title: Gene expression analysis of adult and fetal T-cell progenitors

status: Public on Mar 01 2012

city: Stevenage

first: Nikolai

middle: Nikolaevich

last: Belyaev

address: Gunnels Wood Road

department: Refractory Respiratory Inflammation

institute: GlaxoSmithKline

summary: Development of T-cells provides a unique opportunity to study cell-fate determination due to the accessability and the well defined stages of development. In order to understand the genetic programs underlying fetal and adult T‑cell fate specification we subjected highly purified fetal and adult T-cell progenitor populations to a genome‑wide transcriptional analysis. The aim was to identify molecular elements that govern T-cell fate specification as a whole but ultimately to isolate elements that were specific for a given population in a specific developmental window.

overall_design: FACS purified ETP, DN2 and DN3 progenitor thymocytes from C57BL/6 adult mice and E14.5 embryos were hybridised to Affymetrix Mouse Genome 430A_2.0 GeneChip Arrays.

first: Dimitrios

last: Athanasakis

first: Delmiro

last: Fernandez-Reyes

first: Alexandre

last: Potocnik


title: Global comparative transcriptome analysis of cartilage formation in vivo

status: Public on Feb 10 2012

city: Parkville

first: Trevor

middle: L

last: Cameron

address: Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

summary: We set out to characterize the gene expression changes which take place during chondrogenesis in the developing mouse limb.  RNA derived from pre-condensed mesenchyme, mesenchymal condensations, and cartilage anlagen representing the earliest stages of tibial and fibular development was analysed by whole genome microarray analysis, and revealed 931 genes differentially expressed in these tissues.  Among them were 892 genes not previously identified during the initation of chondrogenesis, including members of the Bmp, Wnt, Gdf, Sox, and Fox gene families.  These microarray data were validated by qPCR, in situ hybridisation, and analysis of numerous genes already implicated in chondrogenesis in the scientific literature.

overall_design: 231 sections from a total of four 11.5dpc mouse hind limbs, three 12.5dpc mouse hind limbs, and four 13.5dpc mouse hind limbs (all from separate mice) were microdissected, and tissues from each time point were pooled.  Thus, this experiment consisted of one replicate only.

first: Daniele

last: Belluoccio

first: Peter

middle: G

last: Farlie

first: Bent

last: Brachvogel

first: John

middle: F

last: Bateman


title: Neonatal genistein and pregnancy day 2 oviduct gene expression

status: Public on Feb 21 2012

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

summary: Neonatal genistein treatment causes complete infertility in adult mice.  Part of their infertility can be attributed to a loss of 50% of the preimplantation embryos during transit through the oviduct between days 2 and 3 of pregnancy.  Comparison of the gene expression signatures of oviducts collected on pregnancy day 2 revealed significant alterations in gene expression, particularly in genes involved in development and the inflammatory response.  These findings were verified by real time PCR and in some cases at the protein level by immunoblotting or immunohistochemistry.

overall_design: Mice were treated with either corn oil (control) or genistein 50 mg/kg/day in corn oil for 5 days from postnatal day 1 (day of birth) through postnatal day 5.  At 6-8 weeks of age, both groups of mice were superovulated and mated.  Vaginal plug-positive mice were euthanized on day 2 of pregnancy (48 hr after hCG administration) and oviducts were collected. Both oviducts from one mouse were combined to form one biological replicate.  Four biological replicates from each group (control and neonatal genistein-treated) were compared.

first: Wendy

middle: N

last: Jefferson

first: Elizabeth

last: Padilla-Banks

first: Carmen

middle: J

last: Williams


title: Identification of  response genes upon neuronal activation in mouse cortical neurons

status: Public on Feb 02 2012

city: Shanghai

first: Xiling

last: Liu

address: 320 Yue Yang Road

country: China

institute: Partner Institute for Computational Biology

summary: We search for developmental changes specific to humans by examining gene expression profiles in the human, chimpanzee and rhesus macaque prefrontal and cerebellar cortex. In both brain regions, developmental patterns were more evolved in humans than in chimpanzees. The major human specific genes in prefrontal cortex was enriched in neuronal functions and regulated by several transcription factors, which were previously implicated in regulation of neuronal functions. To confirm neuronal function of the human prefrontal cortex specific genes, we identifed response genes upon neuronal activation in mouse cortical neurons. Our results show that human specific genes are enriched in the response genes upon neuronal activation, implying the function of human prefrontal cortex specific genes in synaptic development.

overall_design: The cortical neurons from E15 mouse were isolated and cultured. We then exposed neurons to bicuculline (Bic), or potassium chloride (KCl), or without treatment. The cultured neurons under each group were hybridized to Agilent whole mouse genome oligo microarray (4x44k).

first: Zilong

last: Qiu

first: Mehmet

last: Somel

first: Philipp

last: Khaitovich


title: An RNAi screen unveils a new player in stem cell self-renewal and long-term regeneration

status: Public on Feb 07 2012

city: New York

first: Ting

last: Chen

state: NY

institute: Rockefeller University

summary:
Mouse hair follicles undergo synchronized cycles. Cyclical regeneration and hair growth is fueled by stem cells (SCs). Following hair regeneration, SCs within the bulge and its vicinity (upper ORS which becomes the bulge for the next cycle) briefly self-renew to replenish expended SCs and ensure long-term tissue regeneration.
We used microarrays to detect the relative levels of global gene expression influenced by transcription factor Tbx1 in order to gain insight into how Tbx1 is invovled in regulating hair follicle SC self-renewal and long-term regeneration.

overall_design: Fourty eight hours after deplicaiton induced hair regeneration, hair follicle SCs were FACS-purified for RNA extraction and hybridization on Affymetrix microarrays. To obtain homogeneous populations of expression profiles, we applied FASC technique to purify SC according to their cell surface markers.

first: Elaine

last: Fuchs


title: Expression of paraventricular hypothalamus (PVN) from electroconvulsive seizure (ECS) treated C57Bl/6 mice

status: Public on Jan 24 2012

city: Tokyo

first: Eri

last: Segi-Nishida

state: Tokyo

address: Niijuku 6-3-1

country: Japan

institute: Tokyo University of Science

summary: Rationale Electroconvulsive seizure (ECS) therapy is a nonchemical treatment for depression. Since ECS up-regulates expression of c-Fos in the paraventricular nucleus of hypothalamus (PVN), the function of which is frequently influenced in depression, we hypothesized that ECS modulates functions of the PVN and contributes to its antidepressant effects.   Objectives To identify gene expression changes in the mouse PVN by ECS treatment  Material and methods First, we established a method to amplify nucleotides from small quantities of RNA. Mice received one shock of ECS and their brains were collected at 2 or 6 h after shock. The PVN was microdissected from dehydrated brain sections, its total RNA was extracted and microarray analysis was applied.   Results At 2 h after ECS, 2.6% (589 genes) of the probes showed more than 2-fold decrease, and 0.9% (205 genes) showed more than 2-fold increase. To confirm the expression changes, genes showing differential expression with a wide range in the microarray were analyzed by qPCR. Among the genes with more than 2-fold change by ECS, down-regulated 94 genes and up-regulated 24 genes have been reported the association with anxiety, bipolar disorder or mood disorder by the Ingenuity knowledge database. The groups of down-regulated genes, which are suggested to modulate the function of the PVN or associate to psychiatric disorders, include neuropeptides (Cck), kinases (Prkcb, Prkcc, Camk2a), transcription factors (Bcl6, Tbr1), transporters (Aqp4) and others (Fmr1).   Conclusion The present results indicate that ECS treatment can modulate the functions of PVN via a series of gene expression changes, and may contribute to its antidepressant effects at least in part.

overall_design: Mice received one shock of ECS and their brains were collected at 2 h (PVN_ECS2h_1, PVN_ECS2h_2) or 6 h after shock (PVN_ECS6h_1, PVN_ECS6h_2). The brains of sham-treated animals were collected at 2 h after treatment (PVN_sham_1, PVN_sham_2). The PVN was microdissected from dehydrated brain sections, and its total RNA was extracted. RNA samples from two or three animals were pooled to minimize the impact of biological variance. After nucleotide amplification by the ovation amplification, the gene expression profiles were obtained by the Affymetrix microarray analysis. The microarray analysis was performed twice using different sets of animals.

first: Mari

last: Sakaida


title: A defect of the INK4-Cdk4 checkpoint and c-myc collaborate in blastoid mantle cell lymphoma (MCL)-like lymphoma formation in mice

status: Public on Feb 01 2012

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Mantle cell lymphoma (MCL) is a B cell malignancy characterized by a monoclonal proliferation of lymphocytes with co-expression of CD5, CD43 but not CD23. Typical MCL are associated with cyclin D1 overexpression, and blastoid MCL variants are associated with c-myc translocations. We have developed a murine model of MCL-like lymphoma by crossing Cdk4R24C mice with c-myc-3’RR transgenic mice. Cdk4R24C mice is a knock-in strain that express a Cdk4 protein resistant to inhibition by p16INK4a and other INK4 family members. Breeding Cdk4R24C mice with c-myc-3’RR transgenic mice prone to develop aggressive Burkitt lymphoma-like lymphoma leads in c-myc/Cdk4R24C mice to development of clonal blastoid MCL-like lymphoma. A defect of the INK4-Cdk4 checkpoint can participate to lymphomagenesis in conjunction with additional alterations of cell cycle control, a situation which might be reminiscent of the development of human blastoid MCL.

overall_design: B splenocytes from 4 c-myc/Cdk4(R24C) lymphoma mice and 4 wt mice were investigated.

first: Yves

last: Denizot

first: P

last: Barbry

first: K


title: Mouse embryonic kidneys (E13.5): mutant (UB HDAC1,2-/-) vs. wild type

status: Public on Jan 31 2012

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: LA

address: 1430 Tulane Ave

department: Pediatrics

institute: Tulane University School of Medicine

summary: Transcriptional profiling of mouse embryonic kidneys (E13.5) comparing UB HDAC1,2-/- kidneys with wild type kidneys. Studies in our lab showed that histone deacetylase 1 (HDAC1) and 2 (HDAC2) perform redundant, yet essential functions in the developing mouse ureteric bud (UB) tissue. Double deletion of HDAC1 and HDAC2 in the UB results in impaired UB branching morphogenesis, followed by severe kidney dysgenesis. The goal of the microarray analysis was to identify the genetic pathways controlled by HDAC1 and 2 in the UB.

overall_design: Two-condition experiment: E13.5 mutant kidneys (UB HDAC1,2-/-)  vs. E13.5 wild type kidneys . Biological replicates: 4 control replicates, 4 UB HDAC1,2-/- replicates. Two-color Agilent 4x44k chips with dye-swaps on 2 of 4 arrays.

first: Shaowei

first: Dimcho

last: Bachvarov


title: Gene expression profile of oxidative stress-inducible genes of murine embryonic fibroblasts (MEFs)

status: Public on Jan 29 2012

city: Bunkyo-ku

first: Hiroyasu

last: Nakano

address: 2-1-1 Hongo

department: School of Medicine

institute: Juntendo University

summary: To identify a candidate gene that potentially participates in oxidative stress-induced tissue repair,  we have employed whole-genome microarray expression profiling.

overall_design: Oxidative stress-induced gene expression in MEFs was measured at 2 and 4 hours after exposure to doses of 1 mM of H2O2 compared to untreated MEFs.  Two independent experiments were performed at each time point (0, 2, or 4 hours).

first: Sachiko

last: Komazawa-Sakon


title: Comparison of gene expression profiles of MafF-/-: MafG-/-: MafK-/- embryos and MafF-/-: MafG+/+: MafK-/- embyos

status: Public on Jan 09 2012

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

summary:
MafF-/-: MafG+/+: MafK-/- mice are viable, while MafF-/-: MafG-/-: MafK-/- mice are embryonic lethal.  To get an insight into the cause of the lethality of small Maf triple knockout mice, transcriptome analysis was performed using whole embyos of MafF-/-: MafG-/-: MafK-/- at E10.5 and those of MafF-/-: MafG+/+: MafK-/- at  E9.5 or E10.5.
Because MafF-/-: MafG-/-: MafK-/- embryos exhibit growth retardation, the gene expression profile of MafF-/-: MafG-/-: MafK-/- embryos at E10.5 was compared with that of MafF-/-: MafG+/+: MafK-/- embyos at E9.5.  The gene expression profile of MafF-/-: MafG+/+: MafK-/- embryos at E10.5 was also examined as an alternative control.

overall_design: Total RNA was prepared from pooled three embryos for each sample.

first: H

last: Yamazaki

first: F

last: Katsuoka

last: Motohashi

first: J

middle: D

last: Engel

first: M


title: Expression data from naïve and MPTP-exposed cholinergic transgenic mice

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

country: United Kingdom

institute: UCL

summary: PD  is the second most common neurodegenerative disease worldwide with growing prevalence. MPTP is a neurotoxin which causes the appearance of Parkinson's disease (PD) pathology.  The involvement of the cholinergic system in PD has been identified decades ago and anti-cholinergic drugs were upon the first drugs used for symptomatic treatment of PD. Of note, MPTP intoxication is a model of choice for symptomatic neuroprotective therapies since it have been quite predictive. Mice were exposed to the dopaminergic neurotoxin 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP), with or without the protective acetylcholinesterase (AChE-R) variant. Transgenic AChE-S (the synaptic variant), AChE-R (the shorter, protective variant) and FVB/N control mice were included in this study. Two brain regions were examined: the pre-frontal cortex (PFC) and the striatal caudate-putamen (CPu). Each condition (i.e brain region and transgenic variant) was examined on both naive and MPTP-exposed mice.

overall_design: 29 microarrays including hybridizations of control FVB/N PFC, control FVB/N CPu,control S transgenics PFC, control S transgenics CPu, control R transgenics PFC, control R transgenice CPu,  MPTP FVB/N PFC, MPTP FVB/N CPu, MPTP S transgenics PFC, MPTP S transgenics CPu, MPTP R transgenics PFC and MPTP R transgenice CPu mRNA.

first: Yoram

last: Ben-Shaul

first: Liat

middle: B

last: Segal

first: Hermona


title: Gene expression differences between the pancreatic tissues of Pdx1-Cre;KrasLSL-G12D and Pdx1-Cre;KrasLSL-G12D;IKK2/betaF/F mice

city: Houston

first: Paul

last: Chiao

state: Texas

address: 1515 Holcombe Blvd

department: Department of Molecular and Cellular Oncology

institute: The University of Texas M. D. Anderson Cancer Center

summary: Constitutive Kras and NF-kappaB activation is identified as signature alterations in human pancreatic ductal adenocarcinoma (PDAC). However, the mechanisms of constitutive NF-kappaB activation in KrasG12D-induced PDAC are not yet understood. Here, we report that pancreas-targeted IKK2/beta inactivation inhibited NF-kappaB activation and completely suppressed PDAC development in KrasG12D and KrasG12D;Ink4a/Arf mutant mice, demonstrating a genetic link between IKK2/beta and KrasG12D in PDAC inception. Our findings reveal that KrasG12D-activated AP-1 induces IL-1alpha, which in turn activates NF-kappaB and its target genes IL-1alpha and p62, to initiate IL-1alpha/p62 feedforward loops for inducing and sustaining NF-kappaB activity. Furthermore, IL-1alpha overexpression correlates with Kras mutation, constitutive NF-kappaB activity, and poor survival in PDAC patients. Therefore, our findings establish a pathway linking duel feedforward loops of IL-1alpha/p62 through which IKK2/beta/NF-kappaB is activated by KrasG12D.

overall_design: To study Kras-induced inflammatory responses and to identify differentially expressed genes between the pancreatic tissues of Pdx1-Cre;KrasLSL-G12D and Pdx1-Cre;KrasLSL-G12D;IKK2/betaF/F mice, cDNA microarray analysis was performed.

first: Jianhua

last: Ling

first: Ya'an

last: Kang

first: Qianghua

last: Xia

first: Ruiying

last: Zhao

first: Zhe

last: Chang

first: Bailu

last: Peng

first: Jasson

last: Fleming

first: Huamin

last: Wang

first: Mien-Chie

last: Hung


title: Foxa1 and Foxa2 are Required for Sexual Dimorphism in Liver Cancer - Gene Expression

status: Public on Jan 20 2012

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

institute: University of Pennsylvania

summary: Gene expression changes between livers of treated WT and dKO (Foxa1 and Foxa2 KO) male and female mice and untreated female (WT and dKO) mice were measured to identify pathways related to Foxa1/2 regulation of pathways involved in liver cancer.

overall_design: The experiment uses 4 replicates each for 6 conditions

first: Zhaoyu

last: Li

first: Alan

last: Fox

first: Olga

last: Smirnova

first: Klaus

middle: H

last: Kaestner


title: Mouse oocytes: High hydrostatic pressure (HP) treated vs. Control

status: Public on Jan 06 2012

city: Godollo

first: Istvan

last: Bock

address: Aulich Lajos utca 26.

country: Hungary

institute: BioTalentum Ltd.

summary: Transcription profiling of mouse oocytes treated with 20 MPa hydrostatic pressure for 60 minutes at 37 °C comparing control oocytes kept under identical conditions as pressure treated ones, except HHP treatment.

overall_design: One-condition experiment, HP treated oocytes vs. Control oocytes. Biological replicates: 4 HP treated replicates, 4 control replicates.

first: Eszter

last: Losconczi

first: Anita

last: Feher

first: Andras

last: Dinnyes

first: Csaba

last: Pribenszky


title: Evaluating the transcriptomic and metabolic profile of mice exposed to source drinking water

status: Public on Jan 01 2012

city: Nanjing

first: Yan

last: Zhang

address: Xianlin Avenue

institute: Nanjing University

summary: Transcriptomic and metabonomic methods were used to investigate mice’s responses to drinking source water (DSW) exposure. After mice were fed with DSW for 90 days, hepatic transcriptome was characterized by microarray and serum metabonome were determined by 1H nuclear magnetic resonance (NMR) spectroscopy. A total of 243 differentially expressed genes (DEGs) were identified, among which 141 genes were up-regulated and 102 genes were down-regulated. Metabonomics revealed significant changes in concentrations of creatine, pyruvate, glutamine, lysine, choline, acetate, lipids, taurine and trimethylamine oxide. Four biological pathways were identified by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis where both gene expression and metabolite concentrations were altered in response to DSW exposure. These results highlight the significance of combined use of transcriptomic and metabonomic approaches in evaluating potential health risk induced by DSW contaminated with various hazardous materials.

overall_design: Nine mice in each group were selected and the livers of every three mice were homogenized together to obtain a total RNA sample. Three RNA samples in the treated or control group were hybridized separately onto three arrays to compare the genomic expression between the two groups.

first: Xuxiang

first: Bing

last: Wu

first: Shupei

last: Cheng


title: Gene expression profiling in VRK1-deficient testis of Mus musculus

status: Public on Dec 30 2011

city: Singapore

first: Hua

last: Ling

address: 62 Nanyang Drive

department: Department of Chemical and Biomolecular Engineering, SCBE

country: Singapore

institute: Nanyang Technological University

summary: To study effect of VRK1 deletion on spermatogenesis of the mouse, transciptomic analysis of genes in postnatal 8-day testicular cells of wild type and VRK1-deficient Mus musculus was performed.

overall_design: Gene expression in testes from from wild type and VRK1-deficient mutant Mus musculus, respectively, was measured. Four independent experiments for wild type and mutant, respectively, were performed.

first: Aram

last: Kang

first: Matthew

middle: W

last: Chang

first: Kyong

middle: T

last: Kim


title: DNA microarray analysis and functional profile of pituitary transcriptome under core-clock protein BMAL1 control

status: Public on Dec 31 2011

city: MARSEILLE Cedex 15

first: Anne-Marie

last: Francois-Bellan

address: Bd Pierre DRAMARD

institute: CNRS

summary: To find BMAL1-regulated genes in mice pituitary gland we performed a differential microarray  from wild-type vs Bmal1-/- knock-out mice

overall_design: Wild type and clock-deficient Bmal1-/- mice in the C57BL/6J were used at 8 to 12 weeks of age. All animals were housed in a 12-h light/12-h dark cycle (light/dark, 12:12). Mice were sacrificed by decapitation at ZT12 (light off), and three pools of three pituitaries per genotype were used to isolate total RNA. Pituitary glands taken from three mice from the same genotype were removed and frozen in liquid nitrogen until total RNA isolation.

first: F

last: Guillaumond

first: D

last: Becquet

first: B

last: Boyer

first: O

last: Bosler

last: Delaunay

first: J

last: Franc

first: A

middle: M

last: François-Bellan


title: Mouse in vitro fertilized four-cell stage embryos: High hydrostatic pressure (HP) treated vs. Control

first: Istvan

last: Bock

summary: Mouse oocytes were treated with 20 MPa hydrostatic pressure for 60 minutes at 37 °C. The HHP treated oocytes and their untreated controls were fertilized by ICSI and cultured till four-cell stage, when the transcription profiling experiment was performed.

overall_design: One-condition experiment, Four-cell stage embryos from HP treated oocytes vs. four-cell stage embryos from control oocytes. Biological replicates: 3 HP treated replicates, 3 control replicates.

first: Ana

middle: C

last: Carstea

first: Anita

last: Feher

first: Andras

last: Dinnyes


title: Enhancer Decommissioning by LSD1 During Embryonic Stem Cell Differentiation (expression)

status: Public on Jan 03 2012

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Transcription factors and chromatin modifiers play important roles in programming and reprogramming of cellular states during development.  Much is known about the role of these regulators in gene activation, but relatively little is known about the critical process of enhancer silencing during differentiation.  Here we show that the H3K4/K9 histone demethylase LSD1 plays an essential role in decommissioning enhancers during differentiation of embryonic stem cells (ESCs).  LSD1 occupies enhancers of active genes critical for control of ESC state.  However, LSD1 is not essential for maintenance of ESC identity.  Instead, ESCs lacking LSD1 activity fail to fully differentiate and ESC-specific enhancers fail to undergo the histone demethylation events associated with differentiation. At enhancers, LSD1 is a component of the NuRD complex, which contains additional subunits that are necessary for ESC differentiation.  We propose that the LSD1-NuRD complex decommissions enhancers of the pluripotency program upon differentiation, which is essential for complete shutdown of the ESC gene expression program and the transition to new cell states.

overall_design: This represents the expression part of the study.

first: Warren

last: Whyte

first: Steve

last: Bilodeau

first: Heather

last: Hoke

first: David

last: Orlando

first: Garrett

last: Frampton


title: Identification of genes characteristic of primary inguinal or epididymal preadipocyte fibroblasts

city: Boston

first: Rana

middle: K

last: Gupta

address: 44 Binney Street CLSB 11119

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Committed preadipocyte fibroblasts were genetically labelled in transgenic mice by expressing GFP under the control of the locus for Zfp423, a gene controlling preadipocyte determination. These mice are herein referred to as Zfp423-GFP mice. The overall goal was to identify genes differentially expressed between adipogenic GFP+ firboblasts and non-adipogenic GFP- fibroblasts from either inguinal or epididymal fat stromal vascular cultures obtained from Zfp423-GFP mice.

overall_design: Adipose stromal vascular cultures were obtained from inguinal or epididymal fat of 6-8 week-old male Zfp423-GFP mice.  GFP+ and GFP- fibroblasts were sorted from fat stromal vascular cultures and then returned to culture.  Subconfluent cultures of GFP+ and GFP- cells were compared in triplicate for Affymetrix analysis.

first: Bruce

last: Spiegelman


title: MMTV-Myc tumor development in E2F-null backgrounds

status: Public on Dec 29 2011

city: East Lansing

first: Eran

last: Andrechek

state: MI

address: 2120 BPS Building

department: Physiology

institute: Michigan State University

summary: Advances in genomic signatures have begun to dissect breast cancer heterogeneity, and application of these signatures will allow the prediction of which pathways are important in tumor development.  Here we used genomic signatures to predict involvement of specific E2F transcription factors in Myc-induced tumors.  We genetically tested this prediction by interbreeding Myc transgenics with mice lacking various activator E2F alleles.  Tumor latency decreased in the E2F1 mutant background and significantly increased in both the E2F2 and E2F3 mutants.  Investigating the mechanism behind these changes revealed a reduction in apoptosis in the E2F1 knockout strain.  E2F2 and E2F3 mutant backgrounds alleviated Myc effects on the mammary gland, reducing the susceptible tumor target population.   Gene expression data from tumors revealed that the E2F2 knockout background resulted in fewer tumors with EMT, corresponding with a reduction in probability of Ras activation.  In human breast cancer we found that a low probability of E2F2 pathway activation was associated with increased relapse-free survival time.  Together these data illustrate the predictive utility of genomic signatures in deciphering the heterogeneity within breast cancer and illustrate the unique genetic requirements for individual E2Fs in mediating tumorigenesis in both mouse models and human breast cancer.

overall_design: MMTV-Myc tumors were generated in an E2F wild-type, E2F1 null, E2F2 null and E2F3 heterozygous background.  When the primary tumor reached the endpoint, the tumors were flash frozen.  20 tumors from each genotype were selected for microarray analysis.

middle: R

first: Inez

last: Yuwanita

first: Kenichiro

last: Fujiwara


title: Mouse oocytes and in vitro fertilized four-cell stage embryos: High hydrostatic pressure (HP) treated vs. Control

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

overall_design: Refer to individual Series


title: Microarray skeletal muscle PPARbeta overexpressing mice

status: Public on Dec 12 2011

city: Orlando

first: Zhenji

last: Gan

state: FL

address: 6400 Sanger Rd

institute: SBMRI

summary:
This experiment was conducted to identify target genes of the peroxisome proliferator-activated receptor beta (PPARb) in skeletal muscle of transgenic mice that overexpressed PPARb.
The following abstract from the submitted manuscript describes the major findings of this work.

The Nuclear Receptor Transcription Factor PPARbeta/delta Programs Muscle Glucose Metabolism. Zhenji Gan, Eileen Burkart-Hartman, Dong-Ho Han, Brian Finck, Teresa C. Leone, John Holloszy, and Daniel P. Kelly.

To identify new gene regulatory pathways controlling skeletal muscle energy metabolism, comparative studies were conducted on muscle-specific transgenic mouse lines expressing the nuclear receptors, PPARalpha (MCK-PPARalpha) or PPARbeta/delta (MCK-PPARbeta/delta).  MCK-PPARbeta/delta mice are known to have enhanced exercise performance whereas MCK-PPARalpha mice perform at low levels. Transcriptional profiling revealed that the lactate dehydrogenase (Ldh)b/Ldha gene expression ratio is increased in MCK-PPARbeta/delta muscle, an isoenzyme shift that diverts pyruvate into the mitochondrion for the final steps of glucose oxidation. PPARbeta/delta gain- and loss-of-function studies in skeletal myotubes demonstrated that PPARbeta/delta, but not PPARalpha, interacts with the exercise inducible kinase, AMP-activated protein kinase (AMPK), to synergistically activate Ldhb gene transcription by cooperating with myocyte enhancer factor 2A (MEF2A), in a PPARbeta/delta ligand-independent manner. MCK-PPARbeta/delta muscle was shown to have high glycogen stores, increased levels of GLUT4, and augmented capacity for mitochondrial pyruvate oxidation suggesting a broad reprogramming of glucose utilization pathways. Lastly, exercise studies demonstrated that MCK-PPARbeta/delta mice had lower circulating levels of lactate compared to non-transgenic controls, while exhibiting supranormal performance on a high intensity exercise regimen. These results identify a transcriptional regulatory mechanism that increases capacity for muscle glucose utilization in a pattern that resembles the effects of exercise training.
Keywords: muscle, exercise, nuclear receptors, glucose metabolism, gene regulation

overall_design: RNA from two wild-type (non-transgenic (NTG)) and two PPARbeta overexpressing (MCK-PPARb) mice was analyzed. Two replicates of each are provided.

first: Eileen

last: Burkart-Hartman

first: Daniel

middle: P

last: Kelly


title: Gene expression profiling of neural stem cells and their neuronal progeny reveals IGF2 as a regulator of adult hippocampal neurogenesis

city: Zurich

first: Oliver

last: Bracko

address: Schafmattstrasse 18

country: Switzerland

institute: ETH Zurich

summary: Neural stem cells (NSCs) generate new neurons throughout life in two distinct areas of the mammalian brain: the subventricular zone (SVZ) lining the lateral ventricles and the hippocampal dentate gyrus (DG). How gene expression signatures differ among NSCs and immature neurons within and between these adult neurogenic regions is unknown. We isolated NSCs and their progeny using transgenic mice expressing GFP under the control of the Sox2 promoter (labeling NSCs) and transgenic mice expressing DsRed under the control of the doublecortin (Dcx) promoter (labeling immature neurons). Comparison of the transcriptomes of SOX2+ cells derived from both neurogenic areas revealed that NSCs are highly similar but that functionally significant differences in gene expression exist: IGF2, which is expressed only in SOX2+ cells in the DG but not in the SVZ, is required for proliferation of DG-derived but not SVZ-derived NSCs. Gene expression profiles strongly diverged in immature neurons, and we provide evidence that ephrinB3, which was up-regulated only in the DG but not in the SVZ during neuronal differentiation, regulates the survival of newborn granule cells. Thus, the data provided here show that stem cell populations in the adult DG and SVZ are similar but have unique properties that manifest themselves later during neural differentiation, resulting in distinct neuronal populations

overall_design: Hippocampi and SVZ from 6 week old DCX-DsRed and Sox2-GFP Reporter mice were dissected and cell sorted using FACS. cDNA were generated and analysed using Agilent Platform.

first: Tatjana

last: Singer

first: Stefan

last: Aigner

first: Marlen

last: Knobloch

first: Beate

last: Winner

first: Jasodhara

last: Ray

first: Gregory

last: Clemenson

first: Hoonkyo

last: Suh

first: Sebastien

last: Couillard-Despres

first: Ludwig

first: Fred

last: Gage

first: Sebastian

last: Jessberger


title: Transgenic Expression of A238L, a Virus Host Modification Protein, in mouse T cells

status: Public on Dec 01 2011

city: Oeiras

first: Sílvia

middle: Cristina Paiva

last: Almeida

address: Rua da Quinta Grande, n 6

department: Infection and Immunity

country: Portugal

institute: Instituto Gulbenkian de Ciência

summary: The A238L gene has been selectively expressed in mouse T lymphocytes using tissue specific promoter, enhancer and locus control region sequences for CD2. The resulting two independently derived transgenic mice expressed the transgene and developed a metastatic, angiogenic and transplantable CD4+CD8+ CD69- lymphoma. The absence of CD69 from the tumour cells suggests that they were derived from T-cells at a stage prior to positive selection.  In contrast, transgenic mice similarly expressing a mutant A238L, mutA238L, solely inhibiting transcription mediated by NFkappaB, were indistinguishable from wild type mice.  Expression of Rag 1, Rag2, TCRbeta V8.2, CD25, FoxP3, Bcl3, Bcl2 l14, Myc, IL-2, NFAT1, Itk, by purified CD4+CD8+ CD69- thymocytes from A238L transgenic mice was consistent with the phenotype. Similarly evaluated expression profiles of   CD4+CD8+ CD69- thymocytes from the mutant A238L transgenic mice were comparable to those of wild type mice.

overall_design: Purified CD4+CD8+CD69- thymocytes were prepared for wild-type control FVB/N mice, as well as from the FVB/N transgenic mice expressing the A238L and the mutated A238L, mutA238L. Comparisons were performed between the two transgenic mice lines and the control mice.

first: Vivian

middle: L

last: de Oliveira

first: Margarita

last: Bofill

first: Robert

last: Parkhouse


title: Global gene expression profiling in mouse plasma cell tumor precursor and bystander cells revels potential intervention targets for plasma-cell neoplasia

status: Public on Dec 02 2011

city: Iowa City

first: Thomas

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

summary: We extracted nascent plasma cell tumor (PCT) cells from within inflammatory granulomas (OG) isolated from intraperitoneal pristane-injected BALB/c.iMyc  Eμ mice at five different time points during tumor progression. We used laser capture micro-dissection to collect incipient PCT cells and analyzed their global gene expression on Affymetrix Mouse Genome 430A microarrays.  Two independent studies were performed with different sets of mice

overall_design: RNA was extracted from both laser capture samples and whole tissue sections at 5 different times after tumor initiation: 7 days, 17 days, 33 days, 49/46 days and 104/105 days in two independent experiments, studies 1 and 2

first: Jason

last: LeGrand

first: Eun-Sung

last: Park

first: Hongyang

last: Wang

first: Shalu

last: Gupta

first: James

last: Owens Jr

first: Patrick

last: Nelson

first: Wendy

last: DuBois

first: Siegfried

last: Janz

first: J

middle: F

last: Mushinski


title: Transcription profile of B cells isolated from peripheral lymph nodes of wild-type vs CCR7-/- mice

status: Public on Nov 21 2011

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

country: Germany

institute: Medical School Hannover

summary: We investigated the transcriptional profile of B cells isolated from peripheral lymph nodes of CCR7-/-C57BL/6 and C57BL/6 mice respectively. B cells were sorted as follows: CD19+, CD3-, CD11c-, CD11b-, NK1.1-, GR-1-. Very few genes were differentially regulated in CCR7-/- B cells, however the expression of a number of genes associated with B-cell activation was increased in CCR7-/- B cells compared to WT B cells. Our data suggest a role of CCR7 signaling in B-cell activation processes.

overall_design: 12 purified RNA samples (6 samples of each genotype), originated from 12 individually facs-sorted cell samples, were used for the microarray study. 3 RNA samples per genotype were pooled, giving rise to 2 wildtype- and 2 Ccr7 knock-out pools. In each of the 2 dual-color microarray hybridizations, samples from 1 wildtype and 1 Ccr7 knock-out pool were cohybridized. Microarray hybridizations 1 and 2 were performed in a dye-swap approach.

first: Georgios-Leandros

last: Moschovakis

first: Anja

last: Bubke

first: Elisabeth

last: Kremmer

first: Reinhold

last: Förster


title: Gene expression of three prostate lobes, ventral prostate (VP), dorsal lateral prostate (DLP), and anterior prostate (AP), by cholesterol diet

city: Pohang

first: Taek-Kyun

last: Kim

state: Gyeongbuk

address: San 31, Hyoja-dong, Nam-gu

department: Interdisciplinary Bioscience and Bioengineering

country: South Korea

institute: POSTECH

summary: Understanding the systemic regulation of normal prostate gene expression by cholesterol diet is critical for deciphering the mechanisms responsible for the transition from healthy to pathogenic prostate conditions. To understand mechanism under cholesterol effect on prostate, we performed microarray analysis using prostate tissues from SCID or C57BL/6 mice feed with varying diet conditions containing high, low or normal cholesterol.

overall_design: The RNA is obtained from ventral prostate (VP), dorsal lateral prostate (DLP), and anterior prostate (AP) in 18 SCID mice.

first: Daehee

last: Hwang

first: Jayoung


title: Comparison of gene expression in mouse CD4 naïve and activated T-cells

city: Bangalore

first: soumya

last: gupta

address: Bellary Road

country: India

institute: National Centre for Biological Sciences

summary: Gene expression changes when naïve T-cells are stimulated with antigen. We have stimulated these cells with surrogate antigens (aCD3-aCD28 coated beads) for 48 hours, and then did microarray experiment to identify differentially exprssed genes in the two conditions

overall_design: CD4 naïve T-cells from C57/Bl6 mouse were stimulated (activated) with aCD3-aCD28 coated beads for 48 hours and used for microarray experiment

first: K

middle: V

last: Iyer

first: Shovamayee

last: Maharana

first: Soumya

first: G

last: Shivashankar


title: Concerted involvement of Cdx/Hox genes and Wnt signalling in morphogenesis of the caudal neural tube and cloacal derivatives from the posterior growth zone.

city: Utrecht

first: Cesca

last: van de Ven

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Decrease in Cdx dosage in an allelic series of mouse Cdx mutants leads to  progressively more severe posterior vertebral defects. These defects are corrected  by posterior gain of function of the Wnt effector Lef1. Precocious expression of Hox  paralogous 13 genes also induces vertebral axis truncation by antagonizing Cdx  function. We report here that the phenotypic similarity also applies to patterning of  the caudal neural tube and uro-rectal tracts in Cdx and Wnt3a mutants, and in  embryos precociously expressing Hox13 genes. Cdx2 inactivation after placentation  leads to posterior defects including incomplete uro-rectal septation. Compound  mutants carrying one active Cdx2 allele in the Cdx4 null background (Cdx2/4),  transgenic embryos precociously expressing Hox13 genes, and a novel Wnt3a  hypomorph mutant all manifest a comparable phenotype with similar urorectal  defects. Phenotype and transcriptome analysis in early Cdx mutants, genetic rescue  experiments and gene expression studies lead us to propose that Cdx transcription  factors act via Wnt signalling during the laying down of urorectal mesoderm, and that  they are operative in an early phase of these events, at the site of tissue progenitors  in the posterior growth zone of the embryo. Cdx and Wnt mutations and premature  Hox13 expression also cause similar neural dysmorphology including ectopic neural  structures sometimes leading to neural tube splitting at caudal axial levels. These  findings involve the Cdx genes, canonical Wnt signalling, and the temporal control of  posterior Hox gene expression in posterior morphogenesis in the different embryonic  germ layers. They shed a new light on the etiology of the Caudal Dysplasia or  Caudal Regression range of human congenital defects.

overall_design: We used dissected Cdx2 null mutant versus wild type embryos at the 4/5 somite and 7/8 somite stage. RNA was isolated from the posterior part of the embryos (20 embryos of each genotype and stage), dissected at the same axial levels by using the last somite boundary and the base of the allantois as landmarks. Differentially labelled cRNA from the Cdx2 and control embryos were hybridized on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F) in two dye swap experiments and two technical replicates, resulting in eight individual arrays.

first: Jacqueline

last: Deschamps


title: Gene regulation following MIF stimulation.

status: Public on Nov 01 2011

city: Rehovot

first: Idit

last: Shachar

address: 2 Hersel st

country: Israel

institute: Weizmann Institute of Science

summary: Lasting B-cell persistence depends on survival signals that are transduced by cell surface receptors. Here, we describe a novel biological mechanism essential for survival and homeostasis of normal peripheral mature B cells and chronic lymphocytic leukemia (CLL) cells, regulated by the heparin-binding cytokine, midkine (MK), and its proteoglycan receptor, the receptor-type tyrosine phosphatase zeta (RPTPζ). We demonstrate that MK initiates a signaling cascade leading to B cell survival, by binding to RPTPζ. In mice lacking PTPRZ, the proportion and number of the mature B cell population is reduced. Our results emphasize a unique and critical function for MK signaling in the previously described MIF/CD74 induced survival pathway. Stimulation of CD74 with MIF leads to c-Met activation, resulting in elevation of MK expression in both normal mouse splenic B and CLL cells. Our results indicate that MK and RPTPζ are important regulators of the B cell repertoire. These findings could pave the way towards understanding the mechanisms shaping B cell survival, and suggest novel therapeutic strategies based on the blockade of the midkine/RPTPζ-dependent survival pathway.

overall_design: 2 samples were incubated with or without MIF.

first: Sivan

last: Cohen


title: Histone Deacetylase 3 is an Epigenomic Brake in Macrophage Alternative Activation (microarray)

status: Public on Nov 10 2011

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

summary: Macrophages, a key cellular component of inflammation, become functionally polarized in a signal- and context-specific manner.  Th2 cytokines such as IL-4 polarize macrophages to a state of alternative activation that limits inflammation and promotes wound healing.  Alternative activation is mediated by a transcriptional program that is influenced by epigenomic modifications including histone acetylation.  To determine if Histone Deacetylase 3 (HDAC3) has a role in macrophage polarization including alternative activation, we have performed global gene expression analysis in macrophages with and without HDAC3 and with or without IL-4 exposure.  From this data, we conclude that macrophages lacking histone deacetylase 3 (HDAC3) display a polarization phenotype similar to IL-4 induced alternative activation and furthermore are hyper-responsive to IL-4 stimulation.

overall_design: Mouse bone marrow derived macrophages were obtained from both control and HDAC3 KO animals and treated with vehicle control (BSA) or IL-4 for 24 hours.  RNA was isolated and subjected to analysis using an Agilent Whole Genome Microarray Kit.

first: Shannon

middle: E

last: Mullican

first: Christine

last: Gaddis

first: Theresa

last: Alenghat

first: Meera

middle: G

last: Nair

first: Paul

last: Giacomin

first: Dan

last: Feng

first: David

last: Steger

first: Jonathan

last: Schug

last: Artis

first: Mitchell

last: Lazar


title: Role of estrogen related receptor alpha (ERRa) in CD4+ T cell gene expression

status: Public on Oct 21 2011

city: Palo Alto

first: Dmitri

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary:
ERRa is an orphan nuclear receptor with an established role in cell metabolism. Our studies demonstrate that acute or chronic loss of ERRa broadly affects mitochondrial and glycolytic metabolism in CD4+ T cells and results in diminished T cell function and differentation.
In this array, we assessed the contribution of ERRa to changes in gene expression in resting and stimulated CD4+ T cells with the goal of identifying specific metabolic genes that exhibit altered expression in the presence or absence of ERRa. Please see related publication: Michalek, et al. PNAS 2011.

overall_design: CD4+ T cells from 6-8 week old mice were negatively selected (Miltenyi), resulting in >95% purity and cultured in RPMI 1640 (Mediatech) with 10% FBS (Gemini Bio-Products). Wild-type (WT) and ERRa−/− (ERRKO) CD4+ T cells were harvested directly ex vivo or stimulated with anti-CD3 and anti-CD28 antibodies for 12 h in the presence or absence of the pharmacological inhibtors of ERRa XCT790 and Compound A. RNA was harvested using the RNeasy Plus kit from Qiagen.The microarray was prepared and analyzed by the Duke Microarray Facility using Ambion Message Amp Premier labeling and Affymetrix GeneChip Mouse Genome 430A 2.0. Each assay contains three independent biologic replicates.

first: Ryan

last: Michalek

first: Jeff

last: Rathmell


title: Lack of hepatic response of microRNA in mice following chronic benzo(a)pyrene exposure

status: Public on Oct 19 2011

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

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


title: Expression data from mouse T-cell lymphomas

status: Public on Nov 08 2011

city: New York

first: Adolfo

last: Ferrando

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

summary:
Transgenic expression of key transcritpion factors inducing T-cell leukemias in mice.
We used microarrays to identify the gene expression signatures associated with TLX1transgenic /RUNX1 heterozygous tumors compared with different genetic models T acute lymphoblastic lymphoma.

overall_design: RNA extraction from T-cell tumors from mice with different T-cell lymphoma-predisposing genetic backgrounds.

first: Maria

last: Sulis

first: Giusy

last: Della Gatta


title: Protective Role of IL-10 in Ozone-induced Pulmonary Inflammation

city: Research Triangle Park

first: Steven

last: Kleeberger

address: 111 TW Alexander Dr., Building 101, MD D-201

institute: National Institute of Environmental Health Sciences, NIH

summary:
Background: The mechanisms underlying ozone (O3)-induced pulmonary inflammation remain unclear.  Interleukin (IL)-10 is an anti-inflammatory cytokine that is known to inhibit inflammatory mediators.
Objectives: The current study investigated the molecular mechanisms underlying IL-10-mediated attenuation of O3-induced pulmonary inflammation in mice.
Methods: Il10-deficient (Il10-/-) and wild type (Il10+/+) mice were exposed to 0.3-ppm O3 or filtered air for 24, 48 or 72 hr.  Immediately following exposure, differential cell counts, and total protein (a marker of lung permeability) were assessed from bronchoalveolar lavage fluid (BALF).  mRNA and protein levels of cellular mediators were determined from lung homogenates.  We also utilized global mRNA expression analyses of lung tissue with Ingenuity Pathway Analyses (IPA) to identify patterns of gene expression through which IL-10 modifies O3-induced inflammation.
Results: Mean numbers of BALF polymorphonuclear leukocytes (PMNs) were significantly greater in Il10-/- mice than in Il10+/+ mice after exposure to O3 at all time points tested.  O3-enhanced nuclear NF-kB translocation was elevated in the lungs of Il10-/- compared to Il10+/+ mice.  Gene expression analyses revealed several key IL-10 and O3-dependent mediators, including IL-6, MIP-2, IL-1 and CD86.
Conclusions: Results indicated that IL-10 protects against O3-induced pulmonary neutrophilic inflammation and cell proliferation.  Moreover, gene expression analyses identified three response pathways and several novel genetic targets (e.g. Ccr1, Socs3, Il33, Hat1, and Gale) through which IL10 may modulate the innate and adaptive immune response.  These novel mechanisms of protection against the pathogenesis of O3-induced pulmonary inflammation may also provide potential therapeutic targets to protect susceptible individuals.

overall_design: PARALLEL study design with 26 samples. Biological replicates: 2 to 3 replicates per group with wild type air exposed animals as controls for each time point (24, 48, 72 hours). Time-Course, Dose-Response, Strain comparison

first: Gillian

middle: S

last: Backus

first: R

last: Howden

first: Jennifer

last: Fostel

first: A

last: Bauer

first: Hye-Youn

last: Cho

first: Jacqueline

last: Marzec

first: D

middle: B

last: Peden

first: Steve


title: Nuclear Factor I/B is an Oncogene in Small Cell Lung Cancer

status: Public on Dec 08 2011

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Small cell lung cancer (SCLC) is an aggressive cancer often diagnosed only after it has metastasized to distant sites (Meuwissen and Berns 2005; Cooper and Spiro 2006). Despite the need to better understand this disease, SCLC remains poorly characterized at the molecular and genomic levels (Forgacs et al. 2001; Pleasance et al. 2010). Using a genetically-engineered mouse model of SCLC driven by conditional deletion of Trp53 and Rb1 in the lung (Jonkers et al. 2001; Vooijs et al. 2002; Meuwissen et al. 2003; Sage et al. 2003), we identified several frequent, high-magnitude focal DNA copy number alterations in SCLC. We uncovered amplification of a novel, oncogenic transcription factor, Nuclear Factor I/B (Nfib) in the mouse SCLC model and in human SCLC. Functional studies indicate that NFIB regulates cell viability and proliferation during transformation.

overall_design: Gene expression analysis of two replicates each of two independent mSCLC cell lines (3583T3 and 3151T4) stably expressing Nfib, Mycl1 or both Nfib and Mycl1

first: Alison

last: Dooley

first: Monte

last: Winslow

first: Derek

middle: Y

last: Chiang

first: Shantanu

last: Banerji

first: Nicolas

last: Stransky

first: Talya

last: Dayton

first: Eric

last: Snyder

first: Stephanie

last: Senna

first: Roderick

last: Bronson

first: Denise

last: Crowley

first: Jordi

last: Barretina

first: Levi

last: Garraway

first: Matthew

last: Meyerson

first: Tyler

last: Jacks


title: Expression data from active CD4 T cells

status: Public on Oct 01 2011

city: Durham

first: Feng

last: Feng

address: 127 Jone Building, 207 Research Drive

department: Biostatistics&Bioinformatics

institute: Duke University

summary:
miR-17 from the miR-17-92 cluster regulate activation-induced cell death in T cells and modulate inducible regulatory T cell differentiation.
We used microarrays to detail the global program of gene expression modulated by miR-17 and aim to identify the potential targets of miR-17.

overall_design: CD4 T cells from wild type or miR-17-92 deficient mice were activated and transduced with empty vector or that overexpressing miR-17. Potential targets of miR-17 should be upregulated in miR-17-92 deficient CD4 T cells compared to wild type CD4 T cells, and downregulated when miR-17 were reintroduced into the miR-17-92 deficient T cells.

first: Jiang

last: Shan

first: Li

last: Chaoran


title: Pulmonary gene and microRNA expression changes in mice exposed to benzo(a)pyrene by oral gavage

status: Public on Oct 04 2011

first: Andrew

last: Williams

summary:
Polycyclic aromatic hydrocarbons (PAHs) are widely distributed, carcinogenic environmental contaminants produced as a consequence of the incomplete combustion of fossil fuels. Benzo[a]pyrene (BaP) is a very extensively studied prototypical PAH. We recently reported a complete lack of change in microRNA (miRNA) expression in adult mouse liver following oral gavage with BaP despite a robust transcriptome response. We hypothesized that hepatic miRNAs may not be highly responsive to the treatment. Here, we analyse the pulmonary mRNA and miRNA response to BaP in the same mice. Adult male B6C3F1 mice were exposed to 5, 50, 150 and 300 mg/kg BaP by oral gavage for three consecutive days and sacrificed 4 or 24 hours after the last exposure. Serum clinical chemistry and DNA adduct levels in whole lung and liver tissues were analysed at both the time points for all the doses. Acute exposure to BaP resulted in modest decreases in serum inorganic phosphorous, calcium, glucose, alkaline phosphatase and lactate dehydrogenase in animals treated with 300 mg/kg BaP. 32P postlabeling of DNA revealed similar increases in BaP-DNA adducts in both lungs and livers of exposed mice in a dose dependent manner at the 4 hour time point. Using DNA microarrays, pulmonary mRNA and miRNA expression was analysed 4 hours after the final exposure. Over 1,000 genes were statistically differentially expressed (fold change > 1.5 and p < 0.05), encompassing numerous pathways including: oxidative stress, xenobiotic metabolism, cell proliferation, cell cycle, B and T-cell receptor signalling and primary immunodeficiency signalling pathways. Analysis of miRNA profiles revealed downregulation of miR-150, miR-142-5p, 142-3p and upregulation of miR-34c and miR-29b. These miRNAs are involved in various biological processes including immune response, cell proliferation and cell cycle, which are also the main pathways affected at the gene expression level. As BaP exposure does not result in hepatocarcinogenicity, but does cause lung cancer, these miRNAs may play an important role in the outcome of the exposure and be more predictive of carcinogenesis.

Keywords: mRNA, miRNA, Pulmonary, non-target tissue, Toxicogenomics, Benzoapyrene

overall_design: Adult male B6C3F1 mice were exposed to 5, 50, 150 and 300 mg/kg BaP by oral gavage for three consecutive days and sacrificed 4 or 24 hours after the last exposure. Serum clinical chemistry and DNA adduct levels in whole lung and liver tissues were analysed at both the time points for all the doses. Using DNA microarrays, pulmonary mRNA and miRNA expression was analysed 4 hours after the final exposure. This submission only contains the 4hr time point, at control, 150mg/kg and 300mg/kg (except for the liver study where only the control and 300mg/kg samples were used).

first: Sabina

last: Halappanavar

first: Dongmei

last: Wu

first: Byron

last: Kuo

first: Roger

middle: W

last: Godschalk

first: Frederik

last: VanSchooten

first: Carole

last: Yauk


title: Initiation Pausing of 80S Ribosome on mRNA Is Governed by 5’UTR and Responsive to mTORC1 Signaling (Microarray)

status: Public on Nov 12 2011

city: Ithaca

first: Shu-Bing

last: Qian

address: 301 Biotech Bldg.

department: Division of Nutritional Sciences

institute: Cornell University

summary: Recent studies have revealed that the mRNA translation is punctuated by ribosomal pauses through the body of transcripts.  However, little is known about its physiological significance and regulatory aspects.  Here we present a multi-dimensional ribosome profiling approach to quantify the dynamics of initiation and elongation of 80S ribosomes across the entire transcriptome in mammalian cells.  We show that a subset of transcripts have a significant pausing of 80S ribosome around the start codon, creating a major barrier to the commitment of translation elongation.  Intriguingly, genes encoding ribosome proteins themselves exhibit an exceptionally high initiation pausing on their transcripts.  Our studies also reveal that the initiation pausing is dependent on the 5’ untranslated region (5’ UTR) of mRNAs and subject to the regulation of mammalian target of rapamycin complex 1 (mTORC1).  Thus, the initiation pausing of 80S ribosome represents a novel regulatory step in translational control mediated by nutrient signaling pathway.

overall_design: Untreated TSC2 WT MEFs, TSC2 KO MEFs and TSC2 WT MEFs, TSC2 KO MEFs treated with 20nM rapamycin for 30 minutes or 3hours were harvested for ribosme profiling. The fraction samples were pooled into three groups based on velocity sedimentation: single ribosome fraction (Small group), fractions with 2 ~ 4 ribosomes (Medium group), and the one with ≥5 ribosomes (Large group). RNA were extracted from the whole cell lysis and each fraction group.

first: Yan

last: Han

first: Botao

last: Liu

first: Huifeng

last: Jiang

first: Jun

last: Sun

first: Zhenglong

last: Gu


title: IM001: Influenza A/VN/1203/04 infection of C57Bl/6 mouse model - Data from 3 viral doses at 1, 2, 4 and 7 days post infection

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Purpose of experiment was to perform transcriptomic analysis on C57Bl/6 mice infected with different doses of Influenza A/VN/1203/04 at 4 different days post infection.

overall_design:
Twenty-week-old C57BL/6 mice were infected by intranasal instillation of 10^2, 10^3 or 10^4 PFU of VN1203 in 50 µl of PBS or mock-infected with PBS alone.  At days 1, 2, 4 and 7 days post-infection, lungs were harvested and total RNA was isolated and subjected to microarray analysis.  The experimental design was for 4- 5 mice/time point/dose and 3 time-matched mocks.  However due to survival rate, there are only 3 samples at Day 7 at 10^3 PFU and no day 7 samples at 10^4 PFU.
The NIAID Systems Virology Center

first: Chengjun

last: Li

first: Armand

last: Bankhead

first: Jean

last: Chang

first: Amie

last: Eisfeld

first: Yoshihiro

last: Kawaoka

first: Shannon

last: McWeeney


title: Cell-Type-Specific TGF-beta Signaling is Targeted to Genes that Control Cell Identity: Gene Expression

status: Public on Aug 24 2011

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Smad3 co-occupies DNA binding sites with master transcription factors.

overall_design: Treated (Cy5) vs. untreated (Cy3).

first: Alan

middle: C

last: Mullen

first: Jamie

last: Newman

first: David

last: Orlando

first: Roshan

last: Kumar


title: Autocrine IL-1α mediates NF-κB activation by oncogenic ras in keratinocytes

status: Public on Aug 29 2011

city: Frederick

first: Rosalba

last: Salcedo

state: MD

address: 1050 Boyles Street, Bldg. 567

institute: SAIC-NCI

summary: Constitutively active RAS plays a central role in the development of skin cancer in the classical two stage skin carcinogenesis in mice and in a number of human cancers. Ras-mediated tumor formation is commonly associated with upregulation of cytokines and chemokines that mediate an inflammatory response considered relevant to oncogenesis. MyD88 is a crucial intermediate in the expression of multiple innate immune responders through signaling from the Toll-like/IL-1R family. We report that mice ablated for MyD88 or the IL-1R are resistant to topical skin carcinogenesis, and cultured MyD88-/- keratinocytes transduced with an oncogenic ras vector form only a few small tumors in orthotopic grafts. Initiated keratinocytes arising from oncogenic activation of ras are hyperproliferative but also resist signals for induced differentiation and upregulate a host of pro-inflammatory genes. Ras-transduced MyD88-/- keratinocytes are also hyperproliferative but the differentiation response is intact and pro-inflammatory genes are not upregulated. Using both genetic and pharmacological approaches, we find that in keratinocytes, the differentiation and immune regulation functions mediated by oncogenic ras require the establishment of an autocrine loop through IL-1α and its receptor leading to NF-κB activation. In the absence of MyD88 or IL-1R, this loop cannot be established. Further, blocking the IL-1a mediated NF-κB activation in ras-transduced wildtype keratinocytes corrects the defect in both differentiation response and proinflammatory gene expression.  Collectively, these results demonstrate that ras activation converts normal keratinocytes to an initiated phenotype through a series of potentially reversible feedback signals that provide therapeutic opportunities through inhibition of IL-1 signaling.

overall_design: Gene expression comparison of wild type ras-transformed keratinocytes untreated (n=3) or treated (n=3) in vitro with the IL1R antagonist Anakinra.

first: Christophe

last: Cataisson

first: Hakim

last: Shakeeb

first: Andrea

last: Barrett

first: Ming

last: Yi

first: Dai

last: Ren-Ming

first: Lyudmila

last: Lyakh

first: Stuart

middle: H

last: Yuspa

first: Robert

middle: M

last: Stephens

first: Giorgio

last: Trinchieri


title: Laser Capture Microdissection of Hyperlipidemic Mouse Aorta Atherosclerosis

status: Public on Nov 03 2011

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

institute: Ludwig Maximilians Universität München

summary: Atherosclerosis is a transmural chronic inflammatory condition of small and large arteries that is associated with adaptive immune responses at all disease stages. However, impacts of adaptive immune reactions on clinically apparent atherosclerosis such as intima lesion (plaque) rupture, thrombosis, myocardial infarction, and aneurysm largely remain to be identified. It is increasingly recognized that leukocyte infiltrates in plaque, media, and adventitia are distinct but their specific roles have not been defined. To map these infiltrates, we employed laser capture microdissection (LCM) to isolate the three arterial wall laminae using apoE-/- mouse aorta as a model. RNA from LCM-separated tissues was extracted and large scale whole genome expression microarrays were prepared. We observed that the quality of the resulting gene expression maps was compromised by tissue RNA carried over from adjacent laminae during LCM. To account for these flaws, we established quality controls and algorithms to improve the predictive power of LCM-derived microarray data. Our approach creates robust transcriptome atlases of normal and atherosclerotic aorta. Assessing LCM transcriptomes for immunity-related mRNAs indicated markedly distinctive gene expression patterns in the three laminae of the atherosclerotic aorta. These mouse mRNA expression data banks can now be mined to address a wide range of questions in cardiovascular biology.

overall_design: Wild-type and apoE-deficient mice on the C57BL/6J genetic background were maintained on a standard mouse chow. Total aortae were removed at the age of 78 weeks, abdominal aorta was separated from the remainder of the tissue and arterial wall laminae were separated by laser capture microdissection as described (Beer et al. 2011). Following RNA quality controls, microarrays were prepared following MIAME guidelines as described previously (Uzonyi et al. 2006; Graebner et al. 2009; Lotzer et al. 2010).

first: Michael

last: Beer

first: Sandra

last: Doepping

first: Rolf

last: Graebner


title: Lack of hepatic response of microRNA in mice following chronic benzo(a)pyrene exposure (gene expression)

first: Andrew

last: Williams

summary:
Benzo[a]pyrene (BaP) is a very extensively studied prototypical polycyclic aromatic hydrocarbons (PAHs). Previous work in our laboratory showed no changes of microRNA (miRNA) expression in liver following a 3 days exposure to BaP, suggesting a lack of miRNA transcriptional responses to aryl hydrocarbon receptor agonists and/or DNA damage.  Here, we studied 25-week old male MutaTM Mouse exposed to 25, 50, and 75 mg/kg/day BaP by oral gavage for 28 consecutive days.  MAANOVA identified 110 differentially expressed genes (adjusted p < 0.05) with fold change greater than 1.5. The genes most affected included those involved in xenobiotic metabolism, phase II metabolizing enzymes, as well as the downstream targets of p53. Pathway specific RT-PCR was used to confirm the p53 response. A single significant increase in miRNA expression was identified (mir-34a and validated using the Qiagen miScript PCR system). This miRNA is known to be transcriptionally activated by p53. Ingestion of BaP leads to widespread changes in gene expression in mouse liver, with enrichment of genes involved in cell cycle arrest, DNA damage response, and apoptosis via the p53 pathway. In contrast, miRNA expression was relatively unaffected. Only miR-34a was significantly up-regulated, and may therefore play a critical role in the post-transcriptional regulation of p53 and/or its downstream targets.

Keywords: Agilent mouse 4 x 44 oligonucleotide microarrays were used to assess global gene expression in response to 25, 50, and 75 mg/kg BaP treatment

overall_design: Individual total RNA (200 ng) from 5 mice per treatment group (control, 24mg/kg, 50mg/kg, and 75mg/kg) and universal reference total RNA (Stratagene, Mississauga, ON, Canada) was used to synthesize double stranded cDNA.

first: Amal

middle: I

last: Malik

first: Christine

last: Lemieux

first: Paul

middle: A

last: White

first: Carole

last: Yauk


title: Mouse Placenta:Maternal experimental UTI vs Sham UTI infected

status: Public on Sep 10 2011

city: Colubus

first: Sheryl

last: Justice

state: OH

address: 700 Children's Drive

institute: The Research Institute at Nationwide Children's Hospital

summary: Transcriptional profiling to map the changes in placental function subsequent to maternal experimental UTI that result in intrauterine growth restriction.

overall_design: One condition experiment: 2 biological replicates of placenta from mice with maternal experimental UTI, 2 biological replicates of placenta from mice with sham UTI.

last: Bolton

first: Dennis

last: Horvath

first: Birong

last: Li

first: Hanna

last: Cortado

first: David

last: Newsom

first: Peter

first: Santiago

last: Partida-Sanchez


title: Tregs from Bcl11b-deficient versus wild type Tregs (CD4Cre and Foxp3Cre systems)

status: Public on Aug 28 2011

city: albany

first: dorina

last: avram

address: 47 new scotland ave

department: center for immunology and microbial disease

institute: albany medical college

summary:
expression profile in Bcl11b-deficient Treg cells versus wild type Treg cells
Treg cells sorted from Bcl11bF/F/Cd4Cre/Foxp3-GFP+ mice and wild type Foxp3-GFP+ mice
Treg cells sorted from Bcl11bF/F/Foxp3Cre mice and wild type mice

overall_design:
RNA extracted from sorted Bcl11b-deficient Foxp3-GFP Treg cells form Bcl11bF/F/Cd4Cre/Foxp3-GFP+ mice and wild type Foxp3-GFP Treg cells; expression profile by microarray analysis
RNA extracted from sorted Bcl11b-deficient  Treg cells form Bcl11bF/F/Foxp3Cre mice and wild type  Treg cells; expression profile by microarray analysis

first: Dorina

last: Avram


title: Expression data from Sca-1 knockout  mice

city: Washington

first: Robert

last: Glazer

state: DC

address: 3970 Reservoir Rd, NW

department: Oncology

institute: Georgetown University

summary: The role of Sca-1 on mammary tumorigenesis was assessed. Microarrays were used to analyse global gene expression changes in Sca-1 KO mice versus wild-type mice and determine the differential responses to MP and DMBA-induced Mammary carcinogenesis

overall_design: RNA was isolated (RNeasy Mini Kit, Qiagen) from MP-DMBA induced mammary tumor or  mammary gland tissue from nulliparious transgenic and wild-type mice maintained on normal rodent chow

first: Hongyan

last: Yuan


title: Gene expression profile of Tet1 knockout mouse embryonic stem cells (mESCs)

status: Public on Aug 01 2011

first: Albert

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

summary: Global gene expression profile of Tet1 knockout ES cells is compared to wild-type ES cells. All ES lines used are V6.5 (mix 129 C57BL6 backgound).

overall_design: 2 Tet1 KO mice compared to 1 Tet1 wild type mouse.

first: Meelad

last: Dawlaty

first: Rudolf

last: Jaenisch


title: Targeting genes of AP-2d in the mouse midbrain

city: Martinsried

first: Markus

last: Moser

address: Am Klopferspitz 18

institute: Max-Planck-Institute of Biochemistry

summary: Identification of AP-2d target genes in the midbrain of E15 mouse embryos

overall_design: RNA from a pool of 15 E15 mouse midbrains from control and AP-2d knockout embryos


title: Comparative oncogenomics identifies breast tumors enriched in functional tumor initiating cells

status: Public on Aug 15 2011

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

type: Genome variation profiling by genome tiling array

summary: The claudin-low subtype is a recently identified rare molecular subtype of human breast cancer that expresses low levels of tight and adherens junction genes and shows high expression of epithelial-to-mesenchymal transition (EMT) genes.  These tumors are enriched in gene expression signatures derived from human tumor initiating cells (TIC) and human mammary stem cells.  Through cross-species analysis, we discovered mouse mammary tumors that have similar gene expression characteristics as human claudin-low tumors and were also enriched for the human TIC signature.  Such claudin-low tumors were similarly rare, but came from a number of distinct mouse models including the p53 null transplant model. Here we present a molecular characterization of fifty p53 null mammary tumors as compared to other mouse models and human breast tumor subtypes.  Similar to human tumors, the murine p53 null tumors fell into multiple molecular subtypes including two basal-like, a luminal, a claudin-low, and a subtype unique to this model.  The claudin-low tumors also showed high gene expression of EMT inducers, low expression of the miR-200 family, and low to absent expression of both claudin 3 and E-cadherin.  These murine subtypes also contained distinct genomic DNA copy number changes some of which are similarly altered in their cognate human subtype counterpart.  Finally, limiting dilution transplantation revealed that p53 null claudin-low tumors are highly enriched for TICs as compared to the more common adenocarcinomas arising in the same model, thus providing a novel preclinical mouse model to investigate the therapeutic response of TICs.

overall_design: 107 Agilent CGH and expression microarrays

first: Jason

last: Herschkowitz


title: GIF-5 mouse gastric epithelial cells: CD-133-positive vs CD-133-negative

status: Public on Aug 05 2011

city: Bunkyo-ku

first: Hiroshi

last: Fukamachi

state: Tokyo

address: Yushima 5-45-1

department: Department of Molecular Oncology

institute: Tokyo Medical and Dental University

summary:
Transcriptional profiling of GIF-5 mouse gastric epithelial cells comparing CD133-positive and CD133-negative cells. The former formed CD133-positive and CD133-negative cells while the latter only CD133-negative cells, suggesting that CD133-positive cells are mother cells.
The former produced differentiated type tumors while the latter undifferentiated types in vivo, indicating a relationship between CD133-expression and glandular structure formation.

overall_design: One-condition experiment, CD133-positive vs. CD133-negative cells. 2 replicates.

first: Kosei

last: Ito


title: Extinction learning

status: Public on Aug 08 2011

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Extinction learning refers to the phenomenon that a previously learned response to an environmental stimulus, for example the expression of an aversive behavior upon exposure to a specific context, is reduced when the stimulus is repeatedly presented in the absence of a previously paired aversive event. Extinction of fear memories has been implicated with the treatment of anxiety disease but the molecular processes that underlie fear extinctionare only beginning to emerge. Here we show that fear extinction initiates up-regulation of hippocampal insulin-growth factor 2 (Igf2) and down-regulation of insulin-growth factor binding protein 7 (Igfbp7). In line with this observation we demonstrate that IGF2 facilitates fear extinction, while IGFBP7 impairs fear extinction in an IGF2-dependent manner. Furthermore, we identify one cellular substrate of altered IGF2-signaling during fear extinction. To this end we show that fear extinction-induced IGF2/IGFBP7-signaling promotes the survival of 17-19 day-old newborn hippocampal neurons. In conclusion, our data suggests that therapeutic strategies that enhance IGF2-signaling and adult neurogenesis might be suitable to treat disease linked to excessive fear memory.

overall_design: We employed mice to investigate fear extinction in the hippocampus-dependent contextual fear conditioning paradigm. To this end, male C57BL/6J mice were exposed to the fear conditioning box (context) followed by an electric foot-shock which elicits the acquisition of conditioned contextual fear. For extinction training animals were repeatedly reexposed to the conditioned context on consecutive days (24h interval) without receiving the footshockagain (extinction trial, E). This procedure eventually results in the decline of the aversive freezing behavior. Mice that were exposed to the conditioning context without receiving fear conditioning training served as control groups. To gain a better understanding of the molecular processes underlying fear extinction we performed a genome-wide analysis of the hippocampal transcriptome during fear extinction. In the employed paradigm fear extinction is a gradual process. To capture the longitudinal course of fear extinction we decided to perform hippocampal microarray analysis at two time points: (1) After the first extinction trial (E1) when animals display high levels of aversive freezing behavior and (2) at the extinction trial on which the freezing behavior was significantly reduced when compared to E1. This extinction trial, in the case of this experiment E5, we termed “extinction trial low freezing” (ELF). Mice that were exposed to the conditioning context without receiving fear conditioning training served as control groups (3). For all three groups we hybridized 5 samples (biological replicates).

first: Roberto

last: C Agis-Balboa

first: Dario

last: Diaz

first: Jessica

last: Wittnam

first: Nambirajan

last: Govindarajan

first: Kim

last: Blom

first: Susanne

last: Burkhardt

first: Ulla

last: Haladyniak

first: Hope

last: Agbemenyah

first: Anthanasios

last: Zovoilis

last: Salinas-Riester

first: Lennart

last: Opitz

first: Farahnaz

last: Sananbenesi

first: Andre

last: Fischer


title: The effect of HP1-gamma deficiency on primordial germ cells

city: Kanazawa

first: Masahide

last: Asano

state: Ishikawa

department: Advanced Science Research Center,

institute: Kanazawa University

summary: We compared the gene expression profiles of the HP1 gamma -/- vs wild-type PGCs to examine the molecular mechanisms of HP1g in PGC development. Although HP1g is suggested to be involved in PGC proliferation, our microarray data indicated that HP1g does not directly control PGC cell-cycle progression by regulating cell cycle-related genes. However, many genes acting on differentiated tissues were up-regulated in the HP1g-/- PGCs.

overall_design: The mVenus-positive cells from the E11.5 genital ridges were isolated by flow cytometry (JSAN, Bay Bioscience). The total RNA was then prepared from the sorted primordial germ cells (about 500-3,500 cells per embryo) of wild-type or HP1γ-/- embryos with an RNeasy micro kit (Qiagen). The RNA samples were pooled from 5 or 6 embryos of each genotype. Two independent pooled RNA samples of each genotypes were used to verify the reproducibility of the microarray analyses.

first: Kanae

last: Abe

first: Chie

last: Naruse

first: Tomoaki

last: Kato

first: Takumi

last: Nishiuchi

first: Mitinori

last: Saitou


title: Attenuation of early atherogenesis in LDLR-KO mice by proteasome inhibition

status: Public on Jul 14 2011

city: Berlin

first: Antje

last: Ludwig

address: Ziegelstr. 5-9

department: Kardiologie

institute: Charité Universitätsmedizin Berlin

summary: To get further insights into the processes leading to attenuation of early stage atherosclerosis in the bortezomib treated LDLR-KO mice, microarray profiling of gene expression was performed on RNA taken from whole aortae of bortezomib treated LDLR-KO and sham- treated LDLR-KO mice fed a Western diet for 6 weeks and compared the changes in gene expression in both groups to non-atherosclerotic CD animals.

overall_design: Male 10-week-old LDLR-KO mice (B6.129S7-Ldlrtm1Her/J; JAX Mice, Boston) were fed a Western-type diet for 6 weeks ad libitum and received intraperitoneal injections of bortezomib (50 µg/kg body weight; WD+Bor) or saline (WD) twice weekly (n = 4). Mice that were fed normal diet served as chow diet control (CD; n = 4). Gene expression in aortic tissue was measured. Two independent experiments were performed.

first: Nicola

last: Wilck


title: Pre-metastatic expression array day 7

status: Public on Jul 25 2011

city: New York

first: Yupu

last: Liang

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary:
Primary tumors have been shown to prepare distal organs for later colonization of metastatic cells by stimulating organ-specific infiltration of bone marrow-derived cells. Here we demonstrate that neutrophils accumulate in the lung prior to the arrival of metastatic cells in mouse models of breast cancer. Tumor-entrained neutrophils (TENs) inhibit metastatic seeding in the lungs by generating H2O2, and tumor-secreted CCL2 is a critical mediator of optimal anti-metastatic entrainment of G-CSF-stimulated neutrophils. TENs are present in the peripheral blood of breast cancer patients prior to surgical resection but not in healthy individuals. Thus, while tumor-secreted factors contribute to tumor progression at the primary site, they concomitantly induce a neutrophil-mediated inhibitory process at the metastatic site.

To follow the earliest transcriptional changes in pre-metastatic tissues, we orthotopically injected 4T1 cells into the mammary fat pad of female nude mice. Control mice were orthotopically injected with PBS. 7 days post tumor engraftment, the mice were sacrificed and thoroughly perfused with ice cold PBS, and lung and liver samples were flash frozen in liquid nitrogen. Following RNA extraction, the lung and liver RNA samples were analyzed on MOE430A2 Affymetrix arrays using R/Bioconductor software.

overall_design: Expression array was performed on lung or liver tissue from control or tumor-bearing mice. Lung and liver tissues were isolated from 3 control mice (injected with PBS) and 3 tumor-bearing mice (injected with 4T1 cells) 7 days post injection.

first: Zvi

last: Granot

first: Robert

last: Benezra


title: A SUMOylated C-terminus fragment of glutamate transporter EAAT2 linked to inherited ALS mediates motor axon impairment

status: Public on Jul 20 2011

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

summary: Downregulation of expression and activity levels of the astroglial glutamate transporter EAAT2 is thought to be implicated in motor neuron excitotoxicity in amyotrophic lateral sclerosis (ALS). We previously reported that EAAT2 is cleaved by caspase-3 at the cytosolic C-terminus domain, impairing the transport activity and generating a proteolytic fragment found to be SUMO1 conjugated (CTE-SUMO1). We show here that this fragment accumulates in the nucleus of spinal cord astrocytes in vivo throughout the disease stages of the SOD1-G93A mouse model of ALS. In vitro expression in spinal cord astrocytes of the C-terminus peptide of EAAT2 (CTE), which was artificially fused to SUMO1 (CTE-SUMO1fus) to mimic the endogenous SUMOylation reaction, recapitulates the nuclear accumulation of the fragment seen in vivo and causes caspase-3 activation and axonal growth impairment in motor neuron-derived NSC-34 cells and primary motor neurons co-cultured with CTE-SUMO1fus-expressing spinal cord astrocytes. This indicates that CTE-SUMO1fus could trigger non-cell autonomous mechanisms of neurodegeneration. Prolonged nuclear accumulation of CTE-SUMO1fus in astrocytes leads to their degeneration, although the time frame of the cell-autonomous toxicity is longer than the one for the indirect toxic effect on motor neurons. As more evidence on the implication of SUMO substrates in neurodegenerative diseases emerges, our observations strongly suggest that the nuclear accumulation in spinal cord astrocytes of a SUMOylated proteolytic fragment of the astroglial glutamate transporter EAAT2 could take part to the pathogenesis of ALS and suggest a novel, unconventional role for EAAT2 in motor neuron degeneration in ALS.

overall_design: Comparison is made between the toxic fragment (SUMO) and the same fragment without lysines that can be sumo-ylated (CTE). Four replicates have been performed for each sample group.


title: Drosophila_2hr_mated

status: Public on Aug 31 2011

city: College Station

first: Ginger

last: Carney

state: TX

address: 3258 TAMU

department: Biology

institute: Texas A&M University

summary: We hypothesized that social interactions, such as those involved in courtship and mating, would lead to assayable changes in gene expression that may have important effects on individual reproductive success and fitness through alterations in physiology or changes in nervous system function.

overall_design: Five-day-old males were collected two hours after mating with or courting a virgin female compared to males that were left alone for the 2 hrs. After collection, RNA was extracted from male head tissue. Five samples for each treatment were hybridized to Affymetrix Drosophila Genome arrays for a total of 15 arrays. Data were analyzed using dChip PM, dChip PM-MM, MAS5.0, R/Bioconductor GC-RMA, and GeneSpring GC-RMA.

first: Lisa

middle: L

last: Ellis


title: Expression data from GW8510 treatment of pancreatic cells

status: Public on Aug 02 2011

city: Cambridge

first: Dina

middle: A.

last: Fomina-Yadlin

state: MA

address: 7 Cambridge Center, 3112-D

institute: Broad Institute

summary:
Expression of insulin in terminally differentiated non-beta pancreatic cell types could be important for treating type-1 diabetes. We observed that the kinase inhibitor GW8510 up-regulated insulin expression in mouse pancreatic alpha cells.
Gene-expression profiling and gene-set enrichment analysis of GW8510-treated alpha cells suggested coordinate up-regulation of the p53 pathway, which was further implicated in induction of insulin transcript.

overall_design: In order to determine a potential mechanism of insulin induction by GW8510, we treated mouse alpha cells (aTC1) and beta cells (bTC3) with 3.3 µM GW8510 or 0.1% DMSO for five days, and performed gene-expression profiling followed by gene-set enrichment analysis (GSEA). Three biological replicates were included per condition. GW8510 treatment in each cell line was compared to DMSO-treated control.

first: Bridget

last: Wagner


title: Expression profiling of immortalized mature, murine T cells

status: Public on Jul 01 2011

city: Frankfurt am Main

first: Sebastian

last: Newrzela

state: Hessen

address: Theodor-Stern-Kai 7

department: Pathology

institute: University Clinic Frankfurt

summary:
The RNA expression profile of retrovirally immortalized mature, murine T cells was compared to the expression profile of mature naive, murine T lymphocytes and/or murine thymocytes of healthy C57BL/6 mice.
Retroviral insertional mutagenesis can contribute to immortalization of mature T lymphocytes, Newrzela et al. 2011

overall_design:
Mature T lymhpocytes were retrovirally immortalized. To compare the expression profile of immortalized T cells with non-manipulated wild type cells: RNA was isolated from fresh murine T lymphocytes, thymocytes and the immortalized T-cell population (each 1x10E7 cells). For naive T lymphocytes and thymocytes we used 8 weeks old C57BL/6 wild type (WT) donor animals.
Study design: Prof. Dorothee von Laer. Study design and sample preparation: Dr.Sebastian Newrzela
Gene expression profiling was performed as a commercial service by Miltenyi Biotec MACS molecular, Micorarray Service/ Cologne, Germany. Responsible scientist: Alena Fitz, Silvia Rüberg. Performed: March 2008

first: Dorothee

last: von Laer


title: Mouse ES cells vs. iPS cells

city: Minneapolis

first: Nobuaki

last: Kikyo

state: MN

institute: University of Minnesota

summary: Transcriptional profiling of Mouse  iPS cells  and MEFs comparing ES cells.

overall_design: RNA was prepared from the ES cell line CGR8.8, MEFs and and iPSC clone and cRNA was hybridized to Agilent Whole Murine Genome Oligo Microarray.

first: Hiroyuki

last: Hirai


title: Effect of Ursodeoxycholic acid on gene expression in the intestial epithelium

first: christoph

last: Hanski

address: Hindenburgdamm 30

institute: Charité Campus Benjamin Franklin

summary: Background & Aims: Ursodeoxycholic acid (UDCA) attenuates chemical and colitis-induced colon carcinogenesis in animal models. We investigated its mechanism of action on normal intestinal cells, in which carcinogenesis- or inflammation-related alterations do not interfere with the result.   Methods: Alterations of gene expression were identified in Affymetrix arrays in isolated colon epithelium of mice fed with a diet containing 0.4% UDCA and were confirmed in the normal rat intestinal cell line IEC-6 by RT-PCR. The effect of the insulin receptor substrate 1 (Irs-1) expression and of ERK phosphorylation on proliferation was investigated in vitro by flow cytometry, western blotting, siRNA-mediated gene suppression or by pharmacological inhibition of the kinase activity. The ERK1-effect on Irs-1 transcription was tested in a  reporter system.  Results: UDCA-treatment in vivo suppressed potential pro-proliferatory genes including Irs-1 and reduced cell proliferation by more than 30%. In vitro it neutralised the proliferatory signals of IGF-1 and EGF and slowed down the cell cycle. Irs-1 transcription was suppressed due to  high ERK1 activation. Both Irs-1 suppression and the persistent high ERK activation inhibited proliferation. Conversely, the decrease of phosphorylation of ERK1 (but not ERK2) or of its expression partially abrogated the inhibitory effects of UDCA.   Conclusions: UDCA inhibits proliferation of intestinal epithelial cells by acting upon IGF-1 and EGF pathways and targeting ERK1 and, consequently, Irs-1. The inhibition of these pathways adds a new dimension to the physiological and therapeutic action of UDCA and,  since both pathways are activated in inflammation and cancer, suggests new applications of UDCA in chemoprevention and chemotherapy.

overall_design: Six normal mice were used for isolation of control RNA and six mice were used for isolation of RNA after UDCA treatment. RNAs of two animals were pooled i.e. there were six treated samples, named T1+2;T3+4,T5+6 and six nontreated samples named N1+2;N3+4 and N5+6.

first: Santosh

last: Krishna-Subramanian

first: Christoph


title: Gene expression of murine STAT3-KO hearts vs WT

status: Public on Jun 30 2011

city: Hannover

first: Denise

last: Hilfiker-Kleiner

institute: Medical school Hannover

summary: Gene expression analysis of heart tissue probes from a mouse model with a cardiomyocyte-restricted STAT3 deficiency in comparison to corresponding WT mice. (Hilfiker-Kleiner, D. et al. 2004)

overall_design: Comparison of heart left ventricle tissue probes from STAT3-KO and WT mice. Each sample is a pool of 5 tissue probes from each genotype.


title: Pro-invasion metastasis drivers in early stage melanoma are oncogenes

status: Public on Jul 11 2011

city: Boston

first: Yonghong

last: Xiao

address: 450 Brookline Ave., HIM218A

institute: Dana-Farber Cancer Institute

summary: Clinical and genomic evidence support the view that the metastatic potential of a primary tumor may be dictated by transforming events acquired early in the tumorigenic process.  It has been proposed that the presence of such pro-metastatic events in early-stage tumors reflects their additional capability to function as oncogenes.  Here, to test this ‘deterministic’ hypothesis and identify potential pro-metastasis oncogenes, we adopted a comparative oncogenomics-guided functional genetic screening strategy involving (i) global transcriptomic data from two genetically engineered mouse models of melanoma with contrasting metastatic potential, (ii) genomic and transcriptomic profiles of human primary and metastatic melanoma and (iii) an invasion screen in TERT-immortalized human melanocytes and melanoma cells in vitro as well as (iv) evidence of expression selection in human melanoma tissues. This integrated effort led to the identification of 6 genes that are both potently pro-invasive and oncogenic.  Further, we show that one such pro-invasion oncogene, ACP5, can confer spontaneous metastasis in vivo, engages a key pathway governing metastasis and is prognostic in human primary melanomas.

overall_design: The tetracycline-inducible MET-driven mouse (iMet) model (Tyr-rtTA;Tet-Met;Ink4a/Arf-/-) was constructed similar to the previously described iHRAS* model (Tyr-rtTA;Tet-HRASV12G;Ink4a/Arf-/-). RNA from cutaneous melanomas derived from iMet (n=6) or iHRAS* (n=6) models were profiled on Affymetrix M430A_2 chips and resultant transcriptomes were compared to generate a phenotype-based (metastatic capable or not) differentially expressed gene list. Cross-species triangulation to human gene expression and copy number aberrations was based on ortholog mapping.

first: Kenneth

last: Scott

first: Cristina

last: Nogueira

first: Timothy

middle: P

last: Heffernan

first: Remco

last: van Doorn

first: Sabin

last: Dhakal

first: Jason

last: Hanna

first: Chengyin

last: Min

first: Mariela

last: Jaskelioff

first: Chang-Jiun

last: Wu

last: Cameron

first: Samuel

middle: R

last: Perry

first: Rhamy

last: Zeid

first: Tamar

last: Feinberg

first: Minjung

last: Kim

first: George

middle: V

last: Woude

first: Scott

last: Granter

first: Marcus

last: Bosenberg

first: Gerry

last: Chu

first: Ronald

last: DePinho

first: David

last: Rimm

first: Lynda

last: Chin


title: Transgenic expression of polyoma virus middle T antigen in the mouse prostate gives rise to carcinoma

first: Sang Hyun

last: Lee

address: 44 Binney Street, SM970

department: Cancer Biology

summary: Global gene expression profiles of ventral prostates of wild types and transgenic mice created with MT antigen

overall_design: normal prostate vs prostate cancer induced by MT expression

first: S

first: T

last: Roberts


title: Mechanism of action of RPS19R62W mutation in Diamond-Blackfan Anemia (DBA)

status: Public on Jun 29 2011

city: Bethesda

first: Christopher

last: Pan

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

summary:
RPS19 mutations are the most common cause of the human disorder Diamond Blackfan Anemia. The R62W mutation was hypothesized to act in a dominant negative fashion and mice expressing RPS19R62W have many of the characteristics of Diamond Blackfan Anemia.
Diamond-Blackfan Anemia (DBA), is an inherited erythroblastopenia associated with mutations in at least 8 different ribosomal protein genes. Mutations in the gene encoding Ribosomal Protein S19 (RPS19) have been identified in ~25% of DBA families. Most of these mutations disrupt either the translation or stability of the RPS19 protein and are predicted to cause DBA by haploinsufficiency. However, approximately ~30% of RPS19 mutations are missense mutations that do not alter the stability of the RPS19 protein and are hypothesized to act by a dominant negative mechanism. To formally test this hypothesis, we generated a transgenic mouse model expressing an RPS19 mutation in which an Arginine residue is replaced with a Tryptophan residue at codon 62 (RPS19R62W). Constitutive expression of RPS19R62W in developing mice was lethal. Conditional expression of RPS19R62W resulted in growth retardation, a mild anemia with reduced numbers of erythroid progenitors and significant inhibition of terminal erythroid maturation, similar to DBA. RNA profiling demonstrated over 700 dysregulated genes belonging to the same pathways that are disrupted in RNA profiles of DBA patient cells.

overall_design: The samples compared are RNA extracted from CD71 positive erythroblasts sorted from the bone marrow of wild type mice and mice expressing a mutant RPS19 (RPS19R62W) transgene

first: Emily

last: Devlin

last: Bodine


title: Gene expression profiling of small intestine (SI) NKp46+RORgt+ and NKp46+RORgt- Innate Lymphoid Cells (ILCs)

status: Public on Jun 20 2011

city: Marseille

first: elena

last: tomasello

address: 163 avenue de Luminy

institute: CIML

summary: The aim of this study was to analyze the global transcriptional profiles of small intestine (SI) Innate Lymphoid Cells (ILCs) expressing the NK cell marker NKp46. Based on differential expression of the RORgt transcription factor SI NKp46+ ILCs can be divided in NKp46+RORgt- and NKp46+RORgt+ cells. While NKp46+RORgt- cells produce IFN-g, like conventional Natural Killer (NK) cells, NKp46+RORgt+ cells secrete IL-22, like Lymphoid Tissue inducer (LTi) cells. We compared the global transcriptional profiles of both NKp46+RORgt- and NKp46+RORgt+ cells to conventional splenic NK cells and to SI NKp46-RORgt+ cells, which contain adult LTi cells. By following this approach, we showed that SI NKp46+RORγt- ILCs correspond to SI NK cells. We also identified a transcriptional program conserved in adult SI NKp46+RORγt+, NKp46-RORγt+ ILCs and fetal LTi.

overall_design: The various ILC cell populations analyzed in this study were isolated from C57BL/6 RORc(gt)+/GFP reporter mice.  SI NKp46+RORγt- (NKp46+GFP-) cells, SI NKp46+RORγt+ cells (NKp46+GFPlow and NKp46+GFPhigh cells) and NKp46-RORγt+ ILCs, including adult LTi cells , were sorted by flow cytometry from CD3- lamina propria cells of small intestine (SI) of RORc(γt)+/GFP reporter mice . Splenic NKp46+RORγt- (NKp46+GFP-) cells were also sorted as the reference for conventional NK cells. Two replicates of each populations were produced and analyzed.

first: Elena

last: Tomasello

first: Eric

last: Vivier