title: E2F1 loss induces spontaneous tumour development in Rb-deficient epidermis

status: Public on Aug 20 2012

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

institute: CIEMAT

summary: The specific ablation of Rb1 gene in epidermis (RbF/F;K14cre) promotes proliferation and altered differentiation but does not produce spontaneous tumour development. These phenotypic changes are associated with increased expression of E2F members and E2F-dependent transcriptional activity. Here, we have focused on the possible dependence on E2F1 gene function. We have generated mice that lack Rb1 in epidermis in an inducible manner (RbF/F;K14creERTM). These mice are indistinguishable from those lacking pRb in this tissue in a constitutive manner (RbF/F;K14cre). In an E2F1-null background (RbF/F;K14creERTM; E2F1-/- mice), the phenotype due to acute Rb1 loss is not ameliorated by E2F1 loss, but rather exacerbated, indicating that pRb functions in epidermis do not rely solely on E2F1. On the other hand, RbF/F;K14creERTM;E2F1-/- mice develope spontaneous epidermal tumours of hair follicle origin with high incidence. These tumours, which retain a functional p19arf/p53 axis, also show aberrant activation of βcatenin/Wnt pathway. Gene expression studies revealed that these tumours display relevant similarities with specific human tumours. These data demonstrate that the Rb/E2F1 axis exerts essential functions not only in maintaining epidermal homeostasis, but also in suppressing tumour development in epidermis, and that the disruption of this pathway may induce tumour progression through specific alteration of developmental programs.

overall_design: Gene expression was compared between normal mouse skin, skin from transgenic RbF/F;K14creERTM; E2F1-/- , E2F1-/-, and RbF/F;K14creERTM; E2F1-/- mouse, and carcinomas arising in the skin of RbF/F;K14creERTM; E2F1-/- mouse. All mice were treated with tamoxifen.

first: Clotilde

last: Costa

first: Mirentxu

last: Santos

first: Monica

last: Martinez-Fernandez

first: Marta

last: Duenas

first: Corina

last: Lorz

first: Jesus

last: Paramio


title: A timecourse analysis of the genetic extinction of NRAS in an inducible mouse model of melanoma.

status: Public on Aug 09 2012

city: Houston

first: Lawrence

middle: N

last: Kwong

state: TX

address: 1901 East Rd

country: USA

institute: UT MD Anderson Cancer Center

summary:
We sought to understand the pathways involved in NRAS extinction over time using a doxycycline-dependent, inducible mouse model of melanoma. This data provides insights into the temporal dynamics of downstream NRAS signaling and helps to correlate differentially affected pathways.
We used microarrays to determine which transcripts were affected by NRAS-Q61K extinction at 24, 48, and 72 hours after doxycycline withdrawal. This data was used in support of a separate dataset submitted to GEO entitled Comparison of the genetic extinction of NRAS to pharmacological MEK inhibition in an inducible mouse model of melanoma.

overall_design: The iNRAS-475 mouse melanoma cell line was injected intradermally into nude mice which were fed 2mg/ml doxycycline water. Tumors were allowed to reach 200-500mm3 after 6 weeks. Doxycyline was then withdrawn from the diet and tumors harvested at 24, 48, and 72 hours post-withdrawal.

first: Lynda

last: Chin


title: Gene expression analysis of B-ALL cells treated with BET inhibitor

status: Public on Aug 10 2012

city: Boston

first: Christopher

middle: J

last: Ott

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Two human acute lymphoblastic leukemia cell lines were treated with a BET bromodomain inhibitor that blocks BET association with chromatin. These cell lines, MHH-CALL4 and MUTZ-5, each carry translocation of the CRLF2 gene into the IgH locus, and their growth was found to be susceptible to BET inhibition. Gene expression changes were analyzed in each cell line versus vehicle control.

overall_design: Cell were treated for 8 hours with either DMSO or 500nM of the BET bromodomain inhbitor JQ1. Three samples for each treatment were taken and analyzed for each cell line. CEL files were analyzed at both the core and extended gene level by RMA with the Affymetrix Expression Console software.

first: James

middle: E

last: Bradner


title: Oncogenic NRAS Signaling Differentially Regulates Survival and Proliferation in Melanoma.

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

overall_design: Refer to individual Series


title: Surfactant Protein C knockout

status: Public on Aug 21 2012

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Study the Role of Surfactant Protein C in Innate Lung Defense.

overall_design: Gene expression profiles comparison between isolated TYPE II cells from SPC(-/-) and control litter mates.

first: Stephan

last: Glasser

first: Melissa

last: Maxfield

first: Teah

last: Ruetschilling

first: Henry

last: Akinbi

first: John

last: Baatz

first: Joseph

last: Kitzmiller

first: Kristen

last: Page

first: Thomas

last: Korfhagen


title: Selective inhibition of CD4+ T-cell cytokine production and autoimmunity by BET protein and c-Myc inhibitors

status: Public on Aug 04 2012

city: LA JOLLA

first: Jason

last: Greenbaum

state: CA

address: 9420 Athena Circle

department: Bioinformatics Core Facility

institute: LIAI

summary: Bromodomain-containing proteins bind acetylated lysine residues on histone tails and are involved in  the recruitment of additional factors that mediate histone modifications and enable transcription. A compound, I-BET-762, that inhibits binding of an acetylated histone peptide to BRD4 and other proteins of the BET (bromodomain and extra-terminal domain) family, was previously shown to suppress the production of pro-inflammatory proteins by macrophages and block acute inflammation in mice. Here we investigate the effect of I-BET-762 on T cell function. We show that treatment of naïve CD4+ T cells with I-BET-762 during early differentiation modulates subsequent cytokine production, and inhibits the ability of Th1-skewed cells to induce autoimmune pathogenesis in a model  of experimental autoimmune encephalomyelitis (EAE) in vivo. The suppressive effects of I-BET-762 on T-cell mediated inflammation were not due to inhibition of expression of the pro-inflammatory cytokines, IFN-. or IL-17, but correlated with the ability to suppress GM-CSF production from CNS-infiltrating T cells, resulting in decreased recruitment of macrophages and granulocytes. The effects of I-BET-762 were distinct from those of the fumarate ester, dimethyl fumarate (DMF), a candidate drug for treatment of multiple sclerosis (MS). Our data suggest that I-BET and DMF could have complementary roles in the treatment of MS, and provide a strong rationale for inhibitors of BET-family proteins in the treatment of autoimmune diseases, based on their dual ability to suppress granulocyte and macrophage recruitment by T cells as well as production of pro-inflammatory proteins by macrophages.

overall_design: RNA from resting or activated CD4+ T cells grown in the presence of a control substance (DMSO or Control-768) or two different concentrations of I-BET-762, was hybridized to the chip.  There are 3 biological replicates for a total of 2 (cell states) x 4 (conditions) x 3 (replicates) = 24 samples.

first: Hozefa

middle: S

last: Bandukwala

last: Gagnon

first: Susan

last: Togher

middle: A

first: Eward

middle: D

last: Lamperti

first: Nigel

last: Parr

first: Amy

middle: M

last: Molesworth

first: Nicholas

last: Smithers

first: Kevin

last: Lee

last: Witherington

first: David

middle: F

last: Tough

first: Rab

middle: K

last: Prinjha

first: Bjoern

last: Peters

first: Anjana

last: Rao


title: Expression data from anti-EpCAM treated and untreated SP cells compared to lung tissue

status: Public on Aug 08 2012

city: Hannover

last: Krüwel

address: Nikolai-Fuchs-Str. 1

country: Germany

institute: Fraunhofer Institute for Toxicology and Experimental Medicine

summary:
Targeted therapies against cancer stem cells which are enriched in side populations (SP) involves interruption of Wnt-signalling. Furthermore, EpCAM is a SP marker and modulator of Wnt-signalling. Therefore, the effects of an anti-EpCAM treatment on SP-cells and WNT/β-catenin signalling was studied.
SP of the murine lung adenocarcinoma cell line A2C12 was obtained by fluorescence activated cell sorting and whole genome scans helped to define their molecular phenotype after anti-EpCAM antibody treatment.

overall_design: Anti-EpCAM treated and untreated A2C12 cells were subjected to Hoechst 33342 dye exclusion assay and sorted to SP fractions by FACS. Gene expression of SP cells was compared to non-transgenic lung tissue.

first: Astrid

last: Rohrbeck


title: Comparison of the genetic extinction of NRAS to pharmacological MEK inhibition in an inducible mouse model of melanoma

first: Lawrence

last: Kwong

summary:
Since direct pharmacological inhibition of RAS has thus far been unsuccessful, we explored system biology approaches to identify synergistic drug combination(s) that can mimic direct RAS inhibition. Leveraging an inducible mouse model of NRAS-mutant melanoma, we compare pharmacological MEK inhibition to complete NRAS-Q61K extinction in vivo. NRAS-Q61K extinction leads to a complete and durable tumor regression by enhancing both apoptosis and cell cycle arrest. By contrast, MEK inhibition only produces tumor stasis at best and we find that it robustly activates apoptosis but does not significantly impede proliferation.
We used microarrays to determine which transcripts were affected by NRAS-Q61K extinction but insufficiently by MEK inhibition. We selected a  single comparative timepoint, 4 days post-treatment. Downstream analyses included GSEA and TRAP algorithms, leading to the identification of a differentially affected CDK4-driven proliferation network. Immune genes were also identified as significant, but control experiments determined these to be largely the off-target effects of doxycycline and not of NRAS-Q61K extinction.

overall_design: The iNRAS-475 mouse melanoma cell line was injected intradermally into nude mice which were fed 2mg/ml doxycycline water. Tumors were allowed to reach 200-500mm3 after 6 weeks. Mice were then treated with vehicle or 100mg/kg of the AZD6244 MEK inhibitor, or doxycyline was withdrawn from the diet. Each sample represents a distinct tumor and thus provide six biological, not technical replicates per cohort.

first: Lynda

last: Chin


title: Gene expression profiling of experimental granulation tissue in Mmp13-/- mice compared to wild type mice

city: Turku

first: Veli-Matti

last: Kähäri

address: Tykistökatu 6A, 4. floor

country: Finland

institute: University of Turku, Turku University Hospital

summary:
Proteinases play a pivotal role in wound healing by degrading molecular barriers, regulating cell-matrix interactions and availability of bioactive molecules. Matrix metalloproteinase-13 (MMP-13, collagenase-3) is a wide spectrum proteinase. Its expression and function is linked to the growth and invasion of many epithelial cancers such as squamous cell carcinoma. Moreover, the physiologic expression of MMP-13 is associated e.g. to scarless healing of human fetal skin and adult gingival wounds. While MMP-13 is not found in the normally healing skin wounds in human adults, it is expressed in mouse skin during wound healing. Thus, mouse wound healing models can be utilized for studying the role of MMP-13 in the events of wound healing. As the processes such as the migration and proliferation of keratinocytes, angiogenesis, inflammation and activation of fibroblasts are components of wound repair as well as of cancer, many results received from wound healing studies are also adaptable to cancer research.
Classically, the process of wound healing can be devided into three phases which are histologically and functionally separate but temporally overlapping: 1) hemostasis and inflammation, 2) re-epithelialization and granulation tissue formation, and 3) matrix remodeling. Granulation tissue is formed into the wound via fibroplasia, angiogenesis and extracellular matrix (ECM) deposition by fibroblasts. Granulation tissue is rich in inflammatory cells, fibroblasts, myofibroblasts and blood vessels. After epidermal recovery, the granulation tissue is resolved via matrix remodeling and cell apoptosis. A sterile viscose cellulose sponge (VCS) characterized by defined size and structure can be used to experimentally induce formation of subcutaneous granulation tissue. Compared to normal granulation tissue, this model allows easy examination of the granulation tissue in its entirety but leaving out epidermal keratinocytes in the sample preparation. In this study, we studied the role of MMP-13 in the formation of mouse VCS-induced granulation tissue. We performed gene expression profiling of the granulation tissue samples of Mmp13-/- (KO) and wild type (WT) mice harvested at day 7, day 14 and day 21 after VCS implantation.

overall_design: Mmp13-/- (KO) mice were generated as described (Inada et al.  2004, PNAS, 101: 17192-17197) and used in these experiments after backcrossing at least seven generations into C57BL6 mice. The WT mice were generated from the backcrossed heterozygote Mmp13-/- (KO) mice. Granulation tissues were harvested at three time points (7d, 14d, 21d) from Mmp13-/- (KO) and WT mice. One sample of each mouse was analyzed (n=3, 7d; n=4, 14d; n=4, 21d; for each genotype). The samples were processed for RNA extraction and Affymetrix 3'IVT DNA microarray gene expression analysis.

first: Mervi

last: Toriseva


title: Mesp1 induces a subset of hematopoietic-associated transcription factors in ES cell-derived Flk1+Tie2+ endothelium

status: Public on Aug 03 2012

city: St. Louis

first: Mi

last: Cai

state: MO

address: 660 S. Euclid Ave.

department: Immunology and Pathology

institute: Washington University School of Medicine

summary:
Previously, we reported that the transcription factor Mesp1 promotes the cell fates of cardiomyocytes, smooth muscle, and vascular endothelium. Recently, hematopoietic stem cells (HSCs) were shown to derive from hemogenic endothelium.  Since Mesp1 regulates development of endothelium, it potentially could influence gene expression related to hematopoietic development.

Our present fate mapping study found that Mesp1-cre efficiently labeled hematopoietic lineages in vivo. This result suggested that Mesp1 might be expressed in progenitors of the hematopoietic system, such as hemogenic endothelium. To test this, we purified Flk1+ Tie2+ endothelium derived from differentiating ES cells with or without Mesp1 induction, and used microarray expression analysis to identify genes strongly up-regulated by Mesp1.

overall_design: Embryonic stem (ES) cells harboring a doxycycline (dox)-inducible Mesp1 gene (A2lox.Mesp1) were differentiated as embryoid bodies for 5 days in the absence (-) or presence (+) of dox from day 2 to day 4. Flk1+Tie2+ endothelial cells were purified by cell sorting for RNA extraction and hybridization on Affymetrix microarrays.

first: Ellen

last: Langer

first: Jennifer

middle: G

last: Gill

first: Theresa

middle: L

last: Murphy

first: Kenneth


title: Genome-wide analysis of gene expression patterns in the liver tumors of mir-122 knockout mice

status: Public on Aug 07 2012

city: Taipei

first: Ann-Ping

last: Tsou

address: 155, Li-Nong St., Sec.2

department: Inst. Biotechnology in Medicine

country: Taiwan

institute: National Yang-Ming University

summary: To invesigate the physiological roles of mir-122 in hepatocarcinogenesis, we performed expression profiling of the liver tumors of mir-122 knockout mice and the liver tissues of the control B6/129 mice.

overall_design: Total RNA was extracted from three tumors of mir-122 knockout mice and liver tissues of  two control mice of 11 months of age; five tumors of  mir-122 knockout mice and the liver tissues of three control mice of 14 months of age. Gene expression was quantified by robust multi-array analysis (RMA) using the Genomic Suite software from Partek.

first: Wei-Chih

last: Tsai

first: Chu-Sui

last: Hsu

first: Shu-Jen

last: Chen

first: Yi

last: Huang

first: Hua-Chien


title: Scl Represses Cardiomyogenesis in Prospective Hemogenic Endothelium and Endocardium

city: LOS ANGELES

first: Hanna

last: Mikkola

address: 621, Charles E. Young Drive South

department: MCDB

institute: UCLA

summary: Endothelium in embryonic hematopoietic tissues generates hematopoietic stem/progenitor cells; however, it is unknown how its unique potential is specified.  We show that transcription factor Scl/Tal1 is essential for both establishing the hematopoietic transcriptional program in hemogenic endothelium and preventing its misspecification to a cardiomyogenic fate. Scl-/- embryos activated a cardiac transcriptional program in yolk sac endothelium, leading to the emergence of CD31+Pdgfrα+ cardiogenic precursors that generated spontaneously beating cardiomyocytes. Ectopic cardiogenesis was also observed in Scl-/- hearts, where the disorganized endocardium precociously differentiated into cardiomyocytes. Induction of mosaic deletion of Scl in Sclfl/flRosa26Cre-ERT2 embryos revealed a cell-intrinsic, temporal requirement for Scl to prevent cardiomyogenesis from endothelium. Scl-/- endothelium also upregulated the expression of Wnt antagonists, which promoted rapid cardiomyocyte differentiation of ectopic cardiogenic cells. These results reveal unexpected plasticity in embryonic endothelium such that loss of a single master regulator can induce ectopic cardiomyogenesis from endothelial cells.

overall_design: There are 24 samples analyzed, divided into 3 separate experiments. All the samples were performed in biological duplicates.

first: Ben

last: Van Handel

first: Amelie

last: Montel-Hagen

first: Rajkumar

last: Sasidharan

first: Haruko

last: Nakano

first: Roberto

last: Ferrari

first: Cornelis

last: Boogerd

first: Johann

last: Schredelseker

first: Yanling

last: Wang

first: Sean

last: Hunter

first: Tonis

last: Org

first: Jian

last: Zhou

first: Xinmin

last: Li

first: Matteo

last: Pellegrini

first: Jau-Nian

first: Stuart

middle: H

last: Orkin

first: Siavash

last: Kurdistani

first: Sylvia

last: Evans

first: Austin


title: The gene expression analysis of the spinal cord of SBMA (Spinal Bulbar Muscular Atrophy) model mice

city: Nagoya

first: Makoto

last: Minamiyama

address: 65 Tsurumai-Cho, Showa-Ku

department: Neurology

country: Japan

institute: Nagoya University Graduate School of Medicine

summary:
To identify the gene expression changes that are specific to SBMA, we prepared total mRNA samples from the spinal cords of transgenic mice carrying a full-length human AR with 97 CAGs (AR-97Q), transgenic mice bearing a wild-type allele of AR with 24 CAGs (AR-24Q), and the wild-type littermates of the AR-97Q mice (C57BL/6). We used AR-97Q (Line #7-8) male mice because they show progressive muscular atrophy and weakness as well as SBMA-like pathology such as the accumulation of the pathogenic androgen receptor in the nucleus of motor neurons.
Using microarray analysis, we identified the genes with significantly altered expression among the three types of mice.

overall_design: For each group, we examined the male mice at 7-9, 10-12, and 13-15 weeks of age. These stages were chosen because the AR-97Q mice are generally asymptomatic at 7-9 weeks of age (before-onset stage), present with mild motor impairment at 10-12 weeks (early stage), and are severely weakened with profound muscle atrophy at 13-15 weeks (advanced stage). RNA from the total spinal cord, excluding the dorsal root ganglia, was isolated from three mice of each genotype at each stage. For wild-type, pooled sample for three mice were used in each stage.

first: Masahisa

last: Katsuno

first: Gen

last: Sobue


title: Growth inhibition of ovarian tumor-initiating cells by niclosamide

status: Public on Aug 06 2012

first: Hung-Cheng

last: Lai

address: No.250, Wuxing St.

department: Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,

institute: Taipei Medical University

summary: The gene expression profile in treated CP70 side population spheroid cells (CP70sps cells) was analyzed to investigate the effect of niclosamide inhibition on ovarian tumor-initiating cells. CP70sps cells are isolated and characterized as one kind of ovarian tumor-initiating cells, and they show stemness properties and drug resistance capacity. According gene expression profiles and mechanistic analysis, all evidences revealed niclosamide disrupted multiple metabolic pathways affecting biogenetics, biogenesis and redox regulation. These studies support niclosamide as a promising therapeutic agent for ovarian cancer.

overall_design: CP70sps cells were treated with niclosamide for 0, 2, 4 and 6 hours respectively, and then cells were harvested and analyzed their gene expression profiles.

first: Yi-Te

last: Yo

first: Ya-Wen

last: Lin

first: Yu-Chi

first: Curt

last: Balch

first: Rui-Lan

last: Huang

first: Michael-WY

last: Chan

first: Huey-Kang

last: Sytwu

first: Chi-Kuan

last: Chen

first: Cheng-Chang

last: Chang

first: Kenneth

middle: P

last: Nephew

first: Tim

first: Mu-Hsien

last: Yu


title: Expression data from SP and non-SP sorted anti-EpCAM treated A2C12 cells

first: Thomas

last: Krüwel

overall_design: Anti-EpCAM treated and untreated A2C12 cells were subjected to Hoechst 33342 dye exclusion assay and sorted to SP and non-SP fractions by FACS. Three biological replicates.

first: Astrid

last: Rohrbeck


title: Expression data from murine bone marrow-resident plasma cells and spleen mature follicular B cells

city: Cambridge

first: Micah

middle: James

last: Benson

address: 200 Cambridge Park Drive

institute: Pfizer

summary:
CD138+ B220- plasma cells were sorted from bone marrow and B220+ CD23+ mature follicular B cells were sorted from the spleens.  Plasma cells were sorted from C57BL/6 mice 7 days after boosting with antigen, with mice first primed with an i.p. injection of KLH/IFA followed by boost at day 21 with KLH/PBS i.p. Mature B cells were sorted from antigen-naïve C57BL/6 mice.
We compared expression profiles of plasma cells and mature B cells to identify differentially expressed transcripts.

overall_design: Seven days after boosting with KLH, plasma cells were enriched by CD138-PE/anti-PE magnetic bead enrichment and then sorted to purity.  Affymetrix microarrays were performed on 50,000-70,000 plasma cells and 2,000,000-3,000,000 naïve B cells.

first: Anjana

last: Rao

first: Utz

last: Pape


title: Expression Array of Lymphoblastoid Cell lines Under Inflammatory Conditions

status: Public on Sep 07 2012

city: Stanford

first: Simone

last: Thair

address: P226 1201 Welch Rd

department: Emergency Medicine

institute: Stanford University

summary: Comparison of gene expression across 85 cell lines after stimulation with a cocktail of inflammatory cytokines

overall_design: Total RNA extracted from Genotyped Lymphoblastoid cell lines under inflammatory and baseline conditions. 3 biological replicates of stimulated and 2 biological replicates of baseline samples were hybridized to the Illumina Human WG-6 v.3 gene expression chip.

first: Keith

middle: R

last: Walley


title: Increased miR-708 expression in NSCLC and its association with poor survival in lung adenocarcinoma from Never Smokers

city: Rochester

first: Jin Sung

last: Jang

state: MN

address: 200 First St SW

institute: Mayo Clinic

summary: We demonstrate that miR-708 is one of the most highly overexpressed miRNAs in non-small cell lung cancer. High level of miR-708 in tumor is also associated with a reduced overall survival in lung adenocarcinomas from never smokers.  Functionally, miR-708 overexpression increases the proliferation, migration, and invasion in cultured cells and down regulates TMEM88, a negative regulator of Wnt signaling.  Jointly, our results support an oncogenic role of miR-708 by activating Wnt signaling pathway to promote lung cancer progression.

overall_design:
We performed miRNA expression profiling in matched lung adenocarcinoma and uninvolved lung using 47 pairs from formalin-fixed, paraffin-embedded [FFPE] tissues from never smokers.

We performed miRNA expression profiling in matched lung adenocarcinoma and uninvolved lung using 56 pairs of fresh-frozen [FF] samples from never smokers.

first: Jin

last: Jen


title: Tristetraprolin is a tumor suppressor that impairs Myc-induced lymphoma and abolishes the malignant state [Lymphoma].

status: Public on Aug 02 2012

city: Tampa

first: John

middle: Lamoine

last: Cleveland

state: FL

address: 12902 USF Magnolia Drive

institute: H. Lee Moffitt Cancer Center

summary: Myc oncoproteins directly regulate transcription by binding to target genes, yet this only explains a fraction of the genes affected by Myc. mRNA turnover is controlled via AU-binding proteins (AUBPs) that recognize AU-rich elements (AREs) found within many transcripts. Analyses of precancerous and malignant Myc-expressing B cells revealed that Myc regulates hundreds of ARE-containing (ARED) genes and select AUBPs. Notably, Myc directly suppresses transcription of Tristetraprolin (TTP/ZFP36), an mRNA-destabilizing AUBP, and this circuit is also operational during B lymphopoiesis and IL7 signaling. Importantly, TTP suppression is a hallmark of cancers with MYC involvement, and restoring TTP impairs Myc-induced lymphomagenesis and abolishes maintenance of the malignant state. Further, there is a selection for TTP loss in malignancy; thus, TTP functions as a tumor suppressor. Finally, Myc/TTP-directed control of select cancer-associated ARED genes is disabled during lymphomagenesis. Thus, Myc targets AUBPs to regulate ARED genes that control tumorigenesis.

overall_design: Lymphomas collected from Eμ-Myc and Eμ-Myc;Eµ-TTP-1 transgenic mice were investigated. These samples were used for subsequent RNA purification, labeling and hybridization to MOE430 2.0 Affymetrix arrays.

first: Mohammad

last: Fallahi

first: Robert

last: Rounbehler


title: Role of transcriptional regulators IFRD1 and IFRD2 in intestinal lipid absorption and obesity

status: Public on Aug 01 2012

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary:
Because of  the epidemic rise of obesity worldwide, the identification of novel target genes for pharmacological treatment of obesity and related disorders is becoming of high importance. IFRD1 and IFRD2 are members of a novel transcriptional regulators family. Intestinal over-expression of mouse homologue of IFRD1 promoted intestinal triglyceride uptake and induced whole body adiposity in mice. To further elucidate the role of IFRD1 and IFRD2 in vivo, we generated mice lacking both mouse homologues of IFRD1 (TIS7) and IFRD2 (SKMc15) genes. Here, we report that mice deficient in TIS7 and SKMc15 genes, despite  normal calorie intake had severely reduced amount of adipose tissue, were resistant to diet-induced obesity and displayed high glucose tolerance. Lower dietary fat entry into the circulation suggested that this phenotype resulted from impaired intestinal lipid transport. We identified down-regulation of CD36, a fatty acid transporter, both on RNA and protein levels. Reporter assays indicated that TIS7 and SKMc15 transcriptionally regulated CD36 expression and CD36 overexpression partially restored fatty acid uptake in vitro. Hence, our study suggested that TIS7 and SKMc15 play an important role in the regulation of the lipid metabolism and might represent a novel strategy for treatment of disorders caused by excess fat intake.
To determine whether decreased intestinal lipid absorption might be caused by changes in expression of lipid processing and transport molecules, we performed Affymetrix microarray analyses of total RNA samples isolated from the jejunum of HFD-fed WT type and dKO animals. The moderated t-test was used to calculate p-values for significance of differential gene expression between 3 dKO and 3 wild type mice. These raw p-values were adjusted for multiple hypothesis testing using the method from Benjamini and Hochberg for a strong control of the false discovery rate (FDR) and genes with thus adjusted p-values < 0.05 were considered significant.

overall_design: Age-matched (7-10 week old) male wild type and TIS7 (Ifrd1) SKMc15 (Ifrd2) double knock out mice (C57Bl6 background) were caged individually and maintained from 3 weeks up to 8 weeks on a synthetic high saturated fat (HFD) diet (Ssniff). Small intestines (jejunum) were harvested for total RNA isolation. RNAs from 3 WT and 3 dKO mice were subjected to Affymetrix based whole genome gene expression analysis (Mouse 430.2 GeneChip).

first: Domagoj

last: Cikes

first: Ivan

last: Tancevski

first: Philip

last: Eller

first: Ronald

last: Gstir

first: Christian

last: Zwicker

first: Egon

last: Demetz

first: Michael

last: Hess

first: Kristian

last: Pfaller

first: Volker

last: Kuhn

first: Frans

last: Stellaard

first: Herman

last: Dietrich

first: Lukas

last: Huber

first: Ilja

last: Vietor


title: Protein Arginine Methyltransferase 6 dependent gene expression and splicing: Association with breast cancer outcomes

city: St Lucia

middle: Andrew

last: Pearen

state: Queensland

address: The University of Queensland

country: Australia

institute: Institute for Molecular Bioscience

summary: Protein arginine methyltransferase-6 (PRMT6) regulates steroid-dependent transcription and alternative splicing, and is implicated in endocrine system development and function, cell death, cell cycle, gene expression and cancer. Despite its role in these processes, little is known about its function and cellular targets in breast cancer. To identify novel gene targets regulated by PRMT6 in breast cancer cells, we used a combination of small interfering RNA (siRNA) and exon-specific microarray profiling in vitro, coupled to in vivo validation in normal breast and primary human breast tumours. This approach, which allows the examination of genome-wide changes in individual exon usage and total transcript levels, demonstrated PRMT6 knockdown significantly affected: (i) the transcription of 159 genes, and (ii) alternate splicing of 449 genes. Importantly, the levels of PRMT6 itself were significantly decreased in breast cancer, relative to normal breast tissue. The PRMT6 dependent transcriptional and alternative splicing targets identified in vitro, were validated in human breast tumours. Notably, expression of PRMT6 and the corresponding gene signature, correlated with decreased probability of relapse-free or distant metastasis free survival in ER+ breast cancer. These results suggest that dysregulation of PRMT6 dependent transcription and alternative splicing may be involved in breast cancer pathophysiology and the molecular consequences identifying a unique and informative biomarker profile.

overall_design: Total RNA obtained from MCF7 breast cancer cells transfected with siRNA directed against PRMT6 or negative control siRNA (Ambion Silencer Select negative control).

first: Dennis

last: Dowhan

first: Matthew

last: Harrison

first: Natalie

last: Eriksson

first: Peter

last: Bailey

last: Fuller

first: John

middle: W

last: Funder

first: Evan

last: Simpson

last: Leedman

first: Wayne

last: Tilley

first: Melissa

last: Brown

first: Christine

last: Clarke

first: George

last: Muscat


title: Selective knockout of NeuroD1 in the retina and pineal gland

status: Public on Jul 26 2012

city: Bethesda

first: Margaret

last: Ochocinska

address: 49 Convent Dr. Rm.6A71

department: NICHD/PDEGEN

institute: National Institutes of Health

summary:
NeuroD1 encodes a basic helix-loop-helix transcription factor involved in the development of neural and endocrine structures. NeuroD1 mRNA is highly abundant in the adult mammalian pineal gland and exhibits a developmental expression pattern similar to the retina. This is consistent with the common evolutionary origin of pinealocytes and retinal photoreceptors. Pinealocytes and retinal photoreceptors express a shared set of phototransduction genes and submammalian pinealocytes are photosensitive. In contrast to the retina, the pineal gland is a relatively homogeneous structure, composed 95% of pinealocytes. This makes the pineal gland a particularly useful model for understanding photoreceptor cell biology. The loss of NeuroD1 in the retina results in progressive photoreceptor degeneration and the molecular mechanisms underlying this retinal degeneration phenotype remain unknown. Similarly, the role that NeuroD1 plays in the pineal gland is unknown.

To determine the function of NeuroD1 in the pineal gland and retina, a Cre/loxP recombination strategy was used to selectively target a NeuroD1 floxed allele and generate NeuroD1 conditional knockout (cKO) mice. Tissue specificity was conferred using Cre recombinase expressed under the control of the promoter of Crx, a transcription factor selectively expressed in the pineal gland and retina. Pineal and retinal tissues from two-month-old NeuroD1 cKO and control animals were used in microarray studies to identify candidate genes responsible for the photoreceptor degeneration phenotype.

overall_design: The Cre/loxP recombination strategy was used to target a NeuroD1 floxed allele and generate NeuroD1 conditional knockout mice (NeuroD1floxed::Crx-Cre+/-). NeuroD1 floxed mice (NeuroD1floxed::Crx-Cre-/-) served as the controls. Pineal glands and retinas from two-month-old control and conditional knockout mice were collected at ZT6 and ZT20. 3 pools of 6 pineal glands per genotype and respective time of day were collected for each sample. Similarly, 3 pools of 6 retinas each were also collected. RNA from each pool was extracted and hybridized on the Affymetrix Mouse 430 2.0 array.

middle: J

first: Estela

last: Munoz

first: Shobi

last: Veleri

first: Joan

last: Weller

first: Steven

last: Coon

first: Nikita

middle: V

last: Pozdeyev

first: Sandra

last: Goebbels

first: P

last: Iuvone

first: Takahisa

last: Furukawa

first: Klaus

last: Nave

first: David

middle: C

last: Klein


title: Tristetraprolin is a tumor suppressor that impairs Myc-induced lymphoma and abolishes the malignant state [bone marrow B cells].

first: John

last: Cleveland

overall_design: Wild type, Eµ-TTP-1, precancerous Eμ-Myc and precancerous Eμ-Myc;Eµ-TTP-1 transgenic bone marrow B cells (from 4-6 week old littermates; 94% C57BL/6) were investigated. These samples were used for subsequent RNA purification, labeling and hybridization to MOE430 2.0 Affymetrix arrays.

first: Mohammad

last: Fallahi

first: Robert

last: Rounbehler


title: microRNA profiling of formalin-fixed, paraffin-embedded human sarcoma specimens

status: Public on Jul 24 2012

first: Katherine

last: Hill

address: 330 Brookline Avenue, DA-679

department: Medicine

institute: Beth Israel Deaconess Medical Center

summary: A study which examines differences in microRNA expression profiles across different sarcoma histological subtypes

overall_design: Twenty-five unique human FFPE sarcoma samples were used for microRNA profiling; eight of them run in technical duplicate

first: Andrew

last: Kelly


title: Regulation of Pluripotency and Cellular Reprogramming by the Ubiquitin Proteasome System

city: New York

first: Shannon

last: Buckley

state: NY

address: 550 First Ave MSB 504

institute: NYU School of Medicine

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

overall_design: Refer to individual Series

first: Iannis

last: Aifantis


title: Expression data of satellite cells through muscle injury time course

city: Boulder

first: Bradley

middle: B

last: Olwin

state: CO

address: 347 UCB

department: MCD-Biology

institute: University of Colorado

summary:
Satellite cells are resident skeletal muscle stem cells responsible for muscle maintenance and repair.  In resting muscle, satellite cells are maintained in a quiescent state.  Satellite cell activation induces the myogenic commitment factor, MyoD, and cell cycle entry to facilitate transition to a population of proliferating myoblasts that eventually exit the cycle and regenerate muscle tissue.  The molecular mechanism involved in the transition of a quiescent satellite cell to a transit-amplifying myoblast is poorly understood.
We used microarrays to detail the global program of gene expression of in vivo satellite cell activation through muscle injury and identified RNA post-transcriptional regulation as a key component of satellite cell activation.

overall_design: Wild type or Sdc4-/- satellite cells were FACS isolated from resting muscle or from muscle 12h and 48h following barium chloride-induced muscle injury.  5000 cell equivalents of RNA was labeled and hybridized to MOE430v2 GeneChips (Affymetrix) and scanned as per manufacturers protocol.  Probeset intensities were GCRMA normalized for further analysis including UPGMA hierarchical clustering, analysis of variance (ANOVA), and fold change.

first: D

last: Cornelison

first: Nicholas

last: Farina


title: Comparison of EPC vs donor matched HUVEC

status: Public on Jul 31 2012

city: Adelaide

first: Jyotsna

last: Pippal

address: IMVS, Level 3, Frome Road

department: Center for cancer biology

institute: Hanson Research Institute

summary:
Background:  In recent times a subset of bone marrow (BM) derived cells; endothelial progenitor cells (EPCs), have generated tremendous interest, as these cells are suggested to home to sites of neovascularization and neoendothelialization and differentiate into mature endothelial cells (ECs), a process referred to as postnatal vasculogenesis.  EPCs are being considered as a potential regenerative tool for treating various pathophysiological disease states including cardiovascular disorder and as a possible target to restrict vessel growth in tumour pathology.  However, conflicting results have been reported in the field due to lack of EPC specific biomarkers, and the identification, characterization, and the precise role of EPCs in vascular biology still remains a subject of great debate.  Therefore, the objective of this study was to use a bioinformatics approach to identify putative novel EPC specific biomarkers.
Methods:  This study reports a detailed gene expression profile of human umbilical cord blood (UCB) derived non-adherent CD133 + cells at different time points during in vitro differentiation (day 4 and day 7) which were compared with differentiated donor matched human umbilical vein endothelial cells (HUVEC).
Results:  EPC gene expression was profiled at both days 4 and 7, using affymetrix human 1.0ST exon arrays.  Affymetrix gene expression profiling revealed significant expression changes in genes associated with stem/progenitor cell properties such as adhesion, signalling, molecular transport, cell structure organisation and growth.
Conclusions:  This is the first study utilizing gene expression profiling to examine non adherent CD133+ progenitor cells.  Alterations in the gene expression reported in this study may be involved in the cellular processes characteristic of EPC development and differentiation.

overall_design: Gene expression profiling was performed on EPCs cultured for D4 and D7, on Affymetrix human 1.0ST exon array chips.   Gene Spring (version GX11) was used to perform the gene expression analysis on three experimental groups; (a) D4 EPCs versus HUVEC; (b) D7 EPCs versus HUVEC and (c) D4 versus D7 EPCs.

first: Gareth

last: Price

first: Claudine

middle: S

last: Bonder


title: Klf4

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary:
Klf4 is the zinc finger transcription factor indispensable for terminal maturation of epithelial tissues and part of group of proteins for the generation of pluripotent embryonic stem cells from differentiated tissues. No definitive in-vivo-function of Klf4 in the hematopoietic system has been established yet. We show here that Klf4 directly guides the transcriptional program for terminal differentiation of Ly-6Chigh monocytes. Klf4 suppresses transcripts of the interferon immune response and induces a proinflammatory cytokine transcriptional program.
Concordantly, Klf4 hematopoietic deficiency in mice results in an enhanced Th1 but impaired Th17 immune response, and, consequently, those mice are resistant towards the induction of experimental autoimmune encephalitis (EAE). We here identify Klf4 is a transcription factor required for ontogenesis and function of Ly-6Chigh monocytes at the interface of innate and acquired immunity.

overall_design:
The following constructs were used:  Mus musculus  Klf4 full length, (ref|NM_010637.1) cDNA, Mus musculus cyclin-dependent kinase inhibitor 1A (P21) (Cdkn1a), cDNA (ref|NM_007669.3) were fused in frame to the modified oestrogen receptor ERT2 (Feil et al., 1997) and cloned into a retroviral vector (Mieg3) expressing the constructs together with eGFP after an internal ribosomal entry site . (Williams et al., 2000). For Klf4, a mutant comprinsing the zinc- finger domains only  AA 393 – 474 (Klf4 dN) as well as a mutant comprising the entire protein except the zinc fingers AA 1-393 (Klf4-dC) were constructed and fused in frame to the modified oestrogen receptor.
BM cells from 5-FU treated mice were infected with viral constructs, sorted for GFP expression (day8), plated in IMDM , 10% FCS, 2mM Gln, 1% P/S, supplemented with 50ng/ml rSCF, 100ng/ml TPO and 100ng/ml G-CSF and cultured for 72h (day8-day10). On day10 cells were stimulated with 4-OHT (1uM) for 16h. After that time, total RNA was isolated by Trizol method.

Reference List:
Feil,R., Wagner,J., Metzger,D., and Chambon,P. (1997). Regulation of Cre recombinase activity by mutated estrogen receptor ligand-binding domains. Biochem. Biophys. Res. Commun. 237, 752-757.
Williams,D.A., Tao,W., Yang,F., Kim,C., Gu,Y., Mansfield,P., Levine,J.E., Petryniak,B., Derrow,C.W., Harris,C., Jia,B., Zheng,Y., Ambruso,D.R., Lowe,J.B., Atkinson,S.J., Dinauer,M.C., and Boxer,L. (2000). Dominant negative mutation of the hematopoietic-specific Rho GTPase, Rac2, is associated with a human phagocyte immunodeficiency. Blood 96, 1646-1654.

first: Dirk

last: Carstanjen

first: Sandrine

last: Sander


title: Expression data from mandibular arches in mouse embryos

status: Public on Jul 13 2012

city: Tokyo

first: Yuuichi

last: Soeno

address: 1-9-20 Fujimi, Chiyoda-ku

department: Pathology

institute: The Nippon Dental University

summary:
Fusion of branchial arch derivatives is an essential event in the development of craniofacial architecture. A unique feature of the mandibular arch development is medial/lateral compartmentalization for the molecular networks. Those networks give rise to multiple region-specific organs, namely teeth, a tongue, salivary glands, and the supporting matrices such as bones and cartilages.
We aimed to investigate molecular networks that govern the fusion process during mouse mandibular development. To this end, cDNA microarray technology was employed for screening of spatio-temporal gene expression in developing mandibular arch from E9.7 through E14.5.

overall_design: We conducted to divide a mandibular arch medially and laterally to compare both gene expression. From an embryo at E10.5, a medial (M) sample of the mandibular arch was dissected out -at just the distal end of opposed lateral lingual swellings-, and the bulk of remnant lateral region was collected as (L) sample under a stereomicroscope. Forty embryos for each time-point were used to obtain a pool of total RNA.

first: Kazuya

last: FUJITA

last: SOENO

first: Yuji

last: TAYA

first: Takaaki

last: AOBA


title: Expression data from embryonic stem cells following siRNA transfection of UPS members [Differentiation_ES]

summary: While transcriptional regulation of stem cell self-renewal and differentiation has been extensively studied, only a small number of studies have addressed the roles for post-translational modifications in these processes.  A key mechanism of post-translational modification is ubiquitination by the ubiquitin-proteasome system (UPS). Using UPS-targeted RNAi screens, we identify novel regulators of pluripotency and differentiation. We focus on two of these proteins, the deubiquitinating enzyme, Psmd14, and the E3 ligase, Fbxw7, and characterize their importance in ES cell pluripotency and cellular reprogramming.

overall_design: Embryonic stem cells were reverse transfected with siRNA, and differentiated for 48hrs in conditions with retinoic acid, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays


title: The histone demethylase PHF8 is essential for cytoskeleton dynamics

city: Barcelona

first: Elena

last: Asensio

state: Select a State or Province

address: Baldiri Reixac 4-8

department: Molecular Genomics

country: Spain

summary: PHF8 is a histone demethylase associated with X-linked mental retardation (XLMR). It has been described as a transcriptional coactivator involved in cell cycle progression, but its physiological role is still poorly understood. Here we show that PHF8 controls the expression of genes involved in cell adhesion and cytoskeleton organization such as RhoA, Rac1 and GSK3β. A lack of PHF8 not only results in a cell cycle delay but also in a disorganized actin cytoskeleton and impaired cell adhesion. Our data demonstrate that PHF8 directly regulates the expression of these genes by demethylating H4K20me1 at promoters. Moreover, c-Myc transcription factor interacts with PHF8 and binds to the analyzed promoters, suggesting that c-Myc is involved on PHF8 recruitment to these promoters. Further analysis in the neuroblastoma cell line SH-SY5Y and in cortical neurons shows that depletion of PHF8 results in deficient neurite elongation. Overall, our results suggest that the mental retardation phenotype associated with loss of function of PHF8 could be due to abnormal neuronal connections as a result of alterations in cytoskeleton function.

overall_design: HeLa cells were transfected with either control or PHF8 siRNAs. Experiments were performed in biological triplicates. RNA were extracted and sujected to microarray analysis.

last: Asensio-Juan

first: Carme

last: Gallego

first: Marian

last: Martínez-Balbás


title: Expression data from embryonic stem cells following siRNA transfection of UPS members [self_renewal]

first: Shannon

last: Buckley

overall_design: Embryonic stem cells were reverse transfected with siRNA, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays

first: Iannis

last: Aifantis


title: Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [Mouse430_2 Expression]

status: Public on Jul 25 2012

city: Rotterdam

first: frank

last: sleutels

address: Dr Molewaterplein 50

department: cell biology and genetics

country: Netherlands

institute: ErasmusMC

summary: The effect of CTCFL mutation on the transcriptional program in testes

overall_design: Testis RNA extracted from CTCFL wildtype and mutant mice was hybridized on Affymetrix Mouse430_2 arrays

first: Frank

last: Sleutels

first: Widia

last: Soochit

first: Marek

last: Bartkuhn

first: Helen

last: Heath

first: Sven

last: Dienstbach

first: Philipp

last: Bergmaier

first: Vedran

last: Franke

first: Manuel

last: Rosa-Garrido

first: Suzanne

last: van de Nobelen

first: Lisa

last: Caesar

first: Michael

last: van der Reijden

first: Jan

last: Christian Bryne

first: Wilfred

last: van Ijcken

first: J

middle: A

last: Grootegoed

first: M

middle: D

last: Delgado

first: Boris

last: Lenhard

first: Rainer

last: Renkawitz

last: Grosveld

first: Niels

last: Galjart


title: Tristetraprolin is a tumor suppressor that impairs Myc-induced lymphoma and abolishes the malignant state [retrovirally infected ex vivo lymphoma]

first: John

last: Cleveland

overall_design: Ex vivo Eμ-Myc lymphoma cells were infected with MSCV-I-dsRed2 (RFP) and FACS sorted for dsRed2+ cells. These cells were then infected with MSCV-TTP-I-GFP and FACS sorted for GFP expression (TTP-GFP- or TTP-GFP+). These cells were used for subsequent RNA purification, labeling and hybridization to MOE430 2.0 Affymetrix arrays.

first: Mohammad

last: Fallahi

first: Robert

last: Rounbehler


title: Immortalized clonal brown, beige and white adipose cell lines

city: Boston

first: jun

last: wu

address: 450 brookline ave. CLSB11117A

institute: dana-farber cancer institute

summary: Brown fat generates heat via the mitochondrial uncoupling protein UCP1, defending against hypothermia and obesity. Recent data suggest that there are two distinct types of brown fat: classical brown fat derived from a myf-5 cellular lineage and UCP1-positive cells that emerge in white fat from a non-myf-5 lineage. Here, we report the isolation of “beige” cells from murine white fat depots.

overall_design: Microarray analysis of the differentiated clonal inguinal and interscapular adipocytes in the presence of forskolin (10microM). These samples were profiled using Affymetrix mouse 430 2.0 arrays, 26 samples in total.

first: Jun

last: Wu

first: Pontus

last: Boström

first: Lauren

middle: M

last: Sparks

first: Li

last: Ye

first: Jang

last: Choi

first: An-Hoa

last: Giang

first: Melin

last: Khandekar

first: Kirsi

last: Virtanen

first: Pirjo

last: Nuutila

first: Gert

last: Schaart

first: Kexin

last: Huang

first: Hua

last: Tu

first: Wouter

last: van Marken Lichtenbelt

first: Joris

last: Hoeks

first: Sven

last: Enerbäck

first: Patrick

last: Schrauwen

first: Bruce

last: Spiegelman


title: Expression data from primary human skin fibroblasts treated with vehicle (DMSO) and the antioxidant Trolox (0.5 mM, 96 hrs)

status: Public on Jul 15 2012

city: Nijmegen

first: Werner

last: Koopman

state: GLD

address: Geert Grooteplein 26-28

department: 286 Biochemistry

institute: Radboud University Nijmegen Medical Centre

summary: Three (3) independent cell cultures for each condition (DMSO and Trolox) were analyzed. The effect of Trolox was checked on the protein level (being an increased protein level of fully assembled mitochondrial complex I) using blue-native PAGE analysis (as described in Koopman et al., Biochim. Biophys. Acta 1777:853-859, 2008, prior to mRNA extraction.  We used the control cell line #5120 at similar passage number for all six experiments.

overall_design: We generated the following pairwise comparisons Vehicle > Trolox and Vehicle < Trolox. Changes ≥2  and Benjamini Hochberg corrected p-values <0.05 were considered significant.

first: Felix

last: Distelmaier

first: Federica

last: Valsecchi

first: Marleen

last: Forkink

first: Sjenet

last: van Emst-de Vries

first: Herman

middle: G

last: Swarts

first: Hiromi

last: Imamura

first: Eugène

middle: T

last: Verwiel

first: Richard

last: Rodenburg

first: Jan

last: Smeitink

first: Peter

last: Willems


title: Tristetraprolin is a tumor suppressor that impairs Myc-induced lymphoma and abolishes the malignant state

first: John

last: Cleveland

middle: L

first: Mohammad

last: Fallahi

first: Robert

last: Rounbehler


title: Genome-wide analysis of gene expression after tyrosine or methionine/cysteine deprivation in HeLa cells

city: Milan

first: Ilaria

last: Palmisano

address: Via Olgettina, 58

department: Center for Translational Genomics and BioInformatics

institute: San Raffaele Scientific Institute

summary: Limitation of essential amino acids, such as tyrosine or methionine/cysteine, causes upregulation of exogenous integrated transgene expression in mammalian cells. This phenomenon is mediated by histone acetylation and chromatin remodelling, since histone deacetylase (HDAC) inhibitors reproduce starvation-induced transgene upregulation and chromatin immunoprecipitation analysis of amino acid-deprived cells reveals significant changes in total core histones detectable at the CMV promoter. Expression profiling of HeLa cells starved for 5 days in medium without tyrosine or methionine/cysteine provides important information on the cellular response to amino acid deprivation and suggests the involvement of HDAC4 (class II HDAC) in transgene derepression during amino acid starvation.

overall_design: Total RNA obtained from HeLa and HeLaOA1myc cells (HeLa cells with a human ocular albinism type 1 (OA1)+myc tag transgene) subjected to 5 days of tyrosine or methionine/cysteine starvation compared to control cells. Twelve samples are analyzed: HeLa and HeLaOA1myc grown for 5 days in RPMI deprived of tyrosine (Y) vs. complete RPMI; technical duplicates of HeLa and HeLaOA1myc grown for 5 days in DMEM deprived of methionine/cysteine (MC) vs. complete DMEM.

first: Paola

last: Brambilla

first: Filippo

last: Boneschi

first: Maria

last: Schiaffino


title: Expression data for the different phases of ulcerative colitis-associated carcinogenesis in a mouse model

city: Changsha

first: tang

middle: an

last: liu

address: xiangya road #110

country: China

institute: Key Laboratory of Carcinogenesis, Ministry of Health, China

summary: Nonresolving inflammation is correlated to carcinogenesis. Ulcerative colitis-associated colorectal cancer (UC-CRC), one of the typical carcinoma generated by inflammation that cannot be resolved properly, has been widely believed to involve a multistep process contains “inflammation-dysplasia-cancer” sequence. The exact molecular mechanisms underlying the step-wise development of UC-CRC is still not fully understood. Detecting the changes in gene expression profiles may help to reveal why and how does the prolonged inflammatory response lead to carcinogenesis, and to characterize potential diagnostic/prognostic markers or additional therapeutic targets for UC-CRC. There for, we performed temporal genome expression profiling analysis using the Affymetrix genome wide microarray system to identify broad scale changes in gene expression associated with the development of colitis-associated cancer, based on an AOM/DSS induced mouse model of UC-CRC.

overall_design: 6-week-old male ICR mice were given a single intraperitoneal injection of AOM (10mg/kg) at Day 1, followed by three cycles of DSS administration (cycle 1: 2%, Day 8~14; cycle 2: 1.5%, Day 29~33; cycle 3: 1.5%, Day 50~54) in the drinking water. Instead, control group of mice were given a single intraperitoneal injection of saline (10mg/kg) at Day 1 and distilled water drinking from the beginning to the end without DSS. Colorectal tissues were collected at days 14, 28, 42, 56 and 140 (at the end of the 2nd, 4th, 6th, 8th and 20th week) from the AOM/DSS group and at day 14 from the control group. Pathological changes of each sample were identified under microscope. Samples collected at the end of the 2nd week were inflamed mucosae, the 4th week were low grade dysplasias, the 6th week were high grade dysplasias, the 8th week were high grade dysplasias with active inflammation, the 20th week were carcinomas, and the control sample were normal mucosae. Total RNA were extracted and detected by Affymerix GeneChip Mouse Genome 430 2.0 Array.

first: Anliu

last: Tang

last: Li

first: Hongyuan

last: Yang

first: Liyang

last: Zhang

first: Jian

last: Ma

first: Shourong

last: Shen


title: Expression data from early B cell progenitors including CLP,ProB and PreB of Pax5 knockout and wild type C57Bl6 mice

status: Public on Jul 23 2012

city: Toronto

first: Sasan

last: Zandi

state: Ontario

address: 101 college St

country: Canada

institute: UHN

summary: we have investigated molecular and functional properties in  early B-lineage  cells from Pax-5 deficient animals crossed to a B-lineage restricted reporter mouse. Gene expression analysis of ex  vivo isolated progenitor cells revealed that Pax-5 deficiency has a minor impact on Bcell specification.By  comparison  of  gene  expression  patterns  in  ex  vivo isolated Pax-5 and Ebf-1 deficient progenitors, it was possible to identify a set of B-cell restricted genes dependent of Ebf-1 but not Pax-5, supporting the idea that B-cell  specification  and  commitment  is  controlled  by  distinct  regulatory networks.

overall_design: wt λ5 reporter+ and Pax5ko λ5reporter+ fetal liver from d15 embryos isolated and transplanted into sublethaly irradiated mice. After 4 weeks B220+λ5+ cells were sorted out from the bone marrow of the mice and subjected to microarray analyses

first: Josefine

last: Åhsberg

first: Panagiotis

last: Tsapogas

first: Jenny

last: Stjernberg

first: Hong

last: Qian

first: Mikael

last: Sigvardsson


title: Adult and neonatal astrocytes exhibit diverse gene expression profiles during exposure to beta amyloid ex vivo

status: Public on Jul 14 2012

city: Kuopio

first: Antti

middle: Juhani

last: Kurronen

address: Neulaniementie 2

department: A.I. Virtanen Institute for Molecular Sciences

institute: University of Eastern Finland

summary: Research regarding the role of astrocytes as β-amyloid (Aβ) degrading cells has broadened our view about the mechanisms how these common glia cells function in Alzheimer’s disease (AD). Based on previous studies adult mouse astrocytes are able to degrade Aβ deposits from AD mouse model and human brain tissue sections ex vivo, contrary to neonatal astrocytes. In this study, we studied the possible altered gene expression profiles of adult and neonatal astrocytes cultured for 22 h on top of the Aβ burdened tg APdE9 or wild-type mouse brain sections using whole genome microarrays. Quantitative RT-PCR analysis confirmed the significant up-regulation of HtrA serine peptidase 1 (Htra1), metallopeptidase 9 (Mmp9), phosphate regulating gene with homologies to endopeptidases on the X chromosome (Phex) and scavenger receptor class A, member 5 (Scara5) in adult astrocytes, whereas neonatal astrocytes up-regulated Mmp9 and down-regulated genes related to cholesterol transport and synthesis: apolipoprotein E (Apoe), 24-dehydrocholesterol reductase (Dhcr24) and 3-hydroxy-3-methylglutaryl-CoA synthase 1 (Hmgcs1). These findings brought out novel genes which expression is altered during Aβ clearance in adult and neonatal astrocytes ex vivo.

overall_design: Astrocyte cultures: For the adult astrocyte cultures, hippocampi and cortices were isolated from 6-8-week-old C57Bl/6j  wild-type and tg eGFP mice and the tissue was suspended in DMEM/F12 (3:1, Gibco BRL, NY, USA) containing 10 % heat-inactivated fetal bovine serum (Gibco BRL) and 100 U / ml penicillin-streptomycin (Gibco BRL). The cells were treated with Percoll (Sigma-Aldrich, St.Louis, USA) and plated onto poly-L-lysine coated flasks in DMEM/F12 (3:1) containing 10 % heat-inactivated fetal bovine serum, 100 U / ml penicillin-streptomycin and G5 supplement (Gibco BRL). Before the experiments the glial cell cultures were shaken to remove microglia at 200 rpm for 2 h. For the neonatal astrocyte cultures, hippocampi and cortices were isolated from 2-day-old wild-type and eGFP mice according to the protocol described above, except that the culture medium was DMEM (+4500mg/l glucose, + L-glutamine, -pyruvate, Gibco BRL) without G5 supplement and the isolation method included no Percoll treatment. Standard anti-GFAP (1:500; Dako Cytomation, Glostrup, Denmark) immunocytochemistry was used to determine the purity of astrocyte cultures. The cells were  incubated with biotinylated goat anti-rabbit IgG (1:200 dilution; Vector Laboratories, CA) secondary antibody and Vectastain ABC Elite kit was used (Vector Laboratories) according to manufacturer’s protocol.  Hydroxen peroxide (H2O2) and nickel enhanced diaminobenzidine (Ni-DAB) was added to detect the immunoreactivity. Three fields per well and at least three wells per cell type were analyzed for the percentage of Ni-DAB stained cells of all cellular profiles in the field. Adult and neonatal astrocyte cultures both contained on average 99.6 % ± 0.6 % anti-GFAP immunoreactive astrocytes. Anti-Iba (2 µg/ml; Wako, Germany) and anti-CD11b (1:500 dilution; Serotec, UK) antibodies were used to detect possible microglial cells. The cultures contained less than 0.4 % of microglial cells in all experiments. Ex vivo treatments: tg APdE9 / wild-type mouse brain section incubated with neonatal (age 3 d) or adult (age 6-8 wks) mouse eGFP expressing astrocytes (4 x 105 cells / well), n=6. The mouse brain sections used were prepared from tg APdE9 mouse line (created by co-injection of chimeric mouse/human APPSwe and PS1-dE9 vectors, both controlled by their own mouse prion protein promoter element [APdE9 mice (Jankowsky et al. 2004) provided by Prof. Heikki Tanila] and their wild type C57Bl/6j littermates. Before the mRNA isolation process, the samples were pooled (n=3). The purity of the samples was checked with FACS (FACSCalibur, Becton Dickinson, USA) using the analyzing program CellQuestTM version 3.3 (Becton Dickinson, USA). After 22 h incubation the culture medium was removed from the wells and the brain sections with cultured eGFP astrocytes were incubated with 1 x trypsin-EDTA (500 µl /well) for up to 15 min at 37° C.  Partial detachment (at this point, the astrocytes should not lose the grip completely) of the astrocytes from the underlying brain section was monitored with a standard light microscope. After the incubation the brain sections with cultured astrocytes were carefully removed into small petri dishes filled with FBS-containing culture medium to inactivate the trypsin.  Subsequently, the brain sections were immediately examined with fluorescence microscope (Olympus IX-71, Japan). The eGFP astrocytes were separated from the underlying brain section using a special suction hose, which was a modified version from suction hoses typically used for the microinjection techniques. In the other end of the tube there is a pipet tip as a mouthpiece, in the middle of the tube a 0.22 µm filter and in the other end a stretched glass capillary (prepared with a Bunsen burner). The green fluorescent eGFP astrocytes were picked up gently from the underlying brain section (without breaking the brain tissue) using wavelength 468 nm of the fluorescence microscope and simultaneous light microscopy. Data normalization and analysis: The raw data was preprocessed with the robust multichip algorithm (Irizarry et al. 2003), normalized per chip to the median. 12 samples were grouped into 4 sample types: adult_wt, adult_tg, neonatal_wt, neonatal_tg. The change in the astrocyte gene expression was identified according to the sections the astrocytes were incubated (WT or TG). The differentially expressed probe sets were further processed using statistical analysis with Welch unpaired t-test assuming unequal variances (p<0.05; fold change > 2.0 or  < 0.5). Benjamini-Hochberg false-discovery rate (FDR) correction for multiple testing was used to control the number of false-positives results.

first: Rea

last: Pihlaja

first: Eveliina

last: Pollari

first: Katja

last: Kanninen

first: Markus

last: Storvik

first: Garry

last: Wong

first: Milla

last: Koistinaho

first: Jari


title: Comparison of matched primary and metastasis 4T1.2 syngeneic mammary tumor model of spontaneous bone metastasis

status: Public on Jul 18 2012

city: Clayton

first: Sam

last: Forster

state: Victoria

address: 27 - 31 Wright Street

department: Monash Institute

institute: Monash University

summary: Breast cancer metastasis to bone is a critical determinant of long-term survival after treatment of primary tumors. We used a mouse model of spontaneous bone metastasis to determine new molecular mechanisms. Differential transcriptome comparisons of primary and metastatic tumor cells revealed that a substantial set of genes suppressed in bone metastases were highly enriched for promoter elements for the type I interferon (IFN) regulatory factor, Irf7, itself suppressed in mouse and human metastases. The critical function of the Irf7 pathway was demonstrated by restoration of exogenous Irf7 or systemic interferon administration, which significantly reduced bone metastases and prolonged metastasis-free survival. Using mice deficient in the type I receptor (Ifnar1-/-) or mature B, T and NK cell responses (NOD Scid IL-2rγ-/- mice), we demonstrated that Irf7-driven suppression of metastasis was reliant on IFN signaling to host immune cells. Metastasis suppression correlated with decreased accumulation of myeloid-derived suppressor cells and increased CD4++, CD8 T cells and NK cells in the peripheral blood and was reversed by depletion of CD8+ cells and NK cells. Clinical importance of our findings was demonstrated as increased primary tumor Irf7 expression predicted prolonged bone and lung metastasis-free survival. Thus we report for the first time, a novel innate immune pathway, intrinsic to breast cancer cells, whose suppression in turn restricts systemic immunosurveillance to enable metastasis. This pathway may constitute a novel therapeutic target for restricting breast cancer metastases.

overall_design: Microarrays were used to profile transcriptional alterations inherent in tumor cells growing in bone when compared to matched primary tumor cells in the 4T1.2 murine mammary tumor model. Primary and metastasized tumor were isolated from the same mouse with 4 independent biological replicates.

first: Paul

last: Hertzog

first: Belinda

last: Parker

first: Brad

last: Bidwell


title: A mouse model of deregulation of the malt1 oncogene recapitulates the pathogenesis of human malt lymphoma [Spleen dataset]

status: Public on Jul 10 2012

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

institute: FIMA

summary:
Attempts at modeling chromosomal translocations involving MALT1 gene, hallmarks of human mucosa-associated lymphoid tissue (MALT) lymphoma, have failed to reproduce the disease in mice. Here we describe a transgenic model in which MALT1 expression was targeted to mouse hematopoietic stem/progenitor cells. In Sca1-MALT1 mice, MALT1 deregulation activated the NF-kappaB pathway in Sca1+ cells, promoting selective B-cell differentiation and mature lymphocyte accumulation in extranodal tissues, progressively leading to the development of clonal B-cell lymphomas. These tumors recapitulated the histopathological features of human MALT lymphomas, presenting typical lymphoepithelial lesions and plasmacytic differentiation. Transcriptional profiling of Sca1-MALT1 murine lymphomas revealed overlapping molecular signatures with human MALT lymphomas, including MALT1-mediated NFkappaB activation, pro-inflammatory signaling and XBP1-induced plasmacytic differentiation. Moreover, murine Malt1 showed proteolytic activity by cleaving Bcl10 in Sca1-MALT1 lymphomas. Our novel technological approach has allowed modeling human MALT lymphoma in mice, which represent unique tools study MALT lymphoma biology and evaluate anti-MALT1 therapies.

Keywords: Genetic modification, wt vs. transgenic, disease analysis, MALT lymphoma

overall_design: 9 samples were analized of which 5 were splenic lymphomas from Sca1-MALT1 transgenic mice and 4 were spleens from WT mice.

first: Carolina

last: Vicente-Dueñas

first: Lorena

last: Fontán

first: Ines

last: Gonzalez-Herrero

first: Angela

last: Aznar

first: Esther

last: Alonso-Escudero

first: Jose

middle: I

last: Martinez-Ferrandis

first: Fernando

last: Abollo-Jimenez

first: Cristina

last: Bertolo

first: Francisco

last: Garcia-Criado

first: María

last: García-Cenador

first: Federico

last: Garcia-Bragado

first: Ellen

last: Remstein

first: Reiner

last: Siebert

first: Ming

middle: Q

last: Du

first: Xabier

last: Sagaert

first: Izidore

last: Lossos

first: Teresa

last: Flores

first: Cesar

last: Cobaleda

first: Isidro

last: Sanchez-Garcia

last: Martinez-Climent


title: Placental PPARg-Regulated Genes

city: Pittsburgh

first: Yaacov

last: Barak

state: PA

address: 204 Craft Ave

department: OBGYN and Reproductive Sciences

institute: Magee-Womens Research Institute/University of Pittsburgh

summary:
Robust identification of placental PPARg target genes via mutliple PPARg-dependence criteria.
Integration of differential expression data from Pparg-null, Rxra-null, Med1-nul and Ncoa6-null placentas and from WT and Pparg-null Trophoblast stem cells (TSC) differentiated for 2 or 4 days in the presence or absence of the PPARg agonist Rosiglitazone (Rosi).

overall_design:
[Placentas]
Three pools of three WT placentas, each vs a litter-matched pool of three Pparg-null placentas
Three pools of three WT placentas, each vs a litter-matched pool of three Rxra-null placentas
Three pools of three WT placentas, each vs a litter-matched pool of three Med1-null placentas
Three pools of three WT placentas, each vs a litter-matched pool of three Ncoa6-null placentas

[Trophoblast stem cells (TSC)]
Three independent WT TSC lines differentiated for two and four days in the presence or absence of Rosi vs two independent Pparg-null TSC lines differntiated for the same durations in the presence of Rosi


title: A mouse model of deregulation of the malt1 oncogene recapitulates the pathogenesis of human malt lymphoma [MouseSca1 dataset]

first: Victor

last: Segura

summary:
Attempts at modeling chromosomal translocations involving MALT1 gene, hallmarks of human mucosa-associated lymphoid tissue (MALT) lymphoma, have failed to reproduce the disease in mice. Here we describe a transgenic model in which MALT1 expression was targeted to mouse hematopoietic stem/progenitor cells. In Sca1-MALT1 mice, MALT1 deregulation activated the NF-kappaB pathway in Sca1+ cells, promoting selective B-cell differentiation and mature lymphocyte accumulation in extranodal tissues, progressively leading to the development of clonal B-cell lymphomas. These tumors recapitulated the histopathological features of human MALT lymphomas, presenting typical lymphoepithelial lesions and plasmacytic differentiation. Transcriptional profiling of Sca1-MALT1 murine lymphomas revealed overlapping molecular signatures with human MALT lymphomas, including MALT1-mediated NFkappaB activation, pro-inflammatory signaling and XBP1-induced plasmacytic differentiation. Moreover, murine Malt1 showed proteolytic activity by cleaving Bcl10 in Sca1-MALT1 lymphomas. Our novel technological approach has allowed modeling human MALT lymphoma in mice, which represent unique tools study MALT lymphoma biology and evaluate anti-MALT1 therapies.

Keywords: Genetic modification, wt vs. transgenic, MALT1 expression

overall_design: 8 sorting purified Sca1+Lin- samples were analized of which 5 were from Sca1-MALT1 transgenic mice and 3 were from WT mice.

first: Carolina

last: Vicente-Dueñas

first: Lorena

last: Fontán

first: Ines

last: Gonzalez-Herrero

first: Angela

last: Aznar

last: Alonso-Escudero


title: Isolated cardiomyocyte and cardiac fibroblast expression analysis

status: Public on Jul 06 2012

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

institute: Keio University

summary: Some cell type-specific gene expression is maintained in the maturation of cardiomyocytes, where DNA hypomethylation of gene body regions of a set of specific genes. We used microarrays to detail the global gene expression program underlying the maintenance of cardiomyocyte function and maturation and compared it with DNA methylation status.

overall_design: Cardiomyocytes and cardiac fibroblasts were carefully isolated from neonatal and adult hearts and used fresh for the analysis.

first: Shinji

last: Makino


title: Surgical specimens of primary glioblastoma multiform: mRNA and miRNA profiling

city: Beijing

first: Wei

last: Zhang

address: No.6 Tiantan Xili, Dongcheng District

department: Glioma Center, Department of Neurosurgery

institute: Beijing Tiantan Hospital, Capital Medical University

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

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

overall_design: Refer to individual Series


title: Genome-wide analysis of gene expression in surgical specimens of primary glioblastoma multiform

summary: We used a genome-wide coding gene expression profiling to identify a gene signature for the molecular classification or prognostic prediction of primary GBMs.

overall_design: Total RNA obtained from 21 surgical specimens of primary glioblastoma multiform.

first: Tao

last: Jiang


title: zDC (Zbtb46, Btbd4) knockout classical dendritic cells

status: Public on Jul 16 2012

city: New York

first: Matthew

last: Meredith

state: New York

address: 1230 York Ave

institute: The Rockefeller University

type:
Expression profiling by array
Third-party reanalysis

summary: Classical dendritic cells (cDCs) process and present antigens to T cells. Under steady-state conditions, antigen presentation by cDCs induces tolerance. In contrast, during infection or inflammation, cDCs become activated, express higher levels of cell surface MHC molecules, and induce strong adaptive immune responses. We recently identified a cDC-restricted zinc finger transcription factor, zDC, that is not expressed by other immune cell populations, including pDCs, monocytes, or macrophages. Here we define the zDC consensus DNA binding motif and the genes regulated by zDC using chromatin immunoprecipitation and deep sequencing. By deleting zDC from the mouse genome, we show that zDC is primarily a negative regulator of cDC gene expression. zDC deficiency alters the cDC subset composition in the spleen in favor of CD8+ DCs, upregulates activation pathways in steady state cDCs including elevated MHC II expression, and enhances cDC production of VEGF leading to increased vascularization of skin-draining lymph nodes. Consistent with these observations, zDC protein expression is rapidly downregulated after TLR ligation. Thus, zDC is a TLR-responsive cDC-specific transcriptional repressor that is in part responsible for preventing cDC maturation in the steady state.

overall_design:
Splenic classical dendritic cells from mice lacking the second exon of the zDC gene were sorted. DEC-205+ and DCIR2+ cDCs from the zDC knockout mice were collected for comparison with wildtype cDCs. Three replicates per group. The wildtype samples have been previously analyzed and are available in the GEO database in Series GSE6259.

The complete dataset representing: (1) the zDC knockout Samples and (2) the wildtype Samples from Series GSE6259 (re-processed using RMA), is linked below as a supplementary file.


title: Genome-wide analysis of microRNA expression in surgical specimens of primary glioblastoma multiform

summary: MicroRNA has a great potential in predicting survival of cancer patient. We used a genome-wide microRNA expression profiling to identify a miRNA signature for the prediction of clinical outcome of primary GBM patients.

overall_design: Total RNA obtained from 82 surgical specimens of primary glioblastoma multiform and 5 normal brain tissues from areas surrounding arteriovenous malformations (AVM) as control.


title: Expression data from bacterial co-infection study in mice

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary:
Non-typhoidal Salmonella serotypes (NTS) cause a self-limited gastroenteritis while pediatric patients with severe Plasmodium falciparum malaria can develop a life threatening bacteremia that is a major source of child mortality in sub-Saharan Africa.
We used microarrays to detail genome-scale gene expression profiles underlying gastrointestinal immune responses to bacterial infection in mice

overall_design: Responses were measured in mouse cecal mucosa to infection of non-typhodal Salmonella and Plasmodium yoelii, both singularly and in combination.

first: Renee

last: Tsolis


title: Retinal pigment epithelial cells suppress interleukin-17-producing T-helper 17 cells

status: Public on Jul 12 2012

first: Sunao

last: Sugita

address: Yushima 1-5-45, Bunkyo-ku

department: Ophthalmology

institute: Tokyo Medical and Dental Univ.

summary: T cells that encounter cultured ocular pigment epithelial cells in vitro are inhibited from undergoing T cell receptor-triggered activation.  Because retinal pigment epithelial (RPE) cells are able to suppress T-cell activation, we studied whether RPE cells could suppress cytokine production by activated T helper (Th) cells.  In this study we showed that primary cultured RPE cells greatly suppressed activation of bystander CD4+ T cells in vitro, especially the cytokine production by the target T helper cells (Th1 cells, Th2 cells, Th17 cells, but not Th3 cells).  Cultured RPE cells and RPE-supernatants significantly suppressed IL-17 producing CD4+ T cells, and RPE cells fully suppressed polarized Th17 cell lines that induced by recombinant proteins, IL-6 and TGFb2.  Moreover, RPE cells failed to suppress IL-17 producing T cells in the presence of rIL-6.  In addition, Th17 cells exposed to RPE were suppressed via TGFb, which produce RPE cells.  These results indicate that retinal PE cells have immunosuppressive capacity in order to inhibit Th17-type effector T cells.  Thus, ocular resident cells play a role in establishing immune regulation in the eye.

overall_design: Retinal pigment epithelium suppresses Th17 cells


title: Cell-type specific postnatal developmental expression data from mouse cerebellar Purkinje and Stellate/Basket cells

status: Public on Jul 20 2012

city: Hershey

first: Anirban

last: Paul

address: 500 University Drive

department: Neural and Behavioral Sciences

institute: Penn State College of Medicine

summary:
The assembly of neural circuits involves multiple sequential steps such as the specification of cell types, their migration to proper brain locations, morphological and physiological differentiation, and the formation and maturation of synaptic connections. This intricate and often prolonged process is guided by elaborate genetic mechanisms that regulate each developmental event.  Evidence from numerous systems suggests that each cell type, once specified, is endowed with a genetic program that directs its subsequent development.  This cell intrinsic program unfolds in respond to, and is regulated by, extrinsic signals, including cell-cell and synaptic interactions. To a large extent, the execution of this genetic program is achieved by the expression of specific sets of genes that support distinct developmental processes.  Therefore, a comprehensive analysis of the developmental progression of gene expression in synaptic partners of neurons may provide a basis for exploring the genetic mechanisms regulating circuit assembly.
Here we examined the developmental gene expression profiles in well defined cell types in a stereotyped microcircuit of the cerebellar cortex.

overall_design: Manually sorted pure populations of Purkinje cells and Stellate/Basket cells, 3 biological replicates, from Gad67-GFP bac-transgenic (G42) mice were profiled during postnatal developmental stages P3, P7, P14, P21, P28, P35 and P56 using Affymetrix MOE430.2 expression array

first: Z

last: Huang


title: Expression data from mouse muscle

status: Public on Jul 05 2012

city: San Sebastian

first: Amets

last: Saenz

state: Gipuzkoa

address: Pº dr Begiristain s/n

institute: Donostia Hospital

summary:
The knock-out of calpain 3 (C3KO) is a murine model for calpainopathies wich shows a mild dystrophic phenotype with signs of muscle degeneration. Adult (A) mice show a more severe phenotype than young (Y) mice which only present inflammatory infiltrates in most severely affected muscles, such as the soleus. Other muscles (e.g. quadriceps) are much less affected.
We used microarray technology to compare gene expression profiles of young and adult muscles in wild-type (wt) and C3KO mice, in two types of muscle: soleus (affected) and quadriceps (much less affected).

overall_design: 11 wt (7 adult and 4 young) and 11 C3KO (7 adult and 4 young) mice were used in this study for RNA extraction and hybridization on Affymetrix microarrays. The soleus and the quadriceps muscles were obtained from each mouse. All mice were males.

first: Oihane

last: Jaka


title: EMT inducers catalyze malignant transformation of mammary epithelial cells and drive tumorigenesis towards claudin-low tumors [mouse]

city: Lyon

first: stéphane

last: ansieau

address: 28 rue Laennec

department: Centre Léon Bérard

country: France

institute: Inserm U590

summary: The newly identified claudin-low subtype of cancer is believed to represent the most primitive breast malignancies, having arisen from transformation of an early epithelial precursor with inherent stemness properties and metaplastic features. Challenging this hypothesis, we show both in vitro and in vivo that transcription factors inducing epithelial-mesenchymal transition can drive the development of claudin-low tumors from differentiated mammary epithelial cells, by playing a dual role in cell transformation and dedifferentiation.

overall_design: Gene expression profiles of three independent Twist1 + Ras- transgenic mouse-derived metaplastic breast tumors (Breast Tumor A, B and C) and of two luminal MMTV-ERBB2/Neu-breast tumor-derived cell lines (1 and 2) were determined.

first: Anne-Pierre

last: Morel

first: Stéphane

last: Ansieau

first: Alain

last: Puisieux

first: Anne

last: Wierinckx

first: Joël

last: Lachuer

first: Nicolas

last: Nazaret

first: Marjorie

last: Carrere

first: George

last: Hinkal

first: Christelle

last: Lamblot


title: Expression data from FAK null mouse embryonic fibroblasts treated with endothelin-1

status: Public on Jul 01 2012

city: London

first: David

middle: E

last: Carter

state: ON

address: 1151 Richmond Street North

department: London Regional Genomics Centre

institute: Robarts Research Institute

summary:
Endothelin-1 (ET-1) plays a critical role in connective tissue remodeling by fibroblasts during tissue repair and fibrosis. We investigated the molecular pathways in the transmission of ET-1 signals that lead to features of connective tissue remodeling, in particular the role of FAK (focal adhesion kinase).
We used microarrays to investigated whether FAK is required for ET-1 to promote the global programme of gene expression underlying myofibroblast formation and identified distinct classes of up-regulated genes during this process. Genes whose induction by ET-1 required FAK

overall_design: Affymetrix Mouse Genome 430 2.0 GeneChips were used to identify differential gene expression changes bewteen samples.

last: Lagares

first: Oscar

last: Busnadiego

first: Rosa

last: Garcia-Fernandez

first: Mohit

last: Kapoor

first: Shangxi

last: Liu

last: Abraham

first: Xu

last: Shi-Wen

first: Patricia

last: Carreira

first: Benjamin

last: Fontaine

first: Barry

last: Shea

first: Andrew

last: Tager

last: Leask

first: Santiago

last: Lamas

first: Fernando

last: Rodriguez-Pascual


title: Technical and biological variance structure in mRNA-Seq data

status: Public on Jul 17 2012

city: Rochester

first: Brian

last: Bot

address: 200 1st Street SW

institute: Mayo Clinic

type: Expression profiling by high throughput sequencing

summary: mRNA expression data from next generation sequencing platforms is obtained in the form of counts per gene or exon. Counts are generally assumed to follow a Poisson distribution in which the variance is equal to the mean. However, it is common in observed count data with biological variation for over-dispersion to be present, i.e., for the variance to be greater than the mean.

overall_design: examination of technical and biological variance in mRNA-seq count data

first: Ann

last: Oberg

first: Gregory

last: Poland


title: Expression data from cultured c-Kit+Sca-1+Lin- (KSL)cells

status: Public on Jul 04 2012

city: Xian

first: Dengmei

last: Tian

address: Chang-Le Xi Street #17

institute: Fourth Military Medical University

summary:
The Notch signaling pathway plays a critical role in regulating the proliferation and differentiation of stem and progenitor cells including hematopoietic stem and progenitor cells (HSPCs). Notch receptors and ligands are expressed in BM stromal and hematopoietic cells. A large body of evidence has demonstrated that activating Notch signaling enhances HSCs self-renewal and facilitates its expansion ex vivo. We report that an endothelium-targeted soluble Notch ligand, the DSL domain of mouse Delta-like 1 fused with a RGD motif (mD1R), efficiently promotes the expansion ex vivo of mouse bone marrow HSPCs in a Notch signaling and endocytosis dependent manner. HSPCs expanded in the presence of mD1R kept long-term HSPC repopulation capacity.
We used microarrays to  compare the gene expression profiles of HSPCs expanded  in the presence of PBS and mD1R.

overall_design: KSL cells were plated on Human umbilical vein endothelial cells (HUVECs) and cultured in a serum-free medium supplemented with a cocktail containing 5 types of mouse cytokines (m5GF) in the presence of PBS or mD1R for 7 days. Then KSL cells were sorted from these cultured hematopoietic cells for RNA extraction and hybridization on Affymetrix microarrays. The experiments were repeated 3 times.

first: Hua

last: Han

first: Deng-Mei


title: Subtherapeutic antibiotics alter the murine colonic microbiome and early life adiposity

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

summary:
Early life exposure to antibiotics alters the gut microbiome. These alterations lead to changes in metabolic homeostasis and an increase in host adiposity. We used microarrays to identify metabolic genes that may be up- or down-regulated secondary to antibiotic exposure.
Low dose antibiotics have been widely used as growth promoters in the agricultural industry since the 1950’s, yet the mechanisms for this effect are unclear.  Because antimicrobial agents of different classes and varying activity are effective across several vertebrate species, we hypothesized that such subtherapeutic administration alters the population structure of the gut microbiome as well as its metabolic capabilities.  We generated a model of adiposity by giving subtherapeutic antibiotic therapy (STAT) to young mice and evaluated changes in the composition and capabilities of the gut microbiome.  STAT administration increased adiposity in young mice and altered hormones related to metabolism. We observed substantial taxonomic changes in the microbiome, changes in copies of key genes involved in the metabolism of carbohydrates to short-chain fatty acids (SCFA), increases in colonic SCFA levels, and alterations in the regulation of hepatic metabolism of lipids and cholesterol. In this model, we demonstrate the alteration of early life murine metabolic homeostasis through antibiotic manipulation.

overall_design: C57BL6 mice were divided into low-dose penicillin or control groups. Given antibiotics via drinking water after weaning. Sacrificed and liver sections collected for RNA extraction.

first: Ilseung

last: Cho

first: Shingo

last: Yamanishi

first: Laura

last: Cox

first: Barbara

last: Methé

last: Zavadil

first: Kelvin

last: Li

first: Zhan

last: Gao

first: Douglas

last: Mahana

first: Kartik

last: Raju

first: Isabel

last: Teitler

first: Huilin

first: Alexander

last: Alekseyenko

first: Martin

last: Blaser


title: Interleukin-27 priming of T cells controls Interleukin-17-production in trans via induction of Programmed cell death ligand 1

city: Bethesda

first: Golnaz

last: Vahedi

state: MD

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

summary: Interleukin (IL)-27 is a key immunosuppressive cytokine that counters T helper 17 (Th17) cell-mediated pathology. To identify mechanisms by which IL-27 might exert its immunosuppressive effect, we analyzed genes in T cells rapidly induced by IL-27. We found that IL-27 priming of naïve T cells upregulated expression of programmed death ligand 1 (PD-L1) in a signal transducer and activator of transcription (STAT)1-dependent manner. When co-cultured with naïve CD4+ T cells, IL-27-primed T cells inhibited the differentiation of Th17 cells in trans through a PD-1-PD-L1 interaction. In vivo, co-administration of naïve TCR transgenic T cells (2D2 T cells) with IL-27-primed T cells expressing PD-L1 inhibited the development of Th17 cells and protected from severe autoimmune encephalomyelitis. Thus, these data identify a suppressive activity of IL-27, by which CD4+ T cells can restrict differentiation of Th17 cells in trans.

overall_design: The roles of IL-6 and IL-27 in naïve CD4+ T cells was investigated by comparing global gene expression by Affymetrix Mouse Genome 430 2.0 Arrays. The functional outcome of STAT proteins was further evaluated by profiling gene expression changes between WT and STAT-deficient T cells in naïve CD4+ T cells with specific stimulation. All condition were done in biological triplicate.

first: Kiyoshi

last: Hirahara

first: Kamran

last: Ghoreschi

first: Xiang-Ping

last: Yang

first: Hayato

last: Takahashi

first: Arian

last: Laurence

first: Giuseppe

last: Sciumè

first: Aisling

middle: O

last: Hall

first: Christopher

last: Dupont

first: Loise

last: Francisco

first: Qian

last: Chen

first: Masao

last: Tanaka

first: Yuka

last: Kanno

first: Hong-Wei

last: Sun

first: Arlene

middle: H

last: Sharpe

last: Hunter

first: John

last: O’Shea


title: Cell Intrinsic role of Cox-2 in pancreatic cancer development

status: Public on Jun 29 2012

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

summary: Cyclooxygenase-2 (COX-2) is upregulated in pancreatic ductal adenocarcinomas (PDAC). However, how COX-2 promotes PDAC development is unclear. While previous studies have evaluated the efficacy of COX-2 inhibition via the use of non steroidal anti-inflammatory drugs (NSAIDs) or the COX-2 inhibitor celecoxib in PDAC models, none have addressed the cell intrinsic vs. microenvironment roles of COX-2 in modulating PDAC initiation and progression.  We tested the cell intrinsic role of COX-2 in PDAC progression, using both loss-of-function and gain-of-function approaches.  Cox-2 deletion in Pdx1+ pancreatic progenitor cells significantly delays the development of PDAC in mice with K-ras activation and Pten haploinsufficiency.  Conversely, COX-2 over-expression promotes early onset and progression of PDAC in the K-ras mouse model.  Loss of PTEN function is a critical factor in determining lethal PDAC onset and overall survival.  Mechanistically, COX-2 over-expression increases P-AKT levels in the precursor lesions of Pdx1+;K-rasG12D/+;Ptenlox/+ mice in the absence of Pten LOH. In contrast, Cox-2 deletion in the same setting diminishes P-AKT levels and delays cancer progression.  These data suggest an important cell intrinsic role for COX-2 in tumor initiation and progression through activation of the PI3K/AKT pathway.  PDAC that is independent of intrinsic COX-2 expression eventually develops with decreased FKBP5 and increased GRP78 expression, two alternate pathways leading to AKT activation.  Together, these results support a cell intrinsic role for COX-2 in PDAC development and suggest that, while anti-COX-2 therapy may delay the development and progression of PDAC, mechanisms known to increase chemoresistance through AKT activation must also be overcome.

overall_design: Murine mutants with pancreatic specific loss of Pten (Pten +/-) and K-ras activation (K-rasG12D) and either COX-2 over-expression (Cox-2 COE) or knockout (Cox-2 KO) under regulation of the Pdx-1 promoter developed pancreatic ductal adenocarcinoma.  RNA was extracted from pancreatic tumors from individual mutants with pathology thought to closely mimic the human disease.  Pancreatic tissue was subject to RNA extraction and hybridization on Affymetrix cDNA microarrays.

first: Reginald

last: Hill

first: Yunfeng

last: Li

first: Sarah

last: Dry

first: Jospeh

last: Calvopina

first: Alejandro

last: Garcia

first: Christine

last: Kim

first: Ying

last: Wang

first: Timothy

last: Donahue

first: Harvey

last: Herschman

first: Hong

last: Wu


title: Gene expression analysis of inducible ES cells overexpressing Etv2 (induced for 12 hours at day 3 of differentiation)

city: Minneapolis

first: Fengli

last: Fu

state: MN

address: 312 Church Street SE

institute: University of Minnesota

summary:
During embryogenesis, the endothelial and the hematopoietic lineages first appear during gastrulation in the blood island of the yolk sac. We have previously reported that an Ets variant gene 2 (Etv2/ER71) mutant embryo lacks hematopoietic and endothelial lineages, however, the precise roles of Etv2 in yolk sac development remains unclear.
We carried out a transcriptome analysis using an ES cell line that can inducibly express Etv2. Cells were induced  for 12 hours at day 3 of differentiation.

overall_design: An ES cell line (dervied from mouse of background strain 129P2/Ola) with a doxycycline inducible expression casette of Etv2 (ER71 A2Lox.cre) was differentiated in hanging drops. At 3 days of differentiation, cells were treated with doxycycline for 12 hours, and subsequently Flk1(+) cells were sorted. Experiment was done in triplicate and untreated cells were used for control.

first: Naoko

last: Koyano-Nakagawa

first: Junghun

last: Kweon

first: Michelina

last: Iacovino

first: Xiaozhong

last: Shi

first: Tara

last: Rasmussen

first: Luciene

last: Borges

first: Katie

last: Zirbes

first: Tongbin

first: Rita

last: Perlingeiro

first: Michael

last: Kyba

first: Daniel

middle: J

last: Garry


title: Distinct and Overlapping Gene Regulatory Networks in BMP- and HDAC-Controlled Cell Fate Determination in the Embryonic Forebrain

city: Heidelberg

first: Stefan

last: Wolfl

address: Im Neuenheimer Feld 364

department: Institute of Pharmacy and Molecular Biotechnology

institute: Heidelberg University, Heidelberg, Germany

summary: Both bone morphogenetic proteins (BMPs) and histone deacetylases (HDACs) have previously been established to play a role in the development of the three major cell types of the central nervous system: neurons, astrocytes, and oligodendrocytes. We have previously established a connection between these two protein families, showing that HDACs suppress BMP-promoted astrogliogenesis in the embryonic striatum. Since HDACs act in the nucleus to effect changes in transcription, an unbiased analysis of their transcriptional targets could shed light on their downstream effects on BMP-signaling. Using neurospheres from the embryonic striatum as an in vitro system to analyze this phenomenon, we have performed microarray expression profiling on BMP2- and trichostatin A (TSA)-treated cultures, followed by validation of the findings with quantitative RT-PCR and protein analysis.

overall_design: Neurospheres from the embryonic striatum were used to analyze cellular differentiation into neurons and astrocytes in vitro. To analyze the role of BMP2 and the HDAC-inhibitor TSA in this system, neurospheres were treated with TSA or BMP2 for 24 h, and mRNA was extracted after 6 and 24 h of the respective treatment.

first: Catharina

last: Scholl

first: Maya

last: Shaked

first: Kathrin

last: Weißmüller

first: Kerry

last: Tucker


title: Effect on gene expression upon deletion of Ada3

status: Public on Jun 30 2012

city: Omaha

first: Vimla

last: Band

state: NE

address: Room 6011, DRC, 985805 Nebraska Medical Center

department: Genetics, Cell Biology and Anatomy

institute: University of Nebraska Medical Center

summary:
Ada3 (alteration/deficiency in activation) is a transcriptional adaptor that forms a core structural component of multiple HAT complexes. In order to gain insights into physiological roles of Ada3, we made a conditional knockout mouse for Ada3 which was early embryonic lethal. Deletion of Ada3 in MEFs by using Adenovirus-Cre showed changes in global histone acetylation.
We performed microarray analysis after deletion of Ada3 in these cells to compare gene expression changes caused due to Ada3 loss

overall_design: Exponentially growing Ada3FL/FL MEFs were infected with control or Cre adenovirus. After 3 days of infection, we collected RNA from these cells to perform microarray analysis. The experiment was done using biological replicates


title: p38a-dependent gene expression in dendritic cells

city: Charlestown

first: Jin Mo

last: Park

state: MA

address: 149 Thirteenth Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

summary:
Gene expression in wild-type and p38a-knockout dendritic cells (DCs) were compared. Lymph node dendritic cells were isolated from mice, and left unstimulated and stimulated with Pam3CSK4, a toll-like receptor 2 agonist.
C57BL/6 wild-type mice, and dendritic cell-specific p38a-knockout mice on a C57BL/6 background were used for isolation of primary DCs.

overall_design: Gene expression 0, 2, and 4 h after stimulation was analyzed with each time point in duplicate.

first: Patcharee

last: Ritprajak

first: Jin


title: Effects of the long noncoding RNA Malat1 on gene expression

status: Public on Jun 25 2012

city: Wako

first: Yuen Yan

middle: Joanna

last: Ip

state: Saitama

address: 2-1 Hirosawa

department: Advanced Science Institute

institute: RIKEN

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

overall_design: Refer to individual Series