title: Expression profiles of amniotic fluid from human fetuses with Down syndrome and euploid controls

status: Public on May 21 2009

city: Medford

first: Donna

middle: K

last: Slonim

address: 161 College Ave.

department: Computer Science

institute: Tufts University

summary: In order to characterize the differences between second trimester Down syndrome (DS) and euploid fetuses, we compared gene expression in uncultured amniotic fluid supernatant samples. We identified individually differentially expressed genes via paired t-tests in the matched samples, and a set of differentially expressed genes on chromosome 21 using Gene Set Enrichment Analysis.  Functional pathway analysis of the resulting genes highlighted the importance of oxidative stress, ion transport, and G-protein signaling in the DS fetuses.

overall_design: We profiled seven DS expression samples and seven controls matched for gender and approximate gestational age..

first: Keiko

last: Koide

first: Kirby

middle: L

last: Johnson

first: Umadevi

last: Tantravahi

first: Janet

last: Cowan

first: Zina

last: Jarrah

first: Diana

middle: W

last: Bianchi


title: Expression data from human cancer cells treated with UPR modulators under ER stress conditions

status: Public on May 20 2009

city: Ariake

first: Akihiro

last: Tomida

state: Koto-ku, Tokyo

department: Cancer Chemotherapy Center

country: Japan

institute: Japanese Foundation for Cancer Research (JFCR)

summary:
The unfolded protein response (UPR) is a cellular defense mechanism against glucose deprivation, a cell condition that occurs in solid tumors.
A key feature of the UPR is the activation of the transcription program that allows the cell to cope with endoplasmic reticulum (ER) stress. We used micoarrays to show that the UPR transcription program is disrupted by the antitumor macrocyclic compound versipelostatin (VST) and antidiabetic biguanides metformin, buformin and phenformin, depending on cellular glucose availability.

Keywords: stress response, drug response

overall_design:
Total 42 samples were prepared for RNA extraction and hybridization on Affymetrix microarrays.

To induce the UPR, we treated cells (HeLa, HT-29, HT1080, MKN74) for 15 or 18 hours under ER stress conditions by replacing the medium with glucose-free medium or by adding either 2-Deoxy-D-glucose (2DG) or Tunicamycin (TM) to glucose-containing medium. UPR modulators (VST, biguanides or pyrvinium pamoate) were added at various final concentrations immediately after cells were placed in glucose-free medium or just before the chemical stressors were added to glucose-containing culture medium.

first: Sakae

last: Saito

first: Takashi

last: Tsuruo


title: Bioligical pathways of Hsp90 inhibitors in adult T cell leukemia cell lines

status: Public on May 27 2009

city: Tokyo

first: Junko

middle: H

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

institute: Tokyo Medical University

summary: Heat shock protein 90 (Hsp90) is essential for the stability and the function of many client proteins, such as ERB2, C-RAF, CDK4, HIF-1 aplha and AKT. Recent reports demonstrated that inhibition of Hsp90 modulates multiple functions required for survival of human cancer, such as myeloma (Mitsiades et al, Blood:107, 1092, 2006), The aim of this study is evaluate the effect of Hsp90 inhibition, and to identify molecular pathways responsible for anti-proliferative effect on ATL cells. For Hsp90 inhibition, Geldanamycin derivates, 17AAG (17-allylamino -17-demethoxygeldanamycin) and 17DMAG (17-(dimethylaminoethylamino) 17-demethoxygeldanamycin) were used in this study. Interleukin 2-independent ATL cell lines (MT-2 and MT-4) and an interleukin 2-dependent ATL cell line (TaY-E10) were incubated, with or without Hsp90 inhibitors.

overall_design: Three ATL cell lines(TaY-E10, MT-2, and MT-4) were cultured in the presence or absence of Hsp90 inhibitors(17-AAG and 17-DMAG).


title: Molecular Analysis of the Vaginal Response to Estrogens in the Ovariectomized Rat and Postmenopausal Woman

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

country: USA

institute: Pfizer

summary:
Background. Vaginal atrophy (VA) is the thinning of the vaginal epithelial lining, typically the result of lowered estrogen levels during menopause. Some of the consequences of VA include increased susceptibility to bacterial infection, pain during sexual intercourse, and vaginal burning or itching. Although estrogen treatment is highly effective, alternative therapies are also desired for women who are not candidates for hormone replacement therapy (HRT).  The ovariectomized (OVX) rat is widely accepted as an appropriate animal model for many estrogen-dependent responses in humans; however, since reproductive biology can vary significantly between mammalian systems, this study examined how well the OVX rat recapitulates human biology at the transcriptional level. This report describes an analysis of expression profiling data, comparing the responses of rat and human vaginae to estrogen treatment.    Results. The level of differential expression between pre- vs. post- estrogen treatment was calculated for each of the human and OVX rat datasets. Probe sets corresponding to orthologous rat and human genes were mapped to each other using NCBI Homologene. A positive correlation was observed between the rat and human responses to estrogen. Genes belonging to several biological pathways and GO categories were similarly differentially expressed in rat and human.  A large number of the coordinately regulated biological processes are already known to be involved in human VA, such as inflammation, epithelial development, and EGF pathway activation.   Conclusions. At the transcriptional level, there is evidence of significant overlap of the effects of estrogen treatment between the OVX rat and human VA samples.

Keywords: Disease State Analysis: Animal Model Validation

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: We analyzed vaginal biopsies from 19 woman pre and post 3 month estradiol treatment and compared to OVX rats treated with E2 for 6 hr, 3 days or 5 days (N=5)


title: Differential gene expression from azithromycin and SMM treated human airway epithelium

status: Public on May 19 2009

city: Chapel Hill

first: Wanda

middle: K.

last: O'Neal

state: NC

department: Cystic Fibrosis/Pulmonary Research and Treatment Center

institute: University of North Carolina at Chapel Hill

summary:
Microarrays were used to evaluate the effects of azithromycin and an inflammatory stimulus (SMM) on human airway epithelium. Effects of azithromycin treatment were evaluated at 6, 24 and 48 hours. Effects of SMM were evaluated at 6 and 24 hours. In addition, pretreatment with azithromycin was used to evaluate the modulatory effects on SMM-induced inflammation. SMM=supernatant from microcorpulent material from human cystic fibrosis airways.
Keywords: timecourse, treatment comparisons.

overall_design: 10 treatments total, 3-4 samples (patient codes = replicates) per treatment.

first: Carla

last: Ribeiro

first: Harry

last: Hurd

first: Yichao

last: Yu

first: Mary

last: Braun

first: Richard

last: Boucher


title: Analysis of the impact of the method of cell selection on the gene expression profile of human CD4 and CD8 T cells

city: London

first: Rifca

last: Le Dieu

address: 3rd Floor, John Vane Science Building, Charterhouse Square

department: Institute of Cancer

country: United Kingdom

institute: Queen Mary University of London

summary:
Negative immunomagnetic selection has become the method of choice for isolating T cell subsets for functional studies due to concerns that directly binding antibody to the surface of a cell, as occurs with positive selection, results in cross-linking of surface antigens, altered gene transcription and subsequent cellular activation. However there is little data to support this. We therefore examined the impact of the method of immunomagnetic cell selection on the gene expression profile of healthy human CD4 and CD8 T cells in a total of 21 cases.

Keywords: Methodology

overall_design: This study was composed of 4 groups of samples: CD4 Negative Selection (n=5), CD4 Positive Selection (n=5), CD8 Negative Selection (n=5), CD8 Positive Selection (n=6). Two samples (PS6 CD8 and PS9 CD4) were removed from the analysis due to discrepant normalised unscaled standard errors

last: Mitter

first: John

middle: G

last: Gribben


title: Expression data from Crohn's disease (CD) and Ulcerative colitis (UC) human peripheral blood samples

city: Budapest

first: Norbert

last: Solymosi

state: Budapest

address: István u. 2.

country: Hungary

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.

overall_design: Total RNA was extracted from peripheral blood samples of patients with Ulcerative colitis (UC) and Crohn's disease (CD) 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: Expression data from human intestinal biopsies

status: Public on May 05 2009

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

summary:
Whole genome expression profiling of 40 healthy human twins (20 monozygotic, 20 dizygotic)
Keywords: heritability test

overall_design: Sampling was controlled for sampling time, fasting conditions, sampling conditions, sampling storage and processing. 10 twinpairs (20 individuals) were dizygotic and 10 twinpairs (20 individuals) were monozygotic twins.


title: Gene expression profiling of human non-Hodgkins lymphoma (NHL) cell lines

status: Public on May 11 2009

city: South San Francisco

first: Peng

last: Yue

state: CA

address: 1 DNA Way

institute: Genentech Inc

summary:
We profiled 40 NHL cell lines to determine gene expression patterns and molecular subtypes.

Keywords: NHL, cancer, cell lines

overall_design: RNA profiles of NHL cell lines.

first: David

last: Dornan

first: Andrew

last: Polson


title: Identification of genes responsive to the combination of Sonazoid and ultrasound in human leukemia U937 cells

status: Public on May 16 2009

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary: Echo-contrast agents enhance the echogenicity of ultrasound and have been clinically used for diagonosis in current medical fields. Here, the combined effects of Sonazoid, an echo-contrast agent, and ultrasound on the gene expression in human lymphoma U937 cells were investigated using an Affymetrix GeneChip system. The cells were treated with Sonazoid (0.05%; Sonazoid only), ultrasound (0.3 W/cm2 for 1 min; ultrasound only) and the combination of Sonazoid and ultrasound (0.05% Sonazoid plus ultrasound 0.3 W/cm2 for 1 min; Sonazoid + Ultrasound) and followed by incubation for 3 h at 37°C. The percentage of DNA fragmentation 6 h after treatment was 5.8 ± 1.0 (mean ± SD, n = 3), 6.0 ± 0.4, 13.5 ± 1.0, and 18.3 ± 2.3 in cells treated with control, Sonazoid only, ultrasound only and Sonazoid + Ultrasound, respectively. Of approximately 47,000 probe sets analyzed, probe sets that were differentially expressed by a factor 2.0 or greater were 40, 184 and 144 in cells treated with Sonazoid only, ultrasound only and Sonazoid + Ultrasound, respectively.

overall_design: U937 cells, a human lymphoma cell line, were treated with Sonazoid (0.05%), ultrasound (0.3 W/cm2 for 1 min) and the combination of Sonazoid and ultrasound (0.05% Sonazoid plus ultrasound 0.3 W/cm2 for 1 min) and followed by incubation for 3 h at 37°C. Non-treated cells were served as control. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with a Human Genome U133-plus 2.0 array for analysis of over 47,000 transcripts. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Yukihiro

last: Furusawa

first: Ichiro

last: Takasaki

first: Takashi

last: Kondo


title: Longitudinal study of gene expression in healthy individuals

status: Public on May 09 2009

city: Basel

first: Guillemette

last: Duchateau-Nguyen

address: Building 93

department: Pharma Research and Early Development

country: Switzerland

institute: F.Hoffmann-La Roche AG

summary: The gene expression profile of blood drawn from healthy individuals was studied over a period of six months, at five time points. The gene expression profiles appeared to be constant over one month and to slightly vary over three months. A small proportion of genes were found to be differentially regulated according to gender.  Differential gene regulation by age (in subjects 25–55 years of age versus subjects > 55 years of age) was not observed.

overall_design: Healthy subjects were enrolled at a single site, their health status was determined by medical history, physical examination, and standard laboratory test values. Venous blood was drawn in the morning, from fasted subjects at five time points (Day1, Day14, Day28, Day 90 and Day 180). Blood was collected into PAXgene tubes (Becton-Dickinson Diagnostics; Hombrechtikon, Switzerland).

first: Chris

last: Karlovich

first: Andrea

last: Johnson

first: Patricia

last: McLoughlin

first: Mercidita

last: Navarro

first: Carole

last: Fleurbaey

first: Lori

last: Steiner

first: Michel

last: Tessier

first: Tracy

last: Nguyen

first: Monika

last: Wilhelm-Seiler

last: Caulfield


title: Changes in gene expression of hMSCs and NOD/scid mouse lung after IV infusion of hMSCs

status: Public on May 07 2009

city: Temple

first: Joni

last: Ylostalo

state: TX

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

summary: Quantitative assays for human DNA and mRNA were used to examine the paradox that intravenously (IV) infused human multipotent stromal cells (hMSCs) can enhance tissue repair without significant engraftment.  After 2 X 106 hMSCs were IV infused into mice, most of the cells were trapped as emboli in lung.  The cells in lung disappeared with a half-life of about 24 hr but < 1,000 cells appeared in 6 other tissues.  The hMSCs in lung up-regulated expression of multiple genes with a large increase in the anti-inflammatory protein TSG-6.   After myocardial infarction, IV hMSCs but not hMSCs transduced with TSG-6 siRNA decreased inflammatory responses, reduced infarct size, and improved cardiac function. IV administration of recombinant TSG-6 also reduced inflammatory responses and reduced infarct size. The results suggest improvements in animal models and patients after IV infusions of MSCs are at least in part explained by activation of MSCs to secrete TSG-6.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
3 samples containing either mouse lung and human cells or only mouse lung run on a 3 human and 3 mouse arrays.
1) control NOD/scid mouse lung
2) in vitro mix of NOD/scid mouse lung and hMSCs
3) NOD/scid mouse lung 10h after IV infusion of 2 million hMSCs

first: Ryang-Hwa

last: Lee

first: Andrey

last: Pulin

first: Min-Jeong

last: Seo

first: Daniel

last: Kota

first: Benjamin

last: Larson

first: Laura

last: Semprun-Prieto

first: Patrice

last: Delafontaine

first: Darwin

middle: J

last: Prockop


title: Microarray analysis of FoxP3-expressing or non-expressing subsets of human CD4+ T cells

city: Kyoto

first: Makoto

last: Miyara

address: 53 Shogoin Kawahara-cho,

department: Institute for Medical Sciences

institute: Kyoto University

summary:
Gene expression profiles of subsets of CD4+ T cells according to their expression of FoxP3 and CD45RA  were compared.

Abstract:
FoxP3 is a key transcription factor for the development and function of natural CD4+ regulatory T cells (Tregs). Here we show that human FoxP3+CD4+ T cells are composed of three phenotypically and functionally distinct subpopulations: CD45RA+FoxP3low resting Tregs (rTregs) and CD45RA-FoxP3high  activated Tregs (aTregs), both of which are suppressive in vitro, and cytokine-secreting CD45RA-FoxP3low non-suppressive T cells. The proportion of the three subpopulations characteristically altered in cord blood, aged individuals, and patients with immunological diseases. Terminally differentiated aTregs rapidly die while rTregs proliferate and convert into aTregs in vitro and in vivo as shown by the transfer of rTregs into NOD-scid-common gamma-chain-knockout mice and by TCR sequence-based T cell clonotype tracing in peripheral blood of normal individuals. Taken together, the dissection of FoxP3+ cells into subsets enables one to analyze Treg differentiation dynamics and interactions in normal and disease states, and to control immune responses through manipulating particular FoxP3+ subpopulations.

overall_design: RNA was extracted from freshly obtained peripheral blood lymphocytes from a healthy donor that were separated according to their expression of CD25, CD127 and CD45RA after surface staining.

first: Yumiko

last: Yoshioka

first: Akihiko

last: Kitoh

first: Tomoko

last: Shima

first: Kajsa

last: Wing

first: Akira

last: Niwa

first: Christophe

last: Parizot

first: Cécile

last: Taflin

first: Toshio

last: Heike

first: Dominique

last: Valeyre

first: Alexis

last: Mathian

first: Tatsutoshi

last: Nakahata

first: Tomoyuki

last: Yamaguchi

first: Takashi

last: Nomura

first: Masahiro

last: Ono

first: Zahir

last: Amoura

first: Guy

last: Gorochov

first: Shimon

last: Sakaguchi


title: Gene expression data from severe asthmatic children: PBMC profiles during acute exacerbation versus convalescence

city: Perth

first: Kathy

middle: Laura

last: McKenna

state: Western Australia

address: 100 Roberts Rd

country: Australia

institute: Institute for Child Health Research

summary:
Severe asthma exacerbations in children requiring hospitalisation are typically associated with viral infection, and occur almost exclusively amongst atopics, but the significance of these comorbidities is unknown. We hypothesised that underlying interactions between immunoinflammatory pathways related to responses to aeroallergen and virus are involved, and that evidence of these interactions is detectable in circulating cells during exacerbations.
To address this hypothesis we used a genomics-based approach involving profiling of PBMC subpopulations collected during acute exacerbation versus convalescence by microarray and flow cytometry.

overall_design: The study design consisted of 25 atopic subjects, divided into 5 different pools, with each pool containing equal amounts of RNA from 5 subjects, either at acute exacerbation or convalscent stage.

first: L

middle: S

last: Subrata

first: J

last: Bizzintino

first: E

last: Mamessier

first: A

last: Bosco

first: K

first: M

middle: E

last: Wikstrom

last: Goldblatt

first: P

middle: D

last: Sly

first: B

last: Hales

first: W

middle: R

last: Thomas

first: I

middle: A

last: Laing

middle: N

last: LeSouef

last: Holt


title: Transient expression of misfolded surfactant protein C

status: Public on May 14 2009

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Mutations in the SFTPC gene associated with interstitial lung disease in human patients result in misfolding, endoplasmic reticulum (ER) retention, and degradation of the encoded surfactant protein C (SP-C) proprotein. To identify candidate genes involved in ER quality control of SP-C, HEK293 cells were transiently transfected with mutant SP-C (SP-CΔexon4 or SP-CL188Q), SP-CWT, or vector cDNAs, and global changes in gene expression were assessed by microarray analyses. Microarray analysis demonstrated that the SPC exon 4 deletion and SPC L188Q mutations invoke very similar transcriptional profiles including the activation of major players mediating ER response and unfolding protein response (UPR) in transient transfection system. In combination with promoter scan (UPRE, ERSE, XBP1 sites) and protein domain analysis (Finding ER Lumen, ER Membrane retention signal, J-Domain and Leucine Zipper domain), we were able to not only verify the known ERAD components (XBP1, Bip, Erdj4&5), but also identify multiple ER components which may play critical roles in the detection and /or degradation of mutant SPC, which in turn will help us to gain better understanding of the entire mammalian ERAD machinery.

overall_design:
samples consisted of HEK293 cells  transiently transfected with wild-type SP-C (WT), the delta exon4 mutant of SP-C (Ex4) or L188Q mutant
of SP-C (LQ). Groups were performed in triplicate.

first: James

middle: P

last: Bridges

first: Cheng‐Lun

first: Hector

last: Wong

first: Tim

last: Weaver


title: Hypoxia inducible factors 1 and 2 are important transcriptional effectors in primary macrophages experiencing hypoxia

city: sheffield

first: Hsin-Yu

last: Fang

address: Beech Hill Rd

department: Infection & Immunity,School of Medicine & BioMedical Sciences

institute: University of Sheffield

summary:
Ischemia exists in many diseased tissues including arthritic joints, atherosclerotic plaques and malignant tumors. Macrophages accumulate in these sites and upregulate genes  in response to the hypoxia present.
We used microarrays to detail the hypoxia upregulated gene in human primary macrophages.

overall_design: Primary macrophages were differentiated for 7 days in vitro from human peripheral blood (monocyte-derived macrophages, MDMs) and were subjected to severe hypoxia (< 0.5% O2) or normoxia (20.9% O2) in 5% CO2 humidified multi-gas incubators.

first: Paul

last: Heath


title: Gene expression of TCR-alpha/beta CD4- CD8- human T cells

city: Boston

first: Jose

middle: C

last: Crispin

address: 330 Brookline Ave, CLS-928

department: Medicine

institute: Beth Israel Deaconess Medical Center

summary: The origin and function of human double negative (DN) TCR-alpha/beta T cells is unknown.  They are thought to contribute to the pathogenesis of systemic lupus erythematosus because they expand and accumulate in inflamed organs.  Here we provide evidence that human TCR-alpha/beta CD4- CD8- DN T cells derive exclusively from activated CD8+ T cells.  Freshly isolated TCR-alpha/beta DN T cells display a distinct gene expression and cytokine production profile.  DN cells isolated from peripheral blood as well as DN cells derived in vitro from CD8+ T cells, produce a defined array of pro-inflammatory mediators that includes IL-1, IL-17, IFN-gama, CXCL3, and CXCL2.  These results indicate that, upon activation, CD8+ T cells have the capacity to acquire a distinct phenotype that grants them inflammatory capacity.

overall_design: TCR-alpha-beta+ CD25- T cells from healthy human individuals were sorted into CD4+, CD8+, and CD4-CD8- T cells. Cell lysis and RNA extraction was performed immediately.  RNA from each cell subset was pooled.

first: George

last: Tsokos


title: Global Gene Expression in the Human Fetal Testis and Ovary

status: Public on May 01 2009

city: Pullman

first: Lizhong

last: Yang

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

summary:
This study describes a temporal profile of gene expression from normal human fetal testes and ovaries.  Gonads from 34 fetuses between 9 weeks and 20 weeks of gestation were obtained from the Department of Pathology and the Birth Defects Research Laboratory at the University of Washington.  Relative transcript levels were determined using the Affymetrix Human Genome U133A Plus 2.0 arrays.

Sex determination occurs in the human gonad at approximately 6 weeks
gestation with development of the testis driven by expression of SRY.   In this study, SRY transcript was present and elevated at 9 weeks gestation in the testis but absent in the ovary. The transcript levels of other testis-specific factors SOX9, AMH, and the steroidogenic genes CYP17a1, CYP11a1, STAR and HSD17β3 were all significantly higher in the testis.  In contrast, transcripts known to be involved in meiosis including STRA8, SPO11, SYCP3, TEX11, TEX14 and STAG3 showed highest expression in the fetal ovary beginning at week 12.  These gene expression profiles will be a resource for understanding and defining normal gonad development and provide the opportunity to dissect abnormal development.

overall_design: Gonads from 34 fetuses between 9 weeks and 20 weeks of gestation were obtained,  total RNA was extracted and hybridized to Affymetrix microarrays.

first: Chris

last: Small

first: Michael

last: Griswold

first: Brenda

last: Houmard

first: Edith

last: Cheng

first: Theresa

last: Naluai-Cecchini


title: Torcetrapib induces aldosterone and cortisol production in an intracellular calcium-dependent mechanism

status: Public on May 02 2009

city: Salem

first: William

last: Loging

state: CT

address: 73 Skyline Dr

institute: CETP Project Team

summary: ILLUMINATE (Investigation of Lipid Level Management to Understand its Impact in Atherosclerotic Events), the phase 3 morbidity and mortality trial of torcetrapib, a cholesteryl ester transfer protein (CETP) inhibitor, identified previously undescribed changes in plasma levels of potassium, sodium, bicarbonate, and aldosterone. A key question after this trial is whether the failure of torcetrapib was a result of CETP inhibition or of some other pharmacology of the molecule. The direct effects of torcetrapib and related molecules on adrenal steroid production were assessed in cell culture using the H295R as well as the newly developed HAC15 human adrenal carcinoma cell lines. Torcetrapib induced the synthesis of both aldosterone and cortisol in these two in vitro cell systems. Analysis of steroidogenic gene expression indicated that torcetrapib significantly induced the expression of CYP11B2 and CYP11B1, two enzymes in the last step of aldosterone and cortisol biosynthesis pathway, respectively. Transcription profiling indicated that torcetrapib and angiotensin II share overlapping pathways in regulating adrenal steroid biosynthesis. Hormone-induced steroid production is mainly mediated by two messengers, calcium and cAMP. An increase of intracellular calcium was observed after torcetrapib treatment, whereas cAMP was unchanged. Consistent with intracellular calcium being the key mediator of torcetrapib’s effect in adrenal cells, calcium channel blockers completely blocked torcetrapib-induced corticoid release and calcium increase. A series of compounds structurally related to torcetrapib as well as structurally distinct compounds were profiled. The results indicate that the pressor and adrenal effects observed with torcetrapib and related molecules are independent of CETP inhibition.

overall_design:
Experimental Goals: 1. To determine whether or not CETP inhibitors induce activation of RAAS pathway in adrenal derived cells, 2. To determine whether adrenocortical cells show a transcriptional response that can be correlated to BP effects.
Experimental Background:  Aldosterone production by H295R adrenocortical carcinoma cells in response to the treatments described [dimethyl sulfoxide (vehicle), angiotensin II (a CETP inhibitor), or test compound CP-529414 (a CETP inhibitor)] will be analyzed.

first: W

middle: T


title: Metastases of breast cancer (U133plus2)

city: Houston

first: Xiang

last: Zhang

address: One Baylor Plaza, BCM600

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

summary:
Comparisons among breast cancer metastases at different organs revealed distinct microenvironments as characterized by cytokine content.
Such microenvironment distinction might be important to dictate how the cancer cells adapt to survival before they successfully colonize.

Keywords: Disease state analyses

overall_design: 58 breast cancer metastases from different organs were  profiled and compared by the expression level of over 400 cytokines. 29 samples were incuded in this series. 29 others as well as 7 in the present series were profiled on U133A platforms and included in series GSE14018.

first: Joan

last: Massague


title: Transcriptional profiling of ICL670 treated K562 cells

city: Tokyo

first: Junko

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

institute: Tokyo Medical University

summary:
Iron plays a central role in the regulation of many cellular functions. Dysregulation of its metabolism leads an iron overload situation and iron depletion leads to an inhibition of cell proliferation. Recent reports demonstrated that ICL670 (Novartis) acts as a potent NF-kappa-B inhibitor and improves hematological data in a subset of MDS patients (Cilloni et al, Haematologica, s1: 238, 2007). However, the precise mechanism of anti-cancer effect of ICL670 is still uncertain.
To evaluate the effect of ICL670, and to identify the moleclular pathways responsible for the observed reduced transfusion requirement during chelation therapy, we performed gene expression profiling to focus on the pathway involved in the anti-cancer effect of ICL670.

overall_design: A human myeloid leukemia cell line, K562, was incubated with or without  ICL670 for 16hrs.Gene expression profiling was done using an Affymerix GeneChip (U133 Plus 2.0). Statistical analysis was done by GeneSifter vizXlab, Seattle, WA).


title: Characterisation of gene expression changes in T cells from patients presenting with AML compared with healthy T cells

first: Rifca

last: Le Dieu

summary:
Work previously published by our group has demonstrated that T cells from patients with chronic lymphocytic leukaemia (CLL) show differentially regulated genes compared with healthy T cells. This study was initiated to examine if these gene expression changes were unique to CLL T cells or common to an alternative  leukaemia, acute myeloid leukaemia (AML).

Keywords: Comparison of immune cells in health and disease

overall_design: The study was composed of four groups of samples: AML CD4 (n=10), AML CD8 (n=10), Healthy CD4 (n=10), Healthy CD8 (n=11). AML samples were chosen to represent the range of FAB types, prognostic groups and patient outcomes. Healthy T cells were obtained from volunteers. The purity of isolated T cell fractions was greater than 70% in all cases.

first: Richard

last: Mitter


title: Effect of ectopic expression of sFRP1 on MDA-MB-231 human breast cancer cells in vitro and in vivo as xenograft

first: Edward

last: Oakeley

address: Maulbeerstrasse 66

institute: FMI

summary: RNA was isolated from ectopically sFRP1-expressing MDA-MB-231 cells and control MDA-MB-231 cells and as well from tumor lysates arising from these cells as nude mouse xenograft.  Gene expression profiles for these samples were investigated using Affymetrix arrays.

overall_design: MDA-MB-231 human breast cancer cells were stably transfected with human sFRP1 encoding vector or empty vector as control. After the selection with antibiotics, three clones of MDA-MB-231/sFRP1 and three clones of MDA-MB-231/control were selected. These six clones were cultured individually in DMEM 10% FCS with 1mg/ml G-418. When cells reached 70-80% confluence, RNA was isolated from the cells. In parallel, the three clones of MDA-MB-231/sFRP1 and the three clones of MDA-MB-231/control were pooled respectively. One million of cells from each pool were suspended in 100ul PBS and injected to fat pads of female balb/c nude mice (6 mice were injected with MDA-MB-231/sFRP1 and 5 mice were injected with MDA-MB-231/control) to do a xenograft experiment. A few - several weeks after, mice were sacrificed when tumor reached a certain size, tumors were taken and RNA was isolated using trizol reagent.

first: Yutaka

last: Matsuda

first: Thomas

last: Schlange

first: Nancy

last: Hynes


title: CP4-57-deficient vs. wild-type

status: Public on Apr 27 2009

city: State College

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: Previously, we discovered that the global regulator Hha is related to cell death in biofilms and regulates cryptic prophage genes.  Here we show Hha induces excision of prophage CP4-57 and DLP12 by inducing excision genes and by reducing SsrA synthesis.  SsrA is a tmRNA important for rescuing stalled ribosomes, contains an attachment site for CP4-57, and is shown here to be required for CP4-57 excision.  These prophages impact biofilm development as deletion of 35 genes individually of prophage CP4-57 and DLP12 increase biofilm formation up to 17-fold, and 5 genes decrease biofilm formation up to 6-fold.  In addition, CP4-57 excises during early biofilm development but not in planktonic cells, whereas DLP12 excision was detected at all the developmental stages for both biofilm and planktonic cells.  CP4-57 excision leads to a chromosome region devoid of the prophage and formation of a phage circle (which is lost).  These results were corroborated by a whole-transcriptome analysis that showed that complete loss of CP4-57 activated expression of the flg, flh, and fli motility operons and repressed expression of key enzymes in the tricarboxylic acid cycle and enzymes for lactate utilization.  Prophage excision also results in the expression of cell lysis genes that reduce cell viability (e.g., alpA, intA, and intD).  Hence, defective prophage are involved in host physiology via Hha and in biofilm formation by generating a diversified population with specialized functions in terms of motility and nutrient metabolism.

overall_design:
Strain: CP4-57-deficient vs. wild-type

Medium: LB

Culture type:OD=0.5, planktonic cells

first: Xiaoxue

last: Wang

first: Younghoon

last: Kim

middle: K


title: Gene Expression in Peripheral Blood Leucocytes in Monozygotic Twins Discordant for Chronic Fatigue

status: Public on May 12 2009

city: Chapel Hill

first: Patrick

middle: F

last: Sullivan

address: 4109D Neuroscience Research Building, 103 Mason Farm Road

department: Genetics

institute: UNC Chapel Hill

summary: Background. Chronic fatiguing illness remains a poorly understood syndrome of unknown pathogenesis. We attempted to identify biomarkers for chronic fatiguing illness using microarrays to query the transcriptome in peripheral blood leukocytes. Methods. Cases were 44 individuals who were clinically evaluated and found to meet standard international criteria for chronic fatigue syndrome or idiopathic chronic fatigue, and controls were their monozygotic co-twins who were clinically evaluated and never had even one month of impairing fatigue. Biological sampling conditions were standardized and RNA stabilizing media were used. These methodological features provide rigorous control for bias resulting from case-control mismatched ancestry and experimental error. Individual gene expression profiles were assessed using Affymetrix Human Genome U133 Plus 2.0 arrays. Findings. There were no significant differences in gene expression for any transcript. Conclusions. Contrary to our expectations, we were unable to identify a biomarker for chronic fatiguing illness in the transcriptome of peripheral blood leukocytes suggesting that positive findings in prior studies may have resulted from experimental bias.

first: Andrea

last: Byrnes

first: Andreas

last: Jacks

first: Karin

last: Dahlman-Wright

first: Birgitta

last: Evengard

first: Fred

last: Wright

middle: L

last: Pedersen


title: Expression data from human adipose tissue

status: Public on Apr 24 2009

city: Worcester

first: Olga

middle: Theresa

last: Hardy

address: 373 Plantation Street, Biotech Two, Suite 100

department: Molecular Medicine

institute: University of Massachusetts

summary:
Obesity is a risk factor for numerous metabolic disorders; however, not all obese individuals are prone to insulin resistance. The central aim of this study was to identify molecular pathways directly related to insulin resistance independent of BMI in obesity.
We sought to determine the gene expression signature of adipose tissue in a body mass index (BMI)-matched obese cohort of patients that are either insulin sensitive or insulin resistant.

overall_design: We determined the global gene expression signatures of omental and subcutaneous adipose tissue samples obtained from insulin-sensitive obese and insulin-resistant obese patients undergoing gastric bypass surgery.

first: Juerg

last: Straubhaar


title: Sox9 deficiency effect on mouse mammary gland

first: Shaolei

last: Lu

address: 364 Plantation Street

department: Cancer Biology

institute: University of Massachusetts Medical School

summary: RNA from MMTV-Cre;Sox9flox/flox mouse mammary glands were compared to RNA from MMTV-Cre;Sox9+/flox glands. Results indicate that Sox9 regulates several genes that impact ductal morphogenesis in the mammary gland.

overall_design: The portion of the fourth mammary gland that is proximal to the intra-mammary gland lymph nodes was dissected from four 5-week-old MMTV-Cre;Sox9flox/flox females and four MMTV-Cre;Sox9+/flox females of the same age. Total RNA from each gland was extracted and hybridized to separate Affymetrix Gene 1.0 ST chips.

first: Donggoo

last: Bae

first: Lindsey

middle: M

last: Gouvin

first: Arthur

last: Mercurio


title: Dendritic cells activated with LPS IFNg over 48 hours

status: Public on Apr 22 2009

city: Vienna

first: Alexander

last: Dohnal

address: Kinderspitalgasse 6

department: Tumour Immunology

country: Austria

institute: St. Anna Children's Cancer Research Institute

summary:
Pro-inflammation triggered by microbial lipopolysaccharide (LPS) through Toll-like receptor (TLR) 4 in the presence of interferon (IFN)-g induces cytokine secretion in dendritic cells (DCs) tightly regulated by a defined differentiation program. This DC differentiation is characterized by a dynamic immune activating but also tolerance inducing phenotype associated with irreversible down-modulation of cytokines. CD40L on activated T cells further modifies DC differentiation. Using DNA micro arrays we showed down-regulated mRNA levels of TLR signaling molecules while CD40/CD40L signaling molecules were up-regulated at a time when LPS/IFN-g activated DCs have ceased cytokine expression. Accordingly we demonstrated that CD40/CD40L but not TLR4 or TLR3 signaling mediated by LPS or poly (cytidylic-inosinic) acid (poly I:C) and dsRNA re-established the capacity to secret interleukin (IL)-12 in LPS/IFN-g activated DCs, which have exhausted their potential for cytokine secretion. This resulting TH1 polarizing DC phenotype – which lacked accompanying secretion of the crucial immune suppressive IL-10 - enhanced activation of cytotoxic T lymphocytes (CTLs). We therefore conclude that immune modulation is restricted to a secondary T-cell mediated stimulus at an exhausted DC state which prevents an immune tolerant DC phenotype. These findings impacts on the rational design of TLR activated DC-based cancer vaccines for the induction of anti-tumoral CTL responses.
Keywords: time course

overall_design: Monocyte derived DCs were matured for 6 hours with 30 ng/ml lipopolysaccharide (LPS, E. coli strain O111:B4, Calbiochem, San Diego, CA) and 1.000 U/ml IFN-g (Imukin, Boehringer Ingelheim, Austria). RNA of DCs was isolated after 6, 12, 24, or 48 hours of maturation using the RNeasy kit (Qiagen, Hilden, Germany) and analyzed by the RZPD (German Resource Centre for Genome Research, Berlin) using the Affymetrix DNA micro array platform (U133 plus 2.0). DNA array data from different maturation-time experiments were compared to controls that were kept in culture for the same time without stimulation.


title: Human activated Treg cells and retrovirally engineered Th cells, transduced with GARP, FOXP3 or control GFP vector

status: Public on Apr 20 2009

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
Goals and objectives of this study: to identify genes of the Treg signature induced by consitutive expression of GARP or FOXP3 in antigen-specific Th cells with potential role for stabililization & maintenance of the regulatory program.

Keywords: T-cell receptor stimulation, gene-regulation, comparative gene expression profiling, cell type comparison, human, regulatory T cells, FOXP3, GARP

overall_design: Human alloantigen-specific Treg cells (THU) and Th cells (CD4-39), established and described recently (Ocklenburg et al.. Lab Invest.2006; 86: 724-737), were sitmulated for 3 days  with cognate antigen (EBV B cells) and IL2 as described  (Ocklenburg et al.. Lab Invest.2006; 86: 724-737) and analyzed using human Affymetrix U133 2.0 in monoplicate. Th cells had been transduced with a retroviral vector containing human GARP (LRRC32) or FOXP3 and an IRES-driven GFP as marker or empty GFP control, sorted for GFP+, expanded as described recently (Ocklenburg et al.. Lab Invest.2006; 86: 724-737), and characterized functially, phenotypically, and genetically as described (WO/2007/113301). Abbreviations: Treg THU d3 = alloantigen-specific Treg cells; GFP d3 = GFP-transduced alloantigen-specific Th cells (CD4-39); FoxP3 d3 = FOXP-transduced alloantigen-specific Th cells (CD4-39); Garp d3 = GARP-transduced alloantigen-specific Th cells (CD4-39); all stimulated for 3 days (=d3) with EBV B cells and IL2.

first: R

first: M

last: Probst-Kepper


title: Gene expression profile of bladder tissue of patients with ulcerative interstitial cystitis

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

institute: ETH Zurich / University of Zurich

summary:
Interstitial cystitis (IC), a chronic bladder disease with an increasing incidence, is diagnosed using subjective symptoms in combination with cystoscopic and histological evidence. The ultimate goal is the development of a diagnostic assay for IC on a molecular level.
By cystoscopic examination, IC can be classified into an ulcerative and a non-ulcerative subtype. To better understand this debilitating disease on a molecular level, a comparative gene expression profile of bladder biopsies from patients with ulcerative IC and control patients has been performed. Candidate marker genes for ulcerative IC were identified.

overall_design: Five IC patients and six control patients ("healthy") have been selected for the study. All IC patients had Hunner's ulcers and, with the exception of one person, also glomerulations, whereas the control group did not show these cystoscopic findings. From each IC patient, two bladder biopsies were analyzed, one from an ulcer area (“ulcus”), and one from a non-ulcer area (“ni”).

first: Marianne

last: Gamper


title: Expression and methylation data from A2780 (cisplatin-sensitive) and Round5 A2780 (cisplatin-resistant) cell lines

status: Public on Apr 17 2009

city: Bloomington

first: Meng

last: Li

state: IN

address: 1001 E 3rd Street

department: Medical Sciences

institute: Indiana University

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series

first: Curt

last: Balch

first: John

last: Montgomery

first: Mikyoung

last: Jeong

first: JaeHoon

last: Chung

first: Pearlly

last: Yan

first: Tim

last: Huang

first: Sun

last: Kim

first: Kenneth

last: Nephew


title: Expression data from ERG Si treated and Control HUVEC cells

first: Peter

last: Oettgen

address: Harvard Institutes of Medicine, 4 Blackfan Circle

department: Department of Medicine

summary:
ERG (Ets Related Gene) is an ETS transcription factor that was originally described for its role in a number of human cancers.  Our preliminary data demonstrate that ERG exhibits a highly EC restricted pattern of expression in cultured primary cells and several adult tissues including the heart, lung, and brain.  In response to inflammatory stimuli, such as TNF-alpha, we observed a marked reduction of ERG expression in EC.
To further define the role of ERG in the regulation of normal EC function we used RNA interference to knockdown ERG.  Knockdown of ERG in human umbilical vein EC (HUVEC) using siRNA was associated with the reduction of a number known ERG targets.

Keywords: SIRNA Functional Role

overall_design: The functional role of the ERG in the EC cellls was elucidated by comparing gene expression data from HUVEC cells  trasfected with only vector (BERG) , non-sense SiRNA (CERG) vs ERG SiRNA (ERG).

first: Lei

last: Yuan

first: Vesna

last: Nikolova-Krstevski

first: Yumei

last: Zhan

first: Maiko

last: Kondo

first: Manoj

last: Bhasin

first: Laya

last: Varghese

first: Chris

last: Carman


title: Expression data from A2780 (cisplatin-sensitive) and Round5 A2780 (cisplatin-resistant) cell lines.

first: Meng

last: Li

summary: Cisplatin and carboplatin are the primary first-line therapies for the treatment of ovarian cancer. However, resistance to these platinum-based drugs occurs in the large majority of initially responsive tumors, subsequently resulting in a poor long-term prognosis.  To model the onset of drug resistance, we measured gene expression alterations associated with cisplatin resistance.

overall_design: We treated clonally derived, drug-sensitive A2780 epithelial ovarian cancer cells with increasing concentrations of cisplatin.  After 5 cycles of drug selection, the isogenic drug-sensitive (parental A2780) and -resistant (Round5 A2780) cell lines were subjected to mRNA expression microarray analyses.


title: Differential effects of TNFalpha and IL1beta on FLS global gene expression profile

status: Public on Apr 15 2009

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

summary: TNFalpha and IL1beta play a pathogenic role in rheumatoid arthritis. Both cytokines are known to activate cytokine and metalloproteinase secretion by synovial fibroblasts. In the present study, we wanted to investigate whether TNFalpha and IL1beta displayed differential effects on cultured Fibroblast-like Synovial Cells derived from RA patients. Global gene expression analyses indicated that both cytokines induced similar genes in these cells.

overall_design:
Fibroblast-like cells (FLS) were purified from synovial biopsies from RA patients. Briefly, minced synovial fragments were digested in 1 mg/ml hyaluronidase solution (Sigma Aldrich, St Louis, MO) for 15 minutes at 37°C and 6 mg/ml collagenase type IV (Invitrogen, Paisley, UK) for 2 hours at 37°C. Next, cells were washed, resuspended in high-glucose Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 1% antibiotics-antimycotics (Invitrogen) and 1% MEM sodium pyruvate (Invitrogen), and seeded at 10,000 cells/cm2 in 6-well plates. When the cells reached confluence, adherent cells were detached using sterile 0.5% trypsin-EDTA (Invitrogen) and used as FLS between passages 3 and 9.
Cells were seeded in 24-well plated at 25.000/well and incubated overnight with or without the following cytokines : TNF-α (R&D Systems, Minneapolis, MN) 10 ng/ml, IL-1β (R&D Systems) 10 ng/ml. After overnight incubation with the indicated cytokines, cells were harvested and total RNA was extracted using the Nucleospin® RNA II extraction kit (Macherey-Nagel, Düren, Germany), in order to be labeled according to a standard Affymetrix procedure and hybridized on HGU133 Plus 2.0 Human Genome slides.


title: Expression data from MCF-7 Human Breast Cancer Cells

city: Beijing

first: Yupeng

last: Chen

address: Haidian District 38

country: China

institute: Peking University Health Science Center

summary:
SOX genes encode a family of high-mobility group transcription factors that play critical roles in organogenesis. Virtually all members of SOX family have been found to be deregulated in tumors of various origins. However, little is known about the cellular and molecular behaviours involved in the oncogenic potential of SOX proteins.
Cell culture experiments, tissue analysis, and molecular profiling revealed that SOX2 promotes cell proliferation and tumorigenesis through its transcription regulation of cell cycle related genes in breast cancer cells
Keywords: Gene Transfection

overall_design: To delineate the molecular mechanism underlying the cell proliferation and tumorigenic properties of SOX2, we investigated the gene expression profile in MCF-7 cells. Briefly, MCF-7 cells were transfected with pcDNA3.1 and Human SOX2 expression constructs respectively. 24 hours after transfection, total RNA collected from control and SOX2-overexpressing MCF-7 cells was used to probe Human Genome GeneChip array U133 Plus 2.0

first: Yongfeng

last: Shang


title: Effects of PRIMA-1 treatment on Saos-2 p53-null and Saos-2 p53-His273 cells

city: Stockholm

first: Jeremy

last: Lambert

country: Sweden

institute: Karolinska Institutet


title: Remission in Polyarticular Juvenile Idiopathic Arthritis

status: Public on Apr 13 2009

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

summary: Identify biomarkers to predict response to therapy in polyarticular juvenile idiopathic arthritis (JIA) using gene expression microarrays.

overall_design: 42 samples from 13 controls, 14 active patients, 9 patients in clinical remission with medication (CRM), and 6 patients in clinical remission without medication (CR). All patients had polyarticular JIA.

first: Nicholas

last: Knowlton

first: Kaiyu

last: Jiang

first: Mark

middle: B

first: Amita

last: Aggarwal

first: Carol

last: Wallace

first: Ryan

last: McKee

first: Brad

last: Chaser

first: Catherine

last: Tung

first: Laura

last: Smith

first: Yanmin

first: Jeanette

last: Osban

first: Kathleen

last: O’Neil

first: Michael

last: Centola

first: Julie

last: McGhee

first: James

last: Jarvis


title: Expression analysis of Saos-2 p53-null cells

first: Jeremy

summary: Our compound (PRIMA) selectively kills tumor cells expressing mutant p53. Here in our study we decided to investigate the impact of our compound on the transcriptome of Saos2 cells lacking p53.

overall_design: We plated Saos-2 cells, and treated them with our compound for 6h or 12h. We then harvested the cells, extracted the RNA, and followed the protocol to run affymetrix array to analyse the impact of our drug on the whole transcriptome of cells lacking p53.

first: Ali

last: Moshfegh

first: Klas

middle: G

last: Wiman

first: Pierre

last: Hainaut

first: Vladimir

middle: J

last: Bykov


title: L. acidophilus NCFM™, B. lactis 420, L. salivarius Ls-33  and E. coli O157:H7 effect on intestinal epithelial cells

status: Public on Apr 11 2009

city: Turku

first: Ilana

last: Saarikko

address: Linnankatu 55

country: Finland

institute: Genolyze Ltd

summary: Analysis of differentiated Caco-2 intestinal epithelial cell line cocultured with probiotics L. acidophilus NCFM™, B. lactis 420, L. salivarius Ls-33 bacterial cells or treated with cell-free supernatant, and with E. coli O157:H7 cell-free supernatant. Lactobacillus and Bifidobacterium are important genera suggested to be beneficial for human health and E. coli O157:H7 is a pathogen causing hemorrhagic colitis and hemolytic uremic syndrome. Results provide insight into the mechanisms underlying the beneficial effects of probiotics on intestinal epithelial cells and a comparison to pathogenic E. coli.

overall_design: Differentiated Caco-2 cells were cocultured with either L. acidophilus NCFM™, B. lactis 420, and L. salivarius Ls-33 bacteria for 8 hours or with L. acidophilus NCFM™, B. lactis 420, L. salivarius Ls-33, and E. coli O157:H7 cell-free media for 24 hours. As a control a medium-only treatment was used. For probiotics seven samples were analyzed in duplicate with intestinal epithelial cells: three treated with cell-free supernatant, three co-cultures and a control. For EHEC, six samples were analyzed similarly with intestinal epithelial cells: three supernatant samples and three control samples all done as single replica.

first: Rodolphe

last: Barrangou

first: Heli

last: Putaala

first: Gregory

last: Leyer

first: Arthur

last: Ouwehand

first: Egon

last: Bech Hansen

first: Dennis

last: Romero

first: Nina

last: Rautonen


title: Metastases of breast cancer

first: Xiang

last: Zhang

summary:
Comparisons among breast cancer metastases at different organs revealed distinct microenvironments as characterized by cytokine content.

Such microenvironment distinction might be important to dictate how the cancer cells adapt to survival before they successfully colonize.

This SuperSeries is composed of the SubSeries listed below.

middle: H

first: Joan

last: Massague


title: Enhanced differentiation of hESCs into multipotential mesodermal stem cells by inhibition of TGF-b signaling by using SB

city: Odense

first: Amer

last: Mahmood

address: Fyrreparken 66, 2 tv

department: Department of Endocrinology

country: Denmark

institute: University Hospital of Odense &  University of South Denmark

summary:
Directing differentiation of human embryonic stem cells (hESC) into specific cell types using an easy and reproducible protocol is a perquisite for the clinical use of hESC in regenerative medicine protocols.  Here, we report the generation of mesodermal cells with differentiation potential to myocytes, osteoblasts, chondrocytes and adipocytes. We demonstrate that during hESC differentiation as embryoid bodies (EB), inhibition of TGF-b/Activin/Nodal signaling using SB-431542 (SB) markedly up-regulated paraxial mesodermal markers (TBX6, TBX5), early myogenic transcriptional factors (Myf5, Pax7) as well as myocyte committed markers (NCAM, CD34, Desmin, MHC (fast), alpha-smooth muscle actin, Nkx2.5, cTNT).  Establishing EB outgrowth cultures (SB-OG) in the presence of SB (1 uM) led to further enrichment of cells expressing markers for myocyte progenitor cell: CD34+ (33%), NCAM+ (CD56) (73%), PAX7 (25%) and mature myocyte proteins (MYOD1, tropomyocin, fast MHC an
 d SERCA1). Further analysis using DNA microarray revealed differential up-regulation of 117 genes (>2-fold compared to control cells) annotated to myogenic development and function. During ex vivo culture, contracting myocytes were observed (80% of the population) and the cells formed myofibres when implanted intramuscularly in vivo. Furthermore, in the presence of fetal bovine serum (10% FBS), SB-OG cells developed morphologically and phenotypically into a homogeneous stromal (mesenchymal) stem cell (MSC)-like population expressing characteristic MSC CD markers: CD44 (100%), CD73 (98%), CD146 (96%) and CD166 (88%). They were karyotypically normal and were able to differentiate ex vivo and in vivo into osteoblasts, adipocytes and chondrocytes.

overall_design: Human ESCs were differentiated as EBs for 10 days, where after EBs were plated onto fibronectin coated petri dishes. At confluency the outgrowth culture was passaged, at passage 5 3 samples were taken from both control-OG and SB-OG. the samples were mixed and frozen.

first: Basem

last: Abdallah

first: Moustapha

last: Kassem


title: Data integration from two microarray platforms identifies genetic inactivation of RIC8A in a breast cancer cell line

city: Helsinki

first: Henrik

last: Edgren

address: Tukholmankatu 8

institute: Institute for Molecular Medicine, University of Helsinki

type:
Expression profiling by array
Genome variation profiling by array

summary: Using array comparative genomic hybridization (aCGH), a large number of deleted genomic regions have been identified in human cancers. However, subsequent efforts to identify target genes selected for inactivation in these regions have often been challenging. We integrated here genome-wide copy number data with gene expression data and non-sense mediated mRNA decay rates in breast cancer  cell lines to prioritize gene candidates that are likely to be tumour suppressor genes inactivated by bi-allelic genetic events. The candidates were sequenced to identify potential mutations. This integrated genomic approach led to the identification of RIC8A at 11p15 as a putative candidate target gene for the genomic deletion in the ZR-75-1 breast cancer cell line. We identified a truncating mutation in this cell line, leading to loss of expression and rapid decay of the transcript. We screened 127 breast cancers for RIC8A mutations, but did not find any pathogenic mutations. No promoter hypermethylation in these  tumours was detected either. However, analysis of gene expression data from breast tumours identified a small group of aggressive tumours that displayed low levels of RIC8A transcripts. Real-time PCR analysis of 38 breast tumours showed a strong association between low RIC8A expression and the presence of TP53 mutations (P=0.006). We demonstrate a data integration strategy leading to the  identification of RIC8A as a gene undergoing a classical double-hit genetic inactivation in a breast cancer cell line, as well as in vivo evidence of loss of RIC8A expression in a subgroup of aggressive TP53 mutant breast cancers.

overall_design:
Gene expression data: Samples GSM388181-GSM388198.
The experiment utilized six breast cancer cell lines: MDA-MB-468, MDA-MB-231, ZR-75-1, MCF7, BT-474 and T-47D, and three non-malignant cell lines: HMECs (non-malignant human mammary epithelial cells), IMR90 (normal lung fibroblasts) and WS1 (normal skin fibroblasts). All cell lines were obtained from American Type Culture Collection and grown in accordance with the distributor's instructions. Both malignant and non-malignant cell lines were treated with the translation inhibitor emetine dihydrochloride hydrate. For each cell line, parallel cell cultures were grown in 175 cm2 flasks until 70-80 % confluence. Half of the subconfluent cultures were treated with 100 μg ml-1 of emetine dihydrochloride hydrate while the other half were left as untreated controls.

Genome-wide copy number data: Samples GSM388211-GSM388216.
The experiment utilized six breast cancer cell lines; MDA-MB-468, MDA-MB-231, ZR-75-1, MCF7, BT-474 and T-47D. All cell lines were obtained from American Type Culture Collection and grown in accordance with the distributor's instructions. All samples were hybridized once on 44k Agilent Human Genome CGH microarrays according to manufacturers instructions. Genomic DNA pooled from healthy female donors was used as a reference in all hybridizations. DNA from cell line samples were labeled with Cy5 and DNA from reference were labeled with Cy3.

first: Aslaug

last: Muggerud

first: Maija

last: Wolf

first: Kristine

last: Kleivi

first: Emelyne

last: Dejeux

first: Jörg

last: Tost

first: Therese

last: Sørlie

first: Olli

last: Kallioniemi


title: Expression data from human embryonic kidney cells (HEK293) cultivated in high and low glucose

status: Public on Apr 08 2009

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

institute: ETH Zurich

summary: Gene expression profiling of human embryonic kidney (HEK293) cells was performed to determine the effect of high and low glucose on gene expression. Microarrays were used to identify distinct classes of genes up-regulated in HEK293 cells during cultivation for 7 days in medium with physiological (low) glucose compared to high glucose.

overall_design: Human embryonic kidney cells (HEK293) were cultivated for 7 days in commercially available DMEM (supplemented with 10 % FCS) containing high glucose (450 mg/dl) or low glucose (100 mg/dl). Cells were harvested, total RNA was extracted and microarray gene expression profiling was performed to compare differential gene expression between low and high glucose conditions. Two biological replicates for each condition were made (high glucose: HEK-high-gluc-1 and HEK-high-gluc-2;  and low glucose: HEK-low-gluc-1 and HEK-low-gluc-2).

first: Joshua

last: Abd Alla

first: Kristin

last: Reeck

first: Thomas

last: Streichert

first: Said

last: AbdAlla


title: Expression profiles of cancer cells with anchorage-independent growth ability

status: Public on Apr 10 2009

city: Singapore

first: Seiichi

last: Mori

state: Singapore

address: Centre for Life Sciences #02-07, 28 Medical Drive

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore


title: A Genomic Score Prognostic of Outcome in Trauma Patients

city: Boston

first: Wenzhong Xiao

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

summary:
Physiological, anatomical, and clinical laboratory analytic scoring systems (APACHE, Injury Severity Score (ISS)) have been utilized, with limited success, to predict outcome following injury. We hypothesized that a peripheral blood leukocyte gene expression score could predict outcome, including multiple organ failure, following severe blunt trauma.

Contributor: The Inflammation and the Host Response to Injury Large Scale Collaborative Research Program
Keywords: expression profiles

overall_design: cRNA derived from whole blood leukocytes obtained within 12 hours of hospital admission provided gene expression data for the entire genome that were used to create a gene expression score for each patient. Expression profiles from healthy volunteers were averaged to create a reference gene expression profile which was used to compute a difference from reference (DFR) score for each patient. This score described the overall genomic response of patients within the first 12 hours following severe blunt trauma. Regression models were used to compare the association of the DFR, APACHE and ISS scores with outcome.

first: Constance

last: Elson

first: Shaw

last: Warren

first: Douglas

last: Hayden

first: David

last: Schoenfeld

first: Perren

last: Cobb

first: Ronald

middle: V

last: Maier

first: Lyle

last: Moldawer

first: Ernest

middle: E

last: Moore

first: Brian

last: Harbrecht

first: Kimberly

last: Pelak

first: Joseph

last: Cuschieri

last: Herndon

first: Marc

last: Jeschke

first: Celeste

last: Finnerty

first: Bernard

last: Brownstein

first: Laura

last: Hennessy

first: Philip

last: Mason

last: Tompkins


status: Public on Apr 18 2009

city: Bruxelles

first: Basile

last: Stamatopoulos

address: Bd de Waterloo n°121

department: Experimental Hematology

institute: Jules Bordet Institute

summary:
Comparison of Chronic Lymphocytic Leukemia patients expressing high or low levels of ZAP70 mRNA: prognostic factors and interaction with the microenvironment.
Zeta-associated protein 70 (ZAP70) is a widely recognized prognostic factor in chronic lymphocytic leukemia (CLL), but mechanisms by which its higher expression leads to a poor outcome remain to be fully explained.
In an attempt to unveil unfavorable cellular properties linked to high ZAP70 expression, we used gene expression profiling to identify genes associated with disparities in B-cells from CLL patients expressing high versus low ZAP70 mRNA, measured by quantitative real-time PCR.

Keywords: comparison of poor and good prognosis CLL patient transcriptome regarding ZAP70 expression

overall_design: Two groups of seven CLL patients were compared, selected on the basis of either high or low ZAP70 mRNA expression. Total RNA from CD19+ purified cells was exctracted and hybidyzed on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array. Amplification, hybridization and scanning were done according to standard Affymetrix protocols (www.affymetrix.com). CEL files were ,normalized with RMA method.

first: Benjamin

last: Haibe-Kains

first: Carole

last: Equeter

first: Nathalie

last: Meuleman

first: Anne

last: Soree

first: Cécile

last: de Bruyn

first: Delphine

last: Hanosset

first: Dominique

last: Bron

first: Philippe

last: Martiat

first: Laurence

last: Lagneaux


title: Dendritic Cell Vaccine against Glioblastoma Multiforme Patients

status: Public on Apr 03 2009

city: Los Angeles

first: Gretchen

last: Duvall

address: 8700 Beverly BLVD

institute: Cedars Sinai Medical Center

summary:
Human Glioblastoma Multiforme tumors taken before dendritic cell vaccination, the recurrent tumors taken after vaccination and control GBM tumors from non vaccinated patients.
Keywords: Disease State Analysis

overall_design: Six Glioblastoma Multiforme patients underwent surgery. Their brain tumors were removed and analyzed via microarray. The lysate from the tumors were cultured with the patients' dendritic cells and the DCs were injected back into the patients. The patients GBMs returned and they underwent surgery a second time and those tumors were also analyzed via microarray. Tumors from the first and second GBM surgeries of 5 patients who did not receive DC vaccines are included as controls.


title: Expression data from E. coli O157

status: Public on Apr 04 2009

city: SUMMIT

first: SIYUN

last: WANG

state: IL

address: 6502 S ARCHER ROAD

institute: ILLINOIS INSTITUTE OF TECHNOLOGY

summary:
Minimal processing using chlorinated water washes is a common practice in the fresh produce industry to reduce the microbial load and bacterial pathogens attached on produce surfaces.
To evaluate if E. coli O157:H7 strains with different phyllogenetic backgrounds are equally sensitive or display variable resistance to chlorine treatment, we studied the expression profile of Sakai and one 2006 spinach outbreak strain (TW 14359) in response to chlorine and hydrogen peroxide treatment.

overall_design: 2 E. coli O157 strains are incubated with or without chlorine or H2O2 for 30 min for RNA extraction and hybridization on Affymetrix microarrays. We sought to compare the expression profile between the 2 strains with or without oxidative stress.

first: Wei

last: Zhang

first: Siyun

last: Wang

first: Chia-hui

last: Lin


title: Gene expression of E. coli MG1655 pOX38Km at the outside and inside of biofilms

status: Public on Apr 01 2009

city: Sapporo

first: Akinobu

last: Ito

address: North-13, West-8, Kitaku

department: Graduate School of Engineering

institute: Hokkaido University

summary:
Gene expression changes between outside and inside of biofilms were investigated. The gene expression was compared between the outside and inside of the biofilms. At the same time, the gene expressions were also compared with exponential phase and stationary phase in planktonic cells. The gene expression analysis showed that the physiological activities were higher at the outside of the biofilms than those at the inside of the biofilms. The genes induced at the ouside of the biofilms included genes involved in the stress responses and adhesions.

Keywords: different growth phase

overall_design: Affymetrix GeneChip E. coli Genome 2.0 Array was used to compare the gene expression among biofilms (outside and inside) and planktonic cells (exponential phase and stationary phase). All samples were grown in MOPS minimal media with 0.2% glucose at 37ºC. Biofilms were grown on glass surface in flow cells (1 x 4 x 40 mm), and samples were taken at 72 h. Planktonic cell were grown for 6 h (exponential phase) and 24 h (stationary phase). Experiments were repeated 3 times, which resulted in 3 replicates of 4 different samples.

first: Asami

last: Taniuchi

first: Thithiwat

last: May

first: Koji

last: Kawata

first: Satoshi

last: Okabe


title: Gene-expression profiling of peripheral blood mononuclear cells in sepsis

city: Glebe

first: Benjamin

middle: Man Piu

last: Tang

state: NSW

address: 12/29 Cook Street

department: Intensive Care Medicine

institute: Nepean Hospital

summary:
To identify signature genes that help distinguish (1) sepsis from non-infectious causes of systemic inflammatory response syndrome, (2) between Gram-positive and Gram-negative sepsis.
Keywords: Class prediction study

overall_design: A total of 70 critically ill patients were enrolled in a single-centre observational study.  Gene-expression profiling was performed using Affymetrix microarray (U133plus2) with 54,675 transcript.  Data was divided into a training set (n=35) and a validation set (n=35).  A molecular signature was developed in the training set and was then validated in the validation set.

first: Ruby


title: HDAC5 is a repressor of angiogenesis and determines the angiogenic gene expression pattern of endothelial cells

status: Public on Apr 02 2009

city: Frankfurt

first: Carmen

last: Urbich

institute: Molecular Cardiology

summary: Class IIa histone deacetylases (HDACs) are signal-responsive regulators of gene expression involved in vascular homeostasis. To investigate the differential role of class IIa HDACs for the regulation of angiogenesis, we used siRNA to specifically suppress the individual HDAC isoenzymes. Among the HDAC isoforms tested, silencing of HDAC5 exhibited a unique pro-angiogenic effect evidenced by increased endothelial cell migration, sprouting and tube formation. Consistently, overexpression of HDAC5 decreased sprout formation, indicating that HDAC5 is a negative regulator of angiogenesis. The anti-angiogenic activity of HDAC5 was independent of MEF2 binding and its deacetylase activity, but required a nuclear localization indicating that HDAC5 might affect the transcriptional regulation of gene expression. To identify putative HDAC5 targets, we performed microarray expression analysis. Silencing of HDAC5 increased the expression of fibroblast growth factor 2 (FGF2) and angiogenic guidance factors including Slit2. Antagonization of FGF2 or Slit2 reduced sprout induction in response to HDAC5 siRNA. ChIP assays demonstrate that HDAC5 binds to the promoter of FGF2 and Slit2. In summary, HDAC5 represses angiogenic genes, like FGF2 and Slit2, which causally contribute to capillary-like sprouting of endothelial cells. The de-repression of angiogenic genes by HDAC5 inactivation may provide a useful therapeutic target for induction of angiogenesis.

overall_design: 6 samples: 3x siSCRAMBLED transfected HUVEC (control) + 3x siHDAC5 transfected HUVEC 24h after transfection

first: Lothar

last: Rössig

first: David

last: Kaluza

first: Michael

last: Potente

first: Jes-Niels

last: Boeckel

first: Andrea

last: Knau

first: Florian

last: Diehl

first: Jian-Guo

last: Geng

first: Wolf-Karsten

last: Hofmann

first: Andreas

last: Zeiher

first: Stefanie

last: Dimmeler


title: Overexpression of lung developmental transcription factors TTF-1, NKX2-8 and PAX9

city: Durham

first: Chaitanya

middle: R

last: Acharya

address: 203 Research Drive,Medical Sciences Research Building, Suite 433

department: Dept. of Surgery

institute: Duke University

summary:
We investigated the clinical implications of lung developmental transcription factors (TTF-1, NKX2-8, and PAX9) which we recently discovered as cooperating oncogenes activated by way of gene amplification at chromosome 14q13 in lung cancer. Using stable transfectants of human bronchial epithelial cells, RNA expression profiles (signatures) representing activation of the biological pathways defined by each of the three genes were determined and used to risk stratify a non-small cell lung cancer (NSCLC) clinical dataset consisting of ninety-one early stage tumors. Co-activation of the TTF-1 and NKX2-8 pathways identified a cluster of patients with poor survival, representing approximately 20% of patients with early stage NSCLC, whereas activation of individual pathways did not reveal significant prognostic power. Importantly, the poor prognosis associated with co-activation of TTF-1 and NKX2-8 was validated in two other independent clinical datasets. Further, lung cancer cell lines showing co-activation of the TTF-1 and NKX2-8 pathways were shown to exhibit resistance to cisplatin, the standard of care for the treatment of NSCLC. Since TTF-1 and NKX2-8 lack specific inhibitors at the current time, we explored an alternative therapeutic strategy. Using signatures of signaling pathway activation, we identified deregulation of specific oncogenic pathways (Ras and Myc) in the TTF-1/NKX2-8 co-activated cohort.
In vitro experiments demonstrated the ability of a Ras pathway-specific therapy to inhibit tumor cell growth in TTF-1/NKX-2 activated cells, thus, suggesting that modulation of the Ras pathway is a rational strategy to targeted therapy in high risk NSCLC patients with co-activation of specific lung developmental pathways.
Keywords: Transcription factor expression analysis

overall_design: Six controls and six replicates of each transcription factor (TTF1, NKX2-8, PAX9) were prepared and analyzed.

middle: S

last: Hsu

first: Richard

last: Riedel

last: Redman

first: Katherine

last: Garman

first: Bala

last: Balakumaran

first: Ariel

last: Anguiano

first: Sayan

last: Mukherjee

first: William

last: Barry

first: Geoffrey

last: Ginsburg

first: Philip

last: Febbo

first: Joseph

last: Nevins

first: Scott

last: Powers

last: Mu

first: Anil

last: Potti


title: Trap-80-dependence of TNF-alpha-induced genes

city: Nice

first: Dominic

last: van Essen

address: 28 Avenue Valombrose

country: France

institute: Institute for Research on Cancer & Aging, Nice (IRCAN)

summary: In fibroblasts, p65-dependent genes can be sub-divided, depending on whether they are Trap-80-dependent or -independent.  To examine the generality of this grouping, we performed a microarray analysis of wild-type and Trap-80 knock-down fibroblasts, before and after stimulation of NF-kappaB activity using TNF-alpha.

overall_design: RNA was extracted from three independent cultures of wild-type and Trap-80 knock-down fibroblasts, before and after stimulation for 1 hour with 5ng/ml TNF-alpha.  The unstimulated and stimulated wild-type samples, and the stimulated Trap-80 knock-down samples, were used for microarray analysis.

first: Bettina

last: Engist

first: Gioacchino

last: Natoli

first: Simona

last: Saccani


title: Differential gene expression in RA synovial biopsies from responders versus non-responders to adalimumab therapy

city: Brussels

first: Bernard

last: Lauwerys

institute: Université catholique de Louvain

summary:
TNF antagonists are routinely used in severe rheumatoid arthritis (RA) patients who failed conventional DMARD therapy. According to large clinical trials, the three available drugs (adalimumab, infliximab and etanercept) display similar effects in terms of efficacy, tolerability and side effects. These studies also indicate that about 25% of RA patients treated with TNF-antagonists do not display any significant clinical improvement.
The aim of this study was to investigate global molecular patterns in synovial biopsies from RA patients obtained 12 weeks after initiation of adalimumab therapy.

overall_design:
All patients had rheumatoid arthritis (RA), according to the American College of rheumatology criteria for the diagnosis of RA. They had active disease at the time of initiation of adalimumab therapy and were resistant to conventional therapy. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All patients were treated with disease-modifying antirheumatic drugs (DMARD’s), 23 with methotrexate (median dose 15 mg/week, range 7.5 – 20 mg/week), and 2 with leflunomide (20 mg/day); 18 of them were treated with low-dose steroids (prednisolone ≤ 7.5 mg/day). Six patients had been included in double-blind clinical trials before inclusion in the present study (1 in a Golimumab versus placebo trial, 3 in a MapKinase inhibitor versus placebo trial and 2 in a TACE-inhibitor versus placebo trial). These trials were stopped at least 3 months prior to initiation of TNF-blocking therapy. All drug dosages were stable from at least 3 months prior to initiation of TNF blocking therapy until completion of the study. No steroid injections were allowed during the duration of the study.

Adalimumab therapy was initiated at a dosage of 40 mg subcutaneously every other week. Disease activity at baseline and 12 weeks after initiation of therapy (T12) was evaluated using DAS(28)-CRP (3- and 4-variables) scores, and response to therapy was assessed according to the EULAR response criteria that categorize patients in responders (good- or moderate-) and non- (or poor-) responders based on changes in DAS activity between T0 and T12 and absolute DAS values at T12.

Synovial biopsies were obtained by needle-arthroscopy of knee of the patients at T12. The aim of the study was to compare gene expression profiles in synovial tissue of RA patients who responded versus not responded to adalimumab therapy.


title: A Whole Genome Approach to Characterising a Novel Immunodeficiency Disorder

city: Southport

first: Michael

middle: Richard

last: Green

state: Queensland

address: 58 Parklands Drive

department: Griffith Insitute for Health & Medical Research

institute: Griffith University

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

summary: Whole genome gene expression and single nucleotide polymorphism microarrays were used to characterise a novel immunodeficiency disorder, Herbert's Syndrome.

overall_design:
Affymetrix 250K Sty arrays run through genomic DNA from peripheral blood of case and control subjects, used for DNA copy number analysis.
Affymetrix HU133 Plus 2.0 microarrays run through total-RNA from peripheral blood of case and control subjects, used for differential gene expression analysis.

first: Maher

last: Gandhi

first: Lyn

last: Griffiths


title: Senescent Stromal-Derived Osteopontin Promotes Preneoplastic Cell Growth

status: Public on Mar 30 2009

city: St. Louis

first: Sheila

last: Stewart

state: MO

address: 660 S Euclid

institute: Cell Biology & Physiology

summary: Alterations in the tissue microenvironment collaborate with cell autonomous genetic changes to contribute to neoplastic progression.  The importance of the microenvironment in neoplastic progression is underscored by studies demonstrating that fibroblasts isolated from a tumor stimulate the growth of preneoplastic and neoplastic cells in xenograft models.  Similarly, senescent fibroblasts promote preneoplastic cell growth in vitro and in vivo.  Because senescent cells accumulate with age, their presence is hypothesized to facilitate preneoplastic cell growth and tumor formation in older individuals.  To identify senescent stromal factors directly responsible for stimulating preneoplastic cell growth, we carried out whole genome transcriptional profiling and compared senescent fibroblasts to their younger counterparts.  We identified osteopontin (OPN) as one of the most highly elevated transcripts in senescent fibroblasts.   Importantly, reduction of OPN protein levels by RNAi did not impact senescence induction in fibroblasts; however, it dramatically reduced the growth-promoting activities of senescent fibroblasts in vitro and in vivo, demonstrating that OPN is necessary for paracrine stimulation of preneoplastic cell growth.  In addition, we found that recombinant OPN was sufficient to stimulate preneoplastic cell growth.  Finally, we demonstrate that OPN is expressed in senescent stroma within preneoplastic lesions that arise following DMBA/TPA treatment of mice, suggesting that stromal-derived OPN-mediated signaling events impact neoplastic progression.

overall_design:
Human foreskin BJ fibroblasts were mock or Bleomycin sulfate-treated (100ug/ml, Sigma, St. Louis, MO) for 24 hrs.  Replicatively senescent fibroblasts were obtained by continuous passage.  After 72 hr serum-starvation, RNA was collected using TRIzol (Invitrogen, Carlsbad, CA).  Biotinylated cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChips (Affymetrix, Santa Clara, CA) by the Washington University Microarray Facility.

There were 4, 6, and 6 samples for SIPS, RS, and young respectively:
- Stress-induced premature senescence (GSM336347..GSM336379)
- Replicative Senescent (GSM336385..GSM336573)
- Young (GSM336574..GSM336628)

Microarray quality control, analysis, and clustering (UPGMA by Centroid) were performed using dChip (May, 2008 release).  All GeneChip comparisons had a cut-off basis of a lower bound of 90% confidence of fold-change ≥1.5 and expression intensity difference ≥75.

first: Ermira

last: Pazolli

first: Xianmin

last: Luo

first: Sarah

last: Brehm

first: Kelly

last: Carbery

first: Jun-Jae

last: Chung

first: Julie

last: Prior

first: Jason

last: Doherty

first: Shadmehr

last: Demehri

first: Lorena

last: Salavaggione

first: David

last: Piwnica-Worms

middle: A


title: Neuroblastoma cell lines under normoxic and hypoxic conditions

city: Genoa

first: Paolo

last: Fardin

address: Largo G. Gaslini 5

department: Molecular Biology

country: Italy

institute: Istiuto Giannina Gaslini

summary:
Hypoxia is a low oxygen condition that occurs in the developing tumor mass and that is associated with poor prognosis and resistance to chemo- and radio-therapy. The definition of the hypoxia gene signature is fundamental for the understanding of tumor biology, as in the case of neuroblastoma, the most common pediatric solid tumor. The issue of identifying a significant group of variables in microarray gene expression experiments is particularly difficult due to the typical high dimensional nature of the data and great effort has been spent in the development of feature selection techniques.
Our main goal is to define a robust hypoxia gene signature in neuroblastoma cell lines. A set of 9 neuroblastoma cell lines were cultured under normoxic and hypoxic conditions for 18 hours, and their gene expression profiles were measured with Affymetrix GeneChip HG-U133 Plus 2.0. The clustering analysis of the expression profiles based on different clustering methods consistently revealed that hypoxia was not the major factor characterizing the data set. T-test analysis with multiple testing correction fails to identify significantly differentially expressed genes. Conversely the l1-l2 regularization selects 11 significant probesets while building an effective classification rule. The algorithm is cast within a cross-validation framework in order to achieve an unbiased analysis. The estimated cross-validation error is 17% (3 out of 18).
We show that the use of l1-l2 regularization allowed us to model the effect of hypoxia, which was not detected by conventional t-test based approaches and we find a panel of genes able to properly discriminate the normoxic versus the hypoxic status of neuroblastoma cell lines.

overall_design: The expression profile of 9 neuroblastoma cell lines under normoxia vs hypoxia was studied

first: Annalisa

last: Barla

first: Sofia

last: Mosci

first: Lorenzo

last: Rosasco

first: Alessandro

last: Verri

first: Luigi

last: Varesio


title: Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 1.c)

status: Public on Mar 27 2009

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

summary: Human induced pluripotent stem (iPS) cells have previously been derived from somatic cells using viral vectors that integrate transgenes into the genome. Genomic integration, however, can allow persistent leaky expression of the transgenes and can create insertional mutations, thus limiting the utility of these cells for both research and clinical applications. Here, we describe the derivation of human iPS cells free of vector and transgene sequences using non-integrating oriP/EBNA1-based episomal vectors. The resulting iPS cells are similar to human embryonic stem (ES) cells in both proliferative and developmental potential. These results demonstrate that reprogramming of human somatic cells does not require genomic integration or the continued presence of exogenous reprogramming factors, and removes one important obstacle to the clinical applications of these cells.

overall_design: Total of 5 es, 1 fibr, 11 parental clones

first: J

last: Yu

first: K

last: Hu

last: Smuga-Otto

first: S

last: Tian

first: R

last: Stewart

first: I

middle: I

last: Slikvin

last: Thomson


title: Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 4.a)

overall_design: Total of 5 es, 1 fibr, 2 parental, 4 ips sub clones


title: Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors

summary:
Human induced pluripotent stem (iPS) cells have previously been derived from somatic cells using viral vectors that integrate transgenes into the genome. Genomic integration, however, can allow persistent leaky expression of the transgenes and can create insertional mutations, thus limiting the utility of these cells for both research and clinical applications. Here, we describe the derivation of human iPS cells free of vector and transgene sequences using non-integrating oriP/EBNA1-based episomal vectors. The resulting iPS cells are similar to human embryonic stem (ES) cells in both proliferative and developmental potential. These results demonstrate that reprogramming of human somatic cells does not require genomic integration or the continued presence of exogenous reprogramming factors, and removes one important obstacle to the clinical applications of these cells.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Total 21 samples were analyzed to confirm the similarity of human iPS cells derived with episomal vectors with human ES cells, and a dissimilarity with fibroblasts.
Refer to individual Series

first: Junying

first: Kejin

first: Kim

first: Shulan

first: Ron

first: Igor

first: James


title: Synchronized HTC116 cells: time course

status: Public on Mar 31 2009

city: Kamakura

first: Hideaki

last: Mizuno

state: Kanagawa

address: 200 Kajiwara

department: Discovery research dept.

institute: Chugai Pharmaceutical Co., Ltd.

summary: Analysis of synchronized HCT116 cells at various time points up to 10 hours following treatment with DMSO or Nocodazole.

overall_design: HCT116 colorectal cancer cell line was obtained from the American Type Culture Collection (ATCC) and grown in McCOY’S 5A MEDIUM MODIFIED (SIGMA) with 10% FBS (JBS). It was maintained at 37°C and 5% CO2. Synchronous culture was obtained by incubating cells for 19 h in 2 mM of thymidine, followed by a 9 h-incubation in normal medium and a second 16 h-incubation in thymidine (2 mM). Cells were washed with normal medium followed by treatment with DMSO for 0, 2, 4, 6, 7, 8, 9 and 10 h as a control or 0.1 mg/ml Nocodazole (Sigma) for 7, 8, 9 and 10 h.

first: Yoshito

last: Nakanishi

first: Kouta

last: Takahashi


title: DU145 tumor 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: 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: 52 samples were initially run, 45 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 2, 6, and 24 hours post treatment.  Additionally, untreated time zero samples were analyzed as a further control

first: Windy

last: Berkofsky-Fessler


title: Expression data from breast cancer cell lines with various colony-forming ability

city: Singapore

first: Seiichi

last: Mori

institute: National University of Singapore

summary:
Cultured cancer cells exhibit substantial phenotypic heterogeneity when measured in a variety of ways such as sensitivity to drugs or the capacity to grow under various conditions.  Among these, the ability to exhibit anchorage-independent cell growth (colony forming capacity in semisolid media), has been considered to be fundamental in cancer biology, because it has been connected with tumor cell aggressiveness in vivo such as tumorigenic and metastatic potentials, and also utilized as a marker for in vitro transformation.  Although multiple genetic factors for anchorage-independence have been identified, the molecular basis for this capacity is still largely unknown.  To investigate the molecular mechanisms underlying anchorage independent cell growth, we have used genome-wide DNA microarray studies to develop an expression signature associated with this phenotype.  Using this signature, we identify a program of activated mitochondrial biogenesis associated with the phenotype of anchorage-independent growth and importantly, we demonstrate that this phenotype predicts potential for metastasis in primary breast and lung tumors.

Keywords: Breast cancer cell lines with various colony-forming ability

overall_design: To develop an expression signature reflecting the capacity for anchorage-independent cell growth, we first carried out colony formation assays with 19 breast cancer cell lines in suspension culture dish with methyl-cellulose containing media.  Starting with 20,000 plated cells, five cell lines (MDA-MB-361, HCC38, ZR75, Hs578T and BT483) gave rise to less than 20 colonies, while 8 cell lines (MCF7, MDA-MB-231, BT20, SKBR3, MDA-MB-435s, T47D and BT474) showed formation of more than 500 colonies.  The rest of the cell lines showed an intermediate phenotype in colony forming ability (20-200 colonies; HCC1143, HCC1806, HCC1428, MDA-MB-453, CAMA1, BT549 and MDA-MB-157).  Among 19 cell lines, 11 cell lines have duplicates of expression data in a different batch. We removed the batch effect of this Affymetrix expression data using ComBat according to the instruction of http://statistics.byu.edu/johnson/ComBat/Abstract.html. Therefore, this dataset is a combined and standardized data that are originally RMA formatted.

first: Andrea

last: Bild

first: Joseph

last: Nevins


title: Peripheral blood mononuclear cells treated with a CDK inhibitor

overall_design: 40 samples were initially run, 37 passed QC and were analyzed, samples were run in 6 independent replicates and were treated with either vehicle, R547 at the IC90, or R547 at 3 times the IC90.   Additionally, untreated time zero samples were analyzed as a further control


title: Impact of anti-inflammatory agents on the gene expression profile of stimulated human neutrophils

status: Public on Mar 23 2009

city: Quebec

first: Marc

last: Pouliot

state: Qc

address: 2705 boul Laurier

country: Canada

institute: CHUL Research center

summary: Adenosine, prostaglandin E2, or increased intracellular cyclic AMP concentration each elicit potent anti-inflammatory events in human neutrophils by inhibiting functions such as phagocytosis, superoxide production, adhesion and cytokine release. However, the endogenous molecular pathways mediating these actions are poorly understood. In the present study, we examined their impact on the gene expression profile of stimulated neutrophils. We have identified a set of genes that may be part of important resolution pathways that interfere with cell activation. Identification of these pathways will improve understanding of the capacity of tissues to terminate inflammatory responses and contribute to the development of therapeutic strategies based on endogenous resolution

overall_design: Neutrophils were resuspended at a concentration of 25 x 106 cells/ml in Hank's balanced salt solution (HBSS; 37°C) containing 1% fetal bovine serum, 10 mM HEPES pH 7.4, 1,6 mM Ca2+ and no Mg2+. Adenosine deaminase (ADA; 0.1U/mL) was added to cell suspensions 20 min prior to stimulation. Where mentioned, PGE2, CGS 21680, RO 20-1724 and forskolin, dissolved in DMSO, were added to cell suspensions 10 min before stimulation. The final organic solvent concentration was identical in all samples and did not exceed 0.1% (v/v). Neutrophils were stimulated with a mixture of LPS (100 ng/mL), GM-CSF (1.4 nM), TNF-α (100 ng/mL), fMLP (100 nM) and IL-1β (30 nM) for 30 min at 37oC. These experiments were performed 5 times in identical conditions, each time with a different donor.

first: Mireille

last: St-Onge

first: Aline

last: Dumas

first: Annick

last: Michaud

first: Cynthia

last: Laflamme

first: Andrée-Anne

last: Dussault


title: Gene expression of innate immune response in endothelial cells

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
Gene expression in human umbilical vein endothelial cells (HUVEC) was investigated by microarray analysis after 4 h infection with S. aureus isolated from healthy nasal carriers (n=5) and from blood (n=5) of septic patients. All bacterial isolates were spa-typed and characterized with a DNA microarray to determine the presence of virulence genes.

Keywords: infection studies, pathogen, S. aureus

overall_design: Five S. aureus (designated BI-BV) from a collection of blood culture isolates (Department of Clinical Microbiology, Ryhov County Hospital, Jönköping, Sweden) from septic patients were selected. Isolates from patients with diabetes, endocarditis, drug addicts and persons with an operation within the three last years were excluded. Two S. aureus isolates were from patients with an abscess in the psoas muscle, two from patients with spondylitis and one from a wound in the neck. Another five isolates (CI-CV) were randomly selected from a collection of S. aureus obtained from healthy male nasal carriers collected in a previous study.

first: L

last: Stark

first: A

last: Matussek

first: P

last: Lindgren

first: R


title: Conditioning of uropathogenic Escherichia coli to nitrosative stress

status: Public on Mar 21 2009

city: Salt Lake City

first: Matthew

last: Mulvey

address: 15 N. Medical Drive East

department: Pathology

institute: University of Utah

summary: While in transit within and between hosts, uropathogenic E. coli (UPEC) encounter multiple stresses, including substantial levels of nitric oxide and reactive nitrogen intermediates.  Strains of UPEC become conditioned to high concentrations of acidified sodium nitrite (ASN), a model system used to generate nitrosative stress. We used microarrays to define the expression profile of UPEC that have been conditioned for growth in ASN.

overall_design: Separate colonies of the UPEC isolate UTI89 grown on LB agar plates from a -80°C freezer stock were used to start overnight shaking cultures in MES-buffered LB broth (MES-LB, pH 5.0).   Each culture was then diluted 1:100 into 7 ml MES-LB with or without 3 mM ASN in loosely capped 20-by-150-mm borosilicate glass tubes and grown with shaking at 37°C.  Growth was monitored by optical density until OD600 = 1.5, at which point cultures were spun down, and pellets frozen at -80°C for at least 12 h.  RNA was extracted with hot phenol-chloroform and purified by CsCl centrifugation.  cDNA was synthesized, fragmented, and labeled for hybridization to Affymetrix GeneChip® E. coli Genome 2.0 Arrays.

first: M

first: J

last: Bower


title: Comparative transcriptomic profiling of human colon cells (CCD-18Co) exposed to an orange extract rich in flavanones

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

country: Spain

institute: CEBAS-CSIC

summary:
We used microarrays to investigate gene expression changes in human colon normal fibroblasts exposed to a bitter orange extract enriched in flavanones (and previously subjected to in vitro gastro-duodenal digestion) to determine possible modulatory beneficial effects induced by these plant-derived compounds on the colon cells.

Keywords: Comparative gene expression, Control vs Treated cells (response to exposure with xenobiotics plant polyphenols)

overall_design: We used ~90% confluent monolayers of colon CCD-18Co cells exposed to either small doses of pre-digested extract from bitter orange containing a mixture of flavanones (Treated) or equivalent quantities of digestive enzymes and salts (Control). Treatments were done in triplicate.

last: Conesa

first: Jesús

last: Cantalejo

first: Juan

last: Bastida


title: head and neck squamous cell carcinoma samples

status: Public on Mar 22 2009

city: Nashville

first: Christine

middle: H.

last: Chung

state: TN

address: 777 PRB

department: Internal Medicine

country: USA

institute: Vanderbilt University

summary:
Patient selection and specimen collection. Thirty-six freshly frozen tumor samples were prospectively collected from patients undergoing surgery or biopsy for HNSCC at the University of North Carolina (UNC) at Chapel Hill (21 patients) and Vanderbilt University (15 patients). All tissues were snap-frozen in liquid nitrogen within 30 minutes of surgical resection or biopsy, and kept at -80oC until further processing. All patients consented to participation in this study under protocols approved by IRB at the two institutions.
This set includes the samples previously deposited into GEO including 8 additional samples and adjustment for protocol changes. The original 36 before protocol changes (and thus unadjusted) are here: Slebos RJ, Yi Y, Ely K, et al. Gene expression differences associated with human papillomavirus status in head and neck squamous cell carcinoma. Clin Cancer Res 2006;12(3 Pt 1):701-9.
Keywords: disease state analysis

overall_design: 44 primary head and neck tumor samples

first: Joel

last: Parker