title: Transcriptional signature of IFN-alpha in the non-side population of ovarian cancer cells

status: Public on Mar 25 2009

city: Padova

first: Alberto

last: Corradin

state: PD

address: via Tiepolo

department: Dipertimento di Ingegneria dell'Informazione

institute: Università degli Studi di Padova

summary:
To determine the IFN-alpha signature in non-side population of ovarian cancer
Keywords: response to interferon-alpha

overall_design: Affymetrix microarrays for non Side Population cells. 2 phenotypes: treated with interferon alpha and untreated; 2 technical replicates for each phenotypes.

last: Amadori

first: Stefano

last: Indraccolo

first: Lidia

last: Moserle


title: TGFβ/mutant-p53 jointly controlled genes

status: Public on Apr 03 2009

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary:
TGFβ ligands act as tumor suppressors in early stage tumors but are paradoxically diverted into potent prometastatic factors in advanced cancers. The molecular nature of this switch remains enigmatic. We now show that TGFβ-dependent cell migration, invasion and metastasis are empowered by mutant-p53.
To investigate the specific gene expression program by which mutant-p53 and TGFβ control invasion and metastasis in breast cancer cells, we compared the TGFβ transcriptomic profile of control and mutant-p53 depleted MDA-MB-231 cells.

Keywords: expression profiling by array

overall_design: MDA-MB-231 cells, stably expressing either control (shGFP) or anti-p53 (shp53) short-hairpin RNAs, were left untreated or treated with TGFbeta. Samples were then processed for total RNA extraction and hybridization on Affymetrix microarrays. Four biological replicas (A, B, C, D) were used for each of the 4 conditions (1: untreated control; 2: TGFbeta treated control; 3: untreated p53-depleted cells; 4: TGFbeta treated mutant-p53-depleted cells), for a total of 16 samples.

first: Maddalena

last: Adorno

first: Michelangelo

last: Cordenonsi

first: Marco

last: Montagner

first: Sirio

last: Dupont

first: Christine

last: Wong

first: Byron

last: Hann

first: Aldo

last: Solari

first: Sara

last: Bobisse

first: Maria-Beatrice

last: Rondina

first: Enza

last: Guzzardo

first: Anna

last: Parenti

first: Antonio

last: Rosato

first: Allan

last: Balmain

last: Piccolo


title: The effect of a dexamethasone and a FK506 on the induction of chemokines in human mast cells

status: Public on Mar 12 2009

city: Chicago

first: Atsushi

last: Kato

state: IL

address: 240 E. Huron St.

department: Allergy-Immunology Division

country: USA

institute: Northwestern University Feinberg School of Medicine

summary: Mast cells produce a large amount of several chemokines after cross-linking of FceRI and participate in the pathogenesis of allergic diseases. The objective of this study was to comprehensively investigate FceRI-mediated chemokine induction in human mast cells and the effect of a corticosteroid (dexamethasone) and a calcineurin inhibitor (FK506). Human peripheral blood-derived mast cells were stimulated with anti-IgE antibody in the presence of dexamethasone or FK506. Expression of eight chemokines was significantly induced in mast cells by anti-IgE stimulation. Induction of CCL2, CCL7, CXCL3 and CXCL8 by anti-IgE was significantly inhibited by dexamethasone. In contrast, induction of CCL1, CCL3, CCL4 and CCL18 was significantly inhibited by FK506. Combination of dexamethasone and FK506 suppressed production of all chemokines by anti-IgE stimulation. These results suggest that corticosteroids and calcineurin inhibitors inhibit expression of distinct subsets of chemokines and a combination of these drugs almost completely suppresses the induction of all chemokine genes in human mast cells in response to FceRI-dependent stimulation.

overall_design: Human peripheral blood-derived mast cells were stimulated with anti-IgE antibody in the presence of dexamethasone or FK506. Gene expression profiles were evaluated using GeneChip Human Genome U133 plus 2.0 probe arrays (Affymetrix).

first: Hirohisa

last: Saito

first: Kenji

last: Matsumoto


title: Gene expression profile of lung tumors

status: Public on Mar 11 2009

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary:
We have investigated whether the early dissemination of tumor cells into bone marrow is associated with a specific molecular pattern in primary lung cancer
Keywords: primary lung tumor tissue and normal bronchial epithelial tissue

overall_design: two groups of primary lung adenocarcinomas were compared differentiating in the metastatic potential

first: Harriet

last: Wikman

first: Michaela

last: Wrage


title: Tumor Growth and Prognosis of Squamous Cell Carcinoma of the Head and Neck is Linked to Protein Kinase C Alpha

status: Public on Mar 22 2009

city: Nashville

middle: H.

last: Chung

state: TN

address: 777 PRB

department: Internal Medicine

institute: Vanderbilt University

summary:
Protein Kinase C alpha (PKC) is a critical mediator of cell signaling and cancer growth. We show that PKC inhibitors decrease proliferation in squamous cell carcinoma of the head and neck (SCCHN) cells and abrogate growth of SCCHN tumors in mouse xenografts. Analysis of gene expression arrays reveals that PKC regulates cell cycle genes required for DNA synthesis.  In particular, PKC increases cyclin E protein expression, cyclinE/cdk2 complex formation, and transcription of cyclin E and E2F target genes.  Consistent with this mechanism, expression of cyclin E rescues the block in DNA synthesis caused by PKC inhibition.  In SCCHN tissue, PKC and cyclin E expression increase progressively from normal and dysplastic to malignant human head and neck tissue.   Furthermore, PKC  expression correlates with poor prognosis in SCCHN. These results demonstrate that PKC regulates growth by stimulating DNA synthesis through cyclin E and E2F and identify PKC as a therapeutic target that is highly expressed in aggressive SCCHN.
Keywords: time course; dose response

overall_design: 9 samples composed of treated replicates at three time points

middle: H

first: Joel

middle: S

last: Parker


title: Quercetin effect on gene expression in HepG2 hepatocellular cancer cells

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

department: Medicine

country: Greece

institute: University of Crete

summary: Quercetin is a flavonol modifying numerous cell processes with potent antiproliferative effects on cancer cell-lines. The aim of this study was to explore by gene-array analysis the effect of quercetin on cancer-related gene expression in HepG2 cells, followed by verification with RT-PCR and analysis of the expected phenotypic changes (migration, cell cycle, cell proliferation). Quercetin induces significant changes on cell-adhesion related genes, leading to reduced migratory capacity and disorganization of the actin cytoskeleton. Several genes related to DNA functions, cellular metabolism and signal-transducer activities were also modified, while an early effect on G–protein related cascades possibly via protease-activated receptor 2 and phospholipase C-γ1 was identified. Cyclin-D associated events in G1 and ubiquitin-dependent degradation of cyclin-D1 were also affected, resulting in cell-cycle arrest without activation of apoptosis pathways. In conclusion quercetin (3μM) exerts its cellular effects by modifying numerous genes related to mechanisms involved in cancer initiation and promotion.

overall_design: HepG2 cells were serum starved for 24 hours and were then treated with serum free medium with or without quercetin (3μM). Total RNA was collected at 2, 4, 12 and 24 hours and was used for gene-array experiments.

first: Artmisia-Phoebe

last: Nifli

first: Marilena

last: Kampa

first: Vasiliki

last: Pelekanou

first: Joseph

last: Vercauteren

first: Elias

last: Castanas


title: Expression data from human foetal neural stem (NS) cell lines and human glioma neural stem (GNS) cell lines

status: Public on Mar 13 2009

city: Cambridge

first: Steven

middle: Michael

last: Pollard

state: Cambs

address: Tennis Court Road

department: Centre for Stem Cell Research

country: United Kingdom

institute: University of Cambridge

summary:
Gliomas have been proposed to be driven by a population of neural stem-like cells. We isolated a panel of novel human glioma cell lines using adherent neural stem cell conditions.
The normal human foetal (hf) NS cells and the tumorigenic glioma NS cell lines were expanded using growth factors EGF and FGF in adherent culture conditions. In these conditions apoptosis and differentiation are suppressed resulting in more homogeneous populations of stem cells than has been reported previously. We included parallel primary biopsies of non-malignant brain tissue ('Normal Brain').

overall_design: Cell lines were expanded until 70-90% confluent and then harvested for RNA extraction. All cell lines were gorwn in identical culture media. We also include 'Normal Brain' samples which are regions of the adult human cortex.

first: Roslin

last: Russell

first: Ian

last: Clarke

first: Peter

last: Dirks


title: Expression data from E. coli O157:H7 growth in the absence or presence of HEp-2 epithelial cells

status: Public on Mar 19 2009

city: Toronto

first: Philip

middle: M

last: Sherman

state: Ontario

address: 555 University Ave

country: Canada

institute: Hospital for Sick Children

summary:
E. coli O157:H7 global gene expression profile is altered during growth in the presence of Hep-2 cells, relative to the absence of cells
We used Affymetrix E. coli 2.0 genechips to determine gene expression changes

overall_design: E. coli O157:H7 total RNA extracts were collected after a 6 hour regrowth period in either the presence or absence of Hep-2 cells.  E. coli O157:H7 total RNA extracts were collected after a 6 hour regrowth period in minimal media with 5% CO2.

first: Narveen

last: Jandu


title: Childhood Onset Rheumatic Disease Gene Expression Profile

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

summary:
Total RNA from peripheral blood mononuclear cells (PBMC) and neutrophils from children with juvenile dermatomyositis (JDM) and juvenile idiopathic arthritis (JIA) were separately compared to pediatric control samples.
Keywords: pediatric rheumatic disease, blood, PBMC, neutrophil, JIA, JDM

overall_design:
JIA PBMC n = 14
JIA neutrophils n=14
JDM PBMC n = 13
JDM neutrophils n = 14
pediatric control PBMC n = 15
pediatric control neutrophils n = 13

first: Mark

middle: B

first: Shirley

last: Wang

first: Amita

last: Aggarwal

first: Nicholas

last: Knowlton

first: Jiang

last: Kaiyu

first: Yanmin

last: Chen

first: Ryan

last: McKee

first: Brad

last: Chaser

first: Timothy

last: McGhee

first: Jeanette

last: Osban

first: James

middle: N

last: Jarvis


title: Peripheral blood mononuclear, DU145, and HCT116 cells treated with a CDK inhibitor

status: Public on Mar 26 2009

city: Nutley

last: Rosinski

state: NJ

address: 340 Kingsland St

department: In Silico Sciences

institute: Roche

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

overall_design: Refer to individual Series


title: Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue

status: Public on Mar 09 2009

city: Tampa

first: Dung-Tsa

state: FL

address: 12902 Magnolia Drive

department: Biostatistics and Bioinformatics

institute: Moffitt Cancer Center

summary:
Analysis of 143 completely histologically-normal breast tissues resulted in the identification of a “malignancy risk” gene signature that may serve as a marker of subsequent risk of breast cancer development.
Keywords: Tissue from breast cancer and adjacent regions

overall_design: RNA was extracted from microdissected frozen breast tissues for gene array analysis

first: William

middle: J

last: Fulp

first: R

middle: V

last: Chinnambally


title: Identification of human Myc- and Lin-28B-responsive transcripts

city: Baltimore

first: Joshua

middle: T

last: Mendell

state: MD

address: 733 N. Broadway, BRB 471

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

summary: In order to examine the consequences of Myc and Lin-28B induction on the transcriptome, P493-6 cells (human EBV-transformed B lymphocytes) were infected with a retrovirus that produces human Lin-28B or empty virus as a control. Gene expression profiles were then monitored in the high and low Myc state using Affymetrix microarrays.

overall_design: RNA from retrovirally-infected cells with high or low Myc expression was isolated and hybridized to Affymetrix microarrays.

first: Tsung-Cheng

last: Chang


title: Nasopharyngeal carcinoma cell lines (expression analysis)

status: Public on Mar 05 2009

city: Guangzhou

first: Zhong-Xi

last: Huang

address: Tonghe

department: Cancer Institute

country: China

institute: Southern Medical University

summary: Three nasopharyngeal carcinoma cell lines (CNE1, CNE2, and HONE1) expression patterns against an immortalized nasopharyngeal epithelial cell line NP69.

overall_design: This study was done to screen genes consensually overexpressed in NPC. NP69 was used as normal control. The microarray analyses were done in a same batch.

first: Jin

last: Zhao

first: Jing

first: Yun

last: Liu

first: Kai-Tai

last: Yao


title: Nasopharyngeal carcinoma cell lines (expression analysis and copy number analysis)

type:
Expression profiling by array
Genome variation profiling by SNP array

overall_design: This study was designed to screen genes overexpression due to copy number gain.


title: Riboflavin depletion impairs cell proliferation in intestinal cells: Identification of mechanisms and consequences

status: Public on Mar 06 2009

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

summary:
Microarray analysis has been applied to the cell proliferation in a human colonic cel line, Caco-2. We have shown previously that a moderate riboflavin depletion around weaning has a profound impact on the structure and function of the small intestine of the rat, which is not reversible following riboflavin repletion. In this study we have modelled riboflavin deficiency in a human cell line, shown irreversible loss of cell viability associated with impaired mitosis and identified candidate effectors of riboflavin depletion in the cell.
The aim of the present study is to develop a cell culture model of riboflavin depletion and analyse its behaviour using a using a combination of cell biology approaches including microarray analysis.

overall_design: A human colonic cell line, Caco-2, was grown in culture and treated to riboflavin depletion. Treated and untreated cells were collected at appropriate time points and isolated RNA subjected to microarray analysis.

first: Emi

last: Nakano

first: Sohail

last: Mushtaq

middle: R

first: Eun-Sook

last: Lee

first: Jonathan

middle: P

last: Bury

first: Jennifer

last: Waby

first: Stuart

middle: A

last: Riley

first: Hilary

last: Powers

first: Bernard

last: Corfe


title: PC3 cells transfected with androgen receptor treated with various concentration of androgens

status: Public on Mar 04 2009

city: Seattle

first: Biaoyang

last: Lin

state: WA

address: 550 17th Ave, James Tower suite 550

department: Swedish Neuroscience Institute

institute: Swedish Medical Center

summary: We compared PC3 cells with or without harboring the wild-AR construct in the growth conditions of 1nM R1881, 10nM R1881 and ethanol (the solvent for R1881). The MOCK control is PC3 cells transfected with the empty vectors.

overall_design: 2 PC3 Samples transfected with empty vector, without R1881, 2 PC3 Samples transfected with AR, treated with Ethanol, 2 PC3 Samples transfected with AR, treated with 1nM R1881, 1 PC3 transfected with AR, treated with 10nM R1881.


title: Genome-wide analysis of differential methylation and gene expression in a testicular cancer cell line

status: Public on Mar 18 2009

city: Bethesda

first: Hoi Hung

last: Cheung

address: 49 Convent Dr, Rm.2C08 Bldg.49

institute: NICHD

type: Methylation profiling by genome tiling array

summary: Aberrant methylation has been postulated to play an important role in tumorigenesis. We report the use of methylated DNA immunoprecipitation (MeDIP) and whole-genome tiling arrays to investigate methylation changes in testicular germ cell tumor (TGCT) cells. Coupled to expression profiling changes, we found that only 22-26% of differentially methylated genes were also expressed differentially. This phenomenon was independent of the presence of CpG islands in the promoter.  Differential methylation and expression of some of these genes were confirmed in testicular tumor tissue.   A substantial number of differentially methylated regions in the human genome were not linked to annotated gene loci.  Subsequent analysis indicated several microRNAs and small nucleolar RNAs were regulated by these differentially methylated regions.  Our results demonstrate the power of the combination of MeDIP-chip analysis and expression profiling for discovery in cancer cells of epigenetically regulated genes and non-coding RNAs in cancer cells.

overall_design:
MeDIP: Genomic DNA was extracted from the cultured TGCT cell line Ntera2 and a normal testis cell line (CRL-7002). Methylated DNA immunoprecipitation (MeDIP) was performed as previously described (Weber, et al, 2005). Methylation-enriched DNA was amplified and hybridized to Human Tiling Array 2.0R chips (Affymetrix). Triplicate sets of hybridization were performed from 3 independent MeDIP experiments for each cell line. The raw data were analyzed by Tiling Analysis Software (TAS). Arrays from each group (cancer vs normal) were quantile-normalized and differential methylation between groups of tumor and normal was compared by choosing the “two-sample comparison analysis” option in TAS. A two-sided test was performed to evaluate both hypermethylation and hypomethylation. Transfrags (or DMRs) were generated by Interval Analysis with a p-value cutoff at 20 (p < 0.01) and a bandwidth of 275. Transfrags generated by p-value cutoff with a positive signal difference were defined as hypermethylation while those of negative difference were defined as hypomethylation. Genomic bisulfite sequencing was performed to confirm the sensitivity of the observed DMRs.

Expression profiling: Total RNA was extracted from Ntera2 (cancer) and CRL-7002 (normal) cells. Triplicate sets of hybridization were performed for each cell line. Raw data were normalized and analyzed in Partek Genomics Suite Software. Differential gene expression was evaluated using one-way ANOVA.

The supplementary bed files contain 22,452 hypermethylated (GSE15220_Chip_ALL_HYPER.bed) and 12,756 hypomethylated (GSE15220_Chip_ALL_HYPO.bed) regions reported in the paper.

first: Hoi-Hung

first: Tin-Lap

first: Andrew

last: Davis

first: Diana

last: Taft

first: Owen

last: Rennert

first: Wai-Yee

last: Chan


title: Gene expression predictors of extension in oligoarticular juvenile idiopathic arthritis (JIA)

city: London

first: Patricia

middle: Jean

last: Hunter

address: 30 Guilford Street

department: Rheumatology

institute: UCL Institute of Child Health

summary:
Children with oligoarticular JIA (arthritis in 4 or fewer joints) can either continue to have this mild form of arthritis (persistent oligoarticular JIA) or extend to a more sever form involving more than 4 joints (extended oligoarticular JIA)
Synovial fluid mononuclear cell RNA was prepared from 21 recently diagnosed pre-treatment patients and grouped according to whether the patient had extended or persisted at one year after diagnosis

overall_design: Each sample was hybridized to Affymetrix HGU133plus2 microarrays. The mean for each probeset was compared between groups in order to find differentially expressed genes whose expression might predict outcome in a prospective study

first: Lucy

last: Wedderburn


title: Gene expression profiles in muscle tissue from FSHD patients

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary:
Muscle biopsies from biceps and deltoid were taken from 5 patients with FSHD, 5 asymptomatic carriers and 5 normal controls. The genome-wide expression patterns were compared using Affymetrix U133 Plus 2.0 chips.

Keywords: Facioscapulohumeral, FSHD, muscular dystrophy

overall_design: Gene expression profiles were generated for 15 individuals (5 affected patients, 5 asymptomatic carriers and 5 healthy controls)

last: Arashiro

first: Louis

last: Kunkel

first: Mayana

last: Zatz


title: Gene expression profiles in sigmoid colon biopsies from healthy and patients with ulcerative colitis

status: Public on Mar 02 2009

first: John

last: Kwon

address: 720 Rutland Ave.

institute: Johns Hopkins Univ

summary:
Gene expression profiles were performed to compare the difference in sigmoid colon biopsies between from healthy control and patients with ulcerative colitis.
Keywords: disease signature

overall_design: Total RNA was isolated sigmoid biopdy from 5 healthy and 6 UC patients. Pooled 5 ug total RNA equally for each group was used and followed the Affymetrix standard protocol for microarray.

first: Feng

last: Wu


title: miR-155 KO in human dendritic cells

city: Marseille

first: Philippe

last: Pierre

address: Campus Luminy - case 906

country: France

institute: CIML - CNRS - INSERM

summary: In response to inflammatory stimulation, dendritic cells (DCs) have a remarkable pattern of differentiation (maturation) that exhibits specific mechanisms to control immunity. Here, we show that in response to Lipopolysaccharides (LPS), several microRNAs (miRNAs) are regulated in human monocyte-derived dendritic cells. Among these miRNAs, miR-155 is highly up-regulated during maturation. Using LNA silencing combined to microarray technology, we have identified the Toll-like receptor / interleukin-1 (TLR/IL-1) inflammatory pathway as a general target of miR-155. We further demonstrate that miR-155 directly controls the level of important signal transduction molecules. Our observations suggest, therefore, that in mature human DCs, miR-155 is part of a negative feedback loop, which down-modulates inflammatory cytokine production in response to microbial stimuli.

overall_design: We devised a strategy to functionally inhibit the mature form of miR-155 with the aim of identifying the signaling pathways controlled by miR-155 during DC maturation. A LNA-modified oligonucleotide, specifically designed for miR-155 knockdown (anti-miR-155 LNA) was introduced in moDCs by nucleofection prior LPS stimulation. 24h after transfection, a reduction in miR-155 levels of 8- and 32-fold was observed by qPCR in immature and mature moDCs respectively. A comparative microarray analysis (Affymetrix U133 2.0 chip) was performed among miR-155 silenced (anti-miR-155 LNA) and control transfected (scramble LNA) moDCs, exposed or not to LPS. Thus, four samples were totally analyzed. As expected from the limited expression of miR-155 in non-activated DCs, little variation in mRNA expression (177 probe sets differentially expressed employing a cut-off of 1.5) was detected upon miR-155 silencing. Conversely, in LPS-activated cells many mRNAs (1324 probe sets, 770 up-regulated and 554 down-regulated) were affected by miR-155 inhibition.

first: Maurizio

last: Ceppi

last: Pereira

first: Isabelle

last: Dunand-Sauthier

first: Emmanuèle

last: Barras

first: Walter

last: Reith

first: Manuel

last: Santos


title: HCT116 tumor cells treated with a CDK inhibitor

first: James

last: Rosinski

summary: A genomics-based approach to identify pharmacodynamic biomarkers was used for a CDK (cyclin-dependent kinase) inhibitory drug.  R547 is a potent CDK inhibitor with a potent anti-proliferative effect at pharmacologically relevant doses, and is currently in Phase I clinical trials.  Utilizing preclinical data derived from microarray experiments, we identified pharmacodynamic biomarkers to test in blood samples from patients in clinical trials.  These candidate biomarkers were chosen based on several criteria: relevance to the mechanism of action of R547, dose responsiveness in preclinical models, and measurable expression in blood samples. We identified 26 potential biomarkers of R547 action and tested their clinical validity in patient blood samples by quantitative real-time PCR analysis.

overall_design: 77 samples were initially run, 74 passed QC and were analyzed, samples were run in 4 independent replicates and were treated with either vehicle, R547 at the IC50 concentration, R547 at the IC90, or R547 at 3 times the IC90.   Samples were harvested at 1, 2, 4, 6, and 24 hours post treatment.  Additionally, untreated time zero samples were analyzed as a further control

first: Windy

last: Berkofsky-Fessler


title: Profile of rolipram treated B-CLL, normal B, and normal T cells

status: Public on Mar 01 2009

last: Meyers

address: 650 Albany St. Rm. X420

department: Hematology/Oncology

institute: Boston University School of Medicine

summary:
PDE4 inhibitors, which activate cAMP signaling by reducing cAMP catabolism, are known to induce apoptosis in B lineage chronic lymphocytic leukemia (CLL) cells but not normal human T cells. The explanation for such differential sensitivity remains unknown. Here, we report studies contrasting the response to PDE4 inhibitor treatment in CLL cells and normal human T and B cells.
Affymetrix gene chip analysis in the three cell populations following treatment with the PDE4 inhibitor rolipram identified a set of up-regulated transcripts with unusually high fold-changes in the CLL samples, several of which are likely part of compensatory negative feedback loops. The high fold-change were due to low basal transcript levels in CLL cells, suggesting that cAMP-mediated signaling may be unusually tightly regulated in this cell type.

Keywords: drug response

overall_design: Four sets of primary B-CLL, normal B, or normal T cells were each treated with rolipram (20 uM) or vehicle and cultured for 4 hours.  RNA was extracted and subjected to GeneChip analaysis.

first: Adam

last: Lerner


title: Expression data from tibialis anterior muscle

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary:
We generated transgenic mice expressing constitutively SOCS-3 specifically in skeletal muscle. SOCS proteins are implicated in the negative regulation of various pathways including insulin signaling pathway. Our transgenic mice are predisposed to obesity and systemic insulin resistance compared to control mice.
We used microarrays to detail the variations of gene expression in muscle from transgenic mice versus controls.
Keywords: transgenic, tibialis anterior, SOCS-3

overall_design: Tibialis anterior is a mixed muscle easy to extract. Our previous investigations showed that this muscle expressed high level of the SOCS-3 transgene.

first: Emmanuelle

last: Cognard

last: Lebrun

first: Rachel

last: Paul

first: Chantal

last: Filloux

first: Emmanuel

last: Van Obberghen


title: HCT116 PCLKC

status: Public on Feb 26 2009

city: Kisarazu

first: Rui

last: Ose

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Department of Human Genome Research

country: Japan

institute: Kazusa DNA Research Institute

summary:
The gain of Protocadherin LKC (PCDH24) expression in colon carcinoma cell line HCT116 has been shown to induce contact inhibition, thereby completely abolishing tumor formation in vivo.  To clarify the molecular mechanism, we performed DNA microarray analysis and compared gene-expression pattern between control and PCDH24-expressing HCT116 cells.  Approximately 2000 genes were apparently changed their expression.  Further proteomics analysis using 2-DE/MS confirmed the dramatic changes and provided additional information.  We were aware that these changes are quite similar to the changes observed in epithelial-mesenchymal transition (EMT), most drastic changes in development and cancer metastasis.  We thus further analyzed these changes using specific antibodies, and found distinct difference between these two phenomena.  Among the differences, nuclear translocation of catenin beta 1 (CTNNB1) was inhibited by PCDH24-expression, subsequently some of the downstream nodes were suppressed.  Although contact inhibition and cancer metastasis are completely opposite aspect of the cells, we expect that the identified differences will be key nodes to understand the relationship.  We also expect that the nodes will be a target to modulate tumors arising stem cell transplantation (SCT), as well as a therapeutic target for cancer metastasis.
Keywords: dose response

overall_design: Three HCT116 PCLKC cell lines (parental cells and two stable expression clones with random integration of the targeting vector, PCLKC-GFP, GFP) were studied.


title: Analyses of heterogeneous renal allograft biopsies reveal conserved rejection signatures and molecular pathways II

status: Public on Feb 24 2009

city: Basel

first: Friedrich

last: Raulf

department: Novartis Institutes for BioMedical Research / ATDA

country: Switzerland

institute: Novartis Pharma AG

summary:
Specific early diagnosis of renal allograft rejection is gaining importance in the current trend to minimize and individualize immunosuppression. Gene expression analyses could contribute significantly by defining “molecular Banff” signatures. Several previous studies have applied transcriptomics to distinguish different classes of kidney biopsies. However, the heterogeneity of microarray platforms, clinical samples and data analysis methods complicates the identification of robust signatures for the different types and grades of rejection. To address these issues, a comparative meta-analysis was performed across five different microarray datasets of heterogeneous sample collections from two published clinical datasets and three own datasets including biopsies for clinical indications, protocol biopsies, as well as comparative samples from non-human primates (NHP). This work identified conserved gene expression signatures that can differentiate groups with different histopathological findings in both human and NHP, regardless of the technical platform used. The marker panels comprise genes that clearly support the biological changes known to be involved in allograft rejection. A characteristic dynamic expression change of genes associated with immune and kidney functions was observed across samples with different grades of CAN. In addition, differences between human and NHP rejection were essentially limited to genes reflecting interstitial fibrosis progression. This data set here comprises a small validation batch of renal allograft biopsies for clinical indications plus control normal kidney samples from patients at Hôpital Tenon, Paris (second batch) that complements the first batch of 60 samples.
We used microarrays to identify different gene expression signatures of renal allograft biopsies that can classify them according to different types of allograft rejection or CAN.
Keywords: disease state analysis

overall_design: 4 renal allograft core biopsies for clinical indications with different histopathological diagnoses according to Banff'97 criteria and 2 normal kidney samples.

first: Pierre

last: Saint-Mezard

first: Eric

last: Rondeau

first: Hans-Peter

last: Marti


title: CD34 blood cells

city: Milan

first: Gabriele

last: Bucci

address: Via Olgettina 60

department: Center of Translational Genomics and Bioinformatics

institute: Università vita e Salute Ospedale San Raffaele

summary:
CD34+ positively isolated from healthy donors (stimulated by G-CSF) with magnetic beads (after blood leukapheresis)
CD34- obtained from 10dd cytokine cultured CD34+
Keywords: differentiation

overall_design:
5 samples of total RNA.
2 replicates CD34-
3 replicates CD34+

first: gabriele

last: bucci

first: gaetano

last: gargiulo

first: mauro

last: romanenghi

first: saverio

last: minucci


title: Analyses of heterogeneous renal allograft biopsies reveal conserved rejection signatures and molecular pathways I

summary:
Specific early diagnosis of renal allograft rejection is gaining importance in the current trend to minimize and individualize immunosuppression. Gene expression analyses could contribute significantly by defining “molecular Banff” signatures. Several previous studies have applied transcriptomics to distinguish different classes of kidney biopsies. However, the heterogeneity of microarray platforms, clinical samples and data analysis methods complicates the identification of robust signatures for the different types and grades of rejection. To address these issues, a comparative meta-analysis was performed across five different microarray datasets of heterogeneous sample collections from two published clinical datasets and three own datasets including biopsies for clinical indications, protocol biopsies, as well as comparative samples from non-human primates (NHP). This work identified conserved gene expression signatures that can differentiate groups with different histopathological findings in both human and NHP, regardless of the technical platform used. The marker panels comprise genes that clearly support the biological changes known to be involved in allograft rejection. A characteristic dynamic expression change of genes associated with immune and kidney functions was observed across samples with different grades of CAN. In addition, differences between human and NHP rejection were essentially limited to genes reflecting interstitial fibrosis progression. This data set comprises all renal allograft biopsies for clinical indications from patients at Hôpital Tenon, Paris (February 2003 until September 2004) and few respective patients from Hôpital Bicêtre, Paris, Hôpital Pellegrin, Bordeaux, and Hôpital Dupuytren, Limoges, plus control normal kidney samples from Hôpital Tenon, Paris, France (first batch).
We used microarrays to identify different gene expression signatures of renal allograft biopsies that can classify them according to different types of allograft rejection or CAN.
Keywords: disease state analysis

overall_design: 47 renal allograft core biopsies for clinical indications with different histopathological diagnoses according to BANFF'97 criteria, and 13 normal kidney samples as controls.


title: Transcriptomic analyses of renal allograft biopsies reveal conserved rejection signatures and molecular pathways

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

overall_design: Refer to individual Series


title: Parkinson’s disease patient-derived induced pluripotent stem cells free of viral reprogramming factors

city: Cambridge

first: Frank

last: Soldner

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Induced pluripotent stem cells (iPSCs) derived from somatic cells of patients by viral vector-mediated factor transduction represent a powerful tool for biomedical research and may provide a source for cell replacement therapies. However, the proviruses encoding the reprogramming factors represent a major limitation of the current technology because even low vector expression may alter the differentiation potential of the iPSCs and induce malignant transformation. Here we show that fibroblasts from five patients with idiopathic Parkinson’s disease (PD) can be efficiently reprogrammed into hiPSCs and subsequently differentiated into dopaminergic neurons. Moreover, we derived PD specific hiPSCs free of reprogramming factors using Cre-recombinase excisable viruses. Upon factor deletion these cells maintain a pluripotent state and intact karyotype. Importantly, these factor-free hiPSCs show a global gene expression profile, which is more closely related to hESCs than to hiPSCs carrying the transgenes. Our results indicate that residual transgene expression in conventional virus-carrying hiPSCs can affect their molecular characteristics and that factor-free hiPSCs therefore represent a more suitable source of cells for modeling of human disease.

overall_design:
Four types of cells were used for 1-channel expression analysis:
(a) fibroblasts (1 array)
(b) human ES cells (2 different cell lines, 1 array each)
(c) virus-carrying human induced pluripotent stem cells (4 different cell lines, 1 array each)
(d) factor-free human induced pluripotent stem cells (4 different cell lines, 1 array each)

first: Dirk

last: Hockemeyer

first: Caroline

last: Beard

first: Qing

last: Gao

first: George

middle: W

last: Bell

first: Elizabeth

middle: G

last: Cook

first: Gunnar

last: Hargus

first: Alexandra

last: Blak

first: Oliver

last: Cooper

first: Maisam

last: Mitalipova

first: Ole

last: Isacson

first: Rudolf

last: Jaenisch


title: Identification of Tuberculosis Susceptibility Genes with Human Macrophage Gene Expression Profiles

status: Public on Feb 23 2009

city: Ho Chi Minh City

first: Sarah

last: Dunstan

address: 190 Ben Ham Tu, Quan 5

department: Hospital for Tropical Diseases

country: Viet Nam

institute: 1.	Oxford University Clinical Research Unit

summary:
Although host genetics influences susceptibility to tuberculosis, few genes determining disease outcome have been identified. We hypothesized that macrophages from individuals with different clinical manifestations of tuberculosis infection would have distinct gene expression profiles, and that polymorphisms in these genes may also be associated with susceptibility to TB.
We measured gene expression levels of >38,500 genes from ex vivo Mtb- stimulated macrophages in 12 subjects with 3 clinical phenotypes: latent, pulmonary and meningeal tuberculosis (n=4 per group). After identifying differentially expressed genes, we confirmed these results in 34 additional subjects by real-time PCR.  We also used a case-control study design to examine whether polymorphisms in differentially regulated genes were associated with susceptibility to these different clinical forms of TB.
We compared gene expression profiles in Mtb-stimulated and unstimulated macrophages and identified 1608 and 199 genes that were differentially expressed by >2 and >5-fold, respectively. Using cluster analysis, we identified gene expression patterns that distinguished the different clinical forms of tuberculosis.  In an independent sample set of 34 individuals and a subset of highly regulated genes, 90% of the microarray results were confirmed by RT-PCR, including expression levels of CCL1, which distinguished the 3 clinical groups.  Furthermore, 6 single nucleotide polymorphisms (SNPs) in CCL1 were found to be associated with TB in a case-control genetic association study with 273 TB cases and 188 controls.  To our knowledge, this is the first identification of CCL1 as a gene involved in host susceptibility to TB and the first study to combine microarray and DNA polymorphism studies to identify genes associated with TB susceptibility.  These results suggest that genome-wide studies can provide an unbiased method to identify critical macrophage response genes that are associated with different clinical outcomes and that variation in innate immune response genes regulate susceptibility to tuberculosis.
Keywords: tuberculosis, tuberculous meningitis, macrophage, gene expression, microarray

overall_design: Latent TB (LTB) subjects were healthy nursing staff members who had worked at a tuberculosis hospital, for more than 20 years and were positive in ESAT-6 and CFP-10- specific IFN-gamma ELISPOT assays. All subjects with pulmonary (PTB) and meningeal (TBM) disease had been treated and were free of symptoms at the time of venipuncture. Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours. RNA expression was analyzed using a Human Genome U133 Plus 2.0 Array (Affymetrix, USA) which contains probe sets for 47,000 transcripts including 38,500 well-characterized human genes.


title: Type I Interferon: Potential Therapeutic Target for Psoriasis?

status: Public on Feb 20 2009

city: Gaithersburg

first: Brandon

last: Higgs

address: One MedImmune Way

department: Translational Science

institute: MedImmune, LLC

summary:
We observed robust overexpression of type I interferon (IFN)–inducible genes and genomic signatures that indicate T cell and dendritic cell infiltration in lesional skin. Up-regulation of mRNAs for IFN-a subtypes was observed in lesional skin compared with nonlesional skin. Enrichment of mature dendritic cells and 2 type I IFN–inducible proteins, STAT1 and ISG15, were observed in the majority of lesional skin biopsies. Concordant overexpression of IFN-c and TNF-a–inducible gene signatures occurred at the same disease sites.

Keywords: Affymetrix Human Genome U133 Plus 2.0 array

overall_design: A total of 82 Affymetrix HGU133 Plus arrays were run on 54 total subjects. This includes: skin biopsy samples from 21 normal healthy donors (Normal-1 to Normal-21), 56 skin biopsy samples from 28 psoriasis patients who had match lesional and uninvolved (non-lesional) tissue (NS-1/LS-1 to NS-9/LS-9,  NS-11/LS-11 to NS-14/LS-14, and NS-16/LS-16 to NS-30/LS-30), and 5 samples from psoriasis patients that only provided lesional skin biopsies (LS-10, LS-15, and LS-31 to LS-33).


title: mRNA quantitation of human heart left ventricles

status: Public on Feb 19 2009

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

institute: Jichi Medical University

summary:
Left ventricle myocytes were prepared from patients with High or low ejection fraction, and subjected to mRNA profiling.
Keywords: Disease-state analysis

overall_design: Four HighEF and four heart failure specimens were analyzed.


title: Expression data in HTETOP cells following tetracycline or dexrazoxane treatment

city: Mainz

first: Shiwei

last: Deng

address: Obere Zahlbacher Str. 67

institute: Uni Mainz

summary:
HTETOP cells, derived from the human fibrosarcoma cell line HT1080, express human topoisomearse II α (TOP2A) exclusively from a tetracycline (TET)-regulated transgene, we used HTETOP cells to differentiate between TOP2A-dependent and –independent apoptotic effects of doxorubicin and dexrazoxane.
We used microarrays to detect global transcriptional changes in HTETOP cells following tetracycline doxycycline or dexrazoxane treatment.

Keywords: Drug treatment comparison

overall_design:
HTETOP cells were treated with 1 µg/ml doxycycline to inhibit TOP2A expression or vehicle for 24 hours, doxycycline-induced trascriptional changes were identified by comparison of the two groups.

HTETOP cells were treated with 100 µM dexrazoxane to inhibit TOP2A activity or vehicle for 24 hours, global trascriptional changes were identified by comparison of the two groups.


title: Differentation in neuroblastomas

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'Ulm

department: Genetics

institute: Institut Curie

summary: Expression profiling according to differentiation was analysed in 34 neuroblastomas

overall_design:
Unsupervised clusterings were performed to confirm the link between phenotype of differentiation and expression profile
Different groups were compared with SAM-t tests.

first: Franck

last: Bourdeaut

first: Isabelle

last: Janoueix-Lerosey

first: Carlo

last: Lucchesi

first: Regine

last: Paris

first: Agnes

last: Ribeiro

first: Loic

last: de Pontual

first: Jeanne

last: Amiel

first: Stanislas

last: Lyonnet

first: Gaelle

last: Pierron

first: Jean

last: Michon

first: Michel

last: Peuchmaur


title: Effect of MnSOD knockout cells on gene profile expression

status: Public on Feb 18 2009

city: Rehovot

first: Michal

last: pardo

state: Rehovot

address: P.O.Box 12

country: Israel

institute: Hebrew university

summary:
MnSOD is an essential primary antioxidant enzyme that converts superoxide radicals and protons to hydrogen peroxide (H2O2) within the mitochondrial matrix, generated by respiratory chain activity
We used microarrays of cells knocked down for MnSOD and a mock transfected cells as their control (siScramble) to reveal changes in gene expression profile

overall_design:
WT-AML-12 cells silenced (si) for MnSOD were prepared, briefly: The backbone vector pSUPER.retro.puro was used for silencing. Transcripts of 60-nt long oligos constituting hairpin RNAs were designed to generate a low level of MnSOD silencing: a nine-loop (9 L) hairpin with 20 nt of MnSOD sense (siMnSOD) and a 9 L hairpin with 20 nt of scramble-no gene recognition control sense (Scr). Retroviral particles were produced by triple transfection of HEK 293T cells (ATCC No. CRL-11268T) with the retroviral vector (2 ug), pMD-gag-pol (1 ug) and pVSV-G (1 ug) using Trans-IT (Mirusbio Corporation, Madison, WI). For stable transfection, the various retroviruses were introduced with WT-AML-12 hepatocytes using polybrene (Sigma-Aldrich, St. Louis, MO, USA) in a six-well plate followed by selection with 10 ug puromycin for 2 weeks.

To identify sets of genes that are differentially expressed in siMnSOD AML-12 cells compared to Scr-no sense control AML-12 cells, a Gene Chip approach was utilized. Total RNA was extracted (using TRI reagent) and purified using the RNeasy kit (Qiagen, Valencia, CA). Three different batches of frozen cells were taken to microarray analysis. Microarray analysis was performed on an Affymetrix Mouse Gene 1.0 ST chip containing 28,853 genes. The chips were processed and scaled at the Weizmann Institute of Science (Rehovot, Israel) using Affymetrix MAS5.

last: Pardo

first: Oren

last: Tirosh


title: Comparative gene expression profile of 1,25-dihydroxyvitamin D3-treated human monocyte-derived dendritic cells

status: Public on Feb 15 2009

city: DEBRECEN

first: LAJOS

last: SZELES

address: Egyetem tér

country: Hungary

institute: UNIVERSITY OF DEBRECEN

summary: We have carried out global gene expression analysis to clarify the interrelationship between 1,25-dihydroxyvitamin D3 and differentiation-driven gene expression patterns in developing human monocyte-derived dendritic cells. Monocytes were treated with 10 nM 1,25-dihydroxyvitamin D3 or vehicle 14 hours after plating for 12 hours or 5 days. Monocytes, differentiating dendritic cells (+/-1,25-dihydroxyvitamin D3 for 12 hours) and immature dendritic cells (+/-1,25-dihydroxyvitamin D3 for 5 days) were harvested. This design allows one to identify genes regulated by differentiation and/or 1,25-dihydroxyvitamin D3 in human monocyte-derived dendritic cells.

overall_design: Human monocytes were obtained from buffy coats from healthy donors by Ficoll gradient centrifugation followed by immunomagnetic cell separation with anti-CD14-conjugated microbeads. Monocytes were cultured in RPMI-1640 supplemented with 10% FBS, 800 U/ml GM-CSF and 500 U/ml IL-4. Monocytes were treated with 10 nM 1,25-dihydroxyvitamin D3 or vehicle 14 hours after plating for 12 hours or 5 days. Monocytes, differentiating dendritic cells (+/-1,25-dihydroxyvitamin D3 for 12 hours) and immature dendritic cells (+/-1,25-dihydroxyvitamin D3 for 5 days) were harvested. Experiments were performed in biological triplicates representing samples from different donors. 15 samples were processed and hybridized to Human Genome U133 Plus 2.0 Arrays.

first: Lajos

last: Szeles

first: Laszlo

last: Nagy


title: Limb immobilization induces a coordinate down-regulation of mitochondrial and other metabolic pathways in men and women

status: Public on Feb 21 2009

city: Novato

first: Simon

last: Melov

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: Advancements in animal models and cell culture techniques have been invaluable in the elucidation of molecular events and mechanisms regulating muscle atrophy. However, few studies have examined muscle atrophy in humans using modern experimental techniques. The purpose of this study was to examine and validate changes in global gene transcription during immobilization-induced muscle atrophy in humans. Healthy men and women (N=24) were subjected to two weeks of unilateral limb immobilization, with muscle biopsies obtained before, and after 48 hours (48H) and 14 days (14D) of immobilization. Both muscle cross sectional area (~ 5 %) and strength (10-20 %) were significantly reduced in men and women after 14D of immobilization. Micro-array analysis of total RNA extracted from biopsy samples uncovered 575 and 3,128 probes representing multiple genes, which were significantly altered at 48H and 14D, respectively. As a group, genes involved in mitochondrial bioenergetics and carbohydrate metabolism were predominant features at both 48H and 14D, with genes involved in protein synthesis and degradation significantly down-regulated and up-regulated, respectively, at 14D of muscle atrophy. There was also a significant decrease in the protein content of mitochondrial cytochrome c oxidase, and the enzyme activity of cytochrome c oxidase and citrate synthase after 14D of immobilization. Furthermore, protein ubiquitination and oxidative damage were significantly increased by 48H and 14D of immobilization, respectively. These results suggest that transcriptional and post-transcriptional suppression of mitochondrial processes is sustained throughout 14D of immobilization, while protein ubiquitination plays an early but transient role in the progression of immobilization-induced muscle atrophy in humans.

overall_design: 72 samples taken from quadriceps of healthy ambulatory young men and women. Samples were taken at 3 timepoints throughout a 14 day period, the initial sample was taken at time 0 (PRECAST), then the limb was immobilized via a brace, and the 2nd sample was taken at 48 hours (CAST02D). The third sample was taken following 14 days of immobilization (CAST14D).

first: Mark

last: Tarnopolsky


title: Global Chromatin Modifications at Enhancers Correlate with Cell Type-Specific Gene Expression in the Human Genome

city: Dallas

first: Gary

middle: Chung

last: Hon

state: TX

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern

type: Genome binding/occupancy profiling by genome tiling array

summary:
The human body is composed of diverse cell types with distinct functions. While it is known that lineage specification depends on cell specific gene expression, which in turn is driven by promoters, enhancers, insulators and other cis-regulatory DNA sequences for each gene1-3, the relative roles of these regulatory elements in this process is not clear. We have previously developed a chromatin immunoprecipitation-based microarray method (ChIP-chip) to identify promoters, enhancers and insulator elements in the human genome4-6. Here, we use the same approach to identify these active elements in multiple cell types and investigated their roles in cell type-specific gene expression. We observed that chromatin state at promoters and CTCF-binding at insulators are largely invariant across diverse cell types. By contrast, enhancers are marked with highly cell type-specific histone modification patterns, strongly correlate to cell type-specific gene expression programs on a global scale, and are functionally active in a cell type-specific manner. Our results defined over 55, 000 potential transcriptional enhancers in the human genome, significantly expanding the current catalog of human enhancers and highlighting the role of these elements in cell type-specific gene expression.

Keywords: ChIP-chip

overall_design: In HeLa cells, we mapped histone modifications H3K4me1 and H3K4me3, as well as binding of the transcription factor STAT1, genome-wide using ChIP-chip. We predicted almost 40,000 transcriptional enhancers using chromatin signatures, designed condensed microarrays to span these enhancers, and then verified them by examining the following marks in replicate experiments: H3K4me1, H3K4me3, H3K27ac, p300, and MED1. We also performed DNase-chip to map regions of DNase I hypersensitivity. Finally, we repeated these experiments in K562 cells, mapping H3K4me1, H3K4me3, H3K27ac, and STAT1 binding genome-wide using ChIP-chip.


title: Activation of mTOR controls the loss of TCRζ in lupus T cells through HRES-1/Rab4-regulated lysosomal degradation

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: CD3-positive T cells were negatively isolated from 10 SLE patients and 9 healthy controls without SLE.  All of the SLE samples and control samples were compared with one another to identify baseline differences in expression due to the disease.  Next, T cell preparations from 4 of the control subjects were stimulated with either Nitric Oxide (NOC-18) 600 uM for 24hr or stimulated through CD3/CD28 for 24hr to determine which genes were responsive to these signaling mechanisms. Here, we show that activity of the mammalian target of rapamycin (mTOR), which is a sensor of the mitochondrial transmembrane potential, is increased in SLE T cells. Activation of mTOR was inducible by NO, a key trigger of MHP which in turn enhanced the expression of HRES-1/Rab4, a small GTPase that regulates recycling of surface receptors through early endosomes. Expression of HRES-1/Rab4 was increased in SLE T cells and, in accordance with its dominant impact on the endocytic recycling of CD4, it was inversely correlated with diminished CD4 expression. HRES-1/Rab4 over-expression was also inversely correlated with diminished TCRζ protein levels. Combined with follow up studies, these results suggest that activation of mTOR causes the loss of TCRζ in lupus T cells through HRES-1/Rab4-dependent lysosomal degradation.

overall_design:
10 replicate T cell samples from SLE (Lupus) patients
9 replicate T cell samples from healthy control (BC) subjects
4 replicate Nitric Oxide (NOC-18) stimulated T cell samples from 4 of the control subjects
4 replicate CD3/CD28 stimulated T cell samples from 4 of the control subjects

first: David

last: Fernandez

first: Tiffany

last: Telarico

first: Eduardo

last: Bonilla

first: Qing

last: Li

first: Sanjay

last: Banerjee

first: Paul

middle: E

last: Phillips

first: Mary

middle: K

last: Crow

first: Stefanie

last: Oess

first: Werner

last: Muller-Esterl

first: Andras

last: Perl


title: Expression data from rhabdomyosarcoma cells expressing Myod and E-protein heterodimer and controls

status: Public on Feb 14 2009

city: Seatttle

first: Yi

last: Cao

address: 1100 Fairview Ave. N

department: Human Biology

institute: Fred Hutchinson CRC

summary:
Rhabdomyosarcomas (RMS) are characterized by expression of myogenic specification genes, such as MyoD and/or Myf5, as well as their bHLH partners for heterodimerization, the E-proteins.  We have shown that expression of a forced heterodimer of MyoD with one of the E2A proteins, E12, leads to differentiation in a RMS cell culture model when exposed to low serum conditions.

Keywords: RD expressing Myod~E heterodimers and controls

overall_design: RD cells (a type of RMS) were retrovirally infected with either the MyoD~E heterodimer or an empty control vector, differentiated for 24 hours and then RNA collected.

first: Zhihong

last: Yang

first: Kyle

last: MacQuarrie

first: Erwin

last: Analau

first: F

last: Dilworth

first: Scott

last: Diede

first: Stephen

last: Tapscott


title: Expression data from IBS patients before and after treatment

city: Barcelona

first: Cristina

last: Martinez

address: Paseo Valle Hebron 119-129

department: Digestive diseases research unit

country: Spain

institute: Institut de Recerca HUVH

summary:
Increased numbers of mast cells and their products have been linked to symptom onset and severity in patients with chronic diarrhea and abdominal pain.  Although mast-cell inhibition ameliorates clinical manifestations and reduces mucosal inflammation, underlying molecular mechanisms remain unknown.

Keywords: Comparison of gene expression

overall_design: Diarrhea-irritable bowel syndrome (d-IBS) patients were studied at baseline, or 6 months after natural evolution (control) or oral cromoglycate treatment. Jejunal biopsies were subjected to chip analysis (Affymetrix Human Genome U133 Plus 2.0 GeneChips).

first: Javier

last: Santos


title: Human CD4+ memory T cells are preferential targets for bystander activation and apoptosis

status: Public on Feb 11 2009

city: Oxford

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

institute: University of Oxford

summary:
There is much evidence that T cells may be activated via mechanisms which act independently of direct TCR ligation. Despite this, the question of whether such forms of ‘bystander’ T cell activation occur during immune responses is hotly debated.
	To address some outstanding questions, we set up an in vitro system within which to analyse bystander T cell activation in human T cells, in the absence of the possibility for TCR cross-reactivity. In addition, we have investigated the genetic, phenotypic, and functional characteristics of bystander activated T cells.
	Here, we show that bystander T cell activation is, indeed, observed during a specific immune response, and that it occurs preferentially amongst CD4+ memory T cells. Furthermore, bystander activated T cells display a distinct gene expression profile. The mechanism for bystander T cell activation involves soluble factors, and the outcome is an elevated level of apoptosis. This may provide an explanation for the attrition of T cell memory pools of heterologous specificity during immune responses to pathogens such as viruses.

overall_design:
Three conditions tested with 4 biological repilicates in each:
  Resting cells - cells expressing a TCR which does not specifically recognize SEB (Vβ13.1 T cells) and did not upregulate the activation marker CD25 in response to transwell SEB-stimulated co-culture over a 5 day period.
  Bystander activated cells - cells expressing a TCR which does not specifically recognize SEB (Vβ13.1 T cells), but which did upregulate the activation marker CD25 in response to transwell SEB-stimulated co-culture over a 5 day period.
  Directly activated cells - cells expressing a TCR which is known to specifically recognize SEB (Vβ17 T cells), and which did upregulate the activation marker CD25 in response to direct SEB stimulation over a 5 day period.

first: Sarah

middle: C

last: Bangs

first: Helen

last: Cattan

first: Chris

first: Andrew

last: McMichael

first: Xiao-Ning

last: Xu


title: Liver gene expression profiles of TLR3-/- versus TLR3wt (C57Bl/6) mice

status: Public on Feb 08 2009

city: Jerusalem

first: Reba

last: Condiotti

department: Goldyne Savad Institute of Gene Therapy

institute: Hadassah Medical Center

overall_design:
cDNA was prepared from total liver RNA taken from untreated, 3 months old, TLR3-/- and TLR3wt C57Bl/6 mice
each group contained 3 mice

first: Elina

last: Zorde-Khvalevsky

first: Rinat

last: Abramovitch

first: Hila

last: Harel-Barash

first: Irit

last: Spivak-Pohis

first: Ludmila

last: Rivkin

first: Jacob

last: Rachmilewitz

first: Eithan

last: Galun

first: Hilla

last: Giladi


title: Vitamin C-induced gene expression profiling in GM5659 human skin fibroblasts

status: Public on Feb 10 2009

city: Porto

first: Tiago

middle: L

last: Duarte

address: Rua do Campo Alegre, 823

country: Portugal

institute: IBMC - Institute for Molecular and Cell Biology

summary: The skin is a protective barrier against external insults and any lesion must be rapidly and efficiently repaired. Dermal fibroblasts are the major source of extracellular connective tissue matrix and play an important role in wound healing. Vitamin C is an important water-soluble free radical scavenger and an essential cofactor for collagen synthesis by dermal fibroblasts and, consequently, may contribute to the maintenance of healthy skin. Using microarray analysis, we investigated the effects of long-term exposure to a stable vitamin C derivative, ascorbic acid 2-phosphate (AA2P), in contact-inhibited populations of primary human dermal fibroblasts. Compared with "scorbutic" cells, cells exposed to AA2P increased the expression of genes associated with DNA replication and repair and with the G(2)/M phase of the cell cycle. Consistent with the gene expression changes, AA2P increased the mitogenic stimulation of quiescent fibroblasts by serum factors and cell motility in the context of wound healing. Furthermore, AA2P-treated fibroblasts showed faster repair of oxidatively damaged DNA bases. We propose that vitamin C may protect the skin by promoting fibroblast proliferation, migration, and replication-associated base excision repair of potentially mutagenic DNA lesions, and we discuss the putative involvement of hypoxia-inducible transcription factor-1 and collagen receptor-related signaling pathways.

overall_design: Gene expression changes in response to vitamin C were analysed by Microarray technology in GM5659 human skin fibroblasts. Cells were treated with 100 µM of AA or AA2P (or growth medium alone) added fresh every day for a period of 5 days before the vitamin C-induced gene expression changes were investigated. Control, AA- and AA2P-treated samples were collected from three independent experiments each.

first: Marcus

middle: S

last: Cooke

first: George

middle: D

last: Jones


title: Drosha or DGCR8 knockdown effects on mRNA levels in HeLa

status: Public on Feb 05 2009

city: Seoul

first: Jinju

last: Han

address: 599 Gwanangno, Gwanak-gu

country: South Korea

institute: Seoul National University

summary:
Anaysis of mRNA changes in HeLa cells following knockdown of Drosha or DGCR8. Drosha is a nuclear RNase III that carries out microRNA (miRNA) processing by cleaving primary microRNA transcript (pri-miRNA). DGCR8 is an essential co-factor of Drosha.

Keywords: gene expression array-based (RNA / in situ oligonucleotide)

overall_design: siRNA against Drosha or DGCR8 were trasnfected into HeLa cells. siRNA against GFP was used as a control. Biologically duplicated total RNAs were prepared from HeLa cells, 24 hrs and 48 hrs after siRNA transfection.

first: S

last: Kwon

first: Young-Kook

last: Kim

first: Kyu-Hyeon

last: Yeom

first: V

middle: N


title: Beta-catenin status in pediatric medulloblastomas

status: Public on Feb 02 2009

first: Olivier

last: Delattre

summary: Medulloblastoma is the most frequent malignant pediatric brain tumor. Considerable efforts are dedicated to identify markers that help to refine treatment strategies. The activation of the Wnt/beta-catenin pathway occurs in 10-15% of medulloblastomas and has been recently described as a marker for favorable patient outcome. We report a series of 72 pediatric medulloblastomas evaluated for beta-catenin immunostaining, CTNNB1 mutations, and studied by comparative genomic hybridization. Gene expression profiles were also available in a subset of 40 cases. Immunostaining of beta-catenin showed extensive nuclear staining (>50% of the tumor cells) in 6 cases and focal nuclear staining (<10% of cells) in 3 cases. The other cases exhibited either a signal strictly limited to the cytoplasm (58 cases) or were negative (5 cases). CTNNB1 mutations were detected in all beta-catenin extensively nucleopositive cases. The expression profiles of these cases documented a strong activation of the Wnt/beta-catenin pathway. Remarkably, 5 out of these 6 tumors showed a complete loss of chromosome 6. In contrast, cases with focal nuclear beta-catenin staining, as well as tumors with negative or cytoplasmic staining, never demonstrated CTNNB1 mutation, Wnt/beta-catenin pathway activation or chromosome 6 loss. Patients with extensive nuclear staining were significantly older at diagnosis and were in continuous complete remission after a mean follow-up of 75.7 months (range 27.5-121.2) from diagnosis. All three patients with a focal nuclear staining of beta-catenin died within 36 months from diagnosis. Altogether, these data confirm and extend previous observations that CTNNB1-mutated tumors represent a distinct molecular subgroup of medulloblastomas with favorable outcome, indicating that therapy de-escalation should be considered. Yet, international consensus on the definition criteria of this distinct medulloblastoma subgroup should be achieved.

overall_design:
A series of 72 pediatric medulloblastoma tumors has been studied at the genomic level (array-CGH), screened for CTNNB1 mutations and beta-catenin expression (immunohistochemistry). A subset of 40 tumor samples has been analyzed at the RNA expression level (Affymetrix HG U133 Plus 2.0). Correlations between the genomic data, the expression data, the mutational screening, the pathological classification and clinical data is presented in the study.

note: aCGH data not submitted to GEO

first: Sarah

last: Fattet

first: Christine

last: Haberler

first: Patricia

last: Legoix

first: Pascale

last: Varlet

first: Arielle

last: Lellouch-Tubiana

first: Severine

last: Lair

first: Elodie

last: Manie

first: Marie-Anne

last: Raquin

first: Danielle

last: Bours

first: Sabrina

last: Carpentier

first: Emmanuel

last: Barillot

first: Jacques

last: Grill

first: Francois

last: Doz

first: Stephanie

last: Puget

first: Isabelle

last: Janoueix-Lerosey


title: Egr1 regulates the coordinated expression of numerous EGF receptor target genes as identified by ChIP-on-chip

status: Public on Feb 09 2009

city: San Diego

first: Yipeng

last: Wang

institute: Vaccine Research Institute of San Diego

summary:
Previous studies have revealed that UV-stimulation of a variety of cells leads to activation of the EGF receptor, induction of Egr1, growth inhibition and apoptosis.  On the other hand both Egr1 and EGF receptor activation are implicated in promoting the progression of prostate cancer.  We treated M12 tumorigenic prostate epithelial cells which express little Egr1 with UV irradiation which rapidly activated the EGF receptor and elevated Egr1. Treatment with specific EGFR and ERKI/II inhibitors (PD153035 and UO126, respectively) confirmed that the upregulation of Egr1 was downstream of EGFR and ERKI/II Map kinase pathway.  ChIP on chip experiments using Egr1 antibody identified 288 significantly bound promoters upon UV stimulation. Of these target genes, 40% had consensus Egr1 site in their promoters, considerably greater than that expected by chance (p < 0.005).  The array binding results were validated by PCR analysis of 25 genes using DNA from conventional IP experiment. Affymetrix gene expression analysis of UV treated and control cells confirmed that a significant number of these bound promoters showed gene expression changes. Addition of siRNA to Egr1 confirmed that the gene expression changes were dependent upon Egr1 expression.  Addition of EGF led to similar expression changes for nine tested genes.  Proliferation and apoptosis assays confirmed that M12 cells undergo growth arrest and apoptosis following UV irradiation. Moreover, addition of EGF also promoted significant growth inhibition.  These results indicate the M12 cells undergo a EGF receptor dependent apoptosis response upon UV-stimulation and that Egr1 mediates the regulation of numerous genes downstream of the EGF receptor that are associated with this response.
Keywords: UV treatment analysis

overall_design: duplicated experiment for Affymetrix gene expression analysis and Chip-on-Chip analysis.

first: Shilpi

last: Arora

first: Michael

last: McClelland

first: Dan

last: Mercola


title: Identification of HCK and BIN1 as potential mediators of AHI-1 oncogene in primary and transformed CTCL cells

status: Public on Feb 07 2009

city: Vancouver

first: BCGSC

last: BC Cancer Agency

state: BC

address: 675 West 10th Avenue

department: Gene Expression

institute: Canada's Michael Smith Genome Sciences Centre

summary:
AHI-1 is an oncogene often targeted by provirus insertional mutagenesis in murine leukemias and lymphomas.  Aberrant expression of human AHI-1 occurs in cutaneous T-cell lymphoma (CTCL) cells and in CD4+CD7- Sezary cells from patients with Sezary syndrome (SS).  Stable knockdown of AHI-1 using retroviral-mediated RNA interference in CTCL cells inhibits their transforming activity in vitro and in vivo.  To identify genes involved in AHI-1-mediated transformation, microarray analysis was performed to identify differentially expressed genes in AHI-1 suppressed CTCL cells.  Fifteen up-regulated and six down-regulated genes were identified and confirmed by Q-RT-PCR.  Seven were further confirmed in a microarray analysis of CD4+CD7- Sezary cells from SS patients.  HCK and BIN1 emerged as new candidate cooperative genes, with differential protein expression which correlates with observed transcript changes.  Interestingly, changes in HCK phosphorylation and biological response to its inhibitor, dasatinib, were observed in AHI-1 suppressed or overexpressed cells.  The tumor suppressor BIN1 physically interacts with MYC in CTCL cells, which also exhibit differential MYC protein expression.  In addition, aberrant expression of alternative splicing forms of BIN1 was observed in primary and transformed CTCL cells.  These findings indicate that HCK and BIN1 may play critical roles in AHI-1-mediated leukemic transformation of human CTCL cells.

Keywords: Cell type comparison

overall_design: Two groups, each with two subgroups, subgroups having 2 or 3 replicates each

first: Erin

last: Kennah

first: Hong

last: Qian

first: Xiaoyan

last: Jiang


title: Monocyte-derived dendritic cells stimulated with LPS, Poly(I:C), CD40L or a combination of IL-1-b, IL-6, TNF-a and PGE2

status: Public on Jan 29 2009

city: Berlin

first: Elke

last: Krueger

address: Monbijoustr. 2

department: Institute of Biochemistry

institute: Charité Universitaetsmedizin Berlin

summary:
The ubiquitin proteasome system (UPS) is known to possess important regulatory functions in the immune response. To gain a better and first comprehensive insight into the mechanisms underlying the conversion of immature to mature DC in terms of the expression of UPS related genes, we undertook a comparative gene expression profiling during DC maturation in response to four different prototypic maturation stimuli.
Keywords: time course

overall_design: Monocyte-derived DC were harvested at 3 different periods of time following stimulation for RNA extraction and hybridization on Affymetrix microarrays.

first: Frederic

last: Ebstein

last: Krüger


title: In vitro study of gene expression and response to chemotherapy across 50 human-melanoma derived cell lines

city: Durham

first: Christina

last: Augustine

state: NC

address: VAMC RmE4001 508 Fulton St.

department: Surgery

institute: Duke University Medical Center

summary:
To identify patterns of gene expression that correlate with response to treatment with either melphalan or temozolomide we measured both gene expression using microarray genechips and response to drug using a standard in vitro cell proliferation assay.  Senstivity to melphalan was measured 48hrs after drug treatment while sensitivity to temozolomide was measured 12 days after drug treatment.
Keywords: Patterns of gene expression predictive of response to chemotherapy with melphalan or temozolomide in melanoma

overall_design: For each of the 50 melanoma-derived cell lines, 1 flask of cells was grown to 80% confluence and harvested for RNA isolation.  Cells were lysed in buffer with 1% β-mercaptoethanol and RNA isolated using Qiagen RNeasy-plus RNA isolation kit which included a step to eliminate genomic DNA.  RNA concentration was measured and quality assessed using the NanoDrop ND100 spectrophotometer.  RNA was reverse transcribed and biotin-labeled cRNA synthesized.  The product was hybridized to the Affymetrix human genechip HU133 Plus2 according to manufacturer's instructions.  Data was initially assessed for quality and a relative value for expression was calculated as the difference between the perfect match and the mismatch signal intensities using the Affymetrix GeneChip Operating System (GCOS).  A detection call (present, absent or marginal) as well as a detection p-value was also calculated.  Data was normalized by multiplying each signal by a scaling factor such that the mean signal intensity for each GeneChip was equal to 500.  Scaling factors were all under 10.

first: Douglas

last: Tyler


title: Expression data from RNAi SNCA treated human neuroblastoma cell line

status: Public on Feb 01 2009

city: Tuebingen

first: Karina

last: Haebig

address: Calwerstr. 7

department: Medical Genetics

institute: Institute of Human Genetics

summary:
The pre-synaptic protein α-synuclein is a key player in the pathogenesis of Parkinson's disease. Together with accumulation and missfolding of α-synuclein protofibrils serve as seed structures for the aggregation of numerous proteins in the cytoplasm of neuronal cells, the so-called Lewy bodies. Furthermore, missense mutations in the SNCA gene and gene multiplications lead to autosomal dominant forms of familiar PD. However, so far the exact biological role of α-synuclein in normal brain is elusive. To gain more insights into the biological function of this protein we monitored whole genome expression changes in dopaminergic neuroblastoma cells (SH-SY5Y) caused by a 90% reduction of α-synuclein by RNA interference.
Keywords: whole genome expression changes through the loss of α-synuclein

overall_design: comparison of expression profil changes in cells with normal α-synuclein level (control siRNA treatment) and reduced α-synuclein level (siSNCA4 treatment), triplicatesof each condition

last: Bonin

last: Häbig


title: Expression data from 'naïve' and HVC-replicon containing Huh7 cells (Clone A cells)

status: Public on May 03 2009

city: Cambridge

first: Piroska

last: Devay

address: 500 Technology Sq

department: Infectious Disease

institute: NIBRI

summary:
Cyclophilin binding drugs, NIM811 and cyclosporin A (CsA), inhibit the replication of HCV replicon.
We investigated the mode of action of these drugs and identified host factors essential for HCV replication in a subgenomic replicon model.

overall_design: Cultured Huh7 cell were treated with CsA or NIM811 at different concentrations. Cells were harvested after 12, 24 or 48 hours.  The extracted mRNA were hybridized on Affymetrix U133 Plus 2 microarrays.

first: Kara

last: Balabanis

first: Brigitte

last: Wiedmann


title: Effects of labelling fetal MSC with MRI Particles: MGIO and Ferucarbotran

city: Herston

first: Eddy Shoo-Ming

last: Lee

state: Queensland

address: Royal Brisbane and Women's Hospital

country: Australia

institute: University of Queensland

summary: Cell tracking is enabled by incubating ex vivo cells with commercially/clinically available MRI particulate label, such as ferucarbotran. However, the uptake by non-phagocytic cells, such as mesenchymal stem cell (MSC) is poor, and the detection by MRI is impeded. MGIO is a new label that is efficiently taken up by MSC. The proliferation and differentiation capacity of labelled cells are usually assessed to determine cytotoxicity. In this study, we compared the global gene expression profiles of mock-labelled, ferucarbotran-labelled and MGIO-labelled fetal MSC.

overall_design: Fetal MSC were labelled at passage 5, washed with PBS to remove excess labels, detached by trypsin, pelleted by centrfugation and lysed for RNA extraction with the RNeasy mini kit (Qiagen) in triplicates.

first: Eddy

first: Jerry

last: Chan

first: Shih-chang

last: Wang


title: Card9 dependent activation of macrophages by TDB

city: Munich

first: Joerg

last: Mages

address: Trogerstrasse 30

department: Institute of Medical Microbiology, Immunology and Hygiene

institute: Technical University Munich

summary:
Bone marrow derived macrophages from wt and card9 KO mice were stimulated  with CpG, Curdlan or TDB, an analogon to the mycobacterial cord factor TDM for 48h, respectively.
Keywords: card9 knockout, macropphage, TDB

overall_design: wt or card9 KO macrophages stimulated for 48h

first: Roland

last: Lang

first: Jörg

first: Kerstin

last: Werninghaus

first: Angela

last: Servatius


title: Expression data from normal and CRC human peripheral blood samples

city: Budapest

first: Norbert

last: Solymosi

state: Budapest

address: István u. 2.

institute: ATE

summary:
The whole-genome oligonucleotide microarray analysis of peripheral blood samples can contribute to the determination of distant blood markers of local pathophysiological alterations in colorectal diseases. These markers can lead to alternative screening procedures.
Keywords: whole genomic expression

overall_design: Total RNA was extracted from peripheral blood samples of healthy patients and patients with CRC and hybridized on Affymetrix HGU133 Plus 2.0 microarrays

first: Orsolya

last: Galamb

first: Bela

last: Molnar

first: Sandor

last: Spisak

first: Ferenc

last: Sipos


title: U1 Adaptors: a new gene silencing technology

city: Piscataway

first: Samuel

middle: I

last: Gunderson

address: 604 Allison Road

department: Molecular Biology & Biochemistry

institute: Rutgers University

summary: The goal of the microarray experiment was to do a head-to-head comparison of the U1 Adaptor technology with siRNA in terms of specificity at the genome-wide level.  U1 Adaptors represent a novel gene silencing method that employs a mechanism of action distinct from antisense and RNA interference (RNAi).  The U1 Adaptor is a bifunctional oligonucleotide having a “Target Domain” that is complementary to a site in the target gene's terminal exon and a “U1 Domain” that binds to the U1 small nuclear RNA (snRNA) component of the U1 small nuclear ribonucleoprotein (U1 snRNP) splicing factor.  Tethering of U1 snRNP to the target pre-mRNA inhibits 3' end processing (i.e., polyA tail addition) leading to degradation of that RNA species within the nucleus thereby reducing mRNA levels.  We demonstrate that U1 Adaptors can specifically inhibit both reporter and endogenous genes.  Further, targeting the same gene either with multiple U1 Adaptors or with U1 Adaptors and small interfering RNAs (siRNAs), strongly enhances gene silencing, the latter as predicted from their distinct mechanisms of action.  Such combinatorial targeting requires lower amounts of oligonucleotides to achieve potent silencing.

overall_design: For each sample total RNA was prepared from 3 independent transfections and then were pooled and analyzed by QPCR and also by microarray.

first: Rafal

last: Goraczniak

first: Mark

last: Behlke


title: Protein Engineering of the Quorum-Sensing Regulator SdiA of Escherichia coli

status: Public on Jan 28 2009

city: College Station

first: Jintae

department: Chemical Engineering

institute: Texas A&M University

summary: The Escherichia coli quorum-sensing regulator, SdiA, belongs to the LuxR family of transcriptional regulators and is responsible for detecting signals from other bacteria.  Previously we found that SdiA is necessary for E. coli to control its biofilm formation with indole just as SdiA is necessary for E. coli to alter its biofilm formation in the presence of N-acylhomoserine lactones (AHLs).  Here we engineered SdiA by random mutagenesis to further control biofilm formation in the presence of indole and AHLs. After screening of 477?? mutants with indole and two AHLs (N-butyryl-DL-homoserine lactone, and N-(3-oxooctanoyl)-L-homoserine lactone, C6HSL), five SdiA variants were obtained that altered biofilm with and without signals of indole and AHLs.  Two truncation variants (1E11 and 14C3) lacking the C-terminal DNA-binding domain of SdiA showed the reduction of biofilm formation by 5-fold and 10-fold in LB and LB glu, respectively.  DNA microarrays show that the evolved SdiA (1E11) compared to wild-type SdiA influences indole synthesis genes, AI-2 uptake genes, acid-resistance genes, motility related genes, cold-shock protein genes, and several regulatory protein genes. Corroborating DNA microarrays, SdiA variants produced various amounts of indole which led to different survivals in low pH and influenced swimming motility and final cell density. Also, an AHL sensitive variant (2D10) 2-fold increased biofilm formation in the presence of C6HSL, while another variant (6B12) lowered biofilm formation in the presence of C6HSL. Hence, the results clearly showed that mutation of SdiA itself directly controls biofilm formation and SdiA variants could be further recognized by the inter-species signal AHLs. This is the first random protein engineering to control biofilm formation.

overall_design: For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms in 250 mL LB ( 1 mM IPTG + Cm30) in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures diluted that were 1:100.  The cells were shaken at 250 rpm and 30C for 12 hours to form biofilms on the glass wool, and RNA was isolated from the the biofilm cells.

first: Thomas

last: Wood


title: Genes regulated by PRDM5 in U2OS cells.

status: Public on Jan 26 2009

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

summary:
PRDM5 is a recently identified member of the PRDM family of proteins, which functions as a transcriptional repressor by recruiting histone methyltransferase G9A to DNA, and behaves as a putative tumor suppressor in different types of cancer.
We investigated PRDM5 function by identifying its target genes in U2OS cells at different time points after expression of PRDM5 protein.
Keywords: Transcriptional regulation, time course

overall_design: We analyzed gene expression profiles of a U2OS cell line conditionally expressing HA-tagged PRDM5 (U2OS-PRDM5), where PRDM5 is under the transcriptional control of a doxycycline-inducible promoter. Expression of PRDM5 protein is detectable after 8 hours of induction with 2ug/ml doxycycline, and increases steadily up to 48 hours, after which cells begin to undergo apoptosis. U2OS cells containing the empty cloning vector (U2OS-pSG213) were used as controls for each condition.


title: Human adrenocortical carcinomas (33), adenomas (22), and normal adrenal cortex (10), on Affymetrix HG_U133_plus_2 arrays

status: Public on Jan 22 2009

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

country: USA

institute: University of Michigan

summary:
Human samples of 33 adrenocortical carcinomas, 22 adrenocortical adenomas, and 10 normal adrenal cortex samples, each from a different patient, had mRNA assays performed using Affymetrix HG_U133_plus_2 arrays, with 54675 probe-sets.  We note that the same array data is in GEO series GSE33371, where we assayed the cancer samples for Beta-catenin staining or mutation, and make new comparisons based on those assays.
Keywords: disease state analysis

overall_design:
Human samples of 33 adrenocortical carcinomas, 22 adrenocortical adenomas, and 10 normal adrenal cortex samples, each from a different patient, had mRNA assays performed using Affymetrix HG_U133_plus_2 arrays, with 54675 probe-sets.

Two supplementary files are attached below. The Adrenocortical_logs.xls file shows the log-transformed probe-set values and the results of a statistical analysis for each probe-set. The Readme file describes the columns of this log file.

middle: J

last: Giordano

first: Tobias

last: Else

first: Michelle

last: Vinco

first: Juliane

last: Bauersfeld

first: Donita

last: Sanders

first: Dafydd

last: Thomas

first: Paul

last: Gauger

first: Gerard

last: Doherty

first: Gary

last: Hammer


title: Analysis of Ago2-associated transcripts after knockdown of Importin8

city: Martinsried

first: Gunter

last: Meister

address: Am Klopferspitz 18

department: Center for Integrated Protein Science Munich (CIPSM)

country: Germany

institute: Max Planck Institute of Biochemistry

summary: Small regulatory RNAs including small interfering RNAs (siRNAs) and microRNAs (miRNAs) guide Argonaute (Ago) proteins to specific target RNAs leading to mRNA destabilization or translational repression. We recently reported the identification of Importin 8 (Imp8) as a novel component of miRNA-guided regulatory pathways. Imp8 interacts with Ago proteins and localizes to cytoplasmic processing bodies (P-bodies), structures involved in RNA metabolism. For this micro-array dataset, we used immunoprecipitations of Ago2-associated mRNAs followed by micro-array analysis. The results demonstrate that Imp8 is required for recruiting Ago protein complexes to a large set of Ago2-associated target mRNAs allowing for efficient and specific gene silencing. Therefore, we provide evidence that Imp8 is required for cytoplasmic miRNA-guided gene silencing.

overall_design: HeLa cells were transfected with control or Imp8 siRNAs. Each sample was divided into two parts for total RNA extraction and anti-Ago2 immunoprecipitation followed by RNA extraction. In addition to the knockdown of Imp8, total RNA samples were included where the miRNA pathway protein TNRC6B was depleted by RNAi. All micro-array experiments were performed in at least two biological replicates. Total RNA samples and immunoprecipitated RNA samples were hybridized to separate Human Genome U133 Plus 2.0 Affymetrix microarrays. Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. For each array, each measurement was divided by the 50th percentile of all measurements in that sample. The specific enrichment of each individual transcript can be calculated from its normalized value in the immunoprecipitation sample, divided by its normalized value in the corresponding total RNA sample.

first: Lasse

last: Weinmann

first: Julia

last: Höck

first: Tomi

last: Ivacevic

last: Ohrt

first: Jörg

last: Mütze

first: Petra

last: Schwille

first: Elisabeth

last: Kremmer

first: Vladimir

last: Benes

first: Henning

last: Urlaub


title: Expression data from multiple myeloma cells treated with arsenic

status: Public on Jan 23 2009

city: Miami

first: Larry

last: Boise

address: 1600 NW 10th Ave

department: Microbiology and Immunology

institute: University of Miami

summary:
We used microarrays to examine changes in gene expression in multiple myeloma cell lines following treatment with arsenic trioxide and darinaparsin

Keywords: Time course

overall_design: Four multiple myeloma cell lines (U266, MM.1s, KMS11, 8226/S) were treated with either arsenic trioxide (ATO) for 6, 24, or 48 hours or darinaparsin (DAR) for 6 or 24 hours; RNA was extracted from treated and control cells for microarray analysis

first: Lawrence

middle: H

first: Alejo

last: Morales


title: Expression data from primary colorectal cancers

city: Aarhus N.

first: Claus

middle: Lindbjerg

last: Andersen

address: Brenstrupgaardsvej 100

department: Dept. of Molecular Medicine (MOMA)

country: Denmark

institute: Aarhus University Hospital

summary:
Samples were taken from colorectal cancers in surgically resected specimens in 155 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133Plus 2.0 arrays. Our MSI/MSS classifier was applied to these samples.

Keywords: Expression profiling by array

overall_design: mRNA from one-hundred-fifty-five primary colorectal tumour samples were extracted and hybridized to HG-U133Plus 2.0 expression arrays. The MAS5.0 procedure was used to make calls of expression. Data from each sample were quantile normalized and log-2 transformed.

first: Torben

middle: F

last: Ørntoft


title: Genome-wide gene expression in CEBPA mutant and CEBPA silenced AML and in T-ALL

status: Public on Jan 21 2009

city: Rotterdam

first: Bas

last: Wouters

address: P.O. Box 2040, room Ee1330B

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center

summary:
Acute Myeloid Leukemia (AML) is a heterogeneous disease from the molecular and biological standpoints, and even patients with a specific gene expression profile may present clinical and molecular heterogeneity. We studied the epigenetic profiles of a cohort of patients that shared a common gene expression profile but differed in that only half of them harbored mutations of the CEBPA locus, while the rest presented with silencing of this gene and co-expression of certain T cell markers. DNA methylation studies revealed that these two groups of patients could be readily segregated in an unsupervised fashion based on their DNA methylation profiles alone. Furthermore, CEBPA silencing was associated with the presence of an aberrant DNA hypermethylation signature, which was not present in the CEBPA mutant group. This aberrant hypermethylation occurred more frequently at sites within CpG islands. CEBPA silenced leukemias also displayed marked hypermethylation when compared with normal CD34+ hematopoietic cells, while CEBPA mutant cases showed only mild changes in DNA methylation when compared to these normal progenitors.  Biologically, CEBPA silenced leukemias presented with a decreased response to myeloid growth factors in vitro.

Keywords: Gene expression profiling using arrays

overall_design: Direct comparison of gene expression in leukemic blasts from 8 patients with Acute Myeloid Leukemia (AML) carrying a CEBPA mutation and 8 patients with AML without CEBPA mutation but with silencing of CEBPA expression, and with 9 samples of T Acute Lymphoblastic Leukemia (T-ALL) patients.

first: Maria

last: Figueroa

first: Ari

last: Melnick

first: Ruud

last: Delwel


title: Expression data from multiple myeloma cells overexpressing CS1 versus CS1 knockdown

status: Public on Feb 04 2009

city: Boston

first: Yu-Tzu

last: Tai

address: 44 Binney Street

institute: Dana Farber Cancer Institute

summary: We used microarrays to detail the global programme of gene expression underlying CS1-regulated biological processes including increased cell adhesion and cell proliferation.

overall_design: Human multiple myeloma cell lines with and without CS1 expression, either by transffecting CS1 overexpressing vector or lentiviral CS1 shRNA, were subject to total RNA extraction and hybridization on Affymetrix microarrays. We sought to define the common genes underexpressed in CS1 knockdown myeloma cells whereas overexpressed in CS1 overexpressing myeloma cells to gain insight into CS1-targeting genes in order to define the molecular mechanisms regulated by CS1 in multiple myeloma.

first: Y-T


title: Effect of miRNA biogenesis factors on mRNA levels

status: Public on Jan 16 2009

city: Seoul

first: Jinju

last: Han

address: 599 Gwanangno, Gwanak-gu

institute: Seoul National University

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

overall_design: Refer to individual Series


title: Alteration of gene expression profile in HEK293 cells treated with proteasome inhibitor epoxomicin

status: Public on Jan 15 2009

city: Bethesda

first: Allen

middle: HK

last: Chang

address: 50 South Drive, Bldg.50, Rm.2347

institute: NIH\NHLBI

summary:
The objective of this study is to identify the genes that are up-regulated amid proteasome dysfunction to facilitate the discovery of proteolytic pathways that are activated as a compensatory response to proteasome inhibition. Proteasome is a large multi-component proteolytic complex in the cell. It is responsible for the constitutive turn-over of many cellular proteins as well as the degradation of oxidized and/or unfolded proteins. With such a fundamental role in the cell, disruption of proteasome understandably can lead to disastrous outcome. Oxidative stress has been postulated as the driving mechanism for aging. Oxidatively modified proteins, which usually have lost their activity, require immediate removal by proteasome to maintain normal cellular function. Dysfunction of proteasome has also been linked to neuro-degenerative diseases such as Alzheimer’s and Parkinson’s diseases, those that are most commonly seen in aged population. There is more than one proteolytic pathway in the cell, and it has been reported that obstruction of any one of these pathways may enhance the activity of the others. Proteasomal function has been found to have decreased during aging, prompting researchers to hypothesize that failure to remove oxidized proteins may play an important role in aging. It would be interesting to determine the other proteolytic pathways that are activated after proteasome inhibition by a relatively specific inhibitor epoxomicin to help understand their roles in aging processes.

Keywords: time course, proteasome, inhibitor, oxidative stress, epoxomicin

overall_design:
Human embryonic kidney cells (HEK293) were untreated or treated with 1 uM epoxomicin for 1 and 6 hours. Total RNA was extracted for gene expression profiling using Affymetrix human genome U133 2.0 plus chip. A quadrupliate was prepared for each treatment.
contributor: NHLBI Gene Expression Core Facility

first: Rodney

last: Levine


title: Gene expression in mouse heart

city: San Francisco

first: Masaki

last: Ieda

address: 1650 Owens street,

institute: Gladstone Institute

summary:
Growth and expansion of ventricular chambers is essential during cardiogenesis and is achieved by proliferation of cardiac progenitors that are not fully differentiated. Disruption of this process can lead to prenatal lethality. In contrast, adult cardiomyocytes achieve growth through hypertrophy rather than hyperplasia. Although epicardial-derived signals may contribute to the proliferative process in myocytes, the factors and cell types responsible for development of the ventricular myocardial thickness are unclear. Moreover, the function of embryonic cardiac fibroblasts, derived from epicardium, and their secreted factors are largely unknown. Using a novel co-culture system, we found that embryonic cardiac fibroblasts induced proliferation of cardiomyocytes, in contrast to adult cardiac fibroblasts that promoted myocyte hypertrophy. We identified fibronectin, collagen and heparin-binding EGF-like growth factor as embryonic cardiac fibroblast-specific signals that collaboratively promoted cardiomyocyte proliferation in a paracrine fashion. b1 integrin was required for this proliferative response, and ventricular cardiomyocyte-specific deletion of b1 integrin in mice resulted in reduced myocardial proliferation and impaired ventricular compaction. These findings reveal a previously unrecognized paracrine function of embryonic cardiac fibroblasts in regulating cardiomyocyte proliferation.

This SuperSeries is composed of the SubSeries listed below.


title: Gene expression profiling of interferon-beta stimulated cells

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

summary: Cytoplasmic DNA triggers the activation of the innate immune system. While downstream signaling components have been characterized, the DNA sensing components remain largely elusive. We performed a systematic proteomics screen for proteins that associate with DNA, traversed to a screen for IFN-β-induced transcripts. We identified DSIRE (DNA sensor for the IL-1β response, previously called AIM2) as a candidate cytoplasmic sensor. DSIRE showed a marked selectivity for double-stranded DNA. DSIRE can recruit the inflammasome adaptor ASC and gets redistributed to ASC speckles upon coexpression of ASC. RNAi-mediated reduction of DSIRE expression led to an impairment in IL-1β maturation. Reconstitution of unresponsive cells with DSIRE, ASC, caspase 1 and IL-1β showed that DSIRE is sufficient for inflammasome activation. Overall, our data strongly suggest that DSIRE is a cytoplasmic DNA sensor for the inflammasome.

overall_design: In a genomic screen, we used NIH3T3, L929 and RAW264.7 cells to identify genes that were transcriptionally regulated by IFN-β. We stimulated the cells with IFN-β for 4h, isolated the RNA and analyzed global changes in gene expression by microarray analysis. Overall, 225 genes were upregulated at least 3fold, among which numerous well-known interferon-induced genes were found

first: Tilmann

last: Buerckstuemmer

first: Giulio

last: Superti-Furga