title: Indirect Flight Muscle (IFM) expression profiling of actin and myosin nulls in Drosophila melanogaster

status: Public on Jun 25 2015

city: Bangalore

first: Aditi

last: Madan

state: Karnataka

address: GB-03,Dept. of MRDG,New BioSciences Bldg, IISc

department: Dept. of MRDG

institute: Indian Institute of Science

summary:
Expression profiling of IFMs from 1-2 day old adult male flies of 3 genotypes: Canton-S, IFM-specific actin null (Act88FKM88) and IFM-specific myosin null (Mhc7).
Results provide insight into how muscles respond to the absence of major scaffold proteins, and whether these transcriptional responses are filament-specific or generic to the tissue.

overall_design: RNA was extracted from the IFMs of 1-2 day old adult male flies of 3 genotypes (Canton-S, Act88FKM88, Mhc7), labeled, and hybridized on Affymetrix GeneChip Drosophila Genome 2.0 microarrays. 9 microarray experiments from 3 independent biological replicates of each genotype. Data was analyzed using RMA method, and significance was tested using SAM version 3.02, with cut-off parameters of 10% FDR and minimum 2-fold change in expression levels.

first: Divesh

last: Thimmaiya

first: Ari

last: Franco-Cea

first: Mohammed

last: Aiyaz

first: Prabodh

last: Kumar

first: John

last: Sparrow

first: Upendra

last: Nongthomba


title: DIRECT CONVERSION OF FIBROBLASTS INTO FUNCTIONAL ASTROCYTES BY DEFINED TRANSCRIPTION FACTORS

status: Public on Jun 22 2015

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

summary: Direct cell reprogramming has enabled the direct conversion of skin fibroblasts into functional neurons and oligodendrocytes using a minimal set of cell lineage-specific transcription factors. This approach has substantial advantages since it is rapid and simple, generating the cell type of interest in a single step. However, it remains unknown whether this technology can be applied for directly reprogramming skin cells into astrocytes, the third neural lineage. Astrocytes play crucial roles in neuronal homeostasis and their dysfunctions contribute to the origin and progression of multiple human diseases. Herein, we carried out a screening using several transcription factors involved in defining the astroglial cell fate and identified NFIA, NFIB and SOX9 to be sufficient to convert with high efficiency embryonic and post-natal mouse fibroblasts into astrocytes (iAstrocytes). We proved both by gene expression profiling and functional tests that iAstrocytes are comparable to native brain astrocytes. This protocol can be then employed to generate functional iAstrocytes for a wide range of experimental applications.

overall_design: Induced astrocytes (iAstro) were compared to Fibroblasts (Fibro) as negative control and to primary astrocytes (astro) as positive control. Three biological replicates were analyzed for each experimental group.

first: Massimiliano

last: Caiazzo

first: Serena

last: Giannelli

first: Pierluigi

last: Valente

first: Gabriele

last: Lignani

first: Alessandro

last: Sessa

first: Gaia

last: Colasante

first: Rosa

last: Bartolomeo

first: Stefano

last: Ferroni

first: Carmine

last: Settembre

first: Fabio

last: Benfenati

first: Vania

last: Broccoli


title: Peturbation of PICALM Levels Alters Cellular Cholesterol Metabolism

status: Public on Jun 17 2015

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

country: USA

institute: Duke University

summary:
PICALM (Phosphatidyl Inositol Clathrin Assembly Lymphoid Myeloid protein) is a ubiquitously expressed protein that plays a role in clathrin-mediated endocytosis. PICALM also affects the internalization of SNAREs and modulates macroautophagy. Chromosomal translocations that result in the fusion of PICALM to heterologous proteins cause leukemias, and genome-wide association studies have linked Single Nucleotide Polymorphisms (SNPs) of PICALM to Alzheimer’s disease.
To obtain insight into the biological role of PICALM, we performed gene expression studies of PICALM-deficient and PICALM-expressing cells. Pathway analysis demonstrated that PICALM expression influences the expression of genes that encode proteins involved in cholesterol biosynthesis and lipoprotein uptake. GC-MS studies indicated that loss of PICALM increases total cholesterol pool size. Isotopic labeling studies revealed that loss of PICALM alters cholesterol homeostasis via increased scavenging of cholesterol. Measurement of LDL receptor endocytosis further showed that PICALM deficient cells express higher LDLR levels resulting in higher lipoprotein internalization. These findings suggest that PICALM is required for cellular cholesterol homeostasis and point to a novel mechanism by which PICALM alterations may contribute to disease.

overall_design: Total RNA was isolated (Qiagen RNeasy® Micro kit, Valencia, CA) from four replicates of PICALM knockout cells transfected with control vector, and from four replicates of PICALM knockout cells transfected with PICALM.

first: Jacob

middle: L

last: Mercer

first: Joseph

middle: P

last: Argus

first: Donna

last: Crabtree

first: Melissa

middle: M

last: Keenan

middle: A

first: Steven

middle: J

last: Bensinger

first: Catherine

last: Lavau

first: Daniel

middle: S

last: Wechsler


title: Control of stomach smooth muscle development and intestinal rotation by transcription factor BARX1

status: Public on Jun 02 2015

city: New York

first: Chenura

last: Jayewickreme

state: NY

address: 1300 York Avenue

institute: Weill Cornell Medical College

summary:
Diverse functions of the homeodomain transcription factor BARX1 include Wnt-dependent, non-cell autonomous specification of the stomach epithelium, tracheo-bronchial septation, and Wnt-independent expansion of the spleen primordium. Tight spatio-temporal regulation of Barx1 levels in the mesentery and stomach mesenchyme suggests additional roles. To determine these functions, we forced constitutive BARX1 expression in the Bapx1 expression domain, which includes the mesentery and intestinal mesenchyme, and also examined Barx1-/- embryos in further detail. Transgenic embryos invariably showed intestinal truncation and malrotation, in part reflecting abnormal left-right patterning. Ectopic BARX1 expression did not affect intestinal epithelium, but intestinal smooth muscle developed with features typical of the stomach wall. BARX1, which is normally restricted to the developing stomach, drives robust smooth muscle expansion in this organ by promoting proliferation of myogenic progenitors at the expense of other sub-epithelial cells. Undifferentiated embryonic stomach and intestinal mesenchyme showed modest differences in mRNA expression and BARX1 was sufficient to induce much of the stomach profile in intestinal cells. However, limited binding at cis-regulatory sites implies that BARX1 may act principally through other transcription factors. Genes expressed ectopically in BARX1+ intestinal mesenchyme and reduced in Barx1-/- stomach mesenchyme include Isl1, Pitx1, Six2 and Pitx2, transcription factors known to control left-right patterning and influence smooth muscle development. The sum of evidence suggests that potent BARX1 functions in intestinal rotation and stomach myogenesis occur through this small group of intermediary transcription factors.
To investigate how Barx1 regulates gut smooth muscle development in a cell-autonomous manner, we used Affymetrix arrays to profile genes enriched in wild-type stomach and BARX1-overexpressing intestinal mesenchyme, compared to wild-type intestinal mesenchyme.

overall_design: Wildtype stomachs and intestines and Bapx1+/Cre;Rosa26+/Barx1 (Barx1Int) intestines were isolated at embryonic day 13.5. To deplete endoderm and enrich for mesenchyme, tissues were digested using collagenase and trypsin, then cultured for 3 days. RNA was purified using Trizol and processed for hybridization to Affymetrix microarrays.

middle: D

first: Ramesh

last: Shivdasani


title: Expression array of glucosamine-fed Drosophila heart/nephrocyte complexes

status: Public on Jun 12 2015

first: Ross

last: Cagan

address: One Gustave Levy Place, Box 1020

department: Developmental & Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

summary:
Examined the expression effects of supplementing Drosophila food on heart and nephrocyte complexes
30 female flies fed standard diet supplemented with 0.1 M glucosamine were dissected in cold ADH, and heart/nephrocyte complexes were harvested and analyzed.

overall_design: Animals were pre-fed glucosamine or sucrose, and heart/nephrocyte complexes were assessed for differences in gene expression.

first: Jianbo


title: Expression profiling of the E10.5 cardiac conduction system using MinKGFP BAC transgenic mice

status: Public on Aug 19 2015

city: Chicago

first: David

last: Arnolds

state: IL

address: 920 E 57th St

department: Pediatrics

institute: University of Chicago

summary: Proper development of the specialized cardiac conduction system is crucial for function of the mature heart.  Tools for isolation and in-vivo study of the conduction system are limited.  The goal of this study was to identify pathways important for conduction system development.  We generated a BAC transgenic mouse line, minKGFP, that marks the conduction system during embryogenesis and in adulthood.  GFP is expressed in this line at high levels in conduction system myocardium (minkGFP high) and low levels in chamber myocardium (minKGFP low).  We used this mouse line to isolate E10.5 conduction system cells, and performed transcriptional profiling on these cells to identify pathways with potential roles in specification of the developing cardiac conduction system.

overall_design: 8 samples, 4 biological replicates of E10.5 minKGFP high cardiac conduction system cells, 4 biological replicates of E10.5 minKGFP low chamber myocardium cells

middle: E

first: Carolina

last: Vasquez

first: Sylvia

last: Badon

first: Thomas

last: Stricker

first: Gregory

last: Morley

first: Ivan

last: Moskowitz


title: Microarray analysis of a Drosophila dopamine transporter mutant, fumin (fmn)

status: Public on Jun 01 2015

city: Nagoya

first: Jun

last: Tomita

address: 3-1 Tanabe, Mizuho

country: Japan

institute: Nagoya City University

summary:
We previously found a short sleeper mutant, fmn, and identified its mutation in the dopamine transporter gene. In an attempt to discover additional sleep related genes in Drosophila, we carried out a microarray analysis comparing mRNA expression in heads of fmn and control flies and found differentially expressed genes.
Next, using the pan-neuronal Gal4 driver elav-Gal4 and UAS-RNA interference (RNAi) to knockdown individual genes, we performed a functional screen.  We found that knockdown of the NMDA type glutamate receptor channel gene (Nmdar1) reduced sleep.

overall_design: Control (w1118) and fmn flies collected every 4 h at seven time points under 12 h of light (zeitgeber time, ZT 0-12) followed by 12 h darkness (ZT 12-24) (LD) were analyzed.

first: Kazuhiko

last: Kume


title: Transcriptional response of Drosophila S2 cells in response the Drosophila C Virus infection (DCV)

city: Nijmegen

first: Ronald

last: van Rij

address: Geert Grooteplein 28

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences - Radboud University Medical Center

summary: We infected Drosophila S2 cells (invitrogen) with Drosophila C virus (DCV) (Multiplicity of Infection = 10), and harvested samples for further analysis at 8 and 24 hours post-infection.

overall_design: We generated 6 datasets. Each samples was done in duplicate. We thus performed 2 mock infection (S2 medium only), 2 infections harvested 8 hours post-infection, and  2 infections harvested 24 hours post-infection

first: Sarah

last: Merkling


title: Expression data from adult Drosophila females [normoxia and IH]

status: Public on May 30 2015

city: LA JOLLA

first: Erilynn

last: Heinrichsen

state: CA

address: 9500 Gilman Dr, MC0735

institute: UC-San Diego

summary:
High-fat diet (HFD) in normoxia causes a worsened phenotype in adult female flies compared to regular diet (RD). Intermittent hypoxia (IH) causes an opposite phenotype both when flies are on RD in IH compared to normoxia and even more dramatically when on HFD in IH compared to HFD in normoxia.
We used microarrays to examine the transcriptional changes occurring both on a HFD compared to RD in normoxia, and when IH is introduced.

overall_design: Adult female Drosophila were collected at d3-5 and placed on RD or HFD and in normoxia or IH for 1 week. Following this week, flies were immediately frozen on dry ice, RNA was extracted and hybridized on Affymetrix microarrays.

middle: T

first: Gabriel

middle: G

last: Haddad


title: Dazl is required for TET-mediated reprogramming to a naïve pluripotent state

status: Public on Jul 01 2015

city: Utrecht

first: Niels

last: Geijsen

address: Uppsalalaan 8

institute: Hubrecht Institute

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

overall_design: Refer to individual Series


title: Development of gene expression signatures for contact-inhibited and adipogenic-differentiated 3T3-L1 and NIH3T3 fibroblasts

status: Public on May 28 2015

first: Atsushi

last: Enomoto

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Pathology

institute: Nagoya University Graduate School of Medicine

summary: Given previous works showing that, in the process of adipogenic differentiation of 3T3-L1 fibroblasts, the cells need to be cultured to confluency followed by additional incubation before initiating differentiation, we hypothesized that contact inhibition of proliferation (CIP) is requisite for making the cells prone to the differentiation. We screened upregulated genes in contact-inhibited 3T3-L1 fibroblasts, as well as NIH3T3 fibroblasts that are also sensitive to contact inhibition, by a whole genome microarray analysis. We also screened the genes that undergo rapid downregulation after the initiation of adipogenic differentiation.

overall_design: To investigate the mechanism of contact inhibition of proliferation and adipogenic differentiation of 3T3-L1 and NIH3T3 fibroblasts, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish proliferating and contact-inhibited cells and cells that undergo adipogenic differentiation. Total RNAs from 80% confluent (3T3-L1_80%, NIH3T3_80%) and overconfluent (3T3-L1_overconfluent, NIH3T3_overconfluent) cells and cells stimulated with the adipogenic differentiation medium (ZenBio) for 2 hours (3T3-L1_adipo diff med 2 hours, NIH3T3_adipo diff med 2 hours) were harvested and subjected to the microarray analysis.

first: Nobuhisa

last: Nakamura


title: Macrophages recognize the Helicobacter pylori type IV secretion system in the absence of TLR signaling

status: Public on Sep 01 2015

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: Helicobacter pylori conquered the world by colonizing the human stomach. There are two major groups of strains, one with and one without a cag pathogenicity island (cagPAI), which result in different clinical outcomes with increased severity in cagPAI+ H. pylori infections such as higher inflammation and higher rates of gastric carcinogenesis. Since the gastro-intestinal tract is bombarded with nonspecific ligands that would induce innate signaling, tissue-resident immune cells are believed to lack toll-like receptor (TLR) signaling (anergy).To illuminate how anergic innate immune cells respond to H. pylori, we first investigated the transcriptome of H. pylori infected wild type and MyD88/Trif -/- macrophages, which lack TLR signaling. We observed that the majority of regulated genes in wt macrophages were dependent on TLR signaling. In addition, we found that some of the upregulated genes changed their kinetic behavior depending on TLR signaling. Only anergic macrophages were able to differentiate between cagPAI+ and cagPAI- H. pylori via their transcriptional kinetics of specific early response genes. These genes showed a strong bias towards adenylate-uridylate-rich elements (AREs) containing genes, including the prominent pro-inflammatory cytokines IL-1beta and TNF-alpha. Differentiation was dependent on the presence of the cag type 4 secretion system (cagT4SS), but not the CagA effector protein. Thus, we speculate that the direct recognition of the secretion system by tissue-resident macrophages enables the host to differentiate between pathogenic (cagPAI+) and commensal (cagPAI-) H. pylori variants.

overall_design:
Microarray experiments were performed as dual-color hybridizations on Agilent mouse whole genome catalog 44K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

Cells were analyzed at 1h and 3h post infection

first: Manuel

last: Koch

last: Meyer


title: Expression data from 5CC7 T cells stimulated in vivo

status: Public on May 15 2015

city: Bethesda

first: Rachel

last: Gottschalk

state: MD

address: 4 Memorial Dr

institute: NIAID

summary: We used microarrays to determine how the quality and quantity of peptide-MHC impact TCR-induced gene expression in vivo.

overall_design: Adoptively transferred 5CC7 T cells were stimulated in vivo with different doses if two peptides: MCC peptide is a strong agonist and 102S peptide is a weak agonist for the 5CC7 TCR. After 48hours later, T cells were purified and gene expression was assessed using microarray.


title: Microarray data obtained from control, cbtRNAi and cbtOE flies

status: Public on May 08 2015

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

institute: Brandeis University

summary:
Microarray data obtained from control, cbtRNAi (cabut RNAi), and cbtOE (cabut overexpression) flies. From each strain, fly heads at two different time points during the day–night cycle (ZT3 and ZT153) were collected.
Fly heads  were collected and RNA was extracted. RNA  was then used to prepare a probe that was hybridized to Drosophila 2.0 gene expression arrays (Affymetrix).

overall_design: Two  samples of cbtRNAi, two samples of cbtOE and two samples of the control flies (cyo).

first: Ville

last: Hietakangas


title: IFNβ expression is restricted to a subpopulation of splenic pDCs exhibiting a specific immune modulatory transcriptome signature

status: Public on May 27 2015

city: Duesseldorf

first: Stefanie

last: Scheu

state: Nordrhein-Westfalen

address: Universitaetsstr. 1

department: Institute of Medical Microbiology and Hospital Hygiene

institute: University of Duesseldorf

summary: Type I IFNs are critical in initiating protective antiviral immune responses and plasmacytoid DCs (pDCs) represent a major source of these cytokines. Here we show that only few pDCs are capable to produce IFNβ after virus infection or CpG stimulation. Utilizing IFNβ/YFP reporter mice, we identify these IFNβ-producing cells in the spleen as a CCR9+CD9- pDC subset exclusively localized within the T/B cell zones. IFNβ-producing pDCs exhibit a distinct transcriptome profile with higher expression of genes encoding cytokines and chemokines, facilitating T cell recruitment and activation. These distinctive characteristics of IFNβ-producing pDCs are independent of the type I IFN receptor mediated feedback loop. Furthermore, IFNβ-producing pDCs exhibit enhanced CCR7-dependent migratory properties in vitro and in a peritoneal inflammation model they effectively recruit T cells in vivo. We define “professional type I IFN-producing cells” as a distinct subset of pDCs specialized in coordinating cellular immune responses.

overall_design: IFNβ associated gene expression in ex vivo sorted IFNβ/YFPpos vs. IFNβ/YFPneg splenic pDCs was measured at 6 hr after i.v. injection of CpG 1668 complexed to DOTAP. Two independent experiments were performed using pooled samples of at least 12 mice per experiment.

first: Jens

last: Bauer

first: Regine

last: Dress

first: Philipp

last: Dresing

first: Anja

last: Schulze

first: Judith

last: Alferink


title: Transcriptome of globus pallidus from a mouse having a high score of cocaine-dependent conditioned place preference

status: Public on May 10 2015

city: PARIS

first: Gilles

last: Maussion

address: 16 rue Henri Huchard

country: France

institute: INSERM U675

summary: Molecular basis of transition to addiction in vulnerable individuals is largely unknown. We hypothesized that human susceptibility genes can be identified on the basis of conserved molecular mechanisms in rodent brains. We used a short-term cocaine-dependent conditioned place preference (CPP) to identify genetic hallmarks of early steps of reward memory in basal ganglia including accumbens nucleus (NAc), globus pallidus (GP) and subthalamic nucleus (STN). Using genome-wide microarray analysis and CPP as a quantitative trait, we found that synaptic plasticity-related genes are deregulated in these three structures. A significant enrichment in bona fide transcripts involved in dendritic spine local translation was evidenced. mGluR5 is transcriptionally deregulated in Acc and GP of cocaine-treated animals. Grin3a that encodes a NMDA receptor subunit involved in Ca++ permeability is deregulated in NAc. Furthermore, Orexin/Hcrt transcript level is decreased in STN, a region known to be involved in discriminating addictive drugs and natural rewards. We also found that mGluR5 and Grin3a expression deregulation is sufficient to induce changes in synaptic plasticity-related genes. Altogether, these results suggest that a combined deregulation of mGluR5 and Grin3A pathway in NAc, mGluR5 in GP and orexin system in STN may generate an incentive memory contrasted between addictive drugs and natural rewards. Such pathways may include clusters of genes that are potential susceptibility genes for transition to addiction.

overall_design: Agilent Whole Mouse Genome oligomicroarrays (GEO accession no. GPL4134, Agilent Technologies, Palo Alto, CA) were used. They contain 60-mer DNA probes synthesized in situ in a 44k format. Four independent (globus pallidus from mouse treated with cocaine and having a high score of conditioned place preference compared to globus pallidus from mouse treated with saline solution) measurements were carried out for each group of biological conditions using exchanged dye-labeled RNA targets (i.e., Cy3 and Cy5 dyeswapping experiments).

first: Sabah

last: Kelai

first: Aude-Marie

last: Lepagnol-Bestel

first: Evangelos

last: Chortis

first: Sandrine

last: Imbeaud

first: Florence

last: Noble

first: Jean-Marie

last: Moalic

first: Philip

last: Gorwood

first: Michel

last: Simonneau


title: Transcriptome of globus pallidus from a mouse having a low score of cocaine-dependent conditioned place preference

overall_design: Agilent Whole Mouse Genome oligomicroarrays (GEO accession no. GPL4134, Agilent Technologies, Palo Alto, CA) were used. They contain 60-mer DNA probes synthesized in situ in a 44k format. Four independent (globus pallidus from mouse treated with cocaine and having a low score of conditioned place preference compared to globus pallidus from mouse treated with saline solution) hybridizations were carried out for each group of biological conditions using exchanged dye-labeled RNA targets (i.e., Cy3 and Cy5 dyeswapping experiments).


title: Target genes of BRG1 in mouse embryonic stem cells

status: Public on Apr 28 2015

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: BRG1-SWI/SNF complex is an important chromatin remodeling complex that involved in various biological processes. Here we described the genome-wide binding of histone acetylation upon BRG1 depletion in mouse embryonic stem cells.

overall_design: Mouse embryonic stem cells were treated with either scrambled siRNA or siRNA against BRG1 for 48 h, and each treatment has three replicates.

first: Yuan

last: Wang


title: Drosophila ROW RNAi gene expression profiling

status: Public on May 01 2015

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

summary:
Heterochromatin-protein 1 (HP1) is a functionally diverse family of proteins. In particular, Drosophila dHP1c forms a complex with the transcription factors WOC and ROW (dHP1EU) that localizes at euchromatin and regulates gene expression.
We used microarrays to analyse the changes in gene expression after row depletion by RNAi.

overall_design: For expression profiling analyses, total RNAs were prepared from control S2 cells and upon RNAi-mediated depletion of ROW, converted to cDNA and hybridized to Drosophila Genome 2.0 GeneChip (Affymetrix).

first: Joan

last: Font-Burgada

first: Fernando

last: Azorín


title: Target genes of BRG1 in human or mouse embryonic stem cells

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Gene expression in the liver and colon of mice fed diets HH, LL, HL and LH

status: Public on Apr 23 2015

city: Palmerston North

first: Wayne

last: Young

address: Tennent Drive

country: New Zealand

institute: AgResearch

summary: Transcriptional profiling of mice fed a diet deficient in selenium and folate during weaning and in utero (LL), a diet deficient in selenium and folate during weaning but not in utero (HL), a diet sufficient in selenium and folate during weaning but deficient in utero (LH), and a diet sufficient in selenium and folate during weaning and in utero (HH)

overall_design:
2 colour microarray, reference design. Biological replicates: 6 per treatment group.
The reference RNA was extracted from a whole pregnant C57 mouse and foetus.  The whole body was homogenised and RNA was extracted using an AllPrep(r) DNA/RNA/Protein mini kit (Qiagen, Cat number 80004).

first: Matthew

last: Barnett


title: Transcriptomes of subthalamic nuclei, globus pallidus, and accumbens nuclei from mice with low and high scores of cocaine-dependent conditioned place preference


title: Microarray analysis to evaluate the function of USP18 in the mouse CNS

status: Public on Apr 20 2015

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary: Microglia are tissue macrophages of the central nervous system (CNS) that control tissue homeostasis, and as such they are crucially important for organ integrity. Microglia dysregulation is thought to be causal for a group of neuropsychiatric, neurodegenerative and neuroinflammatory diseases, called ‘microgliopathies’. However, how the intracellular stimulation machinery in microglia is controlled is poorly understood. By using expression studies, we identified the ubiquitin-specific protease (Usp) 18 in white matter microglia that essentially contributes to microglial quiescence under homeostatic conditions. We further found that microglial Usp18 negatively regulated the activation of STAT1 and concomitant induction of interferon-induced genes thereby disabling the termination of IFN signalling. Unexpectedly, the Usp18-mediated feedback loop was independent from the catalytic domain of the protease but instead required the interacting region of Ifnar2. Additionally, the absence of Ifnar1 completely rescued microglial activation indicating a tonic IFN signal mediated by receptor interactions under non-diseased conditions. Finally, conditional depletion of Usp18 only in myeloid cells significantly enhanced the disease burden in a mouse model of CNS autoimmunity, increased axonal and myelin damage and determined the spatial distributions of CNS lesions that shared the same STAT1 signature as myeloid cells found in active multiple sclerosis (MS) lesions. These results identify Usp18 as novel negative regulator of microglia activation, demonstrate a protective role of the IFNAR pathway for microglia and establish Usp18 as potential therapeutic target for the treatment of MS.

overall_design: Brain lysate of adult WT, USP18ko, IFNAR1ko and USP18ko:IFNARko mice were analyzed

first: Tobias

last: Goldmann

first: Nicolas

last: Zeller

first: Jenni

last: Raasch

first: Katrin

last: Kierdorf

first: Kathrin

last: Frenzel

first: Lars

last: Ketscher

first: Anja

last: Basters

first: Stefanie

last: Brendecke

first: Alena

last: Spiess

first: Tuan

last: Tay

first: Clemens

last: Kreutz

first: Jens

last: Timmer

first: Grazia

last: Mancini

first: Thomas

last: Blank

first: Guenter

last: Fritz

first: Knut

last: Biber

first: Roland

last: Lang

first: Danielle

last: Malo

first: Doron

last: Merkler

first: Mathias

last: Heikenwalder

first: Klaus

last: Knobeloch

first: Marco

last: Prinz


title: Microarray analysis to evaluate the role of USP18 in primary microglia and the microglia cell line BV-2

first: Ori

last: Staszewski

overall_design: Primary microglia (WT, USP18ko and USP18_C61A mice) and BV-2 cells (treated with control siRNA or siRNA against USP18) were incubated with 500 U/ml IFN-b. At different timepoints (0h, 6h, and 24h) RNA samples were taken and analyzed via Microarray

first: Tobias

last: Goldmann

first: Nicolas

last: Zeller

first: Jenni

last: Raasch

first: Katrin

last: Kierdorf

first: Kathrin

last: Frenzel

first: Lars

last: Ketscher


title: Gene expression in IL-17RA-deficient and wild-type mice following Giardia muris infection

city: Galveston

first: Sara

last: Dann

state: TX

address: 301 University Blvd

department: Internal Medicine

institute: University of Texas Medical Branch

summary: To elucidate IL-17A-dependent immune mechanims involved in regulating host defense, we employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential of regulating protective immunity that failed to be upregulated in the absence of IL-17RA signaling. Whole small intestine tissue collected from IL-17RA-deficient and C57BL/6 (wild-type) mice was collected 2 weeks after Giardia muris infection and from uninfected controls. Expression levels of several genes that may have  anti-parasitic potential (Defb1, Retnlb, Saa1, Saa2) and may be involved in parasite clearance were, on average, lower or unchanged in IL-17RA deficient compared to wild-type mice after infection.

overall_design: Two weeks after Giardia muris challenge, total RNA was extracted and analyzed from tissue of the small intestines of infected IL-17RA-deficient and wild-type mice, and compared to uninfected controls. Each sample contained equal amounts of total RNA from 6 female mice which were pooled and used in the experiment.

last: Eckmann


title: Expression data from larvae body wall expressing LaminC transgenes

status: Public on Apr 16 2015

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

summary:
Expression of mutant lamins in human muscle causes muscular dystrophy.  We have generated a drosophila model that expresses mutant lamins, modeled after those that cause disease in humans.
We used affymetrix microarrays to determine the global changes in gene expression caused by mutant lamins.

overall_design:
Dissected 3rd instar larval body wall from transgenic Drosophila expressing either a full length wildtype Lamin C, an N-terminal Lamin C truncation of the first 42 amino acids or a single amino acid substitution in Lamin C at position 489 from a G residue to a V residue under control of the Gal4-UAS.
RNA was extracted from 3rd instar larval body wall expressing these mutant Lamin C transgenes and microarray analysis using Affymetrix microarrays.

first: George

last: Dialynas

first: Dylan

last: Thiemann

first: Om

middle: K

last: Shrestha

first: Lori

last: Wallrath


title: Identification and Functional Analysis of Healing Regulators in Drosophila

status: Public on Apr 13 2015

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

summary: Wound healing is an essential homeostatic mechanism that maintains the epithelial barrier integrity after tissue damage. Although we know the main events participating in the healing of a wound, many of the underlying molecular mechanisms remain unclear. Genetically amenable systems, such as wound healing in Drosophila imaginal discs, do not model all aspects of the repair process, but allow exploring many unanswered features of the healing response; e.g., which are the signal(s) responsible for initiating tissue remodeling? How is the sealing of the epithelia achieved? Or which are the inhibitory cues that cancel the healing machinery upon completion? Answering these and other questions demands in first place the identification and functional analysis of wound-specific genes. A variety of different microarray analyses of murine and humans have identified characteristic profiles of gene expression at the wound site, however, very few functional studies in healing regulation have been carried out. We developed an experimentally controlled method to culture imaginal discs that allows live imaging and biochemical analysis and is healing-permissive. Employing this approach, we performed a comparative genome-wide profiling between those Drosophila imaginal cells actively involved in healing versus their non-engaged siblings. This lets us identify a set of potential wound-specific genes. Importantly, besides identifying and categorizing new genes, we functionally tested many of their gene products by genetic interference and overexpression in a healing assay. This non-saturated analysis defines a relevant set of new genes whose changes in expression levels are functionally significant for proper tissue repair. There is promise that our newly identified wound-healing genes will guide future work in the more complex mammalian wound response.

overall_design: We developed a healing-permissive in vitro culture system for fly imaginal discs: we used one-channel microarrays for comparing healing-engaged cells (showing activation of the JNK signaling cascade) to cells not participating in healing (silent JNK activity) in wounded wing imaginal discs in culture. Employing this method, we aimed detecting the relevant genes involved in disc healing through microarray analysis. We compared cells actively involved in healing to those not involved and identified a whole set of upregulated or downregulated genes. They were annotated, clustered by expression profiles, chromosomal locations and presumptive functions. Most importantly, we functionally tested them genetically in a healing assay.

last: Martin-Blanco


title: THE UBIQUITIN-SPECIFIC PROTEASE 18 CONTROLS MICROGLIA QUIESCENCE UNDER HOMEOSTATIC AND INFLAMMATORY CONDITIONS


title: Murine hamatopoietic stem cell (HSC): wild type and Skp2 knockout

status: Public on Apr 02 2015

city: Houston

first: JING

last: WANG

address: 1515 Holcombe BLVD

department: Molecular and Cellular Oncology

institute: The University of Texas, MD Anderson Cancer Center

summary: Transcriptional profiling of mouse HSC comparing wild type (WT) and Skp2 knockout

overall_design: Collected bone marrow (BM) cells from WT and Skp2 knockout mice, stained with HSC surface markers for FACS. Collected HSC and extracted total RNA then sent out for microarray analysis.

first: Jing

last: Wang

first: Hui-kuan

last: Lin


title: Bioinformatics Analysis of the Permanent Middle Cerebral Artery Occlusion (PMCAO) Mouse Model Brain Regions Gene Profiles for Unraveling Progression of the Ischemic Core

status: Public on Mar 31 2015

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: Permanent middle cerebral artery occlusion (PMCAO) mouse model has been established and used by our group with a focus on systematically investigating effects of the neuropeptide pituitary adenylate-cyclase activating polypeptide (PACAP38) on the ischemic brain. Using an intracerebroventrically PACAP38 (1 pmol) injection over a control saline (0.9% sodium chloride, NaCl) treatment, we have been successful in generating a vast inventory of gene expression data in both whole hemispheres and specific brain regions of infract/ischemic core (IC) and penumbra (P) with high-throughput Agilent whole genome 4 × 44 K oligo DNA microarray chips. In this study, we first perform a specific analysis of the gene expression in the IC and P compared to the healthy control regions to know the gene profile status of the progression of the IC. We will use this data together with generated biological function and network analysis from our previous studies, and present new insight into the potential mechanism behind PACAP38 neuroprotective function in the ischemic brain.

overall_design: Three mice each in PMCAO groups for ischemic core and penumbra regions in ischemic brain over corresponding controls were used, respectively, that exhibited neurological grades G1 and G2 for the subsequent downstream analysis. Ischemic core and penumbra regions and corresponding healthy core and penumbra were carefully removed with a sterile scalpel, and placed in 2 ml Eppendorf tubes. Samples were then quickly immersed in liquid nitrogen and stored in -80 ºC prior to further analysis. Whole genome DNA microarray analysis was performed on a 4x44K, Agilent DNA Microarray chip.

first: Motohide

last: Hori

first: Tomoya

last: Nakamachi

first: Junko

last: Shibato

first: Randeep

last: Rakwal

first: Seiji

last: Shioda

first: Satoshi

last: Numazawa


title: Integrative analysis of the acquisition of pluripotency in PGCs

status: Public on Apr 08 2015

city: Tokyo

first: Shigeru

last: Saito

address: 6, Yonban-cho Chiyoda-ku

department: Data Science Lab

institute: OPT HOLDING, INC

summary: To elucidate the molecular mechanisms by which PGCs become pluripotent cells, we performed whole transcriptome analysis during the conversion of PGCs into EGCs.

overall_design: There are 3 groups of gene expression profiles, time course analysis of PGCs to EGCs, forced expression of germ cell genes in ESCs, and chemical treatment of PGCs at day2 of the culture

first: Go

last: Nagamatsu


title: Genetic characterization of p27Kip1  and stathmin role in controlling cell proliferation in vivo

status: Public on Apr 01 2015

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

institute: CRO AVIANO

summary: The CDK inhibitor p27Kip1 is a critical regulator of cell cycle progression, but the mechanisms by which p27Kip1 controls cell proliferation in vivo are still not fully elucidated. We recently demonstrated that the microtubule destabilizing protein stathmin is a relevant p27Kip1binding partner involved in the regulation of cell motility.  To get more insights into the in vivo significance of this interaction, we generated p27Kip1 and stathmin double knock out (DKO) mice. Interestingly, thorough characterization of DKO mice demonstrated that most of the phenotypes of p27Kip1 null mice linked to the hyperproliferative behavior, such as the increased body and organ weights, the outgrowth of the retina basal layer and the development of pituitary adenomas, were reverted by co-ablation of stathmin. In vivo analyses showed a reduced proliferation rate in DKO compared to p27kip1 null mice, linked, at molecular level, to decreased kinase activity of CDK4/6, rather than of CDK1 and CDK2. Gene expression profile analyses of mouse thymuses confirmed the phenotypes observed in vivo, demonstrating that DKO clustered with WT and not with p27KO thymuses. Taken together, the results demonstrate that stathmin cooperates with p27Kip1 to control the early phase of G1 to S phase transition and strongly suggest that this function has particular relevance in the contest of tumor progression.

overall_design: Four-conditions experiment (four different mouse genotypes), 6 biological replicates of wild type mouse thymus, 6 biological replicates of p27 knock-out mouse thymus, 6 biological replicates of stathmin knock-out mouse thymus, 6 biological replicates of double knock-out (p27 and stathmin) mouse thymus. Reference design: pool of RNAs derived from mouse fibroblasts of all the genotypes.Reference design;

first: Daniela

last: Marconi

first: Barbara

last: Belletti

first: Stefania

last: Berton

first: Gustavo

last: Baldassarre


title: JAK/STAT coordinates cell proliferation during disc regeneration with Dilp8-mediated developmental delay in Drosophila melanogaster

status: Public on Apr 10 2015

city: Basel

first: Tomonori

last: Katsuyama

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zurich

summary: Regeneration of fragmented Drosophila imaginal discs occurs in an epimorphic manner, involving local cell proliferation at the wound site. Following disc fragmentation, cells at the wound site activate a restoration program through wound healing, regenerative cell proliferation and repatterning of the tissue. However, the interplay of signaling cascades, driving these early reprogramming steps, is not well understood. Here we profiled the transcriptome of regenerating cells in the early phase within twenty-four hours after wounding. We found that JAK/STAT signaling becomes activated at the wound site and promotes regenerative cell proliferation in cooperation with Wingless (Wg) signaling. In addition, we demonstrated that the expression of Drosophila insulin-like peptide 8 (dilp8), which encodes a paracrine peptide to delay the onset of pupariation, is controlled by JAK/STAT signaling in early regenerating discs. Our findings suggest that JAK/STAT signaling plays a pivotal role in coordinating regenerative disc growth with organismal developmental timing.

overall_design: In order to analyze transcriptome change in early regenerating imaginal disc, Drosophila prothorasic leg discs were fragmented (to anterior one-quarter or posterior three-quarters) and cultured ex vivo in adult fly abdomen. Regenerating cells in early regeneration phase (at 12 or 24 hours after wounding) were subjected to transcriptome profiling with Affymetrix microarrays. For control samples, the corresponding regions of uncut-cultured discs and uncut-uncultured discs were used.

first: Federico

last: Comoglio

first: Makiko

last: Seimiya

first: Erik

last: Cabuy

first: Renato

last: Paro


title: Gene expression in hypoxia-tolerant Drosophila melanogaster

city: La Jolla

first: Merril

last: Gersten

address: 9500 Gilman Drive #0412

institute: UCSD

summary: Hypoxia plays a key pathogenic role in the outcome of many pathologic conditions.  To elucidate how organisms successfully adapt to hypoxia, a population of Drosophila melanogaster was generated, through an iterative selection process, that is able to complete its lifecycle at 4% O2, a level lethal to the starting parental population.  Transcriptomic analysis of flies adapted for >200 generations was performed to identify pathways and processes that contribute to the adapted phenotype, comparing gene expression of three developmental stages with generation-matched control flies.  A third group was included, hypoxia-adapted flies reverted to 21% O2 for five generations, to address the relative contributions of genetics and hypoxic environment to the gene expression differences.  We identified the largest number of expression differences in 0.5-3 hr post-eclosion adult flies that were hypoxia-adapted and maintained in 4% O2, and found evidence that changes in Wnt signaling contribute to hypoxia tolerance in flies.

overall_design: A population of flies able to complete their life cycle at 4% O2 was selected from a starting population of 27 isogenic D. melanogaster lines exposed to increasingly  lower O2 levels over many generations.   Transcriptomic analysis of adapted flies maintained at 4% O2 or reverted to room air for five generations, and of generation matched naive controls, was performed to better understand changes in gene expression in adapted flies and to investigate the relative contributions of genetics versus environment to these differences.

first: Dan

last: Zhou

first: Gabriel

last: Haddad

first: Shankar

last: Subramaniam


title: Estradiol Induced Transcriptional Profile of EAAE DNA Binding Deficient ERa Uterus

status: Public on Mar 24 2015

first: NIEHS

last: Microarray Core

summary: To evaluate the ability of a DNA binding deficient ERa to mediate transcriptional responses in the mouse uterus, ovariectomized mice were injected with 100 ul of saline or 250 ng of estradiol (E2) in 100 ul saline, uterine tissue was collected 2 hours filllowing the injection, and RNA was isolated

overall_design: 3 mice each, WT saline, WT E2 2h, EAAE saline, EAAE 2h E2

first: Sylvia

middle: C

last: Hewitt

first: Kenneth

last: Korach


title: Ascites enriches for ovarian cancer stem-like cells that express membrane GRP78

status: Public on Mar 09 2015

city: Durham

first: Jen-Tsan

last: Chi

address: 101 Science Drive, DUMC 3382

institute: Duke University

summary: Ovarian cancer patients are generally diagnosed at stage III/IV, when ascites is common. The volume of ascites positively correlates with the extent of metastasis and negatively with prognosis. Membrane GRP78, a stress-inducible endoplasmic reticulum chaperone which also appears on the plasma membrane (memGRP78) of aggressive cancers, plays a crucial role in the maintenance of embryonic stem cells. Our present study demonstrates that tumor cells isolated from ascites generated by epithelial ovarian cancer (ID8 cells) bearing mice have increased memGRP78 expression compared to ID8 cells in normal culture. We hypothesize that these ascites associated memGRP78+ cells are cancer stem-like cells (CSC) and memGRP78 is functionally important in CSCs. Supporting this hypothesis, we show that memGRP78+ cells isolated from ascites have increased sphere forming and tumor initiating abilities compared to memGRP78- cells. When the tumor microenvironment is recapitulated by adding ascites fluid to cell culture, ID8 cells express more memGRP78 and increased self-renewing ability compared to those cultured in medium alone. Moreover, compared to their counterparts cultured in normal medium, ID8 cells cultured in ascites, or isolated from ascites, show an increased expression of stem cell markers Sca-1, Snail and SOX9. Importantly, antibodies directed against the carboxy (COOH)-terminal domain of GRP78 significantly reduce the self-renewing ability of murine and human ovarian cancer cells pre-incubated with ascites, associated with a decreased phosphorylation of Akt and GSK3α, and reduced level of the transcriptional factor Snail. Based on this data, we suggest that memGRP78 is a logical therapeutic target for late stage ovarian cancer.

overall_design: ID8 cells, murine epithelial ovarian cancer cells, were either cultured in DMEM with 10% FBS  (id8) or 10% ascites developed by ID8 cells bearing mice for 7 days (ASid8).

first: Lihong

last: Mo

first: Salvatore

middle: V

last: Pizzo


title: Genechip analysis of CD4+T cells

status: Public on Mar 17 2015

city: tukuba

first: Yuki

last: Tanaka

state: ibaraki

address: 1-1-1 tennodai

institute: University of tsukuba

summary: 【Objectives】The FPR2 is a G-protein coupled receptor that potently possesses pro- and anti-inflammatory role. Although FPR2 is known to be expressed by T cells, its function in arthritic condition is unclear. We investigated the involvement of FPR2 on T cells in GPI-induced arthritis (GIA) and rheumatoid arthritis (RA).  【Methods】Fluctuated expression of FPR2 mRNA on CD4+T cells was analyzed in GIA. We sorted FPR2+ or FPR2-CD4+T cells from arthritic lymph nodes, then the mRNA expression of various markers from CD4+T cell subsets was examined. Naïve T cells were cultured favoring Th1, Th2 and Th17 cell differentiation, then the expression of FPR2 was analyzed by FACS. In humans, the expression of FPR2 on CD4+T cells from healthy subjects (HS) or patients with RA was compared.  【Results】The expression of FPR2 in CD4+T cells was upregulated in the early phase of arthritis. FPR2+ T cells had higher expression of T-bet and IFNγ than FPR2-T cells. FPR2+ T cells were frequently detected on Th1 condition but not on Th2 and Th17. The expression of FPR2 on CD4+T cells was significantly higher in RA than in HS.  【Conclusion】We identified that FPR2+T cells showed Th1 phenotype in mice and this molecule was highly detected on CD4+T cells in patients with RA, suggesting FPR2+T cells might play a crucial role in RA.

overall_design: To identify the highly expressed molecules on autoreactive-CD4+T cells in GPI-induced arthritis, the mRNA expression profile of splenic CD4+ T cells isolated by Magnetic–activated cell sorting (MACS) was examined by microarray in DBA/1 mice (arthritis susceptible) and C57BL/6 mice (arthritis resistant) after immunization of GPI on day7

first: Isao

last: Matsumoto

first: Asuka

last: Inoue

first: Naoto

last: Umeda

first: Chinatsu

last: Takai

first: Yuko

last: Kurashima

first: Takayuki

last: Sumida


title: Expression data from PPP3R1 cell line starved as compared to PPP3R1 cell line grown in Normal Medium

status: Public on Feb 24 2015

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

summary:
In order to identify the effects of starvation on the PPP3R1 cell line trascriptome, we performed Affymetrix Gene-Chip hybridization experiments for the starved cells
Transcriptome analysis of the starved PPP3R1 cell line

overall_design: For the analysis on the starved PPP3R1 cell line, total RNA was extracted; RNA extracted from PPP3R1 cell line grown in Normal Medium was used as control


title: Shp2 Signaling Suppresses Senescence in PyMT-induced Mammary Gland Cancer in Mice [Mouse430A_2 array]

status: Public on Mar 06 2015

city: Berlin

first: Linxiang

last: Lan

address: Robert-Roessle-Str. 10

department: Cancer Research Program

institute: Max-Delbrueck-Center for Molecular Medicine

summary: In this study, we have used techniques from cell biology, biochemistry, and genetics to investigate the role of the tyrosine phosphatase Shp2 in tumor cells of MMTV-PyMT mouse mammary glands. Genetic ablation or pharmacological inhibition of Shp2 induces senescence, as determined by the activation of senescence-associated β-gal (SA-β-gal), cyclin-dependent kinase inhibitor 1B (p27), p53, and histone 3 trimethylated lysine 9 (H3K9me3). Senescence induction leads to inhibition of self-renewal of tumor cells and blockage of tumor formation and growth. A signaling cascade was identified that acts downstream of Shp2 to counter senescence: Src, Focal adhesion kinase and Map kinase inhibit senescence by activating the expression of S-phase kinase-associated protein 2 (Skp2), Aurora kinase A (Aurka), and the Notch ligand Delta-like 1 (Dll1), which block p27 and p53. Remarkably, the expression of Shp2 and of selected target genes predicts human breast cancer outcome. We conclude that therapies which rely on senescence induction by inhibiting Shp2 or controlling its target gene products may be useful in blocking breast cancer.

overall_design: For Shp2 ablation, primary mammary tumor cells from MMTV-PyMT;Shp2fl/fl mice were transduced with retroviruses expressing control GFP or CreERT2-GFP, and GFP-positive cells were purified by FACS and cultured as mammospheres for 1 week. Mammospheres were then treated with 50 nM 4-OHT for 2 hours, cultured for another 5 days, and subjected to RNA isolation. For pharmacological inhibition, primary mammary tumor cells from the same mice were cultured as mammospheres for 10 days and then treated with the Shp2 inhibitor GS493 for another 2 days. Mammospheres were then subjected to RNA isolation. Each group contains 3 replicates.

first: Jingjing

last: Qi

first: Balázs

last: Györffy

first: Walter

last: Birchmeier


title: The transcriptional response to PPP3R1

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

overall_design: Refer to individual Series


title: Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression

first: Kristen

last: Turner

address: 9500 Gilman Dr

department: Molecular Pathology

institute: Ludwig Institute for Cancer Research

summary: Akt is a robust oncogene that plays key roles in the development and progression of many cancers, including glioma. We evaluated the differential propensities of the Akt isoforms toward progression in the well-characterized RCAs/Ntv-a mouse model of PDGFB-driven low grade glioma. A constitutively active myristoylated form of Akt1 did not induce high-grade glioma (HGG). In stark contrast, Akt2 and Akt3 showed strong progression potential with 78% and 97% of tumors diagnosed as HGG, respectively. We further revealed that significant variations in polarity and hydropathy values among the Akt isoforms in both the pleckstrin homology domain (P domain) and regulatory domain (R domain) were critical in mediating glioma progression. Gene expression profiles from representative Akt-derived tumors indicated dominant and distinct roles for Akt3, consisting primarily of DNA repair pathways. TCGA data from human GBM closely reflected the DNA repair function, as Akt3 was significantly correlated with a 76 gene signature DNA repair panel. Consistently, compared to Akt1 and Akt2 overexpression models, Akt3-expressing human GBM cells had enhanced activation of DNA repair proteins, leading to increased DNA repair and subsequent resistance to radiation and temozolomide. Given the wide range of Akt3-amplified cancers, Akt3 may represent a key resistance factor.

overall_design: 5 different experimental conditions were compared (including GFP, PDGFB, PDGFB in conjunciton with Akt1, Akt2, or Akt3) with 3 mice per treatment

first: Limei

last: Hu


title: Expression data from MEFs wt cells starved as compared to MEFs wt cells grown in Normal Medium

summary:
In order to identify the effects of starvation on the MEFs wt trascriptome, we performed Affymetrix Gene-Chip hybridization experiments for the starved cells
Transcriptome analysis of the starved MEFs wt cells

overall_design: For the analysis on the starved MEFs wt cells, total RNA was extracted; RNA extracted from MEFs wt cells grown in Normal Medium was used as control


title: Gene expression profiling of intraductal papillary mucinous neoplasms (IPMNs) of the pancreas

status: Public on Jan 29 2015

city: Tampa

first: Jennifer

middle: Permuth

last: Wey

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

summary: To exlore whether candidate target genes of certain miRNAs are differentially expressed in high-risk versus low-risk IPMN tissue.

overall_design: Through a pilot project, we identified miRNAs that differentiated between pathologically confirmed high-risk (invasive and high-grade) and low-risk (low- and moderate-grade) IPMN tissue.  Using the current dataset, we explored the expression of gene targets that have been shown to be regulated by  the identified miRNAs by integrating microarray expresssion data from 23 IPMNs (17 high-risk; 6 low-risk).


title: Histone deacetylase inhibition replicates aspects of the adaptive response to exercise and improves muscle metabolism and cardiac function in obesity.

status: Public on Jan 28 2015

city: Waurn Ponds

first: Sean

last: McGee

state: Victoria

address: 75 Pigdons Rd

department: Metolic Research Unit, School of Medicine

country: Australia

institute: Deakin University

summary: Drugs used to treat obesity and type 2 diabetes have limited efficacy in directly normalising muscle metabolism. The discovery of molecules mediating exercise adaptations, and drugs that modulate their activity, is a potential strategy to address this therapeutic gap. Here we show that genetic impairment of HDAC4 and 5 in mice regulated a subset of exercise responsive genes involved in metabolism and increased cell autonomous energy expenditure. Screening of HDAC inhibitors identified Scriptaid as a compound that also replicated aspects of the exercise adaptive response in vitro and in vivo. Treatment of obese mice with Scriptaid increased exercise performance, restored muscle insulin sensitivity and reduced muscle lipids. Scriptaid also increased oxygen consumption and normalised cardiac structure and function in obese mice. These data show that HDAC inhibition replicates aspects of the exercise adaptive response and that pharmacological HDAC inhibition could deliver more efficacious treatment to combat the metabolic diseases.

overall_design: Four-condition experiment, Empty, HDACs, Vehicle and Script-HDACs with five biological replicates for each condition. One replicate per array.

first: Vidhi

last: Gaur

first: Timothy

last: Connor

first: Kylie

last: Venardos

first: Andrew

last: Sanigorski

first: Courtney

last: Swinton

first: Shona

last: Morrison

first: Sheree

last: Martin

first: Lyndal

last: Kerr-Bayles

first: Kathryn

last: Aston-Mourney

first: Cassandra

last: Fleming

first: Darren

last: Henstridge

first: Min

last: Wu

first: Lisa

last: Pike

first: Denise

last: Chen

first: Stefan

last: Gehrig

first: Roelof

last: van Ewijk

first: Gordon

last: Lynch

first: Keith

last: Baar

first: Mark

last: Febbraio

first: Gregory

last: Steinberg

first: Paul

last: Gregorevic

first: Frederick

last: Pfeffer

first: Ken

middle: R

last: Walder

last: Hargreaves


title: Intraductal papillary mucinous neoplasms (IPMNs) of the pancreas

first: Jennifer

last: Wey

type:
Expression profiling by array
Other


title: Gene expression changes during retinal development and rod specification.

status: Public on Jan 20 2015

city: Dublin

first: Fiona

middle: Catherine

last: Mansergh

address: Lincoln Place Gate

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: Photoreceptor disorders are collectively known as retinal degeneration (RD), and include retinitis pigmentosa (RP), cone-rod dystrophy and age related macular degeneration (AMD). These disorders are largely genetic in origin; individual mutations in any one of >200 genes cause RD, making mutation specific therapies prohibitively expensive. A better treatment plan, particularly for late stage disease, may involve stem cell transplants into the photoreceptor or ganglion cell layers of the retina. Stem cells from young mouse retinas can be transplanted, and can form photoreceptors in adult retinas. These cells can be grown in tissue culture, but can no longer form photoreceptors. We have used microarrays to investigate differences in gene expression between cultured retinal progenitor cells (RPCs) that have lost photoreceptor potential, postnatal day 1 (pn1) retinas and the postnatal day 5 (pn5) retinas that contain transplantable photoreceptors. We have also compared FACS sorted Rho-eGFP expressing rod photoreceptors from pn5 retinas with Rho-eGFP negative cells from the same retinas. We have identified over 300 genes upregulated in rod photoreceptor development in multiple comparisons, 37 of which have been previously identified as causative of retinal disease when mutated. It is anticipated that this research should bring us closer to growing photoreceptors in culture and therefore better treatments for RD. This dataset is also a resource for those seeking to identify novel retinopathy genes in RD patients.

overall_design: We extracted whole retinas from postnatal day 1 (Pn1) and postnatal day 5 (Pn5) mice, and compared them with cultured RPCs derived from pn5 retinas, using Affymetrix mouse 430A_2 arrays. We also extracted cells from Rho-eGFP Pn5 retinas and FACS sorted them. GFP+ve cells represent immature rod photoreceptors, as they express the Rho-eGFP fusion protein, which is only expressed in rods. GFP-ve cells represent all other retinal neurons. These samples were amplified and compared using Affymetrix mouse 430A_2arrays, by Source Biosciences GMBH, Berlin, Germany. Results from immature rods were then compared with those from other retinal neurons, while results from whole Pn5 retinas were compared with Pn1 retinas (which don't yet express rod specific genes), and RPCs, which are glial precursors. RPCs were also compared with Pn1 retinas. Genes which showed changed expression profiles in at least 3/4 of comparisons were prioritised for further investigation.

first: Matthew

last: Carrigan

first: Karsten

last: Hokamp

first: G

last: Farrar


title: Expression profile of osteosarcoma cells in which Sox2 maintains cancer stem cells

status: Public on Feb 15 2015

city: New York

first: Alka

last: Mansukhani

address: 550 First Avenue

department: Microbiology

institute: New York University Medical Center

summary:
Sox2 is required to maintain osteosarcoma cell tumor initiation.Knockdown of Sox2 leads tpo loss of tumorigenic properties. To examine gene expression changes upon Sox2 knockdown,  we performed microarray analysis on mouse osteosarcoma cells expressing scrambled or Sox2shRNA.  We found that genes  upregulated upon Sox2 knockdown included osteoblast diffrentiation genes and genes down regulated included cell cycle and RNA processing genes as well as YAP-TEAD target genes.
The Hippo pathway has a profound tumor suppressive role in cancer by restraining the strong growth-promoting function of YAP. We have previously shown that the stem cell transcription factor Sox2 maintains the tumorigenicity of osteosarcoma cancer stem cells (CSCs). In this report, we describe that Sox2 maintains stemness by antagonizing the Hippo pathway via direct repression of Hippo activators, Nf2 (Merlin) and WWC1 (Kibra), thereby leading to exaggerated YAP function. YAP is potently oncogenic in osteosarcoma and its depletion sharply reduces the tumorigenic CSC fraction.  Low Nf2, low WWC1, and high YAP expression mark the CSC fraction of the tumor population, while the more differentiated fraction has high Nf2, high WWC1 and reduced YAP expression.  This Sox2-Hippo axis is conserved and also operates in other Sox2-dependent cancers such as glioblastomas. We propose that disruption of YAP transcriptional activity reduces CSCs and could be a therapeutic strategy for Sox2- dependent tumors.

overall_design: Gene expression of 482 mouse lines mOS482 were analyzed by microarray. 3 replicates each of scrambled and Sox2shRNA were processed and hybridized

first: Upal

last: BasuRoy


title: Ascl2 acts as an R-spondin/Wnt responsive switch to control stemness in intestinal crypts [array]

status: Public on Dec 31 2014

city: Utrecht

first: Jurian

last: Schuijers

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Insitute

summary: Wnt signals control three functions of intestinal crypts: maintenance of Lgr5 stem cells, proliferation of transit-amplifying daughters and formation of Paneth cells. Here, we study how the Wnt effector β-catenin/Tcf4 cooperates with the Wnt-activated transcription factor Ascl2 to control a stem cell transcription program. DNA elements that are co-occupied and synergistically regulated by Ascl2 and Tcf4 specifically map to stem cell genes. In vitro, Tcf4-/- mini-guts are rescued by Ascl2 expression, while Ascl2-/- organoids are rescued by Wnt signaling. A direct auto-activatory loop leads to an on/off expression pattern of Ascl2 with a threshold that depends on the previous state. Wnt/R-spondin1 activates this loop. This mechanism interprets Wnt levels in crypts and translates this continuous signal into a discrete Ascl2 “on” or “off” decision. In turn Ascl2, together with β-catenin/Tcf, activates stem cell genes. Thus, Ascl2 forms a transcriptional 'stemness switch' that is both Wnt-responsive and Wnt-dependent.

overall_design: Expression was profiled from organoids from different genetic backgrounds and under different treatements

first: Hans

last: Clevers


title: Co-chaperone CCRP/DNAJC7-regulated gene regulation in the mouse liver

status: Public on Jan 05 2015

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: Co-chaperone protein CAR Cytoplasmic Retention Protein (CCRP) interacts with various nuclear receptors and determines their localization. However, there is limited information about in vivo role of CCRP especially in nuclear receptor-mediated gene regulation. We have generated CCRP global knockout (KO) mouse and have employed whole genome microarray analysis to reveal the role of CCRP in gene regulation in the mouse liver treated with phenobarbital (CAR activator) or non-treated. Male WT and KO mice were fasted for 24 h followed by the treatment with phenobarbital or vehicle PBS for 6h. Phenobarbital significantly induced or repressed  1302 and 2744 genes in WT and KO, respectively. Interestingly, cholesterol synthesizing genes were significantly up-regulated in KO even without treatment.

overall_design: Mice were fasted for 24 h followed by the intraperitoneally treatment with PBS or phenobarbital at dose of 100 mg/kg body weight for 6 h, or non-treatment.

first: Marumi

last: Ohno


title: Comparison of Control and Tim-Fbl gene expression profiles

status: Public on Jan 12 2015

city: Jerusalem

first: Sebastian

last: Kadener

address: The Alexander Silberman Inst. of Life Sciences, Edmond J. Safra Campus

department: Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

summary: In order to identify genes affected in our model of PANK defficiency we profiled fly heads of female flies control or expressing fumble RNAi by the use of the tim-gal4 driver

overall_design: Female fly heads of the indicated strains were collected at 2 different circadian timepoints, RNA extracted, labeled and hybridized to Affymetrix oligonucleotide microarrays.

first: Hagit

last: Turm


title: The gene expression changes associated with loss of KDM5 (lid) in Drosophila wing discs

city: Bronx

first: Julie

last: Secombe

state: United states

address: 1300 Morris park ave. Ullmann 809

department: Genetics

institute: Albert einstein college of medicne

summary:
To determine the gene expression changes associated with loss of KDM5, we carried out microarray analyses of dissected wing imaginal discs from wildtype (w1118) and kdm510424 homozygous mutant 3rd instar larvae (96hr AED). kdm510424 is >99% homozygous lethal and we are unable to detect KDM5 protein by Western blot, thus it is likely to be a strong loss-of-function allele. Hierarchical cluster analysis of our microarray data revealed that of the 18,500 transcripts represented on the array, 367 genes were up-regulated and 534 genes were down-regulated 1.5-fold or more in kdm5 mutants compared to wildtype (p<0.05).
To highlight biological processes potentially regulated by KDM5, we determined which gene ontology (GO) terms were enriched within the differentially expressed genes. While a total of ten GO terms were significantly enriched (p<0.01), two functionally related and overlapping terms clearly had the largest number of genes: (1) response to stress and (2) oxidation reduction.

overall_design: About 60 dissected w1118 and kdm510424 wing imaginal discs (three replicates each group) were prepared respectively using TRIZOL (Invitrogen) followed by on-column digestion of DNA using the RNeasy Mini Kit (Qiagen). RNA quantity and quality were assessed with a Beckman Coulter DU 640 spectrophotometer and Agilent 2100 Bioanalyzer, following the manufacturer’s protocols. Biotinylated, single-stranded, cDNA was prepared from 100ng total intact RNA. cDNA was hybridized to Drosophila Genome 2.0 GeneChips (Affymetrix).

first: Xingyin

last: Liu


title: Quantitative omics reveals that type I and II IFNs alter bacterial vacuole compositions to restrict infection in macrophages and lungs

status: Public on Jan 01 2015

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: The innate defense mechanisms that control infections with intracellular bacteria are still incompletely understood. Here we show that type I and II IFNs are key regulators of the early gene expression and the host-protective immune response during Legionella pneumophila-induced pneumonia. Using mixed bone marrow-chimeric mice and isolated cells we indicate that both IFNs protect against L. pneumophila by activating an alveolar macrophage-intrinsic antibacterial defense pathway. Quantitative mass spectrometry analysis reveals that both IFNs markedly alter the protein composition of purified Legionella-containing vacuoles, and integrated network analysis defines distinct subsets of IFN-regulated proteins. Subsequent experiments uncover Immunoresponsive gene 1 (Irg1) as a central effector that restricts the bacteria through production of itaconic acid. Collectively, we provide a comprehensive analysis of IFN-mediated effects on gene expression and the bacterial vacuole proteome, and show that L. pneumophila is restricted by an Irg1-dependent production of a bactericidal metabolite.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent mouse whole genome catalog 44K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Jan

last: Naujoks

first: Bastian

last: Opitz

first: Anca

last: Dorhoi


title: Pregnancy-associated alterations in DNA methylation patterns of mammary epithelial stem cells [inhibitor study]

status: Public on Jan 22 2015

city: Cambridge

first: Kendell

last: Clement

address: 7 Divinity Ave.

institute: Harvard University

summary: Mammary gland development and luminal differentiation occur largely postnatally during puberty and pregnancy. To explore the role of DNA methylation in luminal cell differentiation and pregnancy-induced changes, we determined the genome-wide DNA methylation and gene expression profiles of mammary epithelial stem, luminal progenitor, and mature luminal cells at different reproductive stages. We found that pregnancy had the most significant effects on stem cells, inducing a distinct epigenetic state that remained stable through life. Integrated analysis of gene expression, DNA methylation, and histone modification profiles revealed cell type and reproductive stage-specific changes in molecular signatures. We also identified p27 and TGFβ signaling as key regulators of luminal progenitor cell proliferation based on their expression patterns and by the use of explant cultures. Our results suggest relatively minor changes in DNA methylation during luminal cell differentiation as compared to the significant effects of pregnancy on mammary epithelial stem cells.

overall_design: Mammary glands were collected from mice treated with DNA methylation inhibitor 5-azacytidine (AzaC) and histone deacetylase inhibitor valproic acid (VPA) at non-pregnant and pregnant stages for RNA extraction and hybridization on Affymetrix microarrays.

first: Sung

last: Huh

first: Patrick

last: Boyle

first: Alexander

last: Meissner

first: Kornelia

last: Polyak


title: Murine KN6-Lig+ and Lig- DN4 Cells compared to DN3 cells

status: Public on Dec 02 2014

city: philadelphia

first: suraj

last: peri

state: PA

address: 333 cottman ave

department: biostatistics and bioinformatics

institute: Fox chase cancer center

summary: Transcriptomic profiling of  KN6 DN4 TCR Tg thymocytes adopting the γδ fate (Lig+) or the  αβ fate (Lig-)

overall_design: Two-condition experiment, Lig+ vs. KN6-DN3 and Lig- vs. KN6-DN3 cells. Biological replicates: 4 Lig+ (one dye-swap), 3 Lig- (one dye-swap).

first: David

middle: L

last: Wiest

first: Sang

middle: Y

last: Lee


title: Expression data from bone marrow-derived dendritic cells

status: Public on Jan 06 2015

city: Rockville

first: Keiko

last: Ozato

state: Maryland

address: 9000 Rockville Pike

department: NICHD

institute: National Institutes of Health

summary: Dendritic cells are the sentinels of the innate immune system. We used global microarray analysis to identify genes which are regulated by Toll-like receptor signaling pathways.

overall_design: Bone marrow mononuclear cells were isolated from WT B6 mice and differentiated into dendritic cells (DCs). Differentiated DCs were treated with Toll-like receptor ligands (LPS and CpG) for 6 h. mRNA samples from treated and untreated DCs were sent for microarray analysis.

first: Monica

last: Gupta

first: Dong

middle: M

last: Shin

first: Lakshmi

last: Ramakrishna


title: Translational characterization of hepatic miR-301a as a biomarker for acute rejection in experimental and clinical liver transplantation

status: Public on Dec 20 2014

city: Kaohsiung

first: I-Hsuan

middle: Ann

last: Chen

address: 123 Ta-Pei Rd., Niao-Sung

country: Taiwan

institute: CGMH

summary: Using a rat orthotopic liver transplantation (OLT) model and microarray, we compared the expression profiles of microRNAs in naïve and AR livers at day 7 after OLT obtained from the rats with short-term (<14 days, DA-LEW) or long-term (>60 days, DA-PVG) survival fate. AR-related microRNAs and pro-inflammatory cytokines were validated by using a quantitative real-time PCR. AR-related microRNA-mediated inflammatory responses were evaluated by overexpression of a target microRNA in rat primary hepatocytes. Human liver biopsies from recipients with AR or abnormal liver function were used for clinical verification. The microarray revealed that miR-301a was significantly upregulated in lethal AR livers of DA-LEW, while it was comparable to the naïve livers in DA-PVG, which spontaneously overcomes AR.

overall_design: OLT was carried out following the technique previously described by Kamada et al. in the following combinations: DA donor liver into PVG (DA-PVG; natural tolerance model with long-term (>60 days) and DA donor liver into LEW (DA-LEW; AR model with short-term (<14 days).

first: Toshiaki

last: Nakano


title: Uterine Epithelial Cells Specific Estrogen Receptor alpha-Dependent Gene Expression Profiles in Response to Estrogen

status: Public on Dec 01 2014

first: NIEHS

last: Microarray Core

state: NC

department: DIR

summary: Estrogens stimulate hypertrophy and hyperplasia in the uterus and exert their activity through estrogen receptor α (ERα). A uterine epithelial ERα conditional knockout mouse model (Wnt7aCre+;Esr1f/f or cKO) demonstrated that ERα in the epithelial cells was dispensable for an early uterine proliferative response to 17β-estradiol (E2), but required for subsequent uterine biological responses. We compared the gene expression profile in the uterus after E2 treatment in the cKO samples with WT samples. We found that approximately 25% of the genes differentially expressed at 2 h were epithelial ERα independent, as they were preserved in the cKO, indicating they are mediated from the stroma and sufficient to promote initial proliferative responses. However, more than 90% of the differentially expressed transcripts at 24 h were absent in the cKO, indicating the majority of later transcriptional regulation required epithelial ERα and suggesting the loss of regulation of these later transcripts results in the blunted growth response 3 days after treatment. These transcription profiles correlate with our previous biological responses, in which the initial proliferative response is independent of epithelial ERα but dependent on stromal ERα, yet epithelial ERα is essential for subsequent tissue responsiveness. These analyses are now allowing for in vivo determination of the cell specific actions of ERα in the female reproductive tract.

overall_design: The uterine samples were collected from ovariectomized female reproductive tract epithelial ERα knockout (cKO) at 24 h after vehicle (saline) treatment and at 2 and 24 h 17beta-estradiol (0.25 ug/mouse) treatment. Each experimental group contains 3 replicates. Gene expression analysis was conducted by using Agilent Whole Mouse Genome 4×44 multiplex format oligo arrays (no. 014868; Agilent Technologies, Santa Clara, CA).

first: Kenneth

last: Korach

first: Wipawee

last: Winuthayanon


title: Toxicogenomics analysis of placenta samples from mice exposed to different doses of BPA

status: Public on Dec 15 2014

city: Rome

first: Sabrina

last: Tait

state: Italy

address: Viale Regina Elena 299

department: Dpt. Infectious Diseases

institute: Istituto Superiore di Sanità

summary: Bisphenol A (BPA) is a widespread Endocrine Disrupter mainly used in food contact plastics. Several evidences support BPA adverse effects, especially on susceptible groups such as pregnant women. The present study considered placental development - relevant for pregnancy outcomes and fetal nutrition/programming - as a potential target of BPA. Pregnant CD-1 mice were administered per os with vehicle, 0.5 (BPA05) or 50 mg/kg (BPA50) body weight (bw)/die of BPA, from gestational day (GD) 1 to GD11. At GD12, BPA50 induced significant degeneration and necrosis of giant cells, increased vacuolization in the junctional zone in absence of glycogen accumulation and reduction of the spongiotrophoblast layer. BPA05 induced a significant nuclear accumulation of β-catenin in trophoblasts of the labyrinthine and spongiotrophoblast layers, supporting an activation of the Wnt/β-catenin pathway. Transcriptomic analysis indicated a BPA05 promotion and a BPA50 inhibition of blood vessels development and branching supported by the morphological observation of decreased and increased total vessels area in the labyrinth layers upon BPA05 and BPA50 treatments, respectively, with BPA50 also inducing a decrease in vessels number.  These mechanisms involve, respectively, CREB and Wnt/β-catenin pathways for BPA05 and AhR/ARNT pathway for BPA50, as deducted by the transcription factor binding analysis.  These results show that BPA differently affects mouse placental development depending on the dose level. In particular, the 0.5 mg/kw bw, in the range of dose level used to set the Tolerable Daily Intake, may elicit not negligible alterations whose relevance for human health has to be carefully evaluated.

overall_design: Three conidtions experiment: Control, BPA 0.5 mg/kg bw die; BPA 50 mg/kg bw die. Biological replicates: three control replicates; four replicates per treatment. Technical replicates: 2 (dye swap) per biological replica


title: Transcriptome of the bone metastasis associated stroma

status: Public on Dec 09 2014

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

institute: IGBMC

summary:
The reciprocal interaction between cancer cells and the tissue-specific stroma is critical for primary and metastatic tumor growth progression. Prostate cancer cells colonize preferentially bone (osteotropism), where they alter the physiological balance between osteoblast-mediated bone formation and osteoclast-mediated bone resorption, and elicit prevalently an osteoblastic response (osteoinduction). The molecular cues provided by osteoblasts for the survival and growth of bone metastatic prostate cancer cells are largely unknown. We exploited the sufficient divergence between human and mouse RNA sequences together with redefinition of highly species-specific gene arrays by computer-aided and experimental exclusion of cross-hybridizing oligonucleotide probes. This strategy allowed the dissection of the stroma (mouse) from the cancer cell (human) transcriptome in bone metastasis xenograft models of human osteoinductive prostate cancer cells (VCaP and C4-2B).  As a result, we generated the osteoblastic bone metastasis-associated stroma transcriptome (OB-BMST). Subtraction of genes shared by inflammation, wound healing and desmoplastic responses, and by the tissue type-independent stroma responses to a variety of non-osteotropic and osteotropic primary cancers generated a curated gene signature (“Core” OB-BMST) putatively representing the bone marrow/bone-specific stroma response to prostate cancer-induced, osteoblastic bone metastasis. The expression pattern of three representative Core OB-BMST genes (PTN, EPHA3 and FSCN1) seems to confirm the bone specificity of this response. A robust induction of genes involved in osteogenesis and angiogenesis dominates both the OB-BMST and Core OB-BMST. This translates in an amplification of hematopoietic and, remarkably, prostate epithelial stem cell niche components that may function as a self-reinforcing bone metastatic niche providing a growth support specific for osteoinductive prostate cancer cells. The induction of this combinatorial stem cell niche is a novel mechanism that may also explain cancer cell osteotropism and local interference with hematopoiesis (myelophthisis). Accordingly, these stem cell niche components may represent innovative therapeutic targets and/or serum biomarkers in osteoblastic bone metastasis.
Keywords: cancer, transcription-profile, bone, metastasis, stroma

overall_design:
3 samples of VCaP xenografted mouse bones (VCaP xenografts 1/2/3), 3 samples of C4-2B xenografted mouse bones (C4-2B xenografts 1/2/3), 2 samples of Ep156T xenografted mouse bones (Ep156T xenografts 1/2), 2 samples of sham-operated mouse bones (sham-operated bones 1/2) and 3 samples of intact mouse bones (intact bones 1/2/3) were profiled on Affymetrix Mouse Genome 430A 2.0 Arrays.
Sample code: MVX stands for VCaP xenografts, MBM for Intact bone samples, MCX for C4-2B xenografts and MNX for Sham-operated bones samples

first: Berna

last: Özdemir

first: Janine

last: Hensel

first: Chiara

last: Secondini

first: Antoinette

last: Wetterwald

first: Ruth

last: Schwaninger

first: Achim

last: Fleischmann

first: Olivier

last: Poch

first: Mauro

last: Delorenzi

first: Ramzi

last: Temanni

first: Ian

last: Mills

first: Gabri

last: van der Pluijm

first: George

middle: N

last: Thalmann

first: Marco

last: Cecchini


title: Expression data from GNMT and MAT1A knockout models that develop all the stages of non-alcoholic fatty liver disease including hepatocellular carcinoma [MAT1A_15months]

status: Public on Nov 07 2014

city: Alnarp

first: Itziar

last: Frades

address: Sundsvägen 14

department: Plant Protection Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

summary: Liver global gene expression patterns of 15-month-old MAT1A knockout mice histopathologically determined to have hepatocellular carcinoma (HCC). 5 samples are of tumoral tissue and 5 samples are of peritumoral tissue. All these have their respective wild type patterns. These were analyzed to define signatures to study the pathogenesis of NAFLD-derived HCC, explore which subtypes of cancers can be investigated using mouse models and define a signature of HCC differential survival that can be used to characterize HCC subtypes of different survival derived from mixed etiologies.

overall_design: MAT1A-knockout mice liver tumoral and peritumoral tissue samples having hepatocellular carcinoma were selected for RNA extraction and hybridization on Affymetrix microarrays.


title: Undifferentiated Pleomorphic Sarcoma Model Using Tumors from BrafCa

city: Durham

first: Jeffrey

last: Mito

institute: Duke University Medical Center

summary: Analysis of undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma like tumors from BrafCa, p53Fl/Fl mouse model of soft tissue sarcoma

overall_design: Murine soft tissue sarcomas (n = 6) were compared to normal muscle (n = 2)

first: David

last: Kirsch


title: Gene expression profiles of the lung of CD2-T-bet transgenic mice

status: Public on Nov 03 2014

city: Kyoto

first: Shin

last: Kaneko

address: 53 kawaharacho shogoin, sakyo-ku

institute: Kyoto University

summary: To uncover potential mechanisms underlying the observed Pulmonary Alveolar Proteinosis-like phenotype, we performed a microarray analysis using lung mRNAs from T-bet transgenic mice.

overall_design: Gene expression signatures associated with pulmonary alveolar  proteinosis induced by T-bet overexpression in T cells were measured.

first: Shoichi

last: Iriguchi


title: Arid3a modulates the first cell fate decision by direct regulation of both embryonic and extraembryonic gene expression (microarray)

status: Public on Oct 16 2014

city: Austin

first: Jonghwan

last: Kim

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

summary: Arid3a, a transcription factor known for its requirement in B-lymphocyte development, has been recently identified as a member of ES cell pluripotency network. Arid3a is moderately expressed in ES cells, and its expression is gradually increased during differentiation. Since Arid3a shows the highest expression in placenta, we hypothesized that Arid3a may play important roles in TE development. We report that Arid3a is a central regulator of both TE-specific and pluripotency-associated gene expression during ES cell differentiation. While dispensable for self-renewal, we observed that knockdown of Arid3a delays differentiation of ES cells. Induction of Arid3a leads ES cells to promote differentiation, specifically towards TE lineage. Moreover, these Arid3a-overexpressing cells maintained in TE culture media are sufficient to generate functional trophoblast stem-like cells, suggesting roles of Arid3a in TE differentiation. By integrative analyses using the chromosomal targets of Arid3a with expression profiling, we revealed the dual roles of Arid3a, as a direct activator of TE-specific genes and a repressor of pluripotency-associated genes. We further revealed the repressive roles of Arid3a are mediated by histone deacetylases (HDACs). Taken together, our results demonstrate that Arid3a is a critical novel regulator in TE lineage specification.

overall_design:
Arid3a overexpression and Arid3a knockdown
Total RNA was isolated from cultured cells using RNeasy plus mini kit (Qiagen). cDNA were synthesized and labelled, followed by hybridization on Affymetrix GeneChip mouse genome 430A 2.0 arrays.


title: Unraveling the Specific Ischemic Core and Penumbra Transcriptome in Permanent Middle Cerebral Artery Occlusion Model Mice Brain Treated with Neuropeptide PACAP38

status: Public on Oct 31 2014

city: Tsukuba

first: RANDEEP

last: RAKWAL

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: Our group has been systematically investigating effects of the neuropeptide pituitary adenylate-cyclase activating polypeptide (PACAP) on the ischemic brain. To do so, we have established and utilizing the permanent middle cerebral artery occlusion (PMCAO) mouse model, where PACAP38 (1 pmol) injection is given intracerebroventrically in comparison to a control saline (0.9% NaCl) injection, in conjunction with high-throughput DNA microarray analysis. In previous studies, we have accumulated a large volume of data (gene inventory) from the whole brain (ipsilateral and contralateral hemispheres) by this approach. In our latest research, we have targeted specifically infract/ischemic core (hereafter IC) and the penumbra (hereafter P) post-PACA38 injection, for re-examining the transcriptome at 6 and 24 h post-treatment. The aim of the current study is simple – to delineate the specificity of expression and localization of differentially expressed molecular factors influenced by PACAP38. Prior to this highly expensive and time-consuming omic analysis, we checked the validity of our hypothesis and experimental strategy wherein, ischemic core and penumbra were carefully sampled and compared to the corresponding contralateral (healthy) IC and P regions at 6 and 24 h, post PACAP38 or saline injections to reveal expected differences in gene and protein expression by traditional reverse transcriptase-polymerase chain reaction (RT-PCR) and Western blot analyses, respectively (Hori et al., 2014). Our present results using the mouse 4x44K whole genome DNA chip reveal numerous changes (≧/≦ 1.5/0.75-fold) at both 6 h (654 and 456, and 522 and 449 up- and down-regulated genes for IC and P, respectively; and 24 h (2568 and 2684, and 1947 and 1592 up- and down-regulated genes for IC and P, respectively) after PACAP38 treatment. Using bioinformatics analysis by pathway- or specific-disease-state focused gene classifications and Ingenuity Pathway Analysis (IPA), these genes were functionally classified and discussed. Taken together, the DNA microarray analysis provides not only a great resource for further study, but also reinforces the importance of region-specific analyses in genome-wide identification of target molecular factors that might play a role in the neuroprotective function of PACAP38.

overall_design: In the present study, we used three mice each in PMCAO groups for PACAP38 and saline injections, respectively, that exhibited neurological grades G1 and G2 for the subsequent downstream analysis. Six or 24 h post-injection of PACAP38 or saline, the mice were removed from their cages, decapitated, and their brains carefully removed on ice. The right (ipsilateral; ischemic) and left (contralateral) hemispheres were dissected, and from each hemisphere the ischemic core and penumbra regions and corresponding healthy core and penumbra were carefully removed with a sterile scalpel, and placed in 2 ml Eppendorf tubes. The samples were then quickly immersed in liquid nitrogen and stored in -80 ºC prior to further analysis. Effect of the intracerebroventricular PACAP38 administration into ischemic mouse brain was evaluated at the molecular level in the ischemic core and penumbra of ipsilateral (right) hemisphere over the saline injection by whole genome DNA microarray analysis (4x44K, Agilent).

first: Motohide

last: Hori

first: Tomoya

last: Nakamachi

first: Junko

last: Shibato

first: Randeep

last: Rakwal

first: Seiji

last: Shioda

first: Satoshi

last: Numazawa


title: Enhanced adult hippocampal neurogenesis in mice fed the marine-plant derived astaxanthin supplement: A DNA microarray-based analyses

status: Public on Oct 10 2014

summary: Astaxanthin (ASX), the most powerful antioxidant within carotenoids, has not only anti-oxidative stress and anti-infammation, but also neuroprotective effects in the preventatin of oxidative damage on various neurodegenerative diseases in vivo and in vitro. Recent studies demonstrated that ASX enhanced learning and memory performance in human and animal, but its beneficial effects on neuronal mechanism are unknown. Moreover, it is unclelar delving further into ASX-induced the possible molecular mechanisim on adult hippocampal neurogenesis (AHN). Here, we investigated whether ASX enhances AHN depend on concentration, and their related to potential molecular pathway using DNA microarray analysis. Adult male C57BL/6J mice were divided according to different consistency 0% (CON), 0.02%, 0.1%, 0.5% ASX for 4 weeks. All mice received twice injections of BrdU (50 mg/kg, i.p.) before the treatment of ASX to evaluate survival of newly generated cells. We further investigated global gene expression changes in hippocampus with treatment of 0.5% ASX, which contributed to ASX-induced AHN in order to determine potential molecular mechnisim by DNA microarray analysis. There is an increased tendency of proliferation and new-survival cells; although their siginificance is limited in 0.1% and 0.5% ASX groups for proliferation and in 0.5% ASX group for new-survival cells. Moreover, DNA microarray analysis showed upreguation of genes such as PRL, ITGA4 and IL4 associated with hippocampal plasticity and their downstream genes in 0.5% ASX group. Our results suggests that ASX supplementation enhances proliferation by PRL, and survival by ITGA4 and IL4 in the stages of adult hippocampal neurogenesis, respectively.

overall_design: Two-condition experiment, hippocampus tissue 0% (control) and treated 0.5% ASX supplementation. Biological replicates: 4 control replicates, 4 treatment replicates.

first: Jangsoo

last: Yook

first: Masahiro

last: Okamoto

first: Takashi

last: Matsui

first: Joonyong

last: Cho

first: Hyukki

last: Chang

first: Hideaki

last: Soya


title: The Drosophila surface glia transcriptome: insights into conserved blood-brain barrier physiologies

status: Public on Nov 01 2014

city: San Francisco

first: Michael

last: DeSalvo

state: CA

department: Department of Anesthesia

institute: UC San Francisco

summary:
Maintenance of central nervous system (CNS) homeostasis requires tight regulation over the metabolites, drugs, cells, and pathogens entering the brain.  The blood-brain barrier (BBB) carries out these functions, but the regulatory mechanisms underlying BBB physiology are not completely understood. In addition, the BBB has long been an obstacle to the pharmacologic treatment of CNS diseases, thus molecular model systems that can parse BBB functions and understand the complex integration of sophisticated cellular anatomy and highly polarized chemical protection physiology are desperately needed.
In this study, we developed FACS isolation methods for the purification of the surface glia that form the Drosophila BBB. By comparing the transcriptomes (via microarray analyses) of surface glia, FACS isolated neurons, and whole brains, we present a complete catalog of transcripts enriched at the Drosophila BBB. The surface glia transcriptome contains many ABC and SLC transporters, cell adhesion molecules, xenobiotic metabolism pathways, metabolic enzymes, and signaling molecules. Using gene set enrichment analyses and sequence-based comparisons, we compare the Drosophila surface glia to the vertebrate vascular endothelial BBB.

overall_design: Each replicate for the microarray analysis represented sorted cells originating from different growth bottles and processed on different days. Five total replicates were run for each of the following genotypes: wildtype whole brain, and sorted GFP positive cells from Repo, Elav, and 9-137.

first: Roland

middle: J

last: Bainton


title: Follicular helper T cell signature in Type 1 Diabetes

status: Public on Oct 07 2014

city: London

first: Lucy

last: Walker

address: Royal Free Campus

department: Institute of Immunity & Transplantation

country: United Kingdom

institute: University College London

summary: This study set out to examine CD4 T cell differentiation in a mouse model of diabetes based on transgenic expression of ovalbumin under the control of the rat insulin promoter and co-expression of the DO11.10 transgene (DO11 x rip-mOVA mice). The transcriptome of T cells isolated from the pancreatic lymph nodes (lymph nodes draining the site of self antigen expression) was compared with that of T cells isolated from inguinal lymph nodes (non-draining lymph nodes). T cells were sorted based on expression of CD4, DO11.10 TCR (KJ-126), CD25 and CD69.

overall_design: Primary cells from 6 week old DO11 x rip-mOVA mice were isolated ex-vivo from the pancreatic lymph nodes or inguinal lymph nodes. Cells were sorted by flow cytometry using antibodies to CD4, DO11.10 TCR (KJ-126+), CD25 and CD69.  3-6 replicates were collected per experimental group with each replicate deriving from 14 mice. RNA was isolated using the RNeasy micro kit (Qiagen).

first: Rupert

last: Kenefeck

last: Ono


title: Diabetes and Insulin in Regulation of Brain Cholesterol Metabolism

status: Public on Oct 03 2014

city: Boston

first: Jonathan

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: The brain is the most cholesterol-rich organ in the body, most of which comes from in situ synthesis. Here we demonstrate that in insulin-deficient diabetic mice, there is a reduction in expression of the major transcriptional regulator of cholesterol metabolism, SREBP-2, and its downstream genes in the hypothalamus and other areas of the brain, leading to a reduction in brain cholesterol synthesis and synaptosomal cholesterol content. These changes are due, at least in part, to direct effects of insulin to regulate these genes in neurons and glial cells and can be corrected by intracerebroventricular injections of insulin. Knockdown of SREBP-2 in cultured neurons causes a decrease in markers of synapse formation and reduction of SREBP-2 in the hypothalamus of mice using shRNA results in increased feeding and weight gain. Thus, insulin and diabetes can alter brain cholesterol metabolism, and this may play an important role in the neurologic and metabolic dysfunction observed in diabetes and other disease states.

overall_design: Hypothalamus was compared between streptozotocin (STZ)-induced diabetic, ob/ob, and control mice, with 5-6 replicates per goup.

first: R

last: Suzuki

first: K

last: Lee

first: E

last: Jing

first: S

last: Biddinger

first: J

last: McDonald

first: T

last: Montine

last: Craft

first: C

last: Kahn


title: Expression from hemocytes misexpressing Idh-R195H vs. controls

first: Zachary

middle: J.

last: Reitman

address: 159 MSRB1

department: Pathology

institute: Duke Univ. Medical Ctr.

summary: Expression profile for hemocytes from hml-Gal4, UAS-2xEGFP larvae were compared to hemocytes from hml-Gal4, UAS-2xEGFP; UAS-Idh-R195H larvae

overall_design: We sought to determine which genes and pathways were upregulated or downregulated in hemocytes expressing Idh-R195H, the Drosophila homolog of the human cancer-associated IDH1-R132H mutant, in vivo.  We sought to obtain homogeneous populations of hemocytes from each genotype.  We compared larvae expressing Idh-R195H from the hml-Gal4 driver to larvae with the hml-Gal4 driver alone.

first: Hai

last: Yan


title: Lung-resident myeloid-derived suppressor cells display dual functionality in experimental tuberculosis

status: Public on Dec 21 2014

city: Berlin

first: Hans-Joachim

last: Mollenkopf

summary: Using cell-based approaches and experimental mouse models for pulmonary TB we unveiled MDSCs as new myeloid populations directly interacting with Mycobacterium tuberculosis (Mtb). MDSCs readily phagocytosed Mtb, released proinflammatory (IL-6, IL-1α) and immunomodulatory (IL-10) cytokines while retaining their suppressive capacity. MDSCs were identified at the site of infection in disease-resistant and -susceptible mice during pulmonary TB. Excessive MDSC accumulation in lungs correlated with elevated surface expression of IL-4Rα and heightened TB lethality.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent mouse whole genome catalog 44K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Julia

last: Knaul

first: Stefan

middle: H

last: Kaufmann

first: Anca

last: Dorhoi