological pathways that these genes represented were identified. Also identified were mouse genes whose human orthologs are located within uncloned non-syndromic deafness intervals, thus serving as candidates for sequence analysis.
Keywords: Developmental timecourse

overall_design: Inner ear tissues from E9 to E15 were microdissected at half-day intervals. E9 is the earliest stage when the otic placode is clearly visible and able to be microdissected cleanly. E15 is the stage when all the organs of the inner ear have become established, as have the sensory hair and non-sensory support cells within those organs. For each of the stages from E9 to E10, whole inner ears were profiled. For each of the stages from E10.5 to E12, the primordial cochlear and vestibular organs were profiled separately. For each of the stages from E12.5 to E15, the cochlea and the saccule were profiled separately, whereas the utricle and the three ampullae were combined and profiled together. Any given tissue from any given stage was a collection of anywhere between 4 to 17 identical tissues, and was obtained in duplicate (i.e. from different litters). Hence, a total of 58 inner ear samples were obtained. Moreover, non-inner ear tissue found in the immediate vicinity of inner ear tissue was also obtained and profiled. Specifically, all non-inner ear tissue from E9 was profiled in duplicate. Non-inner ear tissue from E9.5 to E10.5 was pooled and profiled together (in duplicate), whereas that from E11 to E15 was pooled and profiled together (also in duplicate). Therefore, a total of 6 non-inner samples were obtained.

first: Mark

last: Warchol

first: Michael

last: Lovett


title: Expression data from Drosophila subjected to artificial selection on locomotion

status: Public on Oct 01 2007

city: Raleigh

first: Katherine

middle: W

last: Jordan

state: NC

address: Campus Box 7614

department: Genetics

institute: North Carolina State University

summary:
Genes relevant to manifestion of and variation in locomotor behavior might be differentially expressed in lines selected for divergent levels of locomotion.
Keywords: selection group

overall_design: Drosophila adults were assessed for  locomotor reactivity levels in a behavioral assay that quantified the locomotor response to a mechanical stimulus.  A subset of the sampled population was selected as parents for the next generation, with High, Low, and Control selection groups maintained.  This artificial selection was continued for 25 generations, with a variety of other behavioral and life history traits assessed for correlation with response to selection for locomotion.  At generation 25, male and female flies were collected for RNA extraction and subsequent gene expression analysis.

first: Theodore

middle: J

last: Morgan

first: MaryAnna

last: Carbone

first: Trudy

middle: F

last: Mackay


title: Expression data from mouse bladder urothelium

status: Public on Feb 02 2007

first: Christopher

middle: Swanson

last: Reigstad

address: 4444 Forest Park Blvd.

department: Center for Genome Sciences

institute: Washington University in St. Louis

summary:
Host responses to intracellular UPEC communities
We used laser capture microdissection and microarrays to identify urothelial transcripts differentially expressed in response to proximity to intracellular UPEC.
Keywords: spatial/cell type analysis

overall_design: Transcription within four distinct populations of urothelial cells was profiled in biological duplicate: (i) uninfected, (ii) mock-infected (sterile 1x PBS), (iii) IBC-distal (cells residing >10 cell diameters from IBCs in the section plane), and (iv) IBC-proximal (cells residing <10 cell diameters from IBCs in the section plane).

first: Scott

last: Hultgren

first: Jeffrey

last: Gordon


title: Gene expression comparison of mouse ES cells and EpiSCs

status: Public on Jun 27 2007

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

summary:
The application of human embryonic stem (ES) cells in medicine
and biology has an inherent reliance on understanding the starting
cell population. Human ES cells differ from mouse ES cells and the
specific embryonic origin of both cell types is unclear. Previous
work suggested that mouse ES cells could only be obtained from
the embryo before implantation in the uterus1–5. Here we show
that cell lines can be derived from the epiblast, a tissue of the postimplantation
embryo that generates the embryo proper. These
cells, which we refer to as EpiSCs (post-implantation epiblastderived
ES cells), express transcription factors known to regulate
pluripotency, maintain their genomic integrity, and robustly differentiate
into the major somatic cell types as well as primordial
germ cells. The EpiSC lines are distinct from mouse ES cells in
their epigenetic state and the signals controlling their differentiation.
Furthermore, EpiSC and human ES cells share patterns of
gene expression and signalling responses that normally function
in the epiblast. These results show that epiblast cells can be maintained
as stable cell lines and interrogated to understand how
pluripotent cells generate distinct fates during early development.
*Note: EpiSCs were previously referred to as post-ES cells
Keywords: cell type comparison

overall_design: 3 biological replicates of each cell type (EpiSC and mouse ES) were compared.

first: Josh

middle: G

last: Chenoweth

first: Ron

last: McKay


title: The Chemotherapeutic Agent, 5,6-Dimethylxanthenone-4-Acetic Acid,

status: Public on Mar 08 2007

first: Stefaine

last: Vogel

address: 660 W. Redwood Street

department: Dept. of Microbiology and Immunology

institute: Univ. of Maryland

summary:
Vascular disrupting agents (VDA) represent a novel approach to the treatment of cancer, resulting in collapse of tumor vasculature and tumor death.  5,6-Dimethylxanthenone-4-acetic acid (DMXAA) is a VDA currently in advanced Phase II clinical trials, yet its precise mechanism of action is unknown despite extensive preclinical and clinical investigations.  The data presented herein demonstrate that DMXAA is a novel and specific activator of the TBK1-IRF-3 signaling pathway.  DMXAA treatment of primary murine macrophages resulted in robust IRF-3 activation, a ~750-fold increase in IFN-beta mRNA and, in contrast to the potent Toll-like receptor 4 (TLR4) agonist, lipopolysaccharide (LPS), signaling was independent of mitogen-activated protein kinase (MAPK) activation and elicited minimal NF-kappaB-dependent gene expression.  DMXAA-induced signaling was critically dependent on the IRF-3 kinase, TBK1, and IRF-3, but MyD88-, TRIF-, IPS-1/MAVS-, and IKKbeta-independent, thus excluding all known TLRs and cytosolic helicase receptors.  DMXAA pretreatment of murine macrophages induced a state of tolerance to LPS and vice versa.  In contrast to LPS stimulation, DMXAA-induced IRF-3 dimerization and IFN-beta expression were inhibited by salicylic acid (SA).  These findings detail a novel pathway for TBK-1-mediated IRF-3 activation and provide new insights into the mechanism of this new class of chemotherapeutic drugs.
Keywords: DMXAA, IRF-3, TBK1, IFN-beta, Salicylic acid, TLR

overall_design: Microarray analysis was carried out using Affymetrix® mouse array 430A_2 exposed to total RNA prepared from C57BL/6J or IFN-beta-/- macrophages that had been treated with medium alone or DMXAA for 3 h.  Fold-induction was calculated using Affymetrix® GeneChip® Operating Software.  A >3-fold increase or decrease between inducible and basal mRNA levels was set as the criteria for inclusion of a gene as modulated.


title: Timepoints 5073 strain

first: Sebastian

last: Kadener

summary:
6 Timepoints from 5073 strain
Keywords: Timepoints 5073 cwo

overall_design: Fly head microarray from 6 Timepoints using 5073 strain


title: Clockwork Orange is a transcriptional repressor and a new Drosophila circadian pacemaker component

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

overall_design: Refer to individual Series


title: CLK targets from fly heads

summary:
CLK targets from fly heads using the TIM-GAL4; UAS-CLKGR line
Keywords: CLK TARGETS

overall_design: Fly heads were stimulated with vehicle + CHX or dexamethasone + CHX


title: Timepoints Control strain

summary:
6 Timepoint microarray from control strain
Keywords: Timepoints yw

overall_design: Fly head microarray from 6 Timepoints using yw strain


title: Methylation of hMTase G9a on a histone-like site regulates protein complex assembly

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

type:
Expression profiling by array
Methylation profiling by array

summary:
Gene expression in eukaryotes is tightly linked to the methylation state of specific lysine residues within the N-terminal region of the core histone proteins. While the mechanisms connecting histone lysine methylation to effector protein recruitment and control of gene activity are increasingly well understood, it remains unknown whether non-histone chromatin proteins are targets for similar modification-recognition systems. Here we show that histone H3 and the H3 methyltransferase G9a share a conserved methylation motif that is both necessary and sufficient to mediate in vivo interaction with the potent epigenetic regulator Heterochromatin Protein 1 (HP1). As with H3, G9a-HP1 interaction is dependent on lysine methylation and can be reversed by adjacent phosphorylation. NMR analysis demonstrates that the HP1 chromodomain recognizes methyl-G9a through a binding mode similar to that used in recognition of methyl-H3, and that adjacent phosphorylation directly antagonizes G9a-HP1 interaction. In addition to uncovering the chromodomain as a generalized methyl-lysine binding module, these data identify histone-like modification cassettes (or “histone mimics”) as an entirely new class of non-histone methylation targets, and directly demonstrate the relevance of the principles underlying the histone code to the regulation of non-histone proteins.
Keywords: methylation analysis

overall_design: Two independent Affymetrix gene expression microarray analyses were performed on samples from G9a-deleted MEFs reconstituted with empty vector (delta), wild type FLAG-G9a (WT), FLAG-G9a K165A (K165A) or FLAG-G9a H1093K catalytic mutant (H1093K).

first: Srihari

middle: C

last: Sampath

first: Alexander

last: Tarakhovsky


title: Liver-specific knockdown of JNK1

status: Public on Oct 02 2007

city: Abbott Park

last: Jung

state: IL

address: 100 Abbott Park Road

department: Gene Expression Analysis

institute: Abbott Laboratories

summary:
Liver-specific Knockdown of JNK1 Up-regulates Proliferator-activated Receptor  Coactivator 1 and Increases Plasma Triglyceride despite Reduced Glucose and Insulin Levels in Diet-induced Obese Mice.

The c-Jun N-terminal kinases (JNKs) have been implicated in the development of insulin resistance, diabetes, and obesity. Genetic disruption of JNK1, but not JNK2, improves insulin sensitivity in diet-induced obese (DIO) mice. We applied RNA interference to investigate the specific role of hepatic JNK1 in contributing to insulin resistance in DIO mice. Adenovirus-mediated delivery of JNK1 short-hairpin RNA (Ad-shJNK1) resulted in almost complete knockdown of hepatic JNK1 protein without affecting JNK1 protein in other tissues. Liver-specific knockdown of JNK1 resulted in significant reductions in circulating insulin and glucose levels, by 57 and 16%, respectively. At the molecular level, JNK1 knockdown mice had sustained and significant increase of hepatic Akt phosphorylation. Furthermore, knockdown of JNK1 enhanced insulin signaling in vitro. Unexpectedly, plasma triglyceride levels were robustly elevated upon hepatic JNK1 knockdown. Concomitantly, expression of proliferator-activated receptor  coactivator 1, glucokinase, and microsomal triacylglycerol transfer protein was increased. Further gene expression analysis demonstrated that knockdown of JNK1 up-regulates the hepatic expression of clusters of genes in glycolysis and several genes in triglyceride synthesis pathways. Our results demonstrate that liver-specific knockdown of JNK1 lowers circulating glucose and insulin levels but increases triglyceride levels in DIO mice.
Keywords: Treatment Response

overall_design: Liver sample from vehicle, GFP Adv-shRNA, or Jnk1 Adv-shRNA treated DIO mice with 5, 4, and 5 replicates, respectively

first: Ruojing

last: Yang

first: Denise

last: Wilcox

first: Deanna

last: Haasch

first: Phong

middle: T

last: Nguyen

first: Martin

last: Voorbach

first: Stella

last: Doktor

first: Sevan

last: Brodjian

first: Eugene

middle: N

last: Bush

first: Emily

last: Lin

first: Peer

middle: B

last: Jacobson

first: Christine

last: Collins

last: Landschulz

first: James

last: Trevillyan

first: Cristina

last: Rondinone

first: Terry

last: Surowy


title: Histone H3K4 and H3K27 trimethylation analysis in ES cells, Mefs and induced pluriptent cells.

status: Public on May 23 2007

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

institute: UCLA

summary:
Mefs were transduced with Oct4 , Sox2, Klf4 and c-myc to induce pluripotency. The histone  H3 K4 and H3 K27 trimethylation status was compared genome wide in ES cells, MEFs, and induced pluripotent cells (iPS).

Keywords: ChIP-Chip

overall_design: Induced pluripotency cells were compared to the ES cells, and MEFs for similar epigenetic marks and gene expression.


title: C2C12 Myotubes in response to Palmitate

status: Public on Jan 18 2007

city: boston

first: Sarah

last: Crunkhorn

address: 1 Joslin Place

department: CMP

institute: Joslin Diabetes Center

summary:
To identify mediators of obesity-linked reductions in PGC-1, we tested the effects of cellular nutrients in C2C12 myotubes.  While overnight exposure to high insulin, glucose, glucosamine, or amino acids had no effect, saturated fatty acids (FA) potently reduced PGC-1a and b mRNA expression.
Keywords: Nutrient Effect

overall_design: Cell culture - Mouse C2C12 myoblasts (ATCC, Manassas, VA) were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 20% fetal bovine serum (Invitrogen), at a confluency of 60-70%.  To initiate differentiation, cells were allowed to reach 100% confluency and medium was changed to DMEM containing 2% horse serum (Invitrogen) and changed every 2 days. Full differentiation, with myotube fusion and spontaneous twitching, was observed at 5 days. Fatty acid stock preparation - Fatty acids were dissolved in 0.1 N sodium hydroxide (final concentration 100 mM) at 65°C for 2 hours and then complexed with 10% fatty acid-free BSA, yielding a final stock of 5 mM.  Three replicates for each fatty-acid.  Microarray analysis - RNA was isolated as described from C2C12 myotubes treated overnight with 500 µM palmitate or 1% BSA, and cRNA was synthesized.  10 mg of cRNA were hybridized to Affymetrix mouse 430A 2.0 arrays.  Intensity values were quantified using MAS 5.0 software.  MAPPFinder (www.genmapp.org) was used to integrate expression data with known pathways.

first: Mary-Elizabeth

last: Patti


title: Transcriptional Response to Alcohol Exposure  in Drosophila melanogaster

status: Public on Jul 27 2006

first: Tatiana

middle: V

last: Morozova

address: campus box 7617

department: zoology

institute: NCSU

summary:
The National Institute on Alcohol Abuse and Alcoholism has estimated that approximately 14 million people in the United States suffer from alcoholism. Alcohol sensitivity, the development of tolerance to alcohol and susceptibility to addiction vary in the population. Whereas environmental factors, such as stress and social experience, contribute to individual variation in sensitivity to chronic alcohol consumption, genetic factors have also been implicated. However, genetic polymorphisms that predispose to alcoholism remain largely unknown due to extensive genetic and environmental variation in human populations.  Drosophila, however, allows studies on genetically identical individuals in controlled environments. Although addiction to alcohol has not been demonstrated in Drosophila, flies show responses to alcohol exposure that resemble human intoxication, including hyperactivity, loss of postural control, sedation, and exposure-dependent development of tolerance. We assessed whole-genome transcriptional responses following alcohol exposure and demonstrate immediate down-regulation of olfactory sensitivity and, concomitant with development of tolerance, altered transcription of enzymes associated with fatty acid biosynthesis. Our results identify key enzymes in conserved metabolic pathways that may contribute to human alcohol sensitivity.
Keywords: Drosophila, model system, alcohol sensitivity, tolerance

overall_design: Alcohol sensitivity in Drosophila melanogaster can be quantified in an inebriometer. The elution time from the column is used as a measure of sensitivity to alcohol intoxication. Overall design:  We collected 3-5 day old Canton S flies either without exposure to ethanol (control group), immediately after passage through the inebriometer, or from a population that had developed tolerance 2h after the initial ethanol exposure.

first: Robert

last: Anholt

first: Trudy

last: Mackay


title: Genome-Wide Identification of Direct Targets of the Drosophila Retinal Determination Protein Eyeless

status: Public on Jan 11 2006

city: Houston

first: rui

last: chen

state: TX

address: One Baylor Plaza

department: HGSC, Department of Molecular and Human Gentics

institute: Baylor College of Medicine

summary:
The discovery of direct downstream targets of transcription factors (TFs) is necessary for understanding the genetic mechanisms underlying complex, highly regulated processes such as development.  In this report, we have used a combinatorial strategy to conduct a genome-wide search for novel direct targets of Eyeless (Ey), a key transcription factor controlling early eye development in Drosophila.  Like many other TFs, little is known for Ey direct downstream targets.  To date, only one gene, sine oculis (so), has been identified as Ey direct targets in Drosophila.  Therefore, it is crucial to identify additional targets in order to gain a better understanding of ey function.  To overcome the lack of high quality consensus binding site sequences, phylogenetic shadowing of Ey binding sites in so was used to construct a position weight matrix (PWM) of the Ey protein.  This PWM was then used for in silico prediction of potential binding sites in the Drosophila melanogaster genome.  To reduce the false positive rate, conservation of these potential binding sites was assessed by comparing the genomic sequences from seven Drosophila species.  In parallel, microarray analysis of wild-type versus ectopic ey-expressing tissue, followed by microarray-based epistasis experiments in an atonal (ato) mutant background, identified 188 genes induced by ey.  Intersection of in silico predicted conserved Ey binding sites with the candidate gene list produced through expression profiling yields a list of 20 putative ey-induced, eye-enriched, ato-independent, direct targets of Ey, including so.  The accuracy of this list of genes was confirmed using both in vitro and in vivo methods.  Initial analysis reveals three genes, eyes absent, shifted, and Optix, as novel direct targets of Ey.  These results suggest that the integrated strategy of computational biology, genomics, and genetics is a powerful approach that can be applied to systematically identify direct downstream targets for any transcription factor genome-wide.
Keywords: genetic modification, cell type comparison

overall_design: biological triplicates were done for all samples


title: Expression data from murine BRD2-mediated lymphomas

status: Public on Oct 28 2006

city: Boston

first: Marc

middle: E.

last: Lenburg

address: 715 Albany Street, E613B

department: Genetics and Genomics

institute: Boston University School of Medicine

summary:
The dual bromodomain protein Brd2 is closely related to the basal transcription factor TAFII250, which is essential for cyclin A transactivation and mammalian cell cycle progression. In transgenic mice, constitutive lymphoid expression of Brd2 causes a malignancy most similar to human diffuse large B cell lymphoma. We compare the genome-wide transcriptional expression profiles of these lymphomas with those of proliferating and resting normal B cells. Transgenic tumors reproducibly show differential expression of a large number of genes important for cell cycle control and lymphocyte biology; expression patterns are either tumor-specific or proliferation-specific. Several of their human orthologs have been implicated in human lymphomagenesis. Others correlate with human disease survival time. BRD2 is underexpressed in some subtypes of human lymphoma and these subtypes display a number of similarities to the BRD2-mediated murine tumors. We illustrate with a high degree of detail that cancer is more than rampant cellular proliferation, but involves the additional transcriptional mobilization of many genes, some of them poorly characterized, which show a tumor-specific pattern of gene expression.
Keywords: disease state analysis

overall_design: 26 samples are included in this series.  Sporadic murine E-mu-BRD2 mediated lymphomas are divided into three classes by disease severity and compared to either resting or mitogen-activated B Cells.  The resting and activated B Cells are either wildtype or E-mu-BRD2 transgenic.  All samples are on the FVB wildtype background.

middle: E

first: Anupama

last: Sinha

first: Douglas

last: Faller

first: Gerald

last: Denis