title: High-fat diet leads to tissue-specific changes reflecting risk factors for diseases in DBA/2J mice

city: Bar Harbor

first: Rachael

last: Hageman

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Analysis of tissues of DBA/2 mice fed a standard breeding diet (SBD) and high fat diet (HFD) revealed tissue specific roles in inflammation and disease, and altered communication between tissues.  The tissues surveyed incuded adipose tissues (brown, inguinal, mesenteric, retro-peritoneal, subcutaneious and gonadal), muscle and liver.

overall_design: After the 6 weeks feeding period with different diets, individual blood and tissues were collected from 12 weeks old mice for the determination of serum factors, gene expression analyses and the determination of fatty acid profiles. Mice were individually fasted for two hours prior to dissection that was carried out between 1 PM and 3 PM on three successive days. After the fasting period, blood was withdrawn from the retroorbital plexus of each mouse through a heparin-coated hematocrit tube into a 1.5 ml tube and placed on room temperature until all samples were centrifuged at 600 x g for 10-15 min to obtain serum for the analysis of lipids, glucose, insulin and leptin. Subsequently, animals were sacrificed by cervical dislocation. After bleeding, the subcutaneous fat pads (mainly inguinal fat pads), the gluteal fat pads (between legs left and right to the after), the quadriceps (musculus rectus femulus, m. vastus intermedius, m. vastus lateralis, m. vastus medialis), the gonadal fat pads (surrounding gonads), the retroperitoneal fat pads (below the kidney), the liver, the mesenteric fat pad (hanging at the intestine), and the brown adipose tissues (surrounded by white adipose tissue) were carefully dissected in the given order and immediately collected in RNAlater (Ambion, Austin, TX). The sampling protocol lasted no longer than 15 min per animal.

first: Asja

last: Wagener

first: Claudia

last: Hantschel

first: Karen

middle: L

last: Svenson

first: Gary

last: Churchill

first: Gudrun

last: Brockmann


title: Liver X receptor beta is the dominant LXR subtype in skeletal muscle

status: Public on Mar 31 2010

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Liver X receptors (LXRs) are important regulators of cholesterol, lipid and glucose metabolism and have been extensively studied in liver, macrophages and adipose tissue. However, their role in skeletal muscle is not yet fully elucidated and the functional role of each of the LXRα and LXRβ subtypes in skeletal muscle is at present unknown. To study the importance of each of the receptor subtypes, myotube cultures derived from wild type (WT), LXRα and LXRβ knockout (KO) mice were established. The present study shows that treatment with the unselective LXR agonist T0901317 increased mRNA levels of LXR target genes such as sterol regulatory element-binding transcription factor 1 (SREBF1), fatty acid synthase (FASN), stearoyl-CoA desaturase 1 (SCD1) and ATP-binding cassette transporter A1 (ABCA1) in myotubes established from WT and LXRα KO mice. However, only minor changes in expression level were observed for these genes after treatment with T0901317 in myotubes from LXRβ KO mice. Gene expression analysis using Affymetrix NuGO Genechip arrays showed that few other genes than the classical, well known LXR target genes were regulated by LXR in skeletal muscle. Furthermore, functional studies using radiolabeled substrates showed that treatment with T0901317 increased lipogenesis and apoA1 dependent cholesterol efflux, in myotubes from WT and LXRα KO mice, but not LXRβ KO mice. The data suggest that the lipogenic effects of LXRs, as well as the LXR-stimulated cholesterol efflux, are mainly mediated by LXRβ in skeletal muscle.

overall_design: To study the importance of each of the receptor subtypes, myotube cultures derived from wild type (WT), LXRa and LXRb knockout (KO) mice were established. Sixteen samples were examined. Half the samples were treated with the unselective LXR agonist T0901317.

first: Nina

middle: P

last: Hessvik

first: Mark

middle: V

last: Boekschoten

first: Mari-Ann

last: Baltzersen

first: Sander

last: Kersten

first: Xiufeng

last: Xu

first: Harriet

last: Andersen

first: Arild

middle: C

last: Rustan

first: Hege

last: Thoresen


title: Comparison of normal mouse hematopoietic stem cells (HSC) to mobilized and leukemia-inducing hematopoietic stem cells

status: Public on Feb 17 2010

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

summary: Highly purified Hematopoietic stem cells (HSC) from mouse bone marrow (BM) were compared to HSC after two days of cytoxan/GCSF treatment (Cyclophosphamide/granulocyte colony-stimulating factor) (Day2Mob) and leukemic HSC from mice lacking JunB. See Forsberg et. al. 2010 for details. CML - chronic myelogenous leukemia.

overall_design: Biological Replicate

first: Susan

last: Prohaska

first: Amy

last: Wager


title: Bortezomib inhibits mTOR pathway in multiple myeloma cells via induced expression of REDD1.

status: Public on Feb 15 2010

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

summary:
The combination of bortezomib and dexamethasone should become the reference induction treatment for multiple myeloma patients younger than 65 years. Pharmacogenomic profiles of genes involved in response to treatment may help to understand resistance. We performed gene expression profiling in 9 myeloma cell lines, incubated or not with bortezomib and dexamethasone for 6 hours. Supervised analysis identified significantly up regulated genes involved in stress responses.
We focused on REDD1 a gene known to be rapidly induced by a wide variety of stress conditions and DNA damages. REDD1 expression was early and highly induced after bortezomib exposure. REDD1 induction was associated with the dephosphorylation of  P70 S6 ribosomal kinase (P70S6K), a key substrate of mTOR. These effects were dependent upon cell line. REDD1 was overexpressed within two hours in bortezomib resistant cell lines in association with a cell size decrease. In sensitive cell lines, neither REDD1 induction nor morphological changes occurred. RNA interference mediated inhibition of REDD1 induction abrogates P70S6K dephosphorylation, early transitory cell size reduction and enhances sensitivity to bortezomib - dexamethasone.
Our results suggest that mTOR regulation could be a resistance mechanism mediated by REDD1 expression in myeloma cells.

overall_design:
Nine cell lines of multiple myeloma studied, incubated or not with bortezomib and dexamethasone, examined with spotted cDNA nylon membrane.
Cell line and Code : JJN3 = Vel_1x; L363 = Vel_2x; LP1 = Vel_3x; MDN = Vel_4x; NCI = Vel_5x; RPMI = Vel_6x; SBN = Vel_7x; U266 = Vel_8x; XG1 = Vel_9x.

first: Olivier

last: Decaux

first: Monique

last: Clément

first: Florence

last: Magrangeas

first: Catherine

last: Charbonnel

first: Loïc

last: Campion

first: Hervé

last: Avet Loiseau

first: Stéphane

last: Minvielle


title: Molecular Sampling of Prostate Cancer: a dilemma for predicting disease progression

status: Public on Mar 05 2010

city: New York

first: Andrea

last: Sboner

state: NY

address: 1305 York Ave, Box 104

department: Pathology; Computational Biomedicine

institute: Weill Cornell Medical College

summary: Current prostate cancer prognostic models are based on pre-treatment prostate-specific antigen (PSA) levels, biopsy Gleason score, and clinical staging but in practice are inadequate to accurately predict clinical disease progression. Hence, we sought to develop a molecular panel for prostate cancer progression by reasoning that molecular profiles might further improve current clinical models. We analyzed a Swedish Watchful Waiting cohort (1977–1999) with up to 30 years of clinical follow up using a novel method for gene expression profiling. This cDNA-mediated annealing, selection, ligation, and extension (DASL) method enabled the use of formalin-fixed paraffin-embedded transurethral resection of prostate (TURP) samples taken at the time of the initial diagnosis. We determined the expression profiles of 6100 genes for 281 men divided in two extreme groups: men who died of prostate cancer or developed metastases and men who survived more than 10 years without metastases (lethals and indolents, respectively). Several models using clinical and molecular features were  evaluated for their ability to distinguish lethal from indolent cases. Surprisingly, none of the predictive models using molecular profiles significantly improved over models using clinical variables only. We reasoned that tumor sampling might preclude the identification of the dominant metastatic nodule. Additional computational analysis confirmed that molecular heterogeneity within both the lethal and indolent classes is widespread in prostate cancer as compared to other types of tumors. Thus the determination of the molecularly dominant tumor nodule may be limited by sampling at time of initial diagnosis, may not be present at time of initial diagnosis, or may occur as the disease progresses preventing the development of molecular biomarkers for prostate cancer progression.

overall_design: 281 cases from the population-based Swedish-Watchful Waiting cohort. The cohort consists of men with localized prostate cancer (clinical stage T1-T2, Mx, N0); Training set: first 186 samples; Validation cohort: remaining 95 cases from the same population.

first: Mark

middle: A

last: Rubin


title: Neonatal starvation response and developmental changes in gene expression revealed by hypothalamic expression profiling

status: Public on Mar 01 2010

city: Ann Arbor

first: Jun

last: Li

state: MI

address: 5789A Medical Science II, Box 5618

institute: University of Michigan

summary: We performed gene expression microarray analysis of the hypothalamic response to starvation in neonatal wild-type mice, and in Snord116del mice that are a mouse model for PWS.  This study is motivated by the neonatal feeding problems observed in several genetic diseases including Prader-Willi syndrome (PWS). Later in life, individuals with PWS develop hyperphagia and obesity due to lack of appetite control. We hypothesize that failure to thrive in infancy and later-onset hyperphagia may be related and could be due to a defect in the hypothalamus. In this study, we performed gene expression microarray analysis of the hypothalamic response to starvation in neonatal wild-type mice, and in Snord116del mice that are a mouse model for PWS. The neonatal starvation response was dramatically different from that reported in adult rodents. Genes that are affected by adult starvation are not changed in the hypothalamus of 5 day-old pups that were starved for 6 hrs.  Unlike in adult rodents, expression levels of Nanos2 and Pdk4 were increased, and those of Pgpep1, Ndph, Brms1l, Mett10d, and Snx1 were decreased after fasting.  In addition, we compared hypothalamic gene expression profiles at days 5 and 13 to document developmental changes.  Notably, the gene expression profiles of Snord116del deletion mice and wild-type littermates were very similar at both postnatal days 5 and 13, and after starvation.

overall_design:
We compared hypothalamic RNA between Snord116del mice with wild type (C57BL/6J) littermates at P5 and P13, with or without fasting treatment.
We are particularly interested in the following comparisons:
Comparison 1: wild type vs. PWS deletion in P5 non-starved mice;
Comparison 2: wild type vs. PWS deletion in P5 fasting mice;
Comparison 3: non-starved vs. fasting in P5 wild type mice;
Comparison 4: non-starved vs. fasting in P5 PWS deletion mice;
Comparison 5: wild type vs. PWD deletion in P13 non-starved mice;
Comparison 6: P5 wild type vs. P13 wild type mice;

first: Feng

last: Ding


title: Ad-MyD88 infected bmDCs: Control vs. Ad-MyD88 infected

status: Public on Jan 29 2010

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

summary: Transcriptional profiling of Bone-Marrow derived mouse Dendritic Cells (bmDCs) infected with Ad-MyD88 vs. Ad-GFP or mock infected

overall_design: Three-condition experiment, Ad-MyD88 vs. Ad-GFP vs. Mock infected cells. Biological replicates: 3 Ad-MyD88, 3 Ad-GFP, 3 mock, independently grown and harvested. One replicate per array.

first: Herbert

last: Lyerly

first: Timothy

last: Clay


title: A Time Course Analysis of the Effects of Prieurianin in the mouse preadipocytes 3T3-L1 cells

status: Public on Feb 08 2010

city: Toledo

first: Khew-Voon

last: Chin

state: OH

address: 3000 Arlington Avenue

department: Medicine

institute: The University of Toledo College of Medicine

summary:
Gene expression profiling to examine the effets of prieurianin in a time-course study (0, 0.25, 0.5, 1, 2, 3, 5, 9, 12, 15, 24, 36, 48, 96, 144, 192, 240, and 288 hrs) on the differentiation of the 3T3-L1 preadipocytes into adipocytes.

The sharp rise in the incidence of obesity in the last two decades has become one of the most serious public health risks worldwide.  Currently approved therapies for obesity exhibit modest efficacy and limiting side effects.  We show here that prieurianin, a limonoid, causes weight loss by reducing energy intake in morbidly obese mice and in mice on high-calorie diet.  Prieurianin is also anti-adipogenic by inhibiting the proliferation and differentiation of preadipocytes into adipocytes, and induces either dedifferentiation or delipidation of mature adipocytes.  Gene expression profiling shows that prieurianin suppresses the expression of genes involved in fat metabolism, and increases the expression of a transcription repressor, zinc finger protein 68 (Zfp68), which inhibits CCAAT/enhancer binding proteins (C/EBPs) and peroxisome proliferator-activated receptor γ (PPARγ), master transcriptional regulators of adipogenesis.  The effects of prieurianin are reminiscent of several cytokines that regulate appetite and adipogenesis, and holds promise as an effective anti-obesity drug.

Keywords: Time course, prieurianin, obesity, differentiation, adipogenesis, preadipocytes, adipocytes, Zfp68

overall_design: L1 Cells were treated either with 0.5% DMSO or 2 µM of prieurianin for the following times: 0, 0.25, 0.5,1, 2, 3, 5, 9, 12, 15, 24, 36, 48, 96, 144, 192, 240, and 288 hrs, and then total RNA was purified at the indicated times using the RNeasy Mini kit according to the manufacturer’s instructions.  Samples were labeled and hybridized to the Mouse OneArray (Phalanx Biotech Group, Palo Alto, CA) and analyzed for gene expression changes, compared to untreated control undergoing normal differentiation.


title: Expression data from the mosquito Anopheles gambiae midgut 3h after a protein meal with or without E. coli.

status: Public on Feb 13 2010

city: Rockville

first: Alvaro

last: Molina-Cruz

state: MD

address: 12735 Twinbrook Parkway

department: NIAID

institute: NIH

summary: The Anopheles gambiae midgut harbors bacteria that proliferate upon a blood feed.  We used microarrays to examine the midgut gene expression response at early stages (3hours) after an artifitial meal containing heat killed bacteria.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: Anopheles gambiae G3 mosquitoes 5-6 day-old  were fed BSA (20% in PBS with fresh 10 mM sodium bicarbonate) with or without heat killed E. coli (equivalent of  2.5 ml of 0.8 OD) .  Three pools of 10 mosquito midguts were dissected after 3h and processed for microarray analysis of gene expression.

first: Carolina

last: Barillas-Mury


title: Gene expression profiling in patients infected with HTLV-1: Identification of ATL and HAM/TSP-specific genetic profiles

status: Public on Feb 14 2010

city: Montreal

first: Eduardo

last: Hernandez

state: Quebec

address: 3755 Cote-Sainte-Catherine Road

department: Molecular Oncology Group

country: Canada

institute: Lady Davis Institute for Medical Research (JGH)

summary: We examined the gene expression profiles of CD4+ T-cells isolated from 7 ATL, 12 HAM/TSP and 11 AC (asymptomatic carriers) to identify gene signatures that may be characteristic for these particular diseases. Using gene expression arrays, we identified ~ 1039 immune-related genes that were differentially expressed in CD4+ T cells; using stringent exclusion criteria, a 122 gene signature could be divided into 3 groups: I) ATL-specific; II) common; and III) HAM/TSP-specific markers

overall_design: To better understand the genetic differences between HTLV-1-associated diseases, we examined the gene expression profile of T lymphocytes from patients either suffering from ATL, HAM/TSP or carrying the HTLV-1 virus without any symptoms. Microarray experiments were performed using the human ImmuneArray cDNA array (UHN Microarray Center, University of Toronto). We used the Stratagene Universal Control, labelled Cy5 for all samples in a competitive hybridization.

first: Stephanie

last: Oliere


title: Ad-MyD88 infected MEFs: Control vs. Ad-MyD88 infected

summary: Transcriptional profiling of Murine Embryonic Fibroblasts (MEFs) infected with Ad-MyD88 vs. Ad-GFP or mock infected.


title: Flag Chromatin IP in Cyclin D1 Flag-HA tagged E.14.5 embryos versus Flag Chromatin IP in wildtype E.14.5 embryos

city: Boston

first: Frederic

middle: Emile

last: Bienvenu

state: MA

address: 1 Jimmy Fund Way

department: Cancer Biology

institute: Dana-Farber Cancer Institute

type: Genome binding/occupancy profiling by array

summary: Cyclin D1 belongs to the core cell cycle machinery1, and it is frequently overexpressed in human cancers2.  The full repertoire of cyclin D1 functions in normal development and in cancer cells is currently unknown. To address this question, here we introduce a novel approach that allows one to determine the set of cyclin D1-interacting proteins  (D1 “interactome”) and cyclin D1-bound genomic fragments (D1 “cistrome”) in essentially any mouse organ, at any point of development or at any stage of cancer progression.   Using this approach, we detected several novel tissue-specific interactors of cyclin D1.  A significant number of these partners represent proteins involved in transcription.  We show, using genome-wide location analysis3, that cyclin D1 occupies promoters of a very large number of genes in the developing mouse, where it binds in close proximity to transcription start sites.  Bioinformatics analyses of cyclin D1-bound genomic segments in the developing embryo revealed DNA recognition sequences for several transcription factors.  By querying SAGE libraries4, promoter CpG content5 and gene expression profiles of cyclin D1-null organs, we demonstrate that cyclin D1 binds promoters of highly expressed genes, and that it functions to activate or to repress gene expression in vivo.  Analyses of cyclin D1 transcriptional targets reveal that cyclin D1 contributes to cell proliferation by upregulating genes required for S-phase entry and progression.  Hence, cyclin D1 plays a broad transcriptional regulatory function in vivo during normal mouse development.

overall_design:
We hypothesized that cyclin D1 may play role in transcription by interacting with transcriptional machinery at the promoters of target genes.
To test this possibility, we employed chromatin immunoprecipitation coupled to DNA microarray analysis (genome-wide location analysis or ChIP-chip) to study association of cyclin D1 with genomic DNA sequences.  In this procedure, a protein of interest is crosslinked to DNA, immunoprecipitated, and the bound DNA is hybridized to an array containing probes that span the genome.  Since anti-FLAG antibodies have been successfully used for ChIP-chip in several different systems including murine cells, knock-in mice expressing tagged cyclin D1 provided us with a novel tool to query the association of cyclin D1 with the genome in vivo, in a living mouse.

middle: E


title: Human T cells isolated from healthy European and African American blood donors: Control vs. Interferon alpha 2b-treated

status: Public on Jan 27 2010

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: Transcriptional profiling of human T cells analyzing the impact of race on the responsiveness to IFNa in healthy blood donors. Control and IFNa-treated samples derived from healthy Caucasian American vs. African American blood donors are compared.

overall_design: Two-condition experiment, Control vs. IFNa-treated. Paired design; untreated and treated samples for each donor.

first: Zoltan

last: Pos

first: Silvia

last: Selleri

first: Tara

last: Spivey

first: Hui

last: Liu

last: Worschech

first: Marianna

last: Sabatino

first: Alessandro

last: Monaco

first: Andras

last: Falus

first: Ena

last: Wang

first: Harvey

middle: J

last: Alter

middle: M


title: Comparison of Genes in Imiquimod-treated and Control Tumors

status: Public on Jan 26 2010

city: Seattle

first: Lynn

last: Amon

state: WA

address: 1100 Fairview, M1-C108

department: Division of Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

summary: The goal of the study is to examine changes in tumor gene expression after imiquimod treatment.  RNA was extracted from spontaneous tumors in control mice (n=4) and in imiquimod-treated mice (n=4).  Gene expression was compared between the control group and the treated group.  In the imiquimod treatment group, the mice received topical treatment of 5% imiquimod cream (Aldara) on shaved skin at the site of spontaneous tumors for one treatment cycle (3 consecutive days).

overall_design: RNA was extracted from 4 spontaneous tumors from neu-tg mice treated with topical imiquimod for 1 cycle and 4 spontaneous tumors from control mice

first: Hailing

last: Lu

first: Hangjun

last: Duan

first: Mary

last: Disis


title: Identification of soluble factors overexpressed in brain endothelial cell (EC) lines compared to non-brain EC lines

status: Public on Feb 11 2010

first: Heather

last: Himburg

address: PO BOX 91013

department: Medicine/Cellular Therapy

institute: Duke University Medical Center

summary: Gene expression in brain lines was compared to non-brain cell lines to identify growth factors uniquely expressed in brain lines

overall_design: In this study, human endothelial cells isolated from brain and non-brain sources were cultured for 1 week & total RNA was isolated from the cells.   RNA was amplified, labeled and hybridized to a spotted array containing oligos from the Operon human H034K chip set.

first: John

last: Chute


title: Comparative Genomic Hybridization: genomic control vs. Ullrich Congenital Muscular Dystrophy and Bethlem myopathy

status: Public on Jan 28 2010

city: Ferrara

first: Matteo

last: Bovolenta

address: 74, Fossato di Mortara

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

type: Genome variation profiling by genome tiling array

summary: Molecular characterization of collagen-VI related myopathies currently relies on standard sequencing, which yields a detection rate approximating 75-79% in Ullrich congenital muscular dystrophy (UCMD) and 60-65% in Bethlem myopathy (BM) patients as PCR-based techniques tend to miss gross genomic rearrangements as well as copy number variations (CNVs) in both the coding sequence and  intronic regions. We have designed a custom oligonucleotide CGH array in order to investigate the presence of CNVs in the coding and non-coding regions of COL6A1, A2, A3, A5 and A6 genes and a group of genes functionally related to collagen VI. A cohort of 12 patients with UCMD/BM negative at sequencing analysis and 2 subjects carrying a single COL6 mutation whose clinical phenotype was not explicable by inheritance were selected and the occurrence of allelic and genetic heterogeneity explored. A deletion within intron 1A of the COL6A2 gene, occurring in compound heterozygosity with a small deletion in exon 28, previously detected by routine sequencing, was identified in a BM patient. RNA studies showed monoallelic transcription of the COL6A2 gene, thus elucidating the functional effect of the intronic deletion. No pathogenic mutations were identified in the remaining analyzed patients, either within COL6A genes, or in genes functionally related to collagen VI. Our custom CGH array may represent a useful complementary diagnostic tool, especially in recessive forms of the disease, when only one mutant allele is detected by standard sequencing. The intronic deletion we identified represents the first example of a pure intronic mutation in COL6A genes.

overall_design: Comparative Genomic Hybridization experiment. Experimental Replicates: twice

first: Marcella

last: Neri


title: Global gene expression analysis of OSKM / N2SKM- infected MEFs over time course

status: Public on Jan 22 2010

city: Singapore

first: Dominic

middle: Jian Chien

last: Heng

address: 60 Biopolis Street #02-01, Genome Building

department: Stem Cell and Developmental Biology

country: Singapore

institute: Genome Institute of Singapore

summary: We used microarrays to detail the global  gene expression profiles of  OSKM and N2OSKM-infected MEFs over a time course (3, 7, 11 dpi).

overall_design: Three biological replicates for each OSKM and N2OSKM time point. The global gene expression profiles of the N2OSKM infected MEFs were compared to OKSM-infected MEFs.

first: J

first: B

last: Feng

last: Han

last: Jianming

first: P

last: Kraus

middle: H

last: Ng

first: Y

last: Orlov

first: M

last: Huss

first: T

last: Lufkin

last: Lim

first: H


title: Global gene expression analyses of the Nr5a2 reprogrammed cells

summary: We used microarrays to detail the global programme of gene expression of  ESCs, Nr5a2 reprogrammed iPSC lines and MEFs.

overall_design: Two biological replicates for ESCs, each iPSC line and each type of MEF. The global gene expression profiles of the Nr5a2 reprogrammed iPS cell lines were compared to ESCs and MEFs.


title: The Nuclear Receptor Nr5a2 can replace Oct4 in the Reprogramming of Murine Somatic Cells to Pluripotent Cells

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

overall_design: Refer to individual Series


title: Amygdalae and hippocampi of C57BL/6J and A/J mouse inbred strains

city: Utrecht

first: Simone

last: de Jong

address: Universiteitsweg 100

department: Medical Genetics

institute: UMC Utrecht

summary:
Gene expression profiling in C57BL/6J and A/J mouse inbred strains reveals gene networks specific for brain regions independent of genetic background

Comparison of whole genome expression data of amygdala and hippocampus of both C57BL/6J and A/J mouse inbred strains using a network approach

overall_design: Amygdala and hippocampus dissected from frozen tissue (adult test-naive A/J and C57BL/6J males) using a punching procedure. N=8-9 per group

first: Tova

last: Fuller

first: Esther

last: Janson

first: Steve

last: Horvath

first: Martien

last: Kas

first: Roel

last: Ophoff


title: Comparative gene expression profiling between cultured and tissue human skeletal muscle

status: Public on Feb 22 2010

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

summary:
Culturing myotubes from skeletal muscle (SM) biopsies enables investigating transcriptional defects and assaying therapeutic strategies. This study compares the transcriptome of aneurally cultured human SM cells versus that of tissue biopsies.
We determined the transcriptomic differences between tissue and cultured SM samples from five individuals. In cultured myotubes compared to the tissue, 1216 genes were regulated: 583 down and 633 up. Downregulated genes were mainly associated with cytoplasm, particularly mitochondria, and involved in metabolism and the muscle-system/contraction process. Upregulated genes were predominantly related to cytoplasm, endoplasmic reticulum, and extracellular matrix. The most significantly regulated pathway was mitochondrial dysfunction. Apoptosis genes were also modulated. Among the most downregulated genes were genes encoding metabolic proteins AMPD1, PYGM, CPT1B and UCP3, muscle-system proteins TMOD4, MYBPC1, MYOZ1 and XIRP2, the proteolytic CAPN3 and the myogenic regulator MYF6. Within the most upregulated group were genes encoding senescence/apoptosis-related proteins CDKN1A and KIAA1199 and potential regulatory factors HIF1A, TOP2A and CCDC80.
In conclusion, cultured muscle cells display reductive metabolic and muscle-system transcriptome adaptations as observed in muscle atrophy and they activate tissue-remodeling and senescence/apoptosis processes. Novel candidate regulators in SM dysfunction are revealed

overall_design:
5 biopsies, 5 cell cultures obtained from the biopsies, paired samples.

The supplementary file 'GSE17503_non-normalized_data.txt' contains non-normalized data for Samples GSM436162, GSM436164, and GSM436432-GSM436439.

first: Anna-Maria

last: Gomez-Foix

first: Sylviane

last: Metairon

first: Martin

last: Kussmann

first: Jaume

last: Colomer

first: Andres

last: Nascimento

first: Celia

last: Garcia-Martinez


title: FoxO3 modulates endothelial gene expression and function by direct and indirect mechanisms

status: Public on Feb 01 2010

city: Mannheim

first: Tobias

last: Czymai

state: Baden-Württemberg

address: Theodor-Kutzer-Ufer 1-3

department: Dermatology

country: Germany

institute: University Medical Center Mannheim, University of Heidelberg

summary:
FoxO transcription factors represent targets of the PI3K/PKB survival pathway controlling important biological processes such as stress responses, cell cycle progression, apoptosis, vascular remodelling and metabolism. Recent studies have demonstrated the existence of alternative mechanisms of FoxO-dependent gene expression beyond classical binding to a FoxO-responsive DNA binding element (FRE). Here we explored the relative contribution of those mechanisms by comparing the transcriptional responses to conditional activation of FoxO3 and a corresponding FRE-binding mutant in primary human endothelial cells. Microarray analysis revealed several functional gene clusters regulated in absence of an intact DNA-binding domain. Notably, both mutants triggered apoptosis albeit with different efficiencies. This was associated with regulation of overlapping and distinct proapototic gene clusters. Subsequent analysis demonstrated important roles for the Bcl2-like family members BIM and NOXA in this process. Remarkably, BIM was effectively induced by the FoxO3 FRE-binding mutant and BIM depletion could rescue its proapoptotic effect.
Our study provides the first comprehensive analysis of alternatively regulated FoxO3 targets in primary cells and underscores the importance of such genes for endothelial function and integrity.

overall_design: HUVEC were infected in 4 independent experiments with either empty pBabe puro vector, pBP-FoxO3.A3.ER, or pBP FoxO3.A3.ER.H212R in three consecutive rounds and 72h post infection.

first: Dorothee

last: Viemann

first: Carsten

last: Sticht

first: Matthias

last: Goebeler

first: Marc

last: Schmidt


title: Transcriptional profile of Epithelial to Mesenchymal Transition in the Ovarian Surface Epithelium

status: Public on Jan 20 2010

city: Cambridge

first: Cristian

last: Brocchieri

address: Hills Road

country: United Kingdom

institute: University of Cambridge

summary: Adult Ovarian Surface Epithelium (OSE) retains the ability to undergo Epithelial to Mesenchymal Transition (EMT). We established a cell culture of murine adult OSE in their epithelial state, and we induced EMT by modifying their culture conditions. In this experiment we compare the transcriptional profile of the OSE before and after EMT.

overall_design: Each of three different cultures of mouse OSE in their epithelial phenotype is split in two: one half is kept epithelial, the other half is cultured under conditions that induce the cells to undergo EMT. After one week the EMT process is complete (as assessed morphologically and biochemically) and the transcriptional profiles of the cells in their respective phenotypes are compared.

first: Natalie

last: Thorne

first: Samuel

last: Aparicio


title: Expression profiles associated with BRCA1 and BRCA2 mutation status in familial breast cancer patients

city: Brisbane

first: Logan

last: Walker

state: QLD

address: PO RBH

country: Australia

institute: Queensland Institute of Medical Research

summary:
Use of DNA damaging agents and RNA pooling to assess expression profiles associated with BRCA1 and BRCA2 mutation status in familial breast cancer patients

Background: A large number of rare sequence variants of unknown clinical significance have been identified in the breast cancer susceptibility genes, BRCA1 and BRCA2. Determining the functional effect of these variants as well as their role in breast cancer susceptibility can be challenging using current classification methods.   Methodology/Principal Findings: To identify predictors of pathogenic mutation status in familial breast cancer patients, we explored the use of gene expression arrays to assess the effect of two DNA damaging agents (irradiation and mitomycin C) on cellular response in relation to BRCA1 and BRCA2 mutation status. A range of regimes were used to treat 27 lymphoblastoid cell-lines (LCLs) derived from affected women in high-risk breast cancer families (nine BRCA1, nine BRCA2, and nine non-BRCA1/2 or BRCAX individuals) and nine LCLs from healthy individuals. Using an RNA pooling strategy, we found that treating LCLs with 1.2 μM mitomycin C and measuring the gene expression profiles 1 hour post-treatment had the greatest potential to discriminate BRCA1, BRCA2 and BRCAX mutation status. A classifier was built using the expression profile of nine QRT-PCR validated genes that were associated with BRCA1, BRCA2 and BRCAX status in RNA pools. These nine genes could distinguish BRCA1 from BRCA2 carriers with 83% accuracy in individual samples, but three-way analysis for BRCA1, BRCA2 and BRCAX had a maximum of 59% prediction accuracy. Conclusions/Significance: Our results suggest that, compared to BRCA1 and BRCA2 mutation carriers, non-BRCA1/2 (BRCAX) individuals are genetically heterogeneous. This study also demonstrates the effectiveness of RNA pools to compare the expression profiles of cell-lines from BRCA1, BRCA2 and BRCAX cases after treatment with irradiation and mitomycin C as a method to prioritize treatment regimes for detailed downstream expression analysis.

overall_design: Total RNA was isolated from 27 lymphoblastoid cell-lines (LCLs) derived from affected women in high-risk breast cancer families (nine BRCA1, nine BRCA2, and nine non-BRCA1/2 women) and nine LCLs from healthy women. LCLs from each of the BRCA1, BRCA2 and BRCAX patient groups, and from healthy controls, were irradiated at 10 Gy using a calibrated Cesium-137 source or treated with MMC at two different doses (0.4 µM or 1.2 µM). Cells were harvested prior to IR or MMC treatment (T0), at 1 h after IR exposure, and at 1 and 2 h after exposure for MMC.

first: Amanda

middle: B

last: Spurdle


title: Hepatic glycosphingolipid deficiency and liver function in mice

status: Public on Feb 04 2010

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Recent studies have reported that glycosphingolipids (GSL) might be involved in obesity induced insulin resistance. Those reports suggested that inhibition of GSL biosynthesis in animals ameliorated insulin sensitivity accompanied with improved glycemic control leading to decreased liver steatosis in obese mice. In addition, GSL depletion altered hepatic secretory function. In those studies, ubiquitously acting inhibitors for GSL-biosynthesis have been used to inhibit function of the enzyme Ugcg (UDP-glucose:ceramide glucosyltransferase), catalyzing the first step of the glucosylceramide based GSL-synthesis pathway.  In the present study, a genetic approach for GSL deletion in hepatocytes was chosen to achieve full inhibition of GSL synthesis and to prevent possible adverse effects caused by Ugcg-inhibitors.  Using the Cre/loxP system under control of the albumin promoter, GSL biosynthesis in hepatocytes and their release into the plasma could be effectively blocked.  Deletion of GSL in hepatocytes did not change quantity of bile excretion through the biliary duct. Total bile salt content in bile-, feces- and plasma from mutant mice showed no difference as compared to control animals. Cholesterol concentration in liver-, bile-, feces- and plasma-samples remained unaffected.  Lipoprotein concentration in plasma-samples in mutant animals reached similar levels as in their control littermates. No alteration in glucose tolerance after intraperitoneal application of glucose and insulin appeared in mutant animals. A preventive effect of GSL-deficiency on development of liver steatosis after high fat diet feeding could not be observed.

Conclusion:
The data suggest that GSL in hepatocytes are not essential for sterol, glucose and lipoprotein metabolism and do not prevent high fat diet-induced liver steatosis, indicating that Ugcg inhibitors exert their effect on hepatocytes either independently of GSL or mediated by other (liver) cell types.

overall_design: Comparison of wildtype mouse liver function versus Ugcg-deficient

first: Richard

last: Jennemann

first: Ulrike

last: Rothermel

first: Shijun

last: Wang

first: Roger

last: Sandhoff

first: Sylvia

last: Kaden

first: Ruud

last: Out

first: Theo

last: van Berkel

first: Johannes

last: Aerts

first: Karen

last: Ghauharali

first: Hermann-Josef

last: Gröne


title: Temporal gene expression by Ephedra herba in brain, heart and liver of mouse

status: Public on Jan 31 2010

city: Daejon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

summary: A microarray analysis was conducted using the brain, heart, and liver tissues of mouse orally administrated aqueous extracts of Ephedra herba, in which the expression level of many genes were altered depending on the duration of treatment time.

overall_design: Aqueous extracts of Ephedra herba were administered orally for 1 hr, 6 hrs, 12 hrs, 24 hrs, 3 days, 5 days and 10 days on mice.


title: Gene expression profiling of tumor cell lines with constitutively active STAT3

status: Public on Jan 15 2010

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

institute: University of Turin

summary: The transcription factor STAT3 is constitutively activated in tumors of different origin but the molecular bases for STAT3 addiction of tumor cells have not yet been clearly identified. We generated knock/in mice carrying the constitutively active Stat3 allele, Stat3C, and showed that Stat3C could enhance Neu oncogenic power, triggering the production of earlier onset, more invasive mammary tumors. Tumor-derived cell lines displayed higher migration and invasion and disrupted distribution of cell-cell junction markers. The tensin family member Cten (C-Terminal Tensin-like), known to mediate EGF-induced migration and highly expressed in inflammatory breast cancer, was up-regulated in both Neu;Stat3C cells and tumors. Both Cten expression and enhanced migration were strictly dependent on Stat3, and Cten silencing normalized cell migration and rescued cell-cell contact defects. Importantly, the pro-inflammatory cytokine IL-6 could mediate Cten induction in MCF10 cells, in an exquisitely Stat3-dependent way. This model allowed us to shed some light on the oncogenic role of Stat3 in the breast, suggesting moreover a mechanism through which inflammatory signals can cooperate with EGF receptors in inflammatory breast cancer.

overall_design: Three cell lines with constitutively active STAT3 and three with wild-type STAT3 were analyzed. Two replicates were analyzed for each cell line.

first: Isaia

last: Barbieri

first: Sara

last: Pensa

first: Tania

last: Pannellini

first: Elena

last: Quaglino

first: Diego

last: Maritano

first: Marco

last: Demaria

first: Alessandra

last: Voster

first: James

last: Turkson

first: Federica

last: Cavallo

first: Christine

last: Watson

first: Piero

last: Musiani

first: Valeria

last: Poli


title: Probiotic-induced differential gene expression during Salmonella challenge in neonatal chicks

status: Public on Jan 14 2010

city: College Park

first: Tom

middle: E.

last: Porter

address: Building 142

department: Animal and Avian Sciences

institute: University of Maryland

summary:
Salmonella remains an important enteric pathogen of poultry, primarily due to concerns regarding food-borne illness in humans consuming contaminated poultry products.  Specific probiotic cultures are efficacious as a treatment for neonatal poultry to prevent enteric infections (competitive exclusion) due to the exquisite susceptibility of young chicks to pathogens in the hatchery and brooding environment.  The objective of this experiment was to analyze transcriptional profiles in the ceca of neonatal chicks using the Arizona Gallus gallus 20.7K Oligo Array v1.0, following treatment with a probiotic culture derived from poultry with and without Salmonella enterica subsp. Enteritidis (SE) challenge.  Chicks were obtained from a commercial hatchery, and challenged with SE upon arrival at the laboratory. One hour post-challenge, chicks were treated with a probiotic culture (FM-B11).  Treatment groups included: Control (no challenge or treatment, vehicle only), SE (challenged only), B11 (treated only) and SE+B11 (challenged and treated).  Samples were obtained at 12h and 24h post-treatment.  We observed that administration of a Lactobacillus-based probiotic culture to chicks following challenge with SE reduced SE colonization of the cecae and resulted in differential expression of genes in the cecae. Among all four treatment groups, 309 genes were differentially expressed (p<0.05) at 12h, and 352 genes were differentially expressed (p<0.05) at 24h.

Keywords: disease state analysis

overall_design: Eight experimental groups with 4 replicates each were analyzed.  A reference RNA design was used for this microarray. Equal amounts of amplified RNA (aRNA) from all samples were pooled and labelled with the Alexa 647 to create the reference pool.  Each individual sample was labelled with Alexa 555.  Each slide was hybridized with both the reference pool and one sample.

first: S

last: Higgins

first: T


title: Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array

city: Beijing

first: Kunlin

last: Zhang

address: DaTun Road A4

country: China

institute: Chinese Academy of Sciences

summary: Methylated DNA enrichment is a key step in a microarray based genome-wide methylation profiling study, and even for future high-throughput sequencing based methylome analysis. In order to evaluate the sensitivity and accuracy of methylated DNA enrichment, we investigated and optimized a number of important parameters to improve the performance of several enrichment assays, including differential methylation hybridization (DMH), microarray-based methylation assessment of single samples (MMASS), and methylated DNA immunoprecipitation (MeDIP). With advantages and disadvantages unique to each approach, we found that assays based on methylation-sensitive enzyme digestion and those based on immunoprecipitation detected different methylated DNA fragments, indicating that they are complementary in their relative ability to detect methylation differences. Our study provides the first comprehensive evaluation for widely used methodologies for methylated DNA enrichment, and could be helpful for developing a cost effective approach for DNA methylation profiling.

overall_design: We optimized several of the experimental parameters in three DNA enrichment methodologies, DMH (-v1 and -v2), MMASS (-v1 and -v2), and MeDIP. For DMH and MMASS assays, where the digested DNA products are amplified using PCR, we assessed the impact of annealing temperature (65°C, 68.5°C, and 72°C) in the PCR amplification of the digested products, and for MeDIP we looked at the incubation time of the 5-methylcytosine antibodies (2 hours and 12 hours) and secondary antibody during immunoprecipitation (1 hour, 2 hours, 3 hours, 4 hours, and 6 hours). Then these three DNA enrichment approaches were utlized to compare the differential methylation profiling of the gastric epithelium cell line Ges-1 and the gastric adenocarcinoma cell line MGC-803.

first: Liu

last: Yang

first: Wei

last: Dai

first: Ximiao

last: He

first: Qian

last: Zhao

first: Jing

last: Wang

first: Zhong

middle: S

last: Sun


title: Multi-component epigenetic control of pro-invasive genes in cancer cells (miRNA)

status: Public on Jan 05 2010

city: La Jolla

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary:
To identify the epigenetic signature that controls cancer cell migration, we performed integrated gene expression, miRNA and epigenetic profiling of 486 selected invasion-associated genes in non-migratory MCF-7 breast carcinoma and highly migratory U251 glioma cells. We used a custom-built chromatin immunoprecipitation (ChIP)-on-Chip microarray that included complimentary oligonucleotide probes for the genes that were functionally linked to proteolysis, migration and tumorigenesis such as extracellular matrix proteins, cellular proteinases and their inhibitors, growth factors and cytokines, and adhesion and signaling receptors. As a result, we determined the role histone H3 modifications [(Lys-4 dimethylation (H3K4me2), Lys-27 trimethylation (H3K27me3) and acetylation (H3ac)] play in transcriptional regulation of the multiple invasion-associated genes. Predominantly, transcriptional silencing of the pro-invasive genes in MCF-7 cells involved the repressive H3K27me3 mark and, frequently, the presence of the stem cell-like bivalent epigenetic mark (enrichment in both H3K27me3 and H3K4me2). In turn, pro-invasive genes in U251 cells were epigenetically stimulated by a gain in H3K4me2 and histone H3 hyperacetylation, and by a global reduction of H3K27me3. Intriguingly, the expression of multiple collagen genes was highly enhanced in glioma cells, thus suggesting that gliomas themselves deposit a specialized, invasion-promoting matrix.
miRNA global profiling complements the ChIP-on-Chip experiment with U251 and MCF-7 cells.

overall_design: Two-condition experiment, MCF7 vs.U251 cells. 2 Biological replicates for each cell line

first: Alex

middle: Y

last: Strongin


title: Cross-platform expression microarray performance in a mouse model of mitochondrial disease therapy

status: Public on Jan 11 2010

city: Philadelphia

first: Marni

last: Falk

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics/ Human Genetics

institute: CHOP

summary: Microarray expression profiling has become a valuable tool in the evaluation of the genetic consequences of metabolic disease.  Although 3’-biased gene expression microarray platforms were the first generation to have widespread availability, newer platforms are gradually emerging that have more up-to-date content and/or higher cost efficiency.  Deciphering the relative strengths and weaknesses of these various platforms for metabolic pathway level analyses can be daunting.  We sought to determine the practical strengths and weaknesses of four leading commercially-available expression array platforms relative to biologic investigations, as well as assess the feasibility of cross-platform data integration for purposes of biochemical pathway analyses.  METHODS: Liver RNA from B6.Alb/cre,Pdss2loxP/loxP mice having primary Coenzyme Q deficiency was extracted either at baseline or following treatment with an antioxidant/antihyperlipidemic agent, probucol.  Target RNA samples were prepared and hybridized to Affymetrix 430 2.0, Affymetrix Gene 1.0 ST, Affymetrix Exon 1.0 ST, and Illumina Mouse WG-6 expression arrays. Probes on all platforms were re-mapped to coding sequences in the current version of the mouse genome. Data processing and statistical analysis were performed by R/Bioconductor functions, and pathway analyses were carried out by KEGG Atlas and GSEA.  RESULTS: Expression measurements were generally consistent across platforms.  However, intensive probe-level comparison suggested that differences in probe locations were a major source of inter-platform variance.  In addition, genes expressed at low or intermediate levels had lower inter-platform reproducibility than highly expressed genes.  All platforms showed similar patterns of differential expression between sample groups, with ‘steroid biosynthesis’ consistently identified as the most down-regulated metabolic pathway by probucol treatment. CONCLUSIONS: This work offers a timely guide for metabolic disease investigators to enable informed end-user decisions regarding choice of expression microarray platform best-suited to specific research project goals.  Successful cross-platform integration of biochemical pathway expression data is also demonstrated, especially for well-annotated and highly-expressed genes.  However, integration of gene-level expression data is limited by individual platform probe design and the expression level of target genes.  Cross-platform analyses of biochemical pathway data will require additional data processing and novel computational bioinformatics tools to address unique statistical challenges.

overall_design: 4 samples are analyzed on each of 4 different Mouse Microarray Expression platforms (Affymetrix Mo430 2.0, Affymetrix Gene, Affymetrix Exon 1.0 ST, and Illumina Whole Genome 6).

first: Zhe


title: Postnatal intestinal response of IUGR piglets to high proteins before weaning

status: Public on Jan 01 2010

city: Saint-Gilles

first: Isabelle

last: Luron

state: Rennes

address: Domaine de la Prise

department: Human Nutrition Division

institute: National Institute for Agronomical Research (INRA)

summary:
Comparison of distal small intestine in IntraUterine Growth Restricted piglets fed either adequate or high protein artificial milks during suckling period. Comparison at 7 and 28 days of life.

Keywords: Nutritional response

overall_design: 22 samples - One sample versus a pool

first: Romain

last: d'Inca

first: Agnès

last: Jamin

first: Véronique

last: Romé

last: Le Huerou-Luron

first: Gaëlle

last: Boudry


title: Altered genes expression profile of Rep2 mutants in Fission Yeast upon HU treatment.

status: Public on Jan 08 2010

first: Zhaoqing

last: Chu

address: 60, Biopolis Streat

summary:
Expression profiles indicate that C-terminal of rep2 is essential for its transactivation activity.
Keywords: rep2 mutants cells treated with 8 mM HU for different time points vs wildtype untreated cells

overall_design: We analyzed 40 arrays for rep2 mutants cells treated with 8 mM HU to wild type cells.

first: Jianhua

last: Liu


title: The genome of a songbird

status: Public on Jan 16 2010

city: Durham

first: Osceola

last: Whitney

address: Research Drive, Bryan Research Building, Room 401E

department: Neurobiology

summary: This study was part of a larger study on the zebra finch genome (Warren et al 2010. Nature). Here we present a summary of the specific experiment on singing-regulated gene expression. To evaluate the genomic landscape of learned vocal communication, we profiled gene expression in the zebra finch song nucleus, Area X, with custom Agilent oligoarrays for up to seven hours following initiation of singing. We developed algorithms to identify singing-regulated transcripts related to time spent singing, and discovered over 800 transcripts in Area X that are significantly regulated by singing. These included known increases of the egr1 and c-fos transcription factors, and a decrease in the FoxP2 transcription factor, a gene associated with spoken language development. We clusted the singing-regulated genes in Area X into 20 temporal dynamic expression patterns, which include rapidly up-regulated and transient, rapidly up-regulated and sustained, slowly up-regulated and sustained, a late upregulated response, and equally diverse clusters of down-regulated patterns. Using promotor motif search algorithms, we found significant over-representation of transcription factor binding sites in the promoters of genes within specific clusters. These binding sites included those of transcription factors known to be activated by neural activity and plasticity, such as CREB, SRF, AP-1, NFKB1, CFOS, EGR1, and MEF2.

overall_design: Gene expression in Area X was measured before singing (0) or after singing for 0.5, 1, 2, 3, 4, 5, 6, and 7hours.  Six independent experiments were performed at each of the 9 timepoints.

first: Andreas

last: Pfenning

first: Jason

last: Howard

first: Charles

last: Blatti

first: Saurabh

last: Sinha

first: Erich

last: Jarvis


title: Prionic protein gene dosage is critical for maintenance of neuronal homeostasis of hippocampal circuits

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

summary:
We demonstrate that Prnp dosage is critical for the maintenance of neuronal homeostasis since both its absence and, more relevantly, its overexpression induce higher sensitivity to kainate (KA) damage. These data correlate with electrophysiological results in freely behaving mutant mice showing an imbalance in activity-dependent synaptic processes, as determined from input/output curves, paired-pulse facilitation, and LTP studies. Gene expression profiling showed that 129 genes involved in canonical pathways such as Ubiquitination or Neurotransmission among  others were co-regulated in knockout and PrPc overexpressing mice. RT-qPCR  analysis of neurotransmission-related genes confirmed GABA-A and AMPA-Kainate  receptor subunit transcriptional co-regulation in both Prnp -/- and Tg20 mice. Our results demonstrate that PrPc is necessary for the proper homeostatic functioning of hippocampal circuits, because of its interactions with GABAA and AMPA-Kainate  receptors.

Keywords: steady state expression; adult brain tissue; hippocampus; genetic modification; transgenic gain of function mutation; targetted deletion loss of function mutation

overall_design: We performed a global transcriptome analysis of three strains that differ in their Prnp gene dose using Illumina Sentrix 6 mouse v1.1 beadarrays. We analyzed mRNA expression in the hippocampi of four individual male mice from each of three strains: 1) Tg20, with a 30 exogenous copies of the Prnp gene within a Prnp -/- background that overexpresses PrPc about 6-7 times the normal wild type levels; 2) littermates lacking the transgene and therefore carrying only the homozygous knock out Prnp -/- strain  which lacks expression of PrPc; and 3) their wild type counterparts carrying two copies of the intact Prnp gene and expressing normal levels of PrPc

first: Jose

last: Del Rio

first: Alejandra

last: Rangel


title: microRNA expression profiles in Aromatase Inhibitor-Resistant, Tamoxifen-Resistant and LTED breast cancer cell lines.

city: Duarte

first: Selma

last: Masri

address: 1500 E Duarte Rd

department: Tumor Cell Biology

institute: City of Hope

summary: Resistance to endocrine therapy agents has presented a clinical obstacle in the treatment of hormone-dependent breast cancer.  Our laboratory has initiated a study of microRNA regulation of signaling pathways that may result in breast cancer progression on aromatase inhibitors (AI).  Microarray analysis of microRNA expression identified 115 significantly regulated microRNAs, of which 49 microRNAs were believed to be hormone-responsive.  Within the AI-resistant cells, microRNAs were differentially expressed between the steroidal and non-steroidal AI-resistant lines.  Also, a group of microRNAs were inversely expressed in the AI-resistant lines versus LTEDaro and tamoxifen-resistant.  We focused our work on hsa-miR-128a which was hormone-responsive and up-regulated in the letrozole-resistant cell lines.  Human miR-128a was shown to negatively target TGFBRI protein expression by binding to the 3’UTR region of the gene.  Loss of TGFBRI resulted in compromised sensitivity to the growth inhibitory effects of TGFB in the letrozole-resistant lines.  Inhibition of endogenous miR-128a resulted in re-sensitization of the letrozole-resistant lines to TGFB growth inhibitory effects.  This data suggests that the hormone-responsive miR-128a can modulate TGFB signaling and survival of the letrozole-resistant cell lines.  To our knowledge, this is the first study to address the role of microRNA regulation as well as TGFB signaling in AI-resistant breast cancer cell lines.  We believe that in addition to estrogen-modulation of gene expression, hormone-regulated microRNAs may provide an additional level of post-transcriptional regulation of signaling pathways critically involved in breast cancer progression and AI-resistance.

overall_design: To look at microRNA expression profiles of breast cancer cell lines derived from MCF-7 cells that are resistant to endocrine therapy agents.  MCF-7 cells that overexpress aromatase (MCF-7aro) were cultured long-term in the presence of endocrine therapy agents until cells acquired resistance.  Three different aromatase inhibitors (letrozole, anastrozole or exemestane) were used, as well as the ER antagonist tamoxifen, or the hormone-free long-term estrogen deprived cells (LTED).  Three replicates of the control cells (MCF-7aro) and all resistant cells were used for microarray experiments.  Total of 23 samples were analyzed by microarray.

first: Shiuan

last: Chen


title: Time-course analysis of intestinal postnatal response to IUGR at 0-2 and 5 days

first: Isabelle

last: Luron

summary:
Kinetic comparative study of distal small intestine and colon of IntraUterine Growth Restricted vs. normal birth weight piglets at the age of 0, 2 and 5 days of life.

Keywords: Nutritional state and time-course comparative analysis.

overall_design: 66 samples  - One sample versus a pool

first: Romain

last: d'Inca

first: Maela

last: Kloareg


title: Thyroid Hormone (TH) Controls The Remodeling Of The Pancreas And The Liver, Part B

city: Baltimore

first: Donald

last: Brown

address: 3520 San Martin Dr

department: Department of Embryology

institute: Carnegie Institution

summary:
Thyroid hormone (TH) controls the remodeling of the pancreas and the liver.  TH-induces dedifferentiation of the exocrine pancreas to a progenitor state (Proc. Nat. Acad Sci. 105, 8962-8967 (2008)) and it remodels the endocrine pancreas (Dev. Biol. 328, 384-391 (2009)). The redifferentiated frog pancreas resembles closely the pancreas of other typical vertebrates. Two pancreas arrays were carried out. The first one studied gene expression changes at different developmental stages of Xenopus laevis during metamorphosis. The second array studies gene expression changes at varying times after the addition of TH to premetamorphic tadpoles.

Keywords: co-expression design,development or differentiation design,reference design,time series design

overall_design:
Overall design: Thyroid hormone (TH) controls remodeling of the liver. The microarray was carried out to identify changes in gene expression at different stages of development during metamorphosis.  This is part 2, done on the 22K Xenopus platform version 1. This dataset was from livers of Xenopus tadpoles (NF52, NF62, and NF66). Each was made in triplicate.
Samples in all 3 parts of the study received the same thyroid hormone levels.


title: Functional Study of the Chicken microRNAs miR-143 and miR-10a

city: Raleigh

first: Nares

last: Trakooljul

address: 120 Broughton Dr

department: Animal Science

institute: North Carolina State University

summary: MicroRNA (miRNA) is a family of small regulatory RNA that post-transcriptionally regulates many biological functions including growth and development. Chicken miR-143 and miR-10a are expressed in both the embryonic and post-hatch chick in a spatio-temporal manner. In order to study the functions of these miRNAs, loss of function and microarray approaches were employed. Spleen cells were isolated from embryonic day 18 chickens and immediately transfected with either a synthetic miR-143 inhibitor or a synthetic miR-10a inhibitor or a negative control oligo-nucleotide (Dharmacon). Cultures were maintained for 48 hrs and microarray analysis was performed using the Arizona Gallus gallus 20.7K long oligoarray (GPL6049). Differentially expressed genes were identified for each miRNA by comparing the miRNA knock-down group to the negative control group. The differentially expressed genes were functionally categorized using the DAVID Functional Annotation Tool (http://david.abcc.ncifcrf.gov/). The 3’-UTR of the up-regulated genes (de-repressed after the miRNAs knock-down) were scanned for potential miR-143 or miR-10a binding sites using the miRanda algorithm version 3.1 (http://www.microrna.org/microrna). In addition, the Chicken (Gallus gallus) Unigene database (NCBI) was also used to predict potential targets of these miRNAs. A set of predicted targets for both miRNAs was selected and validated by dual luciferase reporter gene assay. Overall, many of the identified targets for miR-143 are associated with cell proliferation, tumerigenesis and apoptosis. Many of potential targets for miR-10a are associated with immune response.

overall_design: A reference designed microarray was performed in which samples (Cy3) were co-hybridized with the reference RNA pool (Cy5) on the array. The microarray data set was processed using within- and across-array loess normalization method in JMP Genomics 3.0, SAS (Cary, NC). Data quality was evaluated using the MA plots process and the correlation and grouped scatter plots procedure (JMP Genomics 3.0). Differentially expressed genes were identified using ANOVA process on JMP Genomics 3.0 with fixed effect of treatments and random effect of arrays.


title: Postnatal response of the intestine in 19 d-old IUGR piglets

summary:
Comparison of distal small intestine and colon in IntraUterine Growth Restricted versus normal birth weight piglets at the age of 19 days of life.

Keywords: Nutritional state comparative analysis.

last: Le Huerou-Luron

first: Véronique

last: Romé


title: Integration between Notch- and hypoxia-induced transcriptomes

status: Public on Dec 31 2009

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

institute: National University of Singapore (NUS)

summary: Background: Interaction between key signaling mechanisms is important to generate the diversity in signaling output required for proper control of cellular differentiation and function, although the molecular manifestations of such cross-talk are only partially understood. Notch  signaling and the cellular response to hypoxia intersect at different points in the signaling cascades, and in this report we analyze the consequences of this cross-talk at the transcriptome level.  Results: Mouse ES cells were subjected to various combinations of hypoxia and/or activated Notch signaling, and the transcriptome changes could be grouped into different categories, reflecting various modes of hypoxia and Notch signaling integration. Two principal categories of  novel Notch- and hypoxia-induced genes were identified: i) a larger set of genes induced by one pathway and not significantly affected by the activity status of the other pathway; and ii) a smaller set of genes co-regulated by Notch and hypoxia. In the latter category, we identified  genes that were induced by hypoxia and the expression of which was enhanced by active Notch signaling. In addition, a number of genes were induced by Notch and hypoxia independently, and a final category of genes required simultaneous activation of Notch and hypoxia to be  significantly induced. Several of the hypoxia- and Notch-induced genes were found to be upregulated in various forms of cancer.  Conclusions: We identify novel Notch and hypoxia downstream genes and genes co-regulated by the two pathways, providing a molecular platform to better understand the intersection between the two signaling cascades in normal development and cancer.

overall_design: Total RNA was extracted from 7 treatments in 4 biological replicates of mouse embryonic stem (ES) cells. The 7 treatments consist of 1) ES cell medium for 6 hrs (ESC), 2) N2B27 medium for 6 hrs which is the control condition (N2B27), 3) N2B27 medium supplemented with doxycyline (Dox), 4) Pretreatment with DAPT in ES cell medium for 4 hours followed by switch to N2B27 medium for 6 hours (DAPT), 5) N2B27 under 1% oxygen hypoxic conditions (1% O2), 6) N2B27 supplemented with doxycycline under 1% oxygen hypoxic conditions (1% O2+Dox), 7) Pretreatment with DAPT in ES cell medium for 4 hours followed by switch to N2B27 medium for 6 hours (DAPT) under 1% oxygen hypoxic conditions (1% O2+DAPT).

first: Heather

last: Main

first: Kian

middle: L

last: Lee

first: Henry

last: Yang

first: Saija

last: Haapa-Paananen

first: Henrik

last: Edgren

first: Shaobo

last: Jin

first: Cecilia

last: Sahlgren

first: Olli

last: Kallioniemi

first: Lorenz

last: Poellinger

first: Bing

last: Lim

first: Urban

last: Lendahl


title: Anakinra in Systemic-onset Juvenile Idiopathic Arthritis

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: Background: Systemic-Onset Juvenile Idiopathic Arthritis (SJIA) is a rare disease associated with dysregulated interleukin (IL)-1 activity.  Objectives: To assess the efficacy and safety of Anakinra, an IL-1 receptor antagonist in SJIA and its effects on gene expression profiling.  Methods: We conducted a multicenter, randomized, double-blind placebo-controlled trial. The primary objective was to compare the efficacy of a one-month treatment with anakinra (2 mg/kg subcutaneoulsy daily, maximum 100 mg) to a placebo between 2 groups of 12 SJIA patients each. Response was defined by a 30% improvement of the pediatric American College of Rheumatology criteria for JIA, resolution of systemic symptoms and a decrease of at least 50% of both C-reactive protein and erythrocyte sedimentation rate compared to baseline. An intention-to-treat analyze was performed. After Month 1 (M1), patients taking placebo were switched to Anakinra. Secondary objectives included tolerance and efficacy assessment for 12 months. Results: At M1, concluding the randomized trial, there was a significant difference in the response rate between patients treated with Anakinra (8/12 responders) and placebo (1/12) (p=0.003). The number of adverse events, mainly pain to injections, was similar between both groups. Ten patients from the placebo group switched to Anakinra at M1; nine were responders at M2. Between M1 and M12, six patients stopped treatment for an adverse event (Crohn’s disease, hepatitis), a lack of efficacy or a disease flare (2 cases each). Blood gene expression profiling at enrollment and upon follow-up allowed us to identify one set of dysregulated genes that reverted to normal values in the clinical responders and a second set, including interferon-inducible genes, that was induced by Anakinra.  Conclusion: Anakinra is an effective treatment of SJIA. Its effect is associated with normalization of blood gene expression profiles in clinical responders and de novo induction of an interferon signature. (Clinical trials registration number: NCT00339157)

overall_design: Analyses of treatment effect on blood gene expression profiling were performed on blood taken in 21 SJIA patients at D1, M1 and M6 and 21 healthy donors.


title: Regulatory T cell-mediated resolution of lung injury: Identification of potential target genes via expression profiling

first: Dmitry

middle: N

last: Grigoryev

institute: JHU

summary: We examined early and late gene expression changes using the IT LPS model of Acute Lung Injury (ALI).  In this model, injury peaks at day 4 and is almost completely resolved by day 10 in wild type (WT) C57BL/6 mice.  In contrast to the pattern in WT mice, lymphocyte-deficient Rag-1 -/- mice exhibit strikingly delayed resolution despite similar initial injury.

overall_design: Total RNA was isolated from mouse lung at time 0, 1, 4, and 10 days following LPS treatment of wild type and Rag-1 null mice using TRIzol reagent (Invitrogen Life Technologies), then purified using RNAeasy columns (Qiagen) with DNase I treatment according to the manufacturer’s recommendations.  The quality of RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).

first: Neil

middle: R

last: Aggarwal


title: Differential gene expression in murine neural stem cells (NS5) and neural stem cell-derived astrocytes

city: London

first: Caroline

middle: Emma

last: Johnston

address: 125 Coldharbour Lane

institute: Kings College London

summary:
Gene expression in NS5 murine neural stem cells was compared to that of astrocytes derived from NS5 cells via 3 days of treatment with foetal calf serum (FCS).
Keywords: cell type comparison

overall_design: Four NS5 replicates were compared to four astrocyte replicates

first: Manuela

last: Volta

first: Megan

last: Cooper

first: Kee-Yew

last: Wong

first: Lawrence

last: Stanton

first: Noel

last: Buckley

first: Angela

last: Bithell


title: Important role for secretoglobin(SCGB)3A2 in lung development

status: Public on Dec 26 2009

city: Yokohama

first: Reiko

last: Kurotani

state: Kanagawa

country: Japan

institute: Yokohama City University School of Medicine

summary:
Secretoglobin (SCGB) 3A2 was originally identified as a downstream target in lung for the homeodomain transcription factor NKX2-1, whose null mutation resulted in severely hypoplastic lungs.   A very low level of SCGB3A2 is expressed in lungs at embryonic day (E) 11.5 during mouse development, which markedly increases by E16.5, the time when lung undergoes dramatic morphological changes.  These results suggest that SCGB3A2 may be involved in lung development.  We used microarray to determine whether SCGB3A2 plays a role in lung development.
Keywords: Response to SCGB3A2

overall_design: DNA microarray was performed using RNAs isolated from 4 day-organ cultured Nkx2-1-null lungs with and without SCGB3A2 treatment.

first: Shioko

last: Kimura


title: MicroRNA transcriptional profiling in serum-starved human aortic smooth muscle cells

status: Public on Dec 25 2009

city: Stanford

first: Joshua

middle: M.

last: Spin

state: CA

address: 300 Pasteur Drive

institute: Stanford University

summary: We sought to identify microRNAs that were differentially regulated in cultured primary human aortic smooth muscle cells (SMCs) when exposed to growth arrest via serum starvation over two time points - 48 hours and 72 hours, when compared with serum-fed cells. This treatment leads to increased expression of SMC differentiation markers such as ACTA2, MYH11 and TAGLN. We identified 31 significantly regulated miRNA candidates during this process, 28 rising and 3 falling.

overall_design: Human aortic SMCs (AoSMCs) were propagated in growth media. Control plates were harvested, and the remaining plates were serum starved for 48 (SS48) or 72 hours (SS72) in serum-free basal media.  Several arrays were excluded from final analysis after QC, resulting in a final set of 10.


title: Transcription profiling of Hepatitis C – specific natural CD25pos cells

status: Public on Dec 24 2009

city: Melbourne

first: shuo

last: li

state: VIC

address: 85 Commercial road

institute: Burnet Institute

summary: We reported previously that a proportion of natural CD25+ cells isolated from the PBMC of HCV patients can further upregulate CD25 expression in response to HCV peptides stimulation in vitro, and proposed that virus-specific regulatory T cells (Treg) were primed and expanded during the disease. Here we describe epigenetic analysis of the FOXP3 locus in HCV-responsive natural CD25+ cells and show that these cells are not activated conventional T cells expressing FOXP3, but hard-wired Treg with a stable FOXP3 phenotype and function. Of ~46,000 genes analyzed in genome wide transcription profiling, about 1% were differentially expressed between HCV-responsive Treg, HCV-non-responsive natural CD25+ cells and conventional T cells. Expression profiles, including cell death, activation, proliferation and transcriptional regulation, suggest a survival advantage of HCV-responsive Treg over the other cell populations. Since no Treg-specific activation marker is known, we tested 97 NS3-derived peptides for their ability to elicit CD25 response (assuming it is a surrogate marker), accompanied by high resolution HLA typing of the patients. Some reactive peptides overlapped with previously described T cell epitopes. Our data offers new insights into HCV immune evasion and tolerance and highlights the non-self specific nature of Treg during infection.

overall_design: We analysed 6 patients, 3 different cell fractions in each patient, thus there are 18 RNA samples in total. Illumina Sentrix Human-6 Expression BeadChip-v2.0 was used for the hybridization. The microarray experiments were performed commercially by the Australia Genome Research Facility.

first: Shuo

last: Li

first: Stefan

last: Floess

first: Alf

last: Hamann

first: Silvana

last: Gaudieri

first: Andrew

last: Lucas

first: Margaret

last: Hellard

first: Stuart

last: Roberts

first: Geza

last: Paukovic

first: Magdalena

last: Plebanski

first: Bruce

last: Loveland

first: Campbell

last: Aitken

first: Simon

last: Barry

first: Louis

last: Schofield

first: Eric

last: Gowans


title: Gallus gallus utricle striola vs. extra-striola

city: St. Louis

first: David

middle: Michael

last: Alvarado

state: MO

address: 4565 Scott Ave

department: Genetics

institute: Washington University in St. Louis

summary: The inner ear utilizes sensory hair cells as mechano-electric transducers for sensing sound and balance. In mammals, these hair cells lack the capacity for regeneration. Unlike mammals, hair cells from non-mammalian vertebrates, such as birds, can be regenerated throughout the life of the organism making them a useful model for studying inner ear genetics pathways. The zinc finger transcription factor GATA3 is required for inner ear development and mutations cause sensory neural deafness in humans. In the avian cochlea GATA3 is expressed throughout the sensory epithelia; however, expression is limited to the striola of the utricle. The striola corresponds to an abrupt change in morphologically distinct hair cell types and a 180° shift in hair cell orientation. We used 3 complimentary approaches to identify potential downstream targets of GATA3 in the avian utricle. Specifically we used microarray expression profiling of GATA3 knockdown by siRNA and GATA3 over-expression treatments as well as direct comparisons of GATA3 expressing cells from the striola and non GATA3 expressing cells from the extra-striola.

platform_organism:
Gallus gallus
Homo sapiens
Mus musculus

overall_design: To identify genes that are co-expressed with GATA3 at the striola reversal zone, we compared gene expression in cells micro-dissected from the sensory epithelia of the chick utricle striola to cells from the surrounding extra-striola. There are 2 biological samples and experiments include technical replicates as well as dye-switches for a total of 8 microarrays.

first: Rose

last: Veile

first: Mark

last: Warchol

first: Michael

last: Lovett


title: Identification of potential downstream targets of GATA3 in the avian utricle

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

overall_design: Refer to individual Series


title: GATA3 overexpression in utricle sensory epithelia

overall_design: Dissociated sensory epithelia were plated in 96 well cultures, 5 wells per sample. 4 days post plating, ~ 30% confluency, cells were transfected with a pMES vector containing an internal ribosome entry site regulating expression of GATA3 and eGFP under control of a chick beta-actin promoter. Controls were transfected with a vector containing EGFP only.  There are 2 biological samples and experiments include technical replicates as well as dye-switches for a total of 8 microarrays.


title: Mental Retardation Patients

status: Public on Dec 16 2009

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary:
Profiling the genomic profiles of mental retardation patients.
13 mental retardation patients were selected for detection of genomic aberrations.

overall_design: Patient's DNA were hybridized against Promega control on Agilent G4426B arrays and scanned with the Agilent G2505B scanner.

first: Frederic

last: Lepretre

first: Joris

last: Andrieux


title: KLF2-induced actin shear fibers control both alignment to flow and JNK signaling in vascular endothelium

status: Public on Dec 11 2009

city: Amsterdam

first: Anton

last: Horrevoets

address: van der Boechorststraat 7

department: Molecular Cell Biology

institute: VU University Medical Center

type:
Expression profiling by array
Protein profiling by protein array

summary: The shear stress-induced transcription factor Krüppel-like factor 2 (KLF2) confers anti-inflammatory properties to endothelial cells through inhibition of activator protein 1, presumably by interfering with MAPK cascades. To gain insight into the regulation of these cascades by KLF2, we used antibody arrays in combination with time-course mRNA micro-array analysis. No gross changes in MAPKs were detected, rather phosphorylation of actin cytoskeleton-associated proteins, including Focal Adhesion Kinase, was markedly repressed by KLF2. Furthermore, we demonstrate that KLF2-mediated inhibition of Jun NH2-terminal kinase (JNK) and its downstream targets ATF2/c-Jun is dependent on the cytoskeleton. Specifically, KLF2 directs the formation of typical short basal actin filaments, we term shear fibers, which are distinct from thrombin- or TNF-α-induced stress fibers. KLF2 is shown to be essential for shear stress-induced cell alignment, concomitant shear fiber assembly and inhibition of JNK signaling. These findings link the specific effects of shear-induced KLF2 on endothelial morphology to the suppression of JNK MAPK signaling in vascular homeostasis via novel actin shear fibers.

overall_design:
Tramscriptome profiling: Three independent isolates of Human Umbilical Vein Endothelial cells were transduced with lentiviral vectors expressing Kruppel Like Factor 2 (KLF2) or no protein (mock), and at time after transduction 24 h, 48 h, 72 h , RNA was isolated and hybridized to GPL4868 microarrays using dye swap procedure
Kinome profiling: Two independent isolates of Human Umbilical Vein Endothelial cells were transduced with lentiviral vectors expressing Kruppel Like Factor 2 (KLF2) or no protein (mock), and at time after transduction 72 h , total cellular protein was isolated and hybridized to Kinexus KAM-1.1 phosphoprotein (kinexus) microarrays using dual color procedure in duplicate

first: Reinier

middle: A

last: Boon


title: Differential gene expression in Danio rerio during optic nerve regeneration

city: San Marcos

first: Dana

last: Garcia

address: 601 University Drive

department: Biology

institute: Texas State University-San Marcos

summary: To gain a better understanding of the factors necessary for successful CNS regeneration, a temporal analysis of the changes in gene expression in the eye caused by optic nerve injury was conducted.  Dual color oligonucleotide microarrays were used to compare total RNA harvested from the eyes of sham-operated and optic nerve-injured fish at 3, 24, and 168 hours following surgery. Optic nerve injured fish are compared to sham-operated fish in order to eliminate gene expression due to non-neuronal damage and inflammatory response. Statistical analyses identified 131 genes with a 2.0-fold or greater difference in expression.

overall_design: Wild type zebrafish were obtained from a local pet store. Optic nerve injury was conducted using a severing model accomplished as follows. Zebrafish were anesthetized in 0.2% MS-222 dissolved in tank water.  The muscles surrounding the eye were cut and the eye angled rostrally to expose the nerve. The optic nerve was then severed using microsissors without damaging the ophthalmic artery. In sham operated fish the muscles surrounding the eye were severed but the nerve was not damaged. RNA was extracted from the eye at three time points following surgery 3 hours, 24 hours, and 168 hours. RNA was pooled from multiple fish to achieve 10 ug total RNA.  Samples were collected in triplicate per time point. Gene expression was analyzed on a dual color oligonucleotide array where the optic nerve injured fish were compared to sham-operated fish. Four samples of RNA were also collected from control fish and compared to each other on the microarray to confirm that processing did not create expression differences.

first: Katherine

middle: E

last: Saul

first: Joseph

last: Koke


title: GATA3 siRNA in utricle sensory epithelia

overall_design: Whole utricle specimens were treated with streptomycin for 24 hrs, rinsed and allowed to recover for an additional 24 hrs. Whole utricles were transfected with either GATA3 or GFP 21mer synthetic siRNAs for an additional 48 hrs and pure sensory epithelia were isolated.  There are 2 biological samples and experiments include technical replicates as well as dye-switches for a total of 8 microarrays.


title: Widespread and tissue specific age-related DNA methylation changes in mice

status: Public on Dec 09 2009

city: Houston

first: Jiexin

last: Zhang

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

type: Methylation profiling by genome tiling array

summary: genomic DNA is isolated from C57BL/6 mice intestine at 3.1 months old females and 35.2 months old male.  We used MCAM to identify genes that have age-related methylation changes.

overall_design: Two-condition experiment, old vs. young mice intestine.

first: Shinji

last: Maegawa

first: Jean-Pierre

last: Issa


title: Expression profiling of MRC5 senescent fibroblasts

status: Public on Dec 15 2009

city: Bethesda

first: Ana

middle: I

last: Robles

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

summary:
Microarrays analysis identifies WNT16in senescent fibroblasts.
To identify genes expressed in replicative senescence, microarray experiments were conducted in which we compared the RNA expression profile of young MRC5 fibroblasts at population doubling 28 (PDL28) and replicative senescent MRC5 fibroblasts at PDL63. In total, 177 gene probes were upregulated and 338 gene probes were downregulated in senescent versus young MRC5 fibroblasts. Genes were classified based on mapping to KEGG pathways. Upregulated genes were enriched in three KEGG pathways, the Wingless-type MMTV integration site (WNT) signaling pathway (WNT16, PLCB4, CCND2, SFRP1, WNT5B, RAC2), cytokine-cytokine receptor interaction (TNFRSF10D, TNFRSF10B, TNFRSF10C, IL1R2, IL18, VEGFC), and the p53 signaling pathway (CDKN1A, TNFRSF10B, PERP, STEAP3, ZMAT3). Repressed genes were enriched in three KEGG pathways, cell cycle (PKMYT1, CDC7, CCNE2, MCM4, BUB1, CDC25A, CDKN1B, MCM6, PLK1, CDKN2C, CCNB2, MCM3, BUB1B, CCNA2, CDC2), cytokine-cytokine receptor interaction (KITLG, IL11, TNFSF4, CCL2, PDGFRA, TNFRSF11B, TGFBR1, IL1R1, TNFRSF19), and DNA replication (POLE, RFC2, MCM4, RNASEH2B, POLA1, DNA2, MCM6, PRIM1, RFC4, MCM3). Along with p53 transcriptional targets (CDKN1A, PERP, WIG1), genes encoding secreted factors (WNT16, MMP10, MMP3) were among the most strongly increased in senescent cells.

overall_design: Six arrays were hybridized with complex probes consisting of RNA isolated from MRC5 fibroblasts at population doubling 63 (undergoing replicative senescence) and RNA isolated from MRC5 fibroblats at population doubling 28 (young). The six arrays correspond to three biological replicates, each with a dye-swap technical replicate.

first: Curtis

middle: C

last: Harris

first: Remy

last: Pedeux


title: Thyroid Hormone (TH) Controls The Remodeling Of The Pancreas And The Liver

first: Donald

last: Brown


title: AMD3100 and G-CSF Mobilize Different CD34+ Cell Populations Based on Gene and miRNA Expression

status: Public on Dec 05 2009

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

institute: Sidra Medical and Research Center

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

summary: Plerixafor (AMD3100) and G-CSF mobilize peripheral blood stem cells (PBSCs) by different mechanisms. A rhesus macaque model was used to compare plerixafor and G-CSF-mobilized CD34+ cells. Three PBSC concentrates were collected from 3 macaques treated with G-CSF, plerixafor, or plerixafor plus G-CSF. CD34+ cells were isolated by immunoselection and were analyzed by global gene and micro RNA (miR) expression microarrays. Unsupervised hierarchical clustering of the gene expression data separated the CD34+ cells into three groups based on mobilization regimen. Plerixafor-mobilized cells were enriched for B cells, T cells and mast cells genes and G-CSF-mobilized cells were enriched for neutrophils, and mononuclear phagocytes (MPs) genes. Genes up-regulated in plerixafor plus G-CSF-mobilized CD34+ cells included many that were not up-regulated by either agent alone. Two hematopoietic progenitor cell miR, miR-10 and miR-126, and a dendritic cell miR, miR-155, were up-regulated in G-CSF-mobilized CD34+ cells. A pre-B cell acute lymphocytic leukemia miR, miR-143-3p, and a T cell miR, miR-143-5p, were up-regulated in plerixafor plus G-CSF-mobilized cells. The composition of CD34+ cells is dependent on the mobilization protocol. Plerixafor-mobilized CD34+ cells include more B, T, and mast cell precursors while G-CSF-mobilized cells have more neutrophil and MP precursors.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
human gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus macacae

overall_design: Three rhesus macaques were given all three mobilization protocols and PBSCs were collected from each of these three animals. Two monkeys were given plerixafor first, one was given G-CSF first and all three were given plerixafor plus G-CSF last. This resulted in 6 samples (CD34+ and CD34- cells from each of the 3 mobilizations) from each of the 3 individual animals (biological replicates).


title: Transcriptome analysis of rice in relation to infection with rice tungro spherical virus (RTSV)

status: Public on Dec 07 2009

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

institute: NARO/HARC


title: Duck versus Chicken

status: Public on Dec 03 2009

city: Saint Louis

first: Kara

last: Powder

address: 4566 Scott Ave

institute: Washington University in St Louis

summary:
Avian beaks show extreme species-specific variability in morphology, though they develop from the same primordial structures. In both humans and birds, cranial neural crest cells are the primary source of mesenchyme for the frontonasal prominence; previous work has shown that these cells contain molecular information that regulate species-specific facial variation.  To determine the molecular basis of avian craniofacial patterning, we have gene expression profiled micro-dissected cranial neural crest cells from the frontonasal prominence of three bird species (chickens, quails, and ducks) during embryonic development.  These changes in gene expression were measured on a custom built, cross-species, long oligonucleotide microarray that interrogates the vast majority of transcription factor (TF) genes plus a wide variety of signaling pathways.  Samples were isolated at two developmental stages, before (Hamburger Hamilton stage [HH] 20) and after (HH25) morphological distinctions between the species are evident.
Keywords: cross-species comparison

sample_organism:
Anas platyrhynchos
Gallus gallus

overall_design: Frontonasal mesenchymal cells were micro-dissected two developmental stages, before (Hamburger Hamilton stage [HH] 20) and after (HH25) morphological distinctions between the species are evident.  For each sample, mesenchyme from 40 embryos was pooled. For each stage-matched comparison between duck and chicken, experiments include technical replicates as well as dye-switches for a total of 14 microarrays.

first: Samantha

last: Brugmann

first: Jill

last: Helms

first: Michael

last: Lovett


title: Saccharomyces cerevisiae cells: effect of Top2 depletion without accumulation of positive superhelical stress

city: Barcelona

first: Benjamin

last: Pina

address: Jordi Girona, 18

institute: IDAEA-CSIC

summary: Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in Δtop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the  genome) are gradually unaffected. This positional effect denotes that chromosomal ends are topologically open, thus precluding the accumulation of DNA helical stress in telomere-proximal regions. The progressive escape from the transcription stall observed in all the chromosome extremities indicates also that friction restrictions to DNA twist diffusion, rather than tight topological boundaries, suffice to confine DNA helical tension along eukaryotic chromatin.

overall_design: Two-condition experiment, JCW25 vs top2-ts-TOPA (JCW26). 3 biological replicates per condition and time point, independently grown in leu- selective media and harvested.

first: Ricky

last: Joshi

first: Joaquin

last: Roca

last: Piña


title: Duck versus Quail

sample_organism:
Anas platyrhynchos
Coturnix japonica

overall_design: Frontonasal mesenchymal cells were micro-dissected two developmental stages, before (Hamburger Hamilton stage [HH] 20) and after (HH25) morphological distinctions between the species are evident.  For each sample, mesenchyme from 40 embryos was pooled.  For each stage-matched comparison between duck and quail, experiments include technical replicates as well as dye-switches for a total of 17 microarrays.


title: Expression Analysis of Mammary Epithelial Cells Isolated from 12-16 Week Old Virgin C57Bl6 Lrp5+/+ and Lrp5-/- Mice

status: Public on Dec 01 2009

city: Madison

first: Caroline

last: Alexander

state: WI

address: 1400 University Avenue

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin-Madison

summary:
Investigation of whole-genome gene expression level changes in C57Bl6 Lrp5-/- mammary epithelial cells, compared to the wild-type strain. The mammary epithelial cells were isolated from numbers 4 and 5 mammary glands.
The Lrp5-/- mouse strain described in this study has been further described in Lindvall C, Evans NC, Zylstra CR, Li Y, Alexander CM, Williams BO. 2006. The Wnt signaling receptor Lrp5 is required for mammary ductal stem cell activity and Wnt1-induced tumorigenesis. J Biol Chem. 2006 Nov 17;281(46):35081-7. Epub 2006 Sep 13. PMID: 16973609.

overall_design: Mammary epithelial cells were isolated from 6 groups of Lrp5+/+ and 3 groups of Lrp5-/- mice. The isolated RNA was submitted to the Gene Expression Center, University of Wisconsin-Madison where it was labelled with Cy3. Labelled samples were submitted to Roche Nimblegen and were hybridized to Mus musculus 1-Plex arrays that represent 42,586 mouse genes.


title: Kainic acid-administered Rat brain: control vs Ketogenic diet-fed

status: Public on Dec 02 2009

city: Gangneung

first: Dojun

last: Yoon

state: Gangwon

address: 522 Naegokdong

department: Biochemistry, Medical College

institute: Kwandong University

summary: The ketogenic diet has long been used to treat epilepsy, but its mechanism is not yet clearly understood. To explore the potential mechanism, the changes in gene expression induced by the ketogenic diet in the rat kainic acid (KA) epilepsy model were analyzed.

overall_design: Two-condition experiment, Normal diet-fed rat brain vs. Ketogenic diet-fed rat brain. Duplicate per array


title: Intra-species comparisons

summary:
Avian beaks show extreme species-specific variability in morphology, though they develop from the same primordial structures. In both humans and birds, cranial neural crest cells are the primary source of mesenchyme for the frontonasal prominence; previous work has shown that these cells contain molecular information that regulate species-specific facial variation.  To determine the molecular basis of avian craniofacial patterning, we have gene expression profiled micro-dissected cranial neural crest cells from the frontonasal prominence of three bird species (chickens, quails, and ducks) during embryonic development.  These changes in gene expression were measured on a custom built, cross-species, long oligonucleotide microarray that interrogates the vast majority of transcription factor (TF) genes plus a wide variety of signaling pathways.  Samples were isolated at two developmental stages, before (Hamburger Hamilton stage [HH] 20) and after (HH25) morphological distinctions between the species are evident.
Keywords: developmental time point comparison

sample_organism:
Anas platyrhynchos
Gallus gallus
Coturnix japonica

overall_design: Frontonasal mesenchymal cells were micro-dissected two developmental stages, before (Hamburger Hamilton stage [HH] 20) and after (HH25) morphological distinctions between the species are evident.  For each sample, mesenchyme from 40 embryos was pooled. For each species, the early stage of development was compared to the later stage.  Experiments include technical replicates as well as dye-switches for a total of 4 microarrays per species.


title: Selective inhibition of yeast regulons by daunorubicin

status: Public on Dec 08 2009

summary:
The antitumor drug daunorubicin exerts some of its cytotoxic effects by binding to DNA and inhibiting the transcription of different genes. We analysed this effect in vivo transcriptome level using the budding yeast Saccharomyces cerevisiae as a model and sublethal  concentrations of the drug to minimise general toxic effects. The effects of daunorubicin treatment on the yeast transcriptome are consistent with a model in which this drug impairs binding of different transcription factors by competing for their DNA binding sequences, therefore limiting their effectiveness and affecting the corresponding regulatory networks. This proposed mechanism might have broad therapeutic implications against cancer cells growing under hypoxic conditions.

Keywords: Time course experiment (treated versus non-treated)

overall_design: Treatment with a single concentration of daunorubicin (DNR, 12 mM, IC40) for 1 or 4 hours. Three biological replicates for each sampling time (0, 1 and 4h). Untreated cultures were used as controls.

first: Marta

last: Rojas

first: José

last: Portugal


title: Molecular basis of species-specific variation in beak morphology