title: Environmental Genomics of Calcicole-calcifuge physiology

summary:
The purpose of this set of arrays is to provide a third replicate to use in data analysis addition to the 2 previous replicates for all samples already generated on this project. Our hypothesis is that adaptation to a calcareous environment will be reflected in altered gene expression including genes encoding transporters, ion channels, transcription factors, etc.
To test this hypothesis we grew a laboratory non-calcicole (Col-4) and a laboratory calcicole (Cal-0) ecotypes of A. thaliana at low (1 mM) and high (12.5 mM) rhizospheric Ca2+ and compare the patterns of gene expression by microarray analysis. We then collected from the wild, a putative calcicole ecotype (Elland)and a putative non-calcicole (Penicuik) and grew both at low (1 mM) and high (12.5 mM) rhizospheric Ca2+ and compared expression profiles to the laboratory ecotypes.

Experimenter name = Bev Abram
Experimenter phone = 01524 592931
Experimenter address = Dept Biological Sciences
Experimenter address = Lancaster University
Experimenter address = Bailrigg
Experimenter address = Lancaster
Experimenter zip/postal_code = LA1 4YQ
Experimenter country = UK
Keywords: growth_condition_design;  strain_or_line_design

first: Bev

last: Abram

first: Alan

last: Shirras


title: Response to CBF2 expression

status: Public on Aug 15 2006

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

summary:
This experiment was annotated by TAIR (http://arabidopsis.org).

This experiment looks at changes in gene expression in response to constitutive expression of the transcription factor CBF2.

Experimenter name = Jonathan Vogel
Experimenter phone = 517-355-2299
Experimenter fax = 517-353-5174
Experimenter department = MSU-DOE Plant Research Lab
Experimenter institute = Michigan State University
Experimenter address = East Lansing
Experimenter zip/postal_code = MI 48824
Experimenter country = USA
Keywords: genetic_modification_design

overall_design: 4 samples were used in this experiment

first: Jonathan

last: Vogel

first: Michael

last: Thomashow

first: Henrik

last: Townsend

first: Zoe

last: Emmerson

first: Beatrice

last: Schildknecht


title: Single cell expression profiling of human epidermal stem and transit amplifying cells

status: Public on Aug 04 2006

city: London

first: Kim

middle: B.

last: Jensen

address: 44 Lincoln's Inn Fields

department: London Research Institute

institute: Cancer Research UK

summary:
To explore which signaling pathways are of importance in maintenance of human epidermal keratinocytes we have established a protocol which allows single cell expression profiling. The protocol was applied to cultured human epidermal keratinocytes, and single cell cDNA libraries from stem and transit amplifying cells were identified based on the expression of known SC markers, MCSP and Dll1.
We used microarrays to obtain expression profiles from single cells and identify common denominators that could be important for maintenance and signalling in epidermal stem cells.
Keywords: Timecourse

overall_design: Single cultured epidermal keratinocytes at no later than passage 3 were picked and seeded in 1st strand buffer for generation of cDNA and amplification.

first: Fiona

middle: M

last: Watt

middle: B


title: Gene expression in wild-type and transgenic plants overexpressing rice topoisomerase6 genes

status: Public on Aug 09 2006

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary:
10-day-old wild-type and homozygous transgenic Arabidopsis seedlings (overexpressing OsTOP6A3 and OsTOP6B) grown under normal growth conditions were used for total RNA isolation. The 5 micrograms of each total RNA sample was processed for microarray analysis according to Affymetrix protocol.
Keywords: Arabidopsis, wild-type and transgenic seedlings, differential gene expression

overall_design: The experiment involves the study of differential gene expression in transgenic Arabidopsis seedlings overexpressing rice topoisomerase 6 subunit A (OsTOP6A3) and subunit B (OsTOP6B) cDNAs as compared to wild-type.Two biological replicates for each sample were used for microarray analysis.

first: Akhilesh

middle: K

last: Tyagi

first: Jitendra

middle: P

last: Khurana


title: Expression data from early Drosophila embryo

status: Public on Aug 02 2006

city: Berkeley

first: Soyeon

last: Ahn

state: CA

address: 367 Evans Hall #3860

country: USA

institute: UC Berkeley

summary:
Translational control is critical for early Drosophila embryogenesis and is exerted mainly at the gene-specific level.
To understand the post-transcriptional regulation during Drosophila early embryonic development, we used the sucrose polysomal gradient analyses and GeneChip analysis to illustrate the translation profile of individual mRNAs.
A paper was published in Genome Biology 2007 under the tile "Global analyses of mRNA translational control during early Drosophila embryogenesis".
Keywords: time course, fractionation

overall_design: In this study, we have fractionated embryo extracts from a series of early stages by sedimentation on sucrose density gradients and analyzed the RNA components of these fractions. Our analysis has focused on analyzing ribosomal density, generally and for individual transcripts, global translational activity during the first 10 hours after egg laying and coordination between transcription and translation regulation.

first: Xiaoli

last: Qin


title: Estrogen effects on MCF-7 breast cancer cells co-expressing ERa and ERb

status: Public on Aug 10 2006

city: Santa Monica

first: Edmund

middle: C

last: Chang

state: California

address: 2225 Colorado Ave

institute: Kite Pharma

summary:
Two subtypes of the estrogen receptor, ERalpha and ERbeta, mediate the actions of estrogens, and the majority of human breast tumors contain both ERalpha and ERbeta. To examine the possible interactions and modulatory effects of ERbeta on ERalpha activity, we have used adenoviral gene delivery to produce human breast cancer (MCF-7) cells expressing ERbeta, along with their endogenous ERalpha. We have examined the effects of ERβ expression on genome-wide gene expression by Affymetrix GeneChip microarrays. We find that ERbeta modulated estrogen gene expression on nearly 24% of E2-stimulated genes but only 8% of E2-inhibited genes. We find that ERbeta modulation is gene-specific, enhancing or counteracting ERalpha regulation for distinct subsets of estrogen target genes.  Introduction of ERbeta into ERalpha-containing cells induced up/down-regulation of many estrogen target in the absence of any added ligand.  In addition, ERbeta presence elicited the expression of a unique set of genes that were not regulated by ERalpha alone.  ERbeta modulated the expression of genes in many functional categories, but the greatest numbers were associated with transcription factor and signal transduction pathways. Regulation of multiple components in the TGF beta, SDF1, and semaphorin pathways, may contribute to the suppression of proliferation observed with ERbeta both in the presence and absence of estrogen. Hence, ERbeta modulates ERalpha gene regulation in diverse ways that may contribute to its growth-inhibiting beneficial effects in breast cancer
Keywords: modulatory effects of ERb on ERa

overall_design: MCF-7 cells expressing endogenous ERalpha were infected with adenovirus carrying either estrogen receptor beta (AdERb) or no insert (Ad) at multiplicity of infection (moi) of 5 or 50.  Cells were infected with adenovirus for a period of 48hr before treatment with ligand (vehicle control or 10nM 17beta-estradiol) for a additional period of 24hr before harvest.

first: Benita

middle: S

last: Katzenellenbogen


title: Dilated Cardiomyopathy and Non Failing Biopsies

status: Public on Aug 01 2006

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

summary:
Dilated cardiomyopathy (DCM) is a common cause of heart failure and a leading cause of cardiac transplantation in western countries. The robust predictive expression profile of cardiomyopathic and NF hearts as well as the functional classification can help to identify promising candidates for DCM and may improve the early diagnosis of cardiomyopathy.
Keywords: disease state analysis

overall_design: This series includes single channel hybridizations of 12 independent heart biopsy samples on Affymetrix Array U133A. The twelve independent subendocardial left ventricular tissue samples were collected from seven DCM patients at the time of transplantation and five NF donor hearts which were not transplanted because of palpable coronary calcifications. No technical or biological replicates are included.

first: Andreas

last: Barth

last: Nabauer

first: Stefan

last: Kaab

first: Ulrich

last: Mansmann

first: Sylvia

last: Merck

first: Mathias

last: Gebauer

first: Klaus

last: Steinmeyer


title: Genomic approach to refine prognosis for adjuvant therapy in early stage non-small cell lung carcinoma

city: Durham

first: Joseph

middle: R.

last: Nevins

state: NC

address: 2133 CIEMAS, 101 Science Dr.

department: IGSP

institute: Duke University

summary:
Abstract from paper - Potti A, et al
Keywords: Outcome, recurrence, adjuvant therapy, Early stage Non-small cell Lung Cancer, Lung Metgene Predictor

overall_design: Retrospective analysis of approximately 200 samples obtained from Duke, ACOSOG and CALGB to develop a Lung metagene predictor that would then be used to assess risk of recurrence and thus identify high risk patients with stage Ia non-small cell carcinoma who would be candidates for adjuvant chemotherapy

first: Anil

last: Potti

first: Sayan

last: Mukherjee

first: Rebecca

last: Prince

first: Holly

last: Dressman

first: Andrea

last: Bild

first: Jason

last: Koontz

first: Michael

last: Kelley

first: Geoffrey

last: Ginsburg

first: Mike

last: West

first: David

last: Har


title: Stimulation by LPS and HMGB1 in peripheral blood neutrophils from patients with sepsis-induced acute lung injury

city: Aurora

first: Christopher

middle: D

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

summary:
Peripheral blood neutrophils were isolated from septic patients and treated in vitro with LPS or HMGB1
Keywords: ordered

overall_design: 8 patients, each contributing a control, LPS-treated, and HMGB1-treated neutrophil sample.

first: Eliezer

last: Silva

first: John

middle: J

last: Arcaroli

first: Qianbin

last: He

first: Daiva

last: Svetkauskaite

first: Jerry

middle: A

last: Nick

first: Katie

middle: R

last: Poch

first: Jong

last: Park

first: Mark

middle: W

last: Geraci

first: Edward

last: Abraham


title: Low chronic exposure of Arabidopsis thaliana to Caesium-137

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
Arabidopsis thaliana plants are grown for one week in a hydroponic growth system and transferred to new plant medium containing low levels of Caesium-137 (control is transferred to new medium with no radioactivity) and left for further two weeks. Levels of Caesium-137 are chosen according to research and are reflecting occurring levels found in radioactive contaminated soil. The plants are then harvested and the samples divided into shoot and root samples.

Experimenter name = Yu-Jin Heinekamp
Experimenter phone = 0044-117-3442102
Experimenter address = University of the West of England  (UWE)
Experimenter address = Faculty of Applied Sciences
Experimenter address = Center for Research in Plants, GRI
Experimenter address = Coldharbour Lane
Experimenter address = Bristol
Experimenter zip/postal_code = BS6 5BP
Experimenter country = UK
Keywords: organism_part_comparison_design

overall_design: 12 samples were used in this experiment

first: Yu-Jin

last: Heinekamp

first: Neil

last: Willey

first: Henrik

last: Townsend

first: Zoe

last: Emmerson

first: Beatrice

last: Schildknecht


title: Identifying targets of FLC at 27oC

institute: Nottingham Arabidopsis Stock Centre (NASC)

summary:
FLOWERING LOCUS C (FLC) is a MADS box transcription factor that plays a well characterised role in repressing the vegetative to floral transition of Arabidopsis thaliana. FLC has also been shown to affect the Arabidopsis circadian clock, with mutant seedlings showing short circadian periods. In a previous study, we identified the temperature-dependent circadian period QTL PerCv5b near the FLC locus on the top arm of Chromosome 5. PerCv5b caused a significant period effect at 27oC but not at 12oC or 22oC. Temperature-dependent circadian period phenotypes and a known polymorphism in the Ler allele made FLC a strong candidate gene for PerCv5b. The period effect of FLC was enhanced by combination with alleles of FRIGIDA (FRI), a gene shown to up-regulate FLC's expression.
We were interested in identifying how FLC affects the circadian clock, so we decided to identify its target genes. Greatest phenotypic difference was observed between fri; flc and FRI; FLC genotype seedlings at 27oC, so expression was compared between these lines (previously described in Michaels and Amasino1999 and 2001) on the Affymetrix ATH1 microarray. Seedlings were grown on media (MS 1.5% Agar containing 3% Sucrose) for 6 days under constant cool white fluorescent light (55-60 micro EINSTEINS) at 22oC then entrained for 4 days under (12h , 12h) light , dark cycles at 22oC. At dawn on the fourth day of entrainment they were transferred to constant light (25-30 micro EINSTEINS) at 27oC. Four samples were taken at 6 hour intervals starting 24h after the transfer to continuous conditions at the times 24h, 30h, 36h and 42h.
Equal amounts of total RNA were pooled from the three time points to produce one sample per genotype. The pooling strategy was employed to reduce the effect of circadian regulation on genes expression. This was particularly important in our case as some interesting genes would likely be regulated by the circadian clock and may only show expression differences at particular phases that could easily be missed if using just one time point.

Experimenter name = Kieron Edwards
Experimenter phone = 0131 651 3326
Experimenter fax = 0131 650 5392
Experimenter department = Institute of Molecular Plant Sciences
Experimenter institute = University of Edinbugh
Experimenter address = Kings Buildings
Experimenter address = Mayfield Road
Experimenter address = Edinburgh
Experimenter zip/postal_code = EH9 3JH
Experimenter country = UK
Keywords: genetic_modification_design

first: Kieron

last: Edwards

first: Andrew

last: Millar


title: Sox4 knockdown in ACC3 cells

status: Public on Jul 28 2006

city: Charlottesville

first: Christopher

middle: A.

last: Moskaluk

state: VA

address: P.O. Box 800214, OMS Rm. 3890,  Jefferson Park Ave

department: Pathology

institute: Christopher Moskaluk

summary:
Sox4 is upregulated in adenoid cystic carcinoma (ACC). The ACC3 cell line is the most widely available cell culture model system of this tumor type. RNAi mediated knockdown of Sox4 in ACC3 cells induces apoptosis. Since Sox4 is a transcription factor, it is hypothesized that this apoptotic phenotype is due to changes in transcription from genes under Sox4 control.This experiment was designed to find candidate genes whose expression levels change after Sox4 knockdown that could contribute to the pro-apoptotic phenotype.
Keywords: gene knockdown

overall_design: The ACC3 cell line was subjected to plasmid vector-based shRNA knockdown of the Sox4 gene, with a control group consisting of cells transfected with a plasmid vector expressing shRNA for the bacterial lacZ gene. Both groups were performed in triplicate.The shRNA sequences were expressed from the plasmid pENTR/U6 (Life Technologies Inc). Sox4 sequence: 5’-GACGACCTGCTCGACCTGAcgaaTCAGGTCGAGCAGGTCGTC-3’. RNA was harvested 48 hours after transfection.Labeled cRNA probe was hybridized to Affymetrix U133a probes.

first: Patcharin

last: Pramoonjago

first: Alexander

last: Baras


title: Expression profiling of human adult postmortem brain tissue from subjects with bipolar disorder and healthy controls

status: Public on Jul 27 2006

city: Cambridge

first: Sabine

last: Bahn

address: Tennis Court Road

institute: University of Cambridge

summary:
Bipolar affective disorder is a severe psychiatric disorder with a strong genetic component but unknown pathophysiology. We used microarray technology (Affymetrix HG-U133A GeneChips) to determine the expression of approximately 22 000 mRNA transcripts in post-mortem brain tissue (dorsolateral prefrontal cortex and orbitofrontal cortex) from patients with bipolar disorder and matched healthy controls.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Margaret

last: Ryan

first: Helen

middle: E

last: Lockstone

first: Stephen

last: Huffaker

first: Matthew

middle: T

last: Wayland

first: Maree

last: Webster


title: Adult postmortem brain tissue (orbitofrontal cortex) from subjects with bipolar disorder and healthy controls

summary:
Bipolar affective disorder is a severe psychiatric disorder with a strong genetic component but unknown pathophysiology. We used microarray technology (Affymetrix HG-U133A GeneChips) to determine the expression of approximately 22 000 mRNA transcripts in post-mortem brain tissue (orbitofrontal cortex) from patients with bipolar disorder and matched healthy controls. Orbitofrontal cortex tissue from a cohort of 30 subjects was investigated and the final analysis included 10 bipolar and 11 control subjects. Differences between disease and control groups were identified using a rigorous statistical analysis with correction for confounding variables and multiple testing.
Keywords: disease state analysis

overall_design: RNA extracted from human postmortem brain tissue from adult subjects with bipolar disorder and healthy controls was hybridised to Affymetrix HG-U133A GeneChips to identify differentially expressed genes in the disease state.


title: Classification of serrated colorectal tumors

city: Helsinki

first: Antti

last: Kokko

address: POBOX 63 (Haartmaninkatu 8)

department: Dept of Medical Genetics

country: Finland

institute: University of Helsinki

summary:
Serrated adenocarcinomas are morphologically different from conventional adenocarcinomas. The serrated pathway has recently been proposed to represent a novel mechanism of colorectal cancer (CRC) formation. However, whether they are biologically different and truly form a distinct subclass of CRC, is not known. This study shows that the gene expression profile of serrated and conventional CRCs differs from each others and that serrated CRCs are not only morphologically novel, but also biologically distinct subclass of CRC.
Keywords: molecular classification

overall_design: Total RNA was extracted from fresh frozen tumors with Trizol (GibcoBRL) and purified using RNeasy spin columns (Qiagen). The RNA quality was analyzed using a spectrophotometer and a Agilent 2100 Bioanalyzer (Agilent Technologies). Biotin labeled and fragmented cRNA was prepared from 8 micrograms of total RNA with procedures recommended for the HG-U133 GeneChip expression analysis (Affymetrix). The HG-U133A chips were hybridized, scanned and analyzed with Microarray Suite 5.0 software according to the manufacturer’s instructions (Affymetrix).

first: Päivi

last: Laiho

first: Sakari

last: Vanharanta

first: Reijo

last: Salovaara

first: Heli

last: Sammalkorpi

first: Heikki

last: Järvinen

first: Jukka-Pekka

last: Mecklin

first: Tuomo

last: Karttunen

first: Karoliina

last: Tuppurainen

first: Veronica

last: Davalos

first: Simo

last: Schwartz Jr.

first: Diego

last: Arango

first: Markus

last: Mäkinen

first: Lauri

last: Aaltonen


title: Downstream targets of Nm23-H1: Gene expression profiling of CAL 27 cells using DNA microarray

city: Zagreb

first: Maja

last: Herak Bosnar

address: Bijenicka 54

department: Div. Molecular Medicine

country: Croatia

institute: Rudjer Boskovic Institute

summary:
The human nm23-H1 was discovered as a tumor metastasis suppressor based on its reduced expression in melanoma cell lines with low versus high metastatic potential. It encodes for one of two subunits of the nucleoside-diphosphate kinase. Besides its role in the maintenance of the cells NTP pool, nm23 plays a key role in different cellular processes. The role of nm23-H1 in these processes still has to be elucidated. Our goal was to identify Nm23-H1 downstream targets by subjecting Nm23-H1 overexpressing CAL 27 cells oral squamous cell carcinoma (OSSC) to microarray analysis. The genes with changed expression patterns could be clustered into several groups: transforming growth factor  (TGF) signaling pathway, cell adhesion, invasion and motility, proteasome machinery, cell-cycle, epithelial structural and related molecules and others. Based on the expression patterns observed we presume that nm23-H1 might have a role in OSSCs, which should be confirmed by future experiments.
Keywords: disease state analysis

overall_design: The experiments were conducted on human cell line CAL 27 (poorly differentiated, G3, squamous cell carcinoma of the tongue), obtained by courtesy of Dr. Jeannine Gioanni, Centre Antoine Lacassagne, Nice France).  The cells were transfected with pEGFPC1 and pEGFPC1-nm23-H1 constructs, and total cellular RNA was extracted from clones expressing EGFP-Nm23-H1 and the empty vector-carrying clone for microarray analysis.


title: Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
Pseudomonas syringae pv. tomato DC3000 (Pst) is a virulent pathogen, which causes disease on tomato and Arabidopsis. The type III secretion system (TTSS) plays a key role in pathogenesis by translocating virulence effectors from the bacteria into the plant host cell, while the phytotoxin coronatine (COR) contributes to virulence and disease symptom development.  Recent studies suggest that both the TTSS and and COR are involved in the suppression of host basal defenses.   However, little is known about the interplay between the host gene expression associated with basal defenses and the virulence activities of the TTSS and COR during infection.  The global effects of the TTSS and COR on host gene expression associated with other host cellular processes during bacterial infection are also not well characterized.  In this study, we used the Affymetrix full genome chip to determine the Arabidopsis transcriptome associated with basal defense to Pst DC3000 hrp mutants and the human pathogenic bacterium Escherichia coli O157:H7.   We then used Pst DC3000 virulence mutants to characterize Arabidopsis transcriptional responses to the action of hrp-regulated virulence factors (e.g., TTSS and COR) during bacterial infection.  Additionally, we used bacterial fliC mutants to assess the role of the PAMP flagellin in induction of basal defense-associated transcriptional responses. In total, our global gene expression analysis identified more than 5000 Arabidopsis genes that are reproducibly regulated more than 2-fold in three independent biological replicates of at least one type of comparison.  Regulation of these genes provides a molecular signature for Arabidopsis basal defense to plant and human pathogenic bacteria, and illustrates both common and distinct global virulence effects of the TTSS, COR, and possibly other hrp-regulated virulence factors during Pst DC3000 infection.

Experimenter name = William Underwood
Experimenter phone = 517-353-9182
Experimenter fax = 517-353-9168
Experimenter address = Michigan State University
Experimenter address = 222 Plant Biology Building
Experimenter address = 178 Wilson R.d.
Experimenter address = East Lansing, MI
Experimenter zip/postal_code = 48824
Experimenter country = USA
Keywords: pathogenicity_design

overall_design: 40 samples were used in this experiment

first: William

last: Underwood

first: Sheng-Yang

last: He

first: Henrik

last: Townsend

first: Zoe

last: Emmerson

first: Beatrice

last: Schildknecht


title: Expression data for LMF

status: Public on Jul 07 2006

first: Dave

last: Peck

state: MA

address: 7 Cambridge Center

institute: Broad Institute

summary:
This study compared the expression signatures of HL60 cells +/- tretinoin.  This data was then used for another study showing a method for high-throughput gene expression signature analysis.
Keywords: expression analysis

overall_design: The experiment consists of 3 HL60 samples treated with DMSO and 3 HL60 samples treated with tretinoin.


title: Gene Expression Preferentially Regulated by Tamoxifen in Breast Cancer Cells

first: Edmund

last: Chang

summary:
The beneficial effect of the selective
estrogen receptor modulator (SERM) tamoxifen in the treatment and prevention of breast cancer is assumed to be through its ability to antagonize the stimulatory actions of estrogen, although tamoxifen can also have some estrogen-like
agonist effects.  Here we report that in addition to these mixed agonist/antagonist actions, tamoxifen can also selectively regulate a unique set of more than 60 genes in estrogen receptor alpha
(ERa)-positive MCF-7 human breast cancer cells which are minimally regulated by estradiol or raloxifene.  This gene regulation by tamoxifen is mediated by ERa and is reversed by estradiol or ICI 182,780.  We find that the introduction of ERbeta into MCF-7 cells reverses tamoxifen action on approximately 75% of these genes, suggesting that ERbeta is capable of repressing certain actions of tamoxifen. To examine whether these genes might serve as markers of tamoxifen sensitivity and/or the development of resistance, the expression level of these genes was examined in breast tumors of women who had received treatment with tamoxifen.  High expression of two of the tamoxifen stimulated genes, YWHAZ/14-3-3z and LOC441453, was found to correlate significantly with disease recurrence following tamoxifen treatment in women with ER-positive tumors, and hence appear to be markers of a poor prognosis.
Our data indicate a new dimension in tamoxifen action, involving gene expression regulation that is tamoxifen-preferential, and identify genes that might serve as markers of tumor responsiveness or resistance to tamoxifen therapy.
Keywords: ligand response in two ER backgrounds

overall_design: MCF-7 cells expressing endogenous ERalpha were infected with adenovirus carrying either estrogen receptor beta (AdERb) or no insert (Ad) at multiplicity of infection (moi) of 10. Cells were infected with adenovirus for a period of 48hr before treatment with ligand (vehicle control, 10nM 17beta-estradiol, or 10nM hydroxytamoxifen) for a additional period of 24hr before harvest.

first: Jonna

last: Frasor

first: Benita

last: Katzenellenbogen


title: Longitudinal comparison of monocytes from an HIV viremic vs avirmeic state

status: Public on Jul 04 2006

city: Frederick

first: Richard

last: Lempicki

state: MD

address: PO Box B

department: Clinical Services Program

institute: Leidos Biomedical Research, Inc.

summary:
Longitudinal analysis of monocyte gene expressions patterns before and after cessation of HAART: understanding the impact of HIV viremia on the monocyte tranascritome. We used microarrays to detail the global program of gene expression underlying defects in monocytes from HIV infected patients during viremia..
Diminished Production of Monocyte Proinflammatory Cytokines During HIV Viremia is Mediated by Interferon-alpha:  The in vivo effect of high-level HIV replication on the function of monocytes was investigated.  HIV-positive patients had elevated spontaneous production of monocyte proinflammatory cytokines (IL-1?, IL-6, and TNF-?) compared to uninfected controls.  These levels were highest in patients on-therapy and was diminished, in the context of viremia, following an interruption of therapy.  Diminished production of proinflammatory cytokines during viremia was restored by culturing with autologous CD4+ T cells or monocytes from an on-therapy time point, or by the addition of lipopolysaccharide (LPS).  Microarray analysis demonstrated that diminished monocyte production of proinflammatory cytokines was correlated with elevated levels of type I interferon-stimulated gene transcripts. Addition of exogenous IFN-?2A suppressed the spontaneous production of IL-1?, IL-6, and TNF-? but did not affect responses to LPS, recapitulating the changes observed in HIV viremic patients.  These results suggest that high-level HIV viremia inhibits monocyte function through chronic stimulation by IFN-?.  This effect of viremia on monocytes may play a role in diminished adaptive immune system functions in HIV-infected patients.  Restoration of these functions may contribute to the partial immune reconstitution observed following therapy and may be involved in immune reconstitution and inflammatory syndrome seen in some patients.
Keywords: Longitudinal comparison

overall_design: A longitudinal study was performed on 8 HIV infected individuals looking at gene expression changes in monocytes as a result of rebound of HIV viral load following termination of HAART: 8 patients pre and post HAART cessation.

first: John

last: Tilton

first: Alison

last: Johnson

first: Marlise

last: Luskin

first: Jun

last: Yang

first: Joseph

last: Adelsberger

first: Claire

last: Hallahan

first: JoAnn

last: Mican

first: Julia

last: Metcalf

first: Mark

last: Connors


title: Adult postmortem brain tissue (dorsolateral prefrontal cortex) from subjects with bipolar disorder and healthy controls

first: Sabine

last: Bahn

summary:
Bipolar affective disorder is a severe psychiatric disorder with a strong genetic component but unknown pathophysiology. We used microarray technology (Affymetrix HG-U133A GeneChips) to determine the expression of approximately 22 000 mRNA transcripts in post-mortem brain tissue (dorsolateral prefrontal cortex) from patients with bipolar disorder and matched healthy controls. A cohort of 70 subjects was investigated and the final analysis included 30 bipolar and 31 control subjects. Differences between disease and control groups were identified using a rigorous statistical analysis with correction for confounding variables and multiple testing.
Keywords: disease state analysis

first: Margaret

last: Ryan

first: Helen

last: Lockstone

first: Stephen

last: Huffaker

first: Matthew

last: Wayland

first: Maree

last: Webster


title: Expression data from MCF7/BUS cell culture exposed to xenoestrogens

status: Public on Jul 01 2006

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

summary:
MCF7 cells were exposed to xenoestrogens (vehicle = 0.1% ethanol, 30 pM 17beta-estradiol, 3 micromolar genistein, 10 micromolar genistein, 1 micomolar daidzein, 10 nM bisphenol A, 10 nM para-nonylphenol, 3 nM PPT) for 48 hours.
Keywords: xenoestrogen response

overall_design: MCF7/BUS cells were exposed to xenoestrogens for 48 hours. Experiments were repeated three times independently.

first: Toshi

first: Jessica

last: Chesnes

first: Kathryn

last: Coser

first: Zou

last: Lihua

first: Hua

last: Jingyung

first: Dean

middle: L

last: Kathleen

first: Sonnenschein

last: Carlos

first: Soto

last: Ana

first: Kurt

last: Isselbacher


title: Alveolar Epithelial Cell Injury with EBV Upregulates TGF-beta1 Expression

city: Dublin

first: Andrea

middle: Patricelli

last: Malizia

address: 21, Nelson Street

country: Ireland

institute: University College Dublin

summary:
Idiopathic pulmonary fibrosis (IPF) is a refractory and lethal interstitial lung disease characterized by alveolar epithelial cells apoptosis, fibroblast proliferation and extra-cellular matrix proteins deposition. Epstein - Barr virus (EBV) has previously been localised to alveolar epithelial cells of IPF patients. In this study we utilised a microarray based differential gene expression analysis strategy to identify potential molecular drivers of EBV associated lung fibrosis. We employed an alveolar epithelial cell line infected with EBV (A-Akata). Lytic phase infection induced in the A-Akata cells by TPA/BA treatment resulted in increase of TGFbeta1 and TIEG1 mRNA expression. Treatment of the A-Akata cells with ganciclovir,
resulted in a down regulation of both TIEG1 and TGFbeta1  expression, accompanied by a suppression of the EBV early response genes, Rta and Zta.  This suppression of cell turnover mediators was correlated with an increase in cell activity index. To identify a possible role for Rta in driving apoptotic gene expression, we inhibited the Rta gene expression by silencing RNA, resulting in a decrease in TGFbeta1 and TIEG1 expression. This study identifies an apoptotic role of the EBV early response genes, as enhancer factors of TIEG1 and TGFbeta1 in EBV infected alveolar epithelial cells, potentially providing a possible mechanism for the role of EBV infection in pulmonary fibrosis.
Keywords: EBV lytic phase infection, epithelial cell apoptosis, oligonucleotide array analysis

overall_design: RNA isolation, cDNA synthesis, in vitro transcription and microarray analysis of A549, EBV infected A549 (AAKata) and A549 +TGFbeta1 10ng/ml 4hours were performed as previously reported. All analysis were microarrayed in duplicate. Image files were obtained through Affymetrix GeneChip software (MAS5). Subsequently robust multichip analysis (RMA) was performed.  Expression data was compared to control by ANOVA analysis, p<0.05 correlated values and a signal log ratio of 0.6 or greater (equivalent to a fold change in expression of 1.5 or greater) were taken to identify significant differential regulation. All the SLRs data resulting from the comparative analyses were reported in a graph to determine the reliability of the assay and the linearity by r2. For all the microarray assays r2 value was higher than 0.98. Using gene expression values normalised by RMA, Average Linkage Hierarchical Cluster Analysis was performed and the results visualized by TreeView software.

first: Dominic

last: Keating

first: Sined

last: Smith

first: Dermot

last: Walls

first: Alfred

last: Wood

first: Peter

last: Doran

first: Jim

last: Egan


title: Differential gene expression after treatment of human monocyte-derived dendritic cells with CpG-oligo D19

status: Public on Jun 30 2006

city: Berlin

first: Reinhard

last: Wanner

address: Arnimallee 22

department: Inst. of Molecular Biology and Bioinformatics

institute: Charite-CBF

summary:
Human monocyte-derived dendritic cell cultures devoid of contaminating plasmacytoid dendritic cells were treated with the D-type CpG-oligonucleotide D19, with the non-CpG-oligonucleotide control D, or were left untreated. Cells of all treatment groups stemmed from the same donor. 6 h after addition, cells were harvested, and total RNA was prepared for analysis of D19-dependent differential gene expression on Affymetrix HG-U 133A 2.0.
Keywords: agent response

overall_design: One sample per treatment-group. No replicates.

first: Victoria

last: Hoene

first: Matthias

last: Peiser


title: hTERT effects in CD8 T Lymphocytes HD1

status: Public on Jun 24 2006

city: Lausanne

first: Mauro

last: Delorenzi

address: Génopode Building, Quartier Sorge

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary:
Using CD8+ T lymphocyte clones over-expressing telomerase weinvestigated the molecular mechanisms that regulate T cell proliferation.  Transduction and subcloning procedures were performed on CD8 + naive T-cell clones isolated from two different healthy individuals aged between 30 to 35 years (HD1 and HD2). T-cell cloneswere transduced to express hTERT/GFP or GFP alone. HD2 was profiled on U133Plus 2.0 and submitted as a separate GEO series.
Keywords: Cell Line Comparison.

overall_design: triplicates of 4 conditions, 1 chip (hTERT_YOUNG_HD1_REP2) excluded because of low quality hybridization.

first: Nathalie

last: Rufer

first: Olivier

last: Menzel

first: Marco

last: Migliaccio

first: Darlene

last: Goldstein

first: Sophie

last: Dahoun


title: Expression profiles of ATL patients

status: Public on Jun 14 2006

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

country: Japan

institute: Jichi Medical University

summary:
CD4-positive cells purified from peripheral blood of ATL patients.
Keywords: other


title: A Biologic Definition of Burkitt's Lymphoma from Transcriptional and Genomic Profiling

status: Public on Jun 07 2006

first: Michael

last: Hummel

address: Hindenburgdamm 30

department: Institute of Pathology

institute: Universitätsmedizin Berlin, Campus Benjamin Franklin

summary:
The distinction between the Burkitt lymphoma and diffuse large B-cell lymphoma is imprecise using current diagnostic criteria. We applied transcriptional and genomic profiling to molecularly define Burkitt lymphoma. Gene expression profiling employing Affymetrix GeneChips (U133A) was performed in 220 mature aggressive B-cell lymphomas, including a core group of eight Burkitt lymphomas, which fulfilled all diagnostic criteria of the WHO classification. A molecular signature of Burkitt lymphoma was generated. Chromosomal abnormalities were detected by interphase fluorescence in-situ hybridization and array comparative genomic hybridization. The molecular Burkitt lymphoma signature identified 44 cases. Fifteen of these cases lacked a morphology typical for Burkitt/Burkitt-like lymphoma. The vast majority (88%) of the 176 lymphomas without the molecular Burkitt lymphoma signature represented diffuse large B-cell lymphomas. In 20% of these cases a MYC break was detectable which was associated with complex chromosomal changes. Our molecular definition of Burkitt lymphoma sharpens and extends the spectrum of Burkitt lymphoma. In mature aggressive B-cell lymphomas without a Burkitt lymphoma signature, a chromosomal break in the MYC locus proved to be associated with adverse clinical outcome.
Keywords: Gene expression

overall_design: 220 diffuse large B-cell lymphoma and Burkitt lymphoma samples hybridized to 221 HGU133A Affymetrix GeneChips

first: Stefan

last: Bentink

first: Hilmar

last: Berger

first: Wolfram

last: Klapper

first: Swen

last: Wessendorf

first: Thomas

middle: F

last: Barth

first: Heinz-Wolfram

last: Bernd

first: Sergio

last: Cogliatti

first: Judith

last: Dierlamm

last: Feller

first: Martin-Leo

last: Hansmann

first: Eugenia

last: Haralambieva

first: Lana

last: Harder

first: Dirk

last: Hasenclever

last: Kuehn

first: Dido

last: Lenze

last: Lichter

first: Jose

middle: I

last: Martin-Subero

last: Moeller

first: Hans-Konrad

last: Mueller-Hermelink

first: German

last: Ott

first: Reza

middle: M

last: Parwaresch

first: Christiane

last: Pott

first: Andreas

last: Rosenwald

first: Maciej

last: Rosolowski

first: Carsten

last: Schwaenen

first: Benjamin

last: Stuerzenhofecker

first: Monika

last: Szczepanowski

first: Heiko

last: Trautmann

first: Hans-Heinrich

last: Wacker

first: Rainer

last: Spang

first: Markus

last: Loeffler

first: Lorenz

last: Truemper

first: Harald

last: Stein

first: Reiner

last: Siebert


title: Expression profiles in Blast Bank samples with AML/RAEB

status: Public on May 25 2006

first: Hiroyuki

last: Mano

summary: CD133-positive immature blasts were purified from bone marrow of the patients. Total RNA was extracted by RNeasy mini spin column (Qiagen, Inc).


title: STA1, a stress-upregulated nuclear protein, is required for pre-mRNA splicing, mRNA turnover and stress tolerance

status: Public on Jun 01 2006

city: Riverside

first: Jian-Kang

last: Zhu

address: 2150 Batchelor Hall

department: Botany and Plant Sciences

institute: University of California

summary:
In plants, many gene transcripts are very unstable, which is important for the tight control of their temporal and spatial expression patterns.  To identify cellular factors controlling the stability of unstable mRNAs in plants, we used luciferase imaging in Arabidopsis to isolate a recessive mutant, stabilized 1 (sta1), with enhanced stability of the normally unstable luciferase transcript. The sta1 mutation also causes the stabilization of some endogenous gene transcripts and has a range of developmental and stress response phenotypes. STA1 encodes a nuclear protein similar to the human U5 snRNP-associated 102-kDa protein and to the yeast pre-mRNA splicing factor Prp1p and Prp6p. STA1 expression is up-regulated by cold stress, and the sta1 mutant is defective in the splicing of the cold-induced COR15A gene.  Our results show that STA1 is a pre-mRNA splicing factor required for not only splicing but also the turnover of unstable transcripts and that it has an important role in plant responses to abiotic stresses.
Keywords: Genetic Modification

overall_design: Five replicates for WT (Control) and two replicates for sta1 (mutant) were compared.

first: Byeong-ha

last: Lee

first: Avnish

last: Kapoor

first: Jianhua


title: Novel Molecular Markers for non-melanoma skin cancer

first: Ingo

last: Nindl

address: Schumannstr. 20/21

department: Dermatology

institute: Skin Cancer Center Charite

summary:
normal skin (no), actinic keratosis (ak), and squamous cell carcinoma (scc) of the skin were examined:

Carcinogenesis is a multi-step process indicated by several genes up- or down-regulated during tumor progression. The type and number of genes involved in non-melanoma skin cancer (NMSC) are still unclear. This study examined and identified different expressed genes in NMSC. Fifteen snap-frozen biopsies of five immunosuppressed organ-transplanted recipients each normal skin, actinic keratosis (AK) and invasive squamous cell carcinoma (SCC) were analysed. Total RNA was extracted reverse transcribed and biotin-labeled cRNA was used for hybridization with Affymetrix HG-U133A gene expression cDNA-microarrays containing 22,283 known genes. Confocal scanner evaluated the signals twice and data analysis was performed by predicition analysis of microarrays (PAM) using nearest shrunken centroids with the threshold 3.5 to identify genes best characterizing normal skin and skin cancer. ANOVA analysis was performed as a second independent method to identify differentially expressed genes (p<0.05, and p<0.15). Quantitative verification of 13 up- or down-regulated genes was performed by real-time RT-PCR and genes were confirmed by sequencing. Broad coherent patterns in normal skin vs. AK and SCC were observed for 118 genes. Some of the genes (e.g. annexin, lamin, and metalloproteinases) up-regulated in carcinomas in our study have previously reported as over-expressed in NMSC. In total 42 genes were up-regulated and 76 genes were down-regulated in non-melanoma skin cancer. The majority of genes identified have not been previously reported different expressed during non-melanoma skin carcinogenesis.
Keywords: ordered

first: Chantip

last: Dang

first: Tobias

last: Schmook

first: Ralf

last: Kuban

first: Thomas

last: Meyer

first: Wolfram

last: Sterry

first: Eggert

last: Stockfleth


title: Reprogramming of CTLs into natural killer-like cells in celiac disease

status: Public on May 15 2006

city: Chicago

first: Bana

last: Jabri

state: IL

address: 5841 S Maryland Ave, S354

department: Department of Pathology

institute: University of Chicago

summary:
Celiac disease is an intestinal inflammatory disorder induced by dietary gluten in genetically susceptible individuals. The mechanisms underlying the massive expansion of interferon g–producing intraepithelial cytotoxic T lymphocytes (CTLs) and the destruction of the epithelial cells lining the small intestine of celiac patients have remained elusive. We report massive oligoclonal expansions of intraepithelial CTLs that exhibit a profound genetic reprogramming of natural killer (NK) functions. These CTLs aberrantly expressed cytolytic NK lineage receptors, such as NKG2C, NKp44, and NKp46, which associate with adaptor molecules bearing immunoreceptor tyrosine-based activation motifs and induce ZAP-70 phosphorylation, cytokine secretion, and proliferation independently of T cell receptor signaling. This NK transformation of CTLs may underlie both the self-perpetuating, gluten-independent tissue damage and the uncontrolled CTL expansion leading to malignant lymphomas in severe forms of celiac disease. Because similar changes were detected in a subset of CTLs from cytomegalovirus-seropositive patients, we suggest that a stepwise transformation of CTLs into NK-like cells may underlie immunopathology in various chronic infectious and inflammatory diseases.
Keywords: NKG2C; LAK; CTL; NK receptor; IEL; Mucosal Immunity; Celiac Disease

overall_design: Using a standard GeneChip preparation protocol (Affymetrix, Santa Clara CA), gene array hybridizations and data collection on 5 paired NKG2C+ and NKG2C- IE and PB –CTL samples was preformed at the Functional Genomics Facility, University of Chicago. Briefly, 10ug of total RNA, extracted using the RNeasy Mini kit (Qiagen, Valencia, CA), was used to generate double-stranded cDNA using a T7 linked oligo dT primer and the Superscript II RT system (Invitrogen Carlsbad CA). Purified cDNA was then used to generate biotin-labeled cRNA using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY) according to the manufacturers protocol. This biotinylated-cRNA was then fragmented and hybridized to an Affymetrix GeneChip HG-U133. The arrays were then washed and stained with phycoerythrin-conjugated streptavidin according to the Affymetrix GeneChip protocol and scanned using the Affymetrix Agilent GeneArray Scanner (Affymetrix, Santa Clara CA). Data analyses were preformed using DNA-Chip Analyzer 1.3 (dChip) with the *.CEL files obtained from GeneChip Operating System 1.3 (GCOS 1.3). A PM-only model was used to estimate gene expression level and the invariant set approach was used for normalization. For comparison analyses of the paired NKG2C+ and NKG2C- populations, thresholds for selecting significant genes were set at a relative difference > 1.5 fold, absolute difference > 100 and a significant paired t-test for the signal intensity difference at p < 0.05. Duplicate genes and genes of unknown function were removed. The remaining genes were then grouped based on function and cluster analysis was preformed using dChip.

first: Cezary

last: Ciszewski

first: Shane

last: Curran

first: Bertrand

last: Meresse


title: PCOS patients vs control subjects

status: Public on Jun 17 2006

city: MADRID

first: BELEN

last: PERAL

state: MADRID

address: ARTURO DUPERIER

country: Spain

institute: INSTITUTO DE INVESTIGACIONES BIOMEDICAS, CSIC-UAM

summary:
This experiment was designed to study if there are differences in gene expression in the adipose tissue of women affected by polycystic ovary syndrome (PCOS) compared to non-hyperandrogenic women. PCOS is the most common endocrinopathy in women of reproductive age, and is characterized by hyperandrogenism and chronic anovulation. This disease is frequently associated with obesity, insulin resistance, and defects in insulin secretion, predisposing these women to type 2 diabetes, atherosclerosis, and cardiovascular disease.

We have applied high-density oligonucleotide arrays to omental adipose tissue samples obtained from eight morbidly obese PCOS patients and seven morbidly obese non-PCOS women at the time of bariatric surgery.
Keywords: Disease state analysis

overall_design: We have compared the omental adipose tissue of eight PCOS patients with the same tissue in seven control women without PCOS. All of them are morbidly obese subjects. We also have included two replicates, one biological and one technical.

first: MARTA

last: CORTÓN

first: ALBERTO

last: BENGURIA

first: JOSE

last: SAN MILLÁN

last: BOTELLA-CARRETERO

first: HÉCTOR

last: ESCOBAR-MORREALE

first: BELÉN


title: Time course microarray data following GR activation in MCF10A-Myc breast cells

status: Public on Jun 02 2006

first: Suzanne

middle: Daniela

last: Conzen

address: 5841 S. Maryland Ave, SBRI J301, MC 2115

institute: The University of Chicago

summary:
This series contain time course microarray data from MCF10A-Myc cells treated with either ethanol or Dexamethasone for 30 min, 2 hr, 4 hr, and 24 hr. This series contains three biological replicates that were analyzed as independent replicate experiments (data were normalized within each replicate experiment, not across all samples).
Keywords: time course

overall_design: MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with either vehicle (ethanol) or Dex (10-6 M) for 0.5, 2, 4 or 24 hrs.  Total RNA from each sample was extracted using Qiagen’s RNeasy Kit.  Preparation of biotinylated cRNA and hybridization to oligonucleotide arrays (Affymetrix human genome genechip HG-U133A) were performed at the University of Chicago Microarray Core Facility.  HG-U133A genechip contains 22,215 probe sets that represent approximately 16,000 human genes.  The complete procedure was repeated independently three times.  Gene chips were scanned and analyzed using Robust Multi-array Average (RMA) algorithm.

first: Zou

last: Min

first: Wei

last: Wu

first: Deanna

last: Brickley

first: Travis

last: Pew


title: Cockayne syndrome (CSB) fibroblasts

status: Public on Jul 14 2006

city: Seattle

first: John

middle: C

last: Newman

state: WA

address: 1959 NE Pacific St.

department: Biochemistry

institute: University of Washington

summary:
Cockayne syndrome (CS) is an inherited neurodevelopmental disorder with progeroid features. Although the genes responsible for CS have been implicated in a variety of DNA repair- and transcription-related pathways, the nature of the molecular defect in CS remains mysterious. We sought to define this defect by expression analysis of cells lacking functional CSB, a SWI/SNF-like ATPase that is responsible for most CS cases.
Keywords: primary disease rescue

overall_design: Primary Cockayne fibroblasts (GM00739B) were immortalized with hTERT and rescued with expression of wt CSB cDNA (CSB-wt), ATPase mutant (K538R) CSB (CSB-mut), or eGFP as a negative control (CSB-null). Biological replicates represent independent RNA isolation and target synthesis from a cell line; three were performed for CSB-wt and CSB-null, and two for CSB-mut.

first: Arnold

last: Bailey

first: Alan

last: Weiner


title: A673 inducible-rescue experiment

city: Salt Lake City

first: Stephen

last: Lessnick

state: UT

address: 2000 Circle of Hope

department: Center for Children

institute: Huntsman Cancer Institute

summary:
A673 Ewing's sarcoma cells, with inducible EWS/FLI cDNA, harboring the EF-2-RNAi retrovirus, induced (or uninduced) for the indicated time period.
Keywords: time course

overall_design: Two replicates of a time course series, including the indicated time points, including both induced and uninduced samples.

first: Richard

last: Smith

first: Leah

last: Owen

first: Deborah

last: Trem

first: Jenny

middle: S

last: Wong

first: Jennifer

last: Whangbo

first: Todd

last: Golub


title: A673 Ewing's sarcoma cells: stable-knockdown and inducible-rescue time course experiments

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

overall_design: Refer to individual Series


title: Sphingosine 1-phosphate effect on glioblastoma cells in vitro

status: Public on May 13 2006

first: Chris

last: McCabe

address: 2430 N Halsted

department: Neurobiology

institute: Children's Memorial Hospital

summary:
Abstract

Background
Sphingosine 1-phosphate (S1P), a lysophospholipid, is involved in various cellular processes such as migration, proliferation, and survival. To date, the impact of S1P on human glioblastoma is not fully understood. Particularly, the concerted role played by matrix metalloproteinases (MMP) and S1P in aggressive tumor behavior and angiogenesis remains to be elucidated.

Results
To gain new insights in the effect of S1P on angiogenesis and invasion of this type of malignant tumor, we used microarrays to investigate the gene expression in glioblastoma as a response to S1P administration in vitro. We compared the expression profiles for the same cell lines under the influence of epidermal growth factor (EGF), an important growth factor. We found a set of 72 genes that are significantly differentially expressed as a unique response to S1P. Based on the result of mining full-text articles from 20 scientific journals in the field of cancer research published over a period of five years, we inferred gene-gene interaction networks for these 72 differentially expressed genes. Among the generated networks, we identified a particularly interesting one. It describes a cascading event, triggered by S1P, leading to the transactivation of MMP-9 via neuregulin-1 (NRG-1), vascular endothelial growth factor (VEGF), and the urokinase-type plasminogen activator (uPA). This interaction network has the potential to shed new light on our understanding of the role played by MMP-9 in invasive glioblastomas.

Conclusions
Automated extraction of information from biological literature promises to play an increasingly important role in biological knowledge discovery. This is particularly true for high-throughput approaches, such as microarrays, and for combining and integrating data from different sources. Mining full-text articles, as opposed to abstracts only, may hold the key to unraveling previously unknown relationships between biological entities and could develop into an indispensable instrument in the process of formulating novel and potentially promising hypotheses.
Keywords: Sphingosine 1-phosphate treatment, glioblastoma, epidermal growth factor

first: James

last: Van Brocklyn

first: Eric

middle: G

last: Bremer


title: A673 Stable-Knockdown

summary:
A673 Ewing's sarcoma cells containing either control RNAi retroviral constructs (luc-RNAi), or RNAi retroviral constructs targeting the endogenous EWS/FLI fusion transcript (either EF-2-RNAi or EF-4-RNAi).
Keywords: Expression analysis of RNAi knockdown of endogenous EWS/FLI

overall_design: Eight samples total.  Four luc-RNAi, and four EWS/FLI knockdown constructs (two each of EF-2-RNAi or EF-4-RNAi).


title: Effect of GPI-PLD on global gene expression in HepG2 cells

city: Indianapolis

first: Matthew

last: Grow

state: IN

department: Biochemistry and Molecular Biology

institute: Indiana University

summary:
A time course of the effect of overexpressing GPI-PLD on global gene expression in HepG2 cells was compared to control virus.
Keywords: Expression profiling

overall_design: This experiment compares the global gene expression in HepG2 cells that were either transduced with an adenovirus expressing GPI-phospholipase D or an adenovirus expressing beta galactosidase as a control.  Treatment was for 6 or 12 hrs.  Four replicates for each condition were used.  10 micrograms of total RNA was assayed per genechip using standard Affymetrix protocols.

first: Mark

last: Deeg

first: Nandita

last: Raikwar


title: Effects of metoprolol and nebivolol on gene expresion in human coronary smooth muscle cells

status: Public on May 01 2006

city: Tuebingen

first: Bernhard

middle: R.

last: Brehm

address: Otfried-Mueller-Str. 10

institute: University of Tuebingen

summary:
Human coronary smooth muscle cells were treated with two different ß-blocker (metoprolol and nebivolol). RNA from three replicates of each, treated and the untreated control group, were isolated and the expression profiles were determined using Affymetrix Human Genechip U133A arrays.  Comparisons between the sample groups allow the identification of genes with different expression patterns between the treated and untreated control cells.
Keywords: atherosclerosis, smooth muscle cell, ß-receptor antagonist, inflammation, microarray, nebivolol

overall_design: 3 replicates of control cells (untreated), 3 replicates of metoprolol treated cells and 3 replicates of nebivolol treated cells  were analyzed

first: Gabriele

last: Sauter

first: Sabine

last: Wolf

first: Teut

last: Risler

first: Jürgen

last: Jobst


title: Expression data from MOLT4 human cell line

status: Public on Jun 22 2006

city: Stockholm

first: Ali

last: Moshfegh

department: Oncology and Pathology

country: Sweden

institute: Karolinska Institutet

summary:
To compare The pattern of Gene expression by 7-hydroxymethotrexate-resistant human leukemia cells reveals changes designed to preserve intracellular levels of folate and nucleotide biosynthesis
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.
Keywords: Resistant and non-resistant MOLT4 cell lines

overall_design: Treatment of human T-cell leukemia lines to the major plasma metabolite of methotrexate (MTX), 7-hydroxymethotrexate (7-OHMTX), resulted in an acquired resistance as a results of complete loss of folypolyglutamate synthetase (FPGS) activity. To identify the genes associated with MTX and 7-OHMTX resistance, we analyzed the patterns of gene expression profiles by leukemia sublines and compared with parent cells.

first: Kambiz

last: Fotoohi

first: Freidoun

last: Albertioni


title: Genetic Reclassification of Histologic Grade Delineates New Clinical Subtypes of Breast Cancer

status: Public on May 31 2006

city: Singapore

first: Lance

middle: David

last: Miller

address: 60 Bioplois Street, #02-01 Genome

department: Microarray and Expression Genomics

country: Singapore

institute: Genome Institute of Singapore

summary:
Histological grading of breast cancer defines morphological subtypes informative of metastatic potential, although not without considerable inter-observer disagreement and clinical heterogeneity particularly among the moderately differentiated grade II (G2) tumors. We posited that a gene expression signature capable of discerning tumors of grade I (G1) and grade III (G3) histology might provide a more objective measure of grade with prognostic benefit for patients with moderately differentiated disease. To this end, we studied the expression profiles of 347 primary invasive breast tumors analyzed on Affymetrix microarrays. Using class prediction algorithms, we identified 264 robust grade-associated markers, six of which could accurately classify G1 and G3 tumors, and separate G2 tumors into two highly discriminant classes (termed G2a and G2b genetic grades) with patient survival outcomes highly similar to those with G1 and G3 histology, respectively. Statistical analysis of conventional clinical variables further distinguished G2a and G2b subtypes from each other, but also from histologic G1 and G3 tumors. In multivariate analyses, genetic grade was consistently found to be an independent prognostic indicator of disease recurrence comparable to that of lymph node status and tumor size. When incorporated into the Nottingham Prognostic Index, genetic grade enhanced detection of patients with less harmful tumors, likely to benefit little from adjuvant therapy. Our findings show that a genetic grade signature can improve prognosis and therapeutic planning for breast cancer patients, and support the view that low and high grade disease, as defined genetically, reflect independent pathobiological entities rather than a continuum of cancer progression. Three separate breast cancer cohorts were analyzed: 1) Uppsala (n=249), 2) Stockholm (n=58), 3) Singapore (n=40). The Uppsala and Singapore data can be accessed here. The Stockholm cohort data can be accessed at GEO Series GSE1456.
Keywords: Tumor sample comparisons

overall_design: All tumor specimens were assessed on U133 A and B arrays.

first: Anna

middle: V

last: Ivshina

first: Joshy

last: George

first: Oleg

last: Senko

first: Benjamin

last: Mow

first: Thomas

last: Putti

first: Johanna

last: Smeds

last: Lindahl

first: Yudi

last: Pawitan

first: Per

last: Hall

first: Hans

last: Nordgren

first: John

last: Wong

first: Edison

last: Liu

first: Jonas

last: Bergh

first: Vladimir

last: Kuznetsov

middle: D


title: Distinct Transcription Profiles of Primary and Secondary Glioblastomas

status: Public on Jun 20 2006

city: Los Angeles

first: Cho-Lea

last: Tso

address: 10833 Le Conte Avenue

department: Surgery

institute: University of California, Los Angeles

summary:
Gene expression data of primary and secondary glioblastoma subgroups.
Keywords: glioblastoma, transcription profiles

overall_design: Total RNA was extracted from eighty-three glioblastoma biopsies in total. Probes were synthesized using the commercial Affymetrix kits and hybridized onto U133A Arrays.

first: William

middle: A

last: Freije

first: Allen

last: Day

first: Zugen

last: Chen

first: Barry

last: Merriman

first: Ally

last: Perlina

first: Yohan

last: Lee

first: Ederlyn

middle: Q

last: Dia

first: Koji

last: Yoshimoto

first: Paul

last: Mischel

first: Linda

last: Liau

first: Timothy

last: Cloughesy

first: Stanley

last: Nelson


title: Analysis of target genes induced by the Amyloid Precursor Protein Intracellular Domain

city: Muenster

first: Thorsten

last: Mueller

address: Domgakstr. 19

department: University Hospital Muenster

institute: Institute of Neuropathology

summary:
The amyloid precursor protein (APP) plays a central role in the pathogenesis of Alzheimer’s disease (AD). Processing of APP by β- and γ-secretase activities results in the production of ß-amyloid (Aß), the main constituent of Alzheimer plaques, but also in the generation of the APP intracellular domain (AICD). Recently, it has been demonstrated that AICD has transactivation potential, however, the targets of AICD dependent gene regulation and hence the physiological role of AICD remain largely unknown. In this work we analysed transcriptome changes during AICD dependent gene regulation using a human neural cell culture system inducible for expression of AICD, its co-activator Fe65, or the combination of both. Induction of AICD was associated with increased expression of genes with known function in the organization and dynamics of the actin cytoskeleton as well as genes involved in the regulation of apoptosis.
Keywords: (Tet-Off)

overall_design: Inducible cell culture system

last: Müller

first: Caoimhin

last: Concannon

first: Manus

last: Ward

first: Donat

last: Kögel

first: Jochen

last: Prehn

first: Rupert

last: Egensperger


title: Endothelial Cell Morphogenesis

status: Public on Apr 08 2006

city: Argonne

first: suneeta

last: mandava

address: 9700 S Cass ave

department: Bio

institute: Argonne National Lab

summary:
Human microvascular endothelial cells were stimulated to either proliferate or undergo tubulogenesis over an 8 hour time period.
Keywords: Time Series

overall_design: 5 timepoints for each time series were assayed

first: David

last: Glesne

first: Diane

middle: J

last: Rodi


title: Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling

status: Public on Apr 27 2006

city: Pullman

first: Ajin

last: Mandaokar

address: 447, Clark hall

department: Institute of Biological Chemistry

institute: Washington State University

summary:
In Arabidopsis, jasmonate is required for stamen and pollen maturation.  Mutants deficient in jasmonate synthesis, such as opr3, are male-sterile but become fertile when jasmonate is applied to developing flower buds. We have used ATH1 oligonucleotide arrays to follow gene expression in opr3 stamens for 22 hours following jasmonate treatment.  In these experiments, a total of 821 genes were specifically induced by jasmonate and 480 repressed.  Comparisons with data from previous studies indicate that these genes constitute a stamen-specific jasmonate transcriptome, with a large proportion (70%) of the genes expressed in the sporophytic tissue but not in the pollen.  Bioinformatics tools allowed us to associate many of the induced genes with metabolic pathways that are likely up-regulated during jasmonate-induced maturation.  Our pathway analysis led to the identification of specific genes within larger families of homologues that apparently encode stamen-specific isozymes.  Extensive additional analysis of our dataset identified 13 transcription factors that may be key regulators of the stamen maturation processes triggered by jasmonate.  Two of these transcription factors, MYB21 and MYB24, are the only members of subgroup 19 of the R2R3 family of MYB proteins.  A myb21 mutant obtained by reverse genetics exhibited shorter anther filaments, delayed anther dehiscence and greatly reduced male fertility.  A myb24 mutant was phenotypically wild type, but production of a myb21 myb24 double mutant indicated that introduction of the myb24 mutation exacerbated all three aspects of the myb21 phenotype.  Exogenous jasmonate could not restore fertility to myb21 or myb21 myb24 mutant plants.  Together with the data from transcriptional profiling, these results indicate that MYB21 and MYB24 are induced by jasmonate and mediate important aspects of the jasmonate response during stamen development.
Keywords: Time course analysis

overall_design: Three replicates for opr3 at each time point of 0 hour, 30 minutes, 2 hours, 8 hours and 22 hourss of either JA or OPDA treatment. One replicate of wild-type stamens

first: Bryan

last: Thines

first: Byongchul

last: Shin

first: Markus

last: Lange

first: Goh

last: Choi

first: Yeonjong

last: Koo

first: Yungjoon

last: Yoo

first: Yangdo

first: Giltsu

first: John

last: Browse


title: Expression data from hormone-starved MCF7/BUS cell culture

status: Public on Apr 14 2006

city: Charlestown

first: Kathryn

last: Coser

address: Blg 149 13th St

department: DNA Microarray Core

institute: Mass General Hospital Cancer Center

summary:
To obtain comprehensive information on 17beta-estradiol (E2) sensitivity of genes that are inducible or suppressible by this hormone, we designed a method that determines ligand sensitivities of large numbers of genes using DNA microarray and a set of simple Perl computer scripts implementing the standard metric statistics, and employed it to characterize effects of low (0-100 pM) concentrations of E2 on the transcriptome profile of MCF7/BUS human breast cancer cells, whose E2 dose-dependent growth curve saturated with 100 pM E2. Evaluation of changes in mRNA expression for all genes covered by the DNA microarray indicated that, at a very low concentration (10 pM), E2 suppressed 3~5 times larger numbers of genes than it induced, whereas at higher concentrations (30-100 pM) it induced 1.5~2 times more genes than it suppressed. Using clearly defined statistical criteria, E2-inducible genes were categorized into several classes based on their E2 sensitivities. This approach of hormone sensitivity analysis revealed that expression of two previously reported E2-inducible autocrine growth factors, TGF-? and SDF-1, was not affected by 100 pM and lower concentrations of E2 but strongly enhanced by 10 nM E2, which was far higher than the concentration that saturated the E2 dose-dependent growth curve of MCF7/BUS cells. These observations suggested that biological actions of E2 are derived from expression of multiple genes whose E2 sensitivities differ significantly and, hence, dependent on the E2 concentration especially when it is lower than the saturating level, emphasizing the importance of characterizing the ligand dose-dependent aspects of E2 actions. (paper abstract)
Keywords: Dose Response, Time Course

overall_design:
MCF7/BUS cells were exposed to varying concentrations of 17beta-estradiol (E2) for 48 hours. Experiments were repeated five times independently.
In another experiment, MCF7/BUS cells were subjected to hormone starvation. At day 0, 1, and 2, RNA samples were isolated from cell culture. Experiments were repeated three times independently.


title: Profiling of MCF-7 cell lines stably overexpressing (ca)Raf-1, (ca)MEK, (ca)erbB-2, or ligand-activatable EGFR.

status: Public on Apr 06 2006

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
Profiling of MCF-7 cell lines stably overexpressing constitutively active Raf-1, constitutively active MEK, constitutively active c-erbB-2, or ligand-activatable EGFR as models of overexpressed growth factor signaling, as well as control vector transfected cells (coMCF-7) and control vector transfected cells long-term adapted for estrogen-independent growth (coMCF-7/lt-E2).
Keywords: Cell Line Comparison

overall_design: Cell lines were profiled in biological triplicates, 18 arrays in all.

first: Dorraya

last: El-Ashry


title: Nitric Oxide Activation of Erk Regulates the Stability and Translation of mRNA Transcripts Containing CU-Rich Elements

status: Public on Jul 27 2006

city: Bethesda

first: Shuibang

last: Wang

address: 10 Center Drive

department: Critical Care Medicine Dept

institute: Clinical Center

summary:
Nitric oxide (NO) can stabilize mRNA by activating p38 mitogen-activated protein kinase (MAPK). Here, transcript stabilization by NO was investigated in human THP-1 cells using microarrays. After LPS pre-stimulation, cells were treated with actinomycin D and then exposed to NO without or with the p38 MAPK inhibitor SB202190. The decay of 220 mRNAs was affected; most were stabilized by NO. Unexpectedly, SB202190 often enhanced rather than antagonized transcript stability. NO activated p38 MAPK and Erk1/2; SB202190 blocked p38 MAPK, but further activated Erk1/2. PCR confirmed that NO and SB202190 could additively stabilize mRNA, an effect abolished by Erk1/2 inhibition. In affected genes, these responses were associated with CU-rich elements (CURE) in 3' un-translated regions. NO stabilized the mRNA of a CURE-containing reporter gene, while repressing translation. Dominant-negative Mek1, an Erk1/2 inhibitor, abolished this effect. NO similarly stabilized, but blocked translation of MAP3K7IP2, a natural CURE-containing gene. NO increased hnRNP translocation to the cytoplasm and binding to CURE. Over-expression of hnRNP K, like NO, repressed translation of CURE-containing mRNA. These findings define a sequence-specific mechanism of NO-triggered gene regulation that stabilizes mRNA, but represses translation.
Keywords: time course and dose response

overall_design: THP-1 cells were first stimulated with LPS (1 µg/ml) for 4 h to boost transcript levels. After 30 min treatment with ActD (2.5 µg/ml), a transcription inhibitor, in the absence or presence of p38 MAPK inhibitor SB (0.1 µM), cells were then further incubated for 0-180 min with 400 µM of GSNO or GSH control (N = 4). Total RNA at different time points (0, 45, 90 and 180 min) was extracted, labeled and hybridized to human U133A microarrays, which were then scanned using Agilent GeneArray Scanner. Affymetrix MAS5 signal values were analyzed and first normalized to the 97th percentile, a value corresponding to the expression level of the 678th most intense probeset on the array.  This normalization strategy assumed that the most intense probesets corresponded to mRNA species which were most stable and were generally unaffected by the treatments studied here.  Then logarithmically transformed normalized data were subject to linear regression with respect to the 4 time points studied (0, 45, 90, 180 min following the start of incubation with GSH or GSNO), to estimate a slope corresponding to a first-order decay rate. The decay slope was calculated for each probeset, for each of the four conditions (GSH, GSNO, SB/GSH and SB/GSNO) using an Analysis of Covariance (ANCOVA), constraining the time 0 expression value to be identical for the pair of conditions without SB and the pair with SB, as necessitated by the design of the experiment.  Further, since the experiment was replicated in 4 distinct batches, a blocked ANCOVA was utilized. The analysis results were then used to select genes which decayed, and whose decay rate changed following treatment.  The p-value for a one-way, four level ANCOVA was calculated and used to compute a false discovery rate (FDR).  The probesets with the lowest p-values, corresponding to a FDR of 10%, were selected and annotated based on information presented by Affymetrix at the NetAffx web-site as of April 12, 2004.

first: Jianhua

last: Zhang

first: Stephanie

last: Theel

first: Jennifer

last: Barb

first: Peter

last: Munson

first: Robert

last: Danner


title: Periodontal regeneration study

status: Public on Apr 13 2006

city: Potomac Falls

first: Agnieszka

middle: Maria

last: Lichanska

institute: Tessarae, LLC

summary:
Periodontal regeneration study.
Periodontitis is a common chronic inflammatory disease which may lead to tooth loss. The ultimate goal of periodontal therapy is complete regeneration of the tissues lost as a result of periodontitis. However, most regenerative clinical procedures are unpredictable, largely because there is a lack of understanding of how the various tissues comprising the periodontium (gingival epithelium, gingival connective tissue, periodontal ligament, aveolar bone and cementum) interact during the regenerative process.
The aim of this study was to investigate the molecular mechanisms that are involved in periodontal regeneration. For this purpose, paired sets of gingival, ligament and regenerating cells were isolated from patients that have been treated for periodontitis via a regenerative surgical procedure. A microarray analysis using the Hu133A Affymetrix arrays was used to identify the genes and pathways that were characteristic of the three different tissues. We have identified over 500 transcripts in global comparison and intrapatient comparisons that were differentially expressed between ligament and gingival samples, and approximately 30 transcripts that characterized the regenerating cell population. By using a functional classification based on Gene Ontology we were able to group the transcripts into 12 groups. Proteases/Protease inhibitors were differentially expressed between the ligament and gingiva highlighting high ECM remodelling activity by gingival cells. On the other hand, ligament cells were shown to have increased protein synthesis by increasing their nucleolar and ribosomal gene complement. We were able to identify 57 various DNA binding proteins, among them were some well characterised transcription factors, transcriptional regulators, including DNA polymerases and transcriptional co-activators. Furthermore, we have also identified changes in expression of their targets in the two tissues.
This is the first study to characterise the gene expression profile of periodontal regenerating cells and allowed us to gain valuable insights into the cellular and molecular mechanisms that occur during the regenerative process. We have identified signalling pathways which are consistent with clinical observations of the regenerative properties of gingival and periodontal ligament cells. These pathways provide candidate targets that can be manipulated in order to achieve a superior regenerative clinical outcome.
Keywords: other

first: Saso

last: Ivanovski

first: Elisabetta

last: d'Aniello

first: Michael

last: Waters


title: Variations in gene expression among different types of human skeletal muscle

city: Boston

last: Kang

address: 300 Longwood Avenue

institute: Children's Hospital Boston

summary:
There is a consistent variation in the response of different skeletal muscle groups to mutations in genes known to cause muscular dystrophy, yet these muscles appear histologically similar. To better understand these phenotypic differences, we analyzed gene expression patterns in control muscle specimens obtained from four sites at autopsy: deltoid, quadriceps, gastrocnemius, and tibialis anterior (TA). A total of 35 muscle samples from nine individuals (four pediatric and five geriatric) were studied. Factors potentially influencing gene expression in the different samples included individuality, age, muscle type, gender, cause of death, postmortem interval, and ethnicity. The first three factors, in decreasing order, were found to have a significant impact on the stratification of muscle specimens. A novel analytic method, using a second round of normalization, was used to elicit differences between muscle types. This approach may be extended to a broader survey, potentially elucidating a molecular classification of the skeletal muscles.
Keywords: anatomic comparison of different human skeletal muscles

overall_design: Skeletal muscles obtained at autopsy from 35 muscles, representing 9 individuals and 4 muscle types.  RNA targets generated and run on Affymetrix U133A and U133B GeneChips.

middle: B

first: Alvin

middle: T

last: Kho

first: Despina

last: Sanoudou

first: Judith

middle: N

last: Haslett

middle: P

last: Dow

first: Mei

last: Han

first: Jessica

last: Blasko

first: Hart

last: Lidov

first: Alan

middle: H

last: Beggs

first: Louis

last: Kunkel


title: Differential redulation of gene expression by an RTI SARM and canonical agonist of androgen receptor

status: Public on Apr 11 2006

city: Palo Alto

first: Dmitri

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary:
We have previously identified a family of novel androgen receptor (AR) ligands that, upon binding, enable AR to adopt structures distinct from that observed in the presence of canonical agonists. In this report, we describe the use of these compounds to establish a relationship between AR structure and biological activity with a view to defining a rational approach with which to identify useful Selective Androgen Receptor Modulators (SARMs). As one of the approaches, we used a DNA microarray analysis to demonstrate that differently conformed receptors facilitate distinct patterns of gene expression in LNCaP cells. Interestingly, we observed a complete overlap in the identity of genes expressed following treatment with mechanistically distinct AR ligands. However, it was differences in the kinetics of gene regulation that distinguished these compounds. Follow-up studies, in cell-based assays of AR action, confirmed the importance of these alterations in gene expression. Together these studies demonstrate an important link between AR structure, gene expression and biological outcome.
Keywords: Comparative gene expression analysis, cell culture, prostate carcinoma, androgen receptor, selective modulators of androgen receptor, SARM

overall_design:
In this experiment LNCaP cells (400,000 per 75 cm2 flask) were first incubated in DMEM/8% charcoal-stripped serum to reduce the background hormone exposure, and then were treated with Vehicle (ethanol), DHT (10 nM) or RTI-6413-018 (100 nM). Treatment was done for 6 and 24 hrs. At the end of treatment, cells were collected by trypsization and immediately frozen in liquid nitrogen. Isolation of mRNA was performed using Qiagen Oligotex midi kit. cRNA synthesis, labeling and hybridization were performed by Expression Analysis Institute, Durham, NC. Samples were hybridized to Affymetrix HG.U133 A and B chips.
The entire experiment was repeated 3 times.

first: Donald

last: McDonnell


title: The effect of moderate hypothermia on gene expression by THP-1 cells

status: Public on Apr 05 2006

city: Richmond

first: Larry

middle: A.

last: Sonna

address: 2020-I Timbers Hill Road

institute: Gene Expression Consulting

summary:
Background:  Moderate hypothermia (32oC for 12 – 72 hours) has therapeutic applications, but the mechanisms by which it affects cellular function are unclear.  We tested the hypothesis that moderate hypothermia produces broad changes in gene expression by human cells at the level of mRNA.
Methods:  Acute monocytic leukemia THP-1 cells were incubated under control conditions (37oC) or moderate hypothermia (32oC) for 24 hours.  Cellular mRNA was extracted and a cold stress response was confirmed by examining the expression of the cold-inducible gene CIRBP by reverse transcription PCR (RT-PCR).  Gene expression analysis was performed on seven sets of samples with Affymetrix U133A chips, using established statistical methods.  Sequences were considered to be affected by cold if they showed statistically significant changes in expression and also met published post-hoc filter criteria (changes in geometric mean expression of 2-fold or greater and detection calls of “present” or “marginal” in at least half of the experiments).  The changes in expression of a select number of these sequences were further confirmed by PCR.
Results:  167 sequences met our prospectively defined criteria for a change in expression; 67 showed increases in expression and 100 showed decreases in expression.  Consistent with prior literature, the cold-inducible genes CIRBP and RBM3 showed increases in expression.  Functional categories affected by cold stress included genes involved in immune responses, cell growth, proliferation, and differentiation, and metabolism and biosynthesis.  Several heat shock proteins (HSPs) showed decreases in expression.
Conclusions:  Moderate hypothermia produces substantial changes in cellular gene expression, in categories potentially of importance to systemic function.  Interestingly, cold exposure without re-warming decreased the expression of several HSPs.  Our in vitro findings suggest that moderate hypothermia in vivo might produce physiologically important changes in gene expression by circulating leukocytes.
Keywords: Stress response / hypothermia

overall_design: Seven sets of paired THP-1 samples, grown under either control (37oC) or hypothermic (32oC) conditions for 24 hours

first: Matthew

middle: M

last: Kuhlmeier

first: Heather

last: Carter

first: Jeffrey

last: Hasday

first: Craig

last: Lilly

first: Karen

last: Fairchild


title: Gene expression signatures for predicting prognosis of squamous cell lung carcinomas

status: Public on Mar 30 2006

city: San Diego

first: Jack

last: Yu

address: 3210 Merryfield Row

institute: Veridex, LLC

summary:
Gene signatures were derived to separate high risk patients from low risk ones..
Keywords: prognosis analysis

overall_design: 130 samples from 129 patients


title: First bone marrow relapse with or without initial diagnosis

status: Public on Mar 20 2006

city: New York

first: Deepa

last: Bhojwani

state: NY

address: Smilow Research Building 1206-B, 522 First Avenue

department: Pediatric Hematology Oncology

institute: New York University School of Medicine

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

overall_design: Refer to individual Series

first: William

middle: L

last: Carroll


title: Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas.

city: Zürich

first: Keith

middle: S

last: Hoek

address: private

institute: Currently unaffilliated

summary:
Affymetrix oligonucleotide microarrays were used to assess global differential gene expression comparing normal human melanocytes with six independent melanoma cell strains from advanced lesions. The data, validated at the protein level for selected genes, confirmed the overexpression in melanoma cells relative to normal melanocytes of several genes in the growth factor/receptor family that confer growth advantage and metastasis. In addition, novel pathways and patterns of associated expression in melanoma cells not reported before emerged.
Keywords: class comparison study (melanoma vs melanocyte)

overall_design: Six melanoma cultures and two melanocyte cultures.  The melanoma cultures are considered, for the purposes of this investigation, replicates from the point of view that they are all melanomas.

first: David

last: Rimm

first: Kenneth

middle: R

last: Williams

first: Hongyu

last: Zhao

first: Stephan

last: Ariyan

first: Aiping

last: Lin

first: Harriet

last: Kluger

first: Aaron

last: Berger

first: Elaine

last: Cheng

first: Sergio

last: Trombetta

first: Terence

last: Wu

first: Michio

last: Niinobe

first: Kazuaki

last: Yoshikawa

first: Gregory

middle: E

last: Hannigan

first: Ruth

last: Halaban


title: 35 patients at diagnosis and relapse

first: Deepa

last: Bhojwani

summary:
35 paired samples from initial diagnosis and first marrow relapse. Genes and pathways differentiating diagnosis and relapse were identified. Potential therapeutic targets were also identified.
Keywords: paired

overall_design: 35 patients with samples from initial diagnosis and first marrow relapse.


title: 60 samples obtained at relapse

summary:
Gene expression profiles were analyzed from 60 children with first bone marrow relapse. Genes and pathways differentiating early vs. late relapse were identified. Signatures predicting early response to therapy were also identified.
Keywords: ordered

overall_design: 60 patients at relapse were analyzed

first: William

last: Carroll


title: Constitutive expression of misfolded surfactant protein C

city: Cincinnati

first: James

middle: Patrick

last: Bridges

state: OH

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

summary:
Mutations in the gene encoding surfactant protein C (SFTPC) have been linked to interstitial lung disease in children and adults.  Expression of the index mutation, SP-Cdeltaexon4, in transiently transfected cells and type II cells of transgenic mice resulted in misfolding of the proprotein, activation of ER stress pathways and cytotoxicity.  In the current study we show that stably transfected cells adapted to chronic ER stress imposed by constitutive expression of SP-Cdeltaexon4 via an NF-kB-dependent pathway.  However, infection of cells expressing SP-Cdeltaexon4 with respiratory syncytial virus resulted in significantly enhanced cytotoxicity associated with accumulation of the mutant proprotein, pronounced activation of the unfolded protein response and cell death.  Adaptation to chronic ER stress imposed by misfolded SP-C was associated with increased susceptibility to viral-induced cell death.  The wide variability in the age of onset of ILD in patients with SFTPC mutations may be related to exposure to an environmental insult that ultimately overwhelms the homeostatic, cytoprotective response.
Keywords: transcriptional response to misfolded protein due to genetic modification

overall_design: samples consisted of HEK293 cells stably transfected with wild-type SP-C (WT), the delta exon4 mutant of SP-C (Exon4) or empty vector (EVcontrol).  Groups were performed in triplicate.

first: Yan

last: Xu

first: Cheng-Lun

first: Hector

last: Wong

first: Timothy

last: Weaver


title: Leukotriene D4- and Thrombin-Triggered Transcriptomes in Human Umbilical Vein Endothelial Cells

status: Public on Mar 14 2006

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

institute: Ludwig Maximilians Universität München

summary:
Cysteinyl leukotrienes (cysLT), i.e. LTC4, LTD4, and LTE4, are lipid mediators derived from the 5-lipoxygenase pathway. The cysLT receptors cysLT1-R and cysLT2-R are expressed on different target cells and mediate inflammatory reactions in tissue- and LT-R-specific ways. Though endothelial cells (ECs) predominantly express cysLT2-Rs, their role in vascular biology remains to be defined. To delineate cysLT2-R´s action, we stimulated human umbilical vein EC with 100 nM LTD4 for 60 min, determined gene signatures by microarrays, and characterized the resulting EC phenotypes. As controls, we compared LTD4-induced genes with those induced by 10 nM thrombin, a prototype vasoactive activator of EC that binds to protease-activated receptor 1 (PAR-1). Following application of stringent filters 37 LTD4-upregulated genes were identified (> 2.5fold stimulation). Surprisingly, most of the LTD4-regulated genes were also induced by thrombin and expression of cysLT2-R- and PAR-1-regulated genes strongly correlated (Pearson correlation coefficient: r = 0.90). Moreover, LTD4 + thrombin, when added together, augmented expression of LTD4- or thrombin-stimulated genes (Wilcoxon signed rank test: p < 0.01). Prominently induced genes that may play roles in vascular injury were studied in detail: Early growth response (EGR) and nuclear receptor subfamily 4 group A; E-selectin; CXC ligand 2; interleukin 8 (IL-8); a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif 1 (ADAMTS-1); and tissue factor (TF). Transcripts of these genes peaked at approximately 60 min, were unaffected by the cysLT1-R antagonist montelukast, and were superinduced by cycloheximide. The EC phenotype was markedly altered: LTD4 induced de novo synthesis of EGR1 protein and EGR1 localized in the nucleus in LTD4-stimulated cells; LTD4 upregulated IL-8 formation and secretion; and LTD4 raised TF protein and TF-dependent EC pro-coagulant activity. These data show that cysLT2-R activation results in a pro-inflammatory EC phenotype through activation of immediate-early genes that resemble those induced by PAR-1. As LTD4 and thrombin are formed concomitantly during vascular injury and pro-thrombotic states, cysLT2-R and PAR-1 may collaborate in vivo to mediate vascular injury and repair.
Keywords: Leukotriene Transcriptome, Thrombin Transcriptome, HUVEC, Immediate-Early Gene Expression, Cysteinyl Leukotriene 2 Receptor Gene Signature in HUVEC

overall_design: HUVEC in passage 1 were cultured in serum-free EC medium until cells reached confluency. HUVEC were stimulated by 100 nM LTD4 (n = 4) or 10 nM thrombin (n = 4) or both agonists concomitantly (n = 3). The immediate-early gene programs of these experimental groups were identified at 60 minutes. In addition, one HUVEC preparation was stimulated with 100 nM LTD4 for 6 h and 24 h.


title: Ca2+-dependent Transcription Patterns in Human Cerebrovascular Smooth Muscle

status: Public on Mar 16 2006

city: Burlington

first: Anjanette

middle: D

last: Watson

state: VT

address: 120A Marsh Life Science

department: Bioinformatics Core

institute: University of Vermont

summary:
Altered Ca2+ handling has both immediate physiological effects and long-term genomic effects on vascular smooth muscle function.  Previously we have shown that elevation of cytoplasmic Ca2+ through voltage-dependent Ca2+ channels (VDCCs) or store-operated Ca2+ channels (SOCCs) results in phosphorylation of the Ca2+/cAMP response element binding protein (CREB) in cerebral arteries.  Here we demonstrate that stimulation of these different Ca2+ influx pathways results in transcriptional activation of a distinct, yet overlapping set of genes, and that the induction of selected CRE-regulated genes is prevented by the addition of corresponding Ca2+ channel blockers.  Using oligonucleotide array analysis, changes in mRNA levels were quantified following membrane depolarization with K+ or depletion of intracellular Ca2+ stores with thapsigargin in human cerebral vascular smooth muscle cells.  Array results for differentially regulated genes containing a CRE were confirmed by quantitative RT-PCR, and corresponding changes in protein expression were shown by Western blot analysis and immunofluorescence.  Membrane depolarization induced a transient increase in c-fos mRNA and a sustained increase in early growth response-1 (Egr-1) mRNA and protein that were inhibited by application of the VDCC blocker, nimodipine, and the SOCC inhibitor, 2-aminoethoxydiphenylborate (2-APB).  Thapsigargin induced a sustained increase in c-fos mRNA and MAP kinase phosphatase-1 (MKP-1) mRNA and protein, and these effects were decreased by 2-APB but not by nimodipine.  Our findings thus indicate that Ca2+ entry through VDCCs and SOCCs can differentially regulate CRE-containing genes in vascular smooth muscle and imply that signals involved in growth modulation are both temporally and spatially regulated by Ca2+.
Keywords: stress response

overall_design:
each of three experiments cell cultures were split three ways; one of the resulting samples was left untreated (C), another was treated with thapsigargin (TG), and the third was treated with elevated K+ (K).   The resulting nine samples were used for triplicate estimates of the response of each gene to TG and K treatments.
We tested the prospective hypothesis that genes having a CRE are differentially expressed after TG or K treatment using a permutation test: each of the 22,283 probe sets on the Affymetrix GeneChip was categorized two ways based on 1) whether or not it contains a CRE or not  .   Independence of CRE and threshold differential expression was rejected by Fisher’s exact test for both TG treatment ( ) and K treatment ( ).   Target genes (c-fos, egr-1, and mkp-1 ) were identified based on    ranking.

first: Karen

last: Lounsbury

first: Renee

middle: A

last: Pulver-Kaste

first: Christy

last: Barlow

first: Paul

last: Penar

first: Bruce

last: Tranmer

first: Jeffrey

last: Bond


title: Gene profiling of primary cultures from human prostate tumors

status: Public on Mar 09 2006

city: Roma

first: Antonella

last: Farsetti

address: Via delle Messi d'Oro 156

department: Centro Ricerca Sperimentale

country: Italy

institute: Istituto Regina Elena

summary:
The histopathological and molecular heterogeneity of prostate cancer and the limited availability of human tumor tissue make unraveling the mechanisms of prostate carcinogenesis a challenging task. Our goal was to develop an ex vivo model that could be reliably utilized to define a prognostic signature based on gene expression profiling of cell cultures that maintained the tumor phenotype. To this end, we derived epithelial cultures from tissue explanted from 59 patients undergoing radical prostatectomy or cistoprostatectomy because of Prostate Benign Hyperplasia/Prostate Cancer or Bladder Carcinoma. Patient selection criteria were absence of hormonal neo-adjuvant treatment before surgery and diagnosis of clinically localized disease. Using this unique experimental material we analyzed expression of 22.500 transcripts on the Affymetrix Human U133A Gene Chips platform. Cultures from normal/hyperplastic tissues with a prevalent luminal phenotype, and from normal prostate epithelial tissue with basal phenotype (PrEC) served as controls.
We have established a large number of prostate primary cultures highly enriched in the secretory phenotype. From them we derived an epithelial-restricted transcriptional signature that: 1) differentiated normal from tumor cells; and 2) clearly separated cancer derived lines into two distinct groups which correlated with indolent and aggressive clinical behavior of the disease.
Our findings provide:1) a method to expand human primary prostate carcinoma cells with a luminal phenotype; 2) a powerful experimental model to study primary prostate cancer biology; and 3) a novel  means to characterize these tumors from a molecular genetic standpoint for prognostic and/or predictive purposes.
Keywords: prostate cancer; gene profile; primary cultures; prognosis; molecular pathology.

overall_design: Gene expression profiling: normal versus PCa-derived cells. RNA was isolated from 22 tumor cultures and hybridized to U133A Affymetrix GeneChips arrays. Since cultures representing matched case controls could not be generated from normal prostate tissue adjacent or controlateral to the lesion, cultures derived from normal/hyperplastic tissues (N1, C10, C17, C16sx) with a prevalent luminal phenotype, and from normal prostate epithelial cells with the basal phenotype (PrEC) were used as controls.This analysis was performed using  30 samples (22 cancer-derived cultures, 4 from normal/hyperplastic tissues, 3 different batches of commercial PREC and 1 LNCAP).

first: Simona

last: Nanni

first: Carmen

last: Priolo

first: Annalisa

last: Grasselli

first: Manuela

last: D'Eletto

first: Roberta

last: Merola

first: Fabiola

last: Moretti

first: Michele

last: Gallucci

first: Piero

last: De Carli

first: Steno

last: Sentinelli

first: Anna

last: Cianciulli

first: Marcella

last: Mottolese

first: Paolo

last: Carlini

first: Diego

last: Arcelli

first: Mauro

last: Helmer-Citterich

first: Carlo

last: Gaetano

first: Massimo

last: Loda

first: Alfredo

last: Pontecorvi

first: Silvia

last: Bacchetti

first: Ada

last: Sacchi


title: Expression profiling of acute megakaryoblastic leukemia

city: Zurich

first: Jean-Pierre

last: Bourquin

address: Steinwiesstrasse 75

department: Pediatric Oncology

institute: University Children's Hospital Zurich

summary:
mononuclear cells were isolated on a density gradient and RNA extracted using Trizol and the Promega SV column RNA purification. Affymetrix U133A chips were hybridised using standard procedures at the core facility of Dana Farber Cancer Institute.
Keywords: disease state analysis

overall_design: This series includes samples of acute megakaryoblastic leukemia from 24 patients with Down Syndrome, 28 patients without Down Syndrome, 9 samples with acute myelomonocytic leukemia of patients without Down Syndrome, 8 samples from neonates with Down Syndrome and with transient myeloproliferative disease

first: Stuart

last: Orkin


title: A Modular Analysis of Breast Cancer Reveals a Novel Low-Grade Molecular Signature in Estrogen Receptor-Positive Tumors

status: Public on Feb 18 2006

city: Singapore

first: Kun

last: Yu

department: Cellular & Molecular Research

institute: National Cancer Centre

summary:
Primary human breast tumors were obtained from the National Cancer Centre of Singapore (NCC) Tissue Repository, after appropriate approvals from the NCC Repository and Ethics Committees. Profiled samples contained at least 50% tumor content.
Keywords = Gene expression
Keywords = Breast Cancer
Keywords: other

first: Patrick

last: Tan