title: Differential expression pattern in AICD resistent TReg vs. CD4+CD25high TReg cells

status: Public on Jun 15 2006

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
In this screen we compared cDNA from rTreg (AICD resistent TReg cells) against cDNA derived from all CD4+CD25hi Treg  for further molecular characterization of rTreg
Keywords: cell type comparison

overall_design: Single comparison of rTReg vs. TReg. We pooled rTreg-cDNA derived from FACS-sorted CD4+CD25hi Treg of eight healthy blood donors and performed gene chip microarray analysis.

first: Benedikt

last: Fritzsching

first: Nina

last: Oberle

first: Eva

last: Pauly

first: Jan

last: Buer

first: Johannes

last: Pöschl

first: Peter

middle: H

last: Krammer

first: Otwin

last: Linderkamp

first: Elisabeth

last: Suri-Payer


title: TGF-beta1 target genes in hematopoietic stem/progenitor cells and dendritic cells

status: Public on Jun 29 2006

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

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

overall_design: Refer to individual Series


title: TGF-beta1 target genes in human hematopoietic stem/progenitor cells.

summary:
CD34+ hematopoietic stem/progenitor cells were isolated from human cord blood and amplified in vitro for 10-14 days in serum-free medium with specific cytokines (Ju et al., Eur. J. Cell Biol. 82, 75-86, 2003; Hacker et al., Nat. Immunol. 4, 380-386, 2003). Cells were then treated with TGF-beta1 for various periods of time (2, 4, 16 hours) and RNA was prepared and subjected to microarray analysis.
Keywords: Response to cytokine treatment for various periods of time.

overall_design:
CD34+ hematopoietic stem/progenitor cells (HPC) were amplified in vitro and treated with TGF-beta1 (10 ng/ml) for 2, 4 and 16 hours.
HPC untreated
HPC + TGF-beta1 for 2 hours
HPC + TGF-beta1 for 4 hours
HPC + TGF-beta1 for 16 hours

first: Xing-Sheng

last: Ju

first: David

last: Ruau

first: Christiane

last: Becker


title: TGF-beta1 target genes in human dendritic cells (DC).

summary:
CD34+ hematopoietic stem/progenitor cells were isolated from human cord blood and amplified in vitro for 10-14 days in serum-free medium with specific cytokines (Ju et al., Eur. J. Cell Biol. 82, 75-86, 2003; Hacker et al., Nat. Immunol. 4, 380-386, 2003). Cultured progenitor cells were induced to differentiate into DC in RPMI medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 microM Beta-mercaptoethanol, 100 U/ml penicillin and streptomycin (GIBCO-BRL) and 500 U/ml GM-CSF, 500 U/ml IL-4 for 6 days with or without 10 ng/ml TGF-beta1 as indicated (0.5x10E6 cells/ml). Every 2 days growth factors were added and cells were maintained at 0.5x10E6 cells/ml cell density. RNA was prepared and subjected to microarray analysis.
Keywords: Response to cytokine treatment for various periods of time.

overall_design:
Dendritic cells (DC) were treated for various periods of time (4, 16 and 36 hours) with TGF-beta1 (10 ng/ml) or left untreated.
DC untreated
DC + TGF-beta1 for 4 hours
DC + TGF-beta1 for 16 hours
DC + TGF-beta1 for 36 hours


title: Total RNA from human venous blood from male and female probands

status: Public on Aug 12 2006

city: Muenster

last: Eisenacher

address: von-Esmarch-Str. 56

department: Integrierte Funktionelle Genomik (IFG)

summary:
The aim of the project was to explore the feasibility of gene expression profiles as a general diagnostic tool. Therefore the most frequently used and easy to use white blood cells have been profiled. We wanted to examinate, whether phenotypes created by organs different from blood cells have enough influence on these cells to allow the diagnosis of their presence. As a proof of principle we tried to identify surrogate markers for human sex (excluding markers on sex chromosomes).
Keywords: indirect phenotype classification, surrogate marker classification, genetic differences

overall_design: 14 HG-U95A and 9 HG-U95Av2 arrays have been hybridized with material from 5 male and 5 female probands with no known diseases; different number of replicates in the range 1 to 4 resulting into 12 experiments in the male group and 11 experiments in the female group.

first: Harald

last: Funke


title: Gene-expression profiling of HIV-1 infection and perinatal transmission in Botswana

status: Public on Jul 01 2006

city: Boston

first: Monty

last: Montano

state: MA

address: 650 Albany Street, Bldg X, room 640

department: Medicine

country: USA

institute: Boston Medical Center

summary:
We used Affymetrix U133A 2.0 chips to better understand transcriptional changes associated with HIV-1 infection and perinatal transmission in human PBMCS obtained from young adult mothers with infants in Botswana in vivo.
HIV seropositive and drug naïve samples:
GSM94333, GSM94334, GSM94335, GSM94336, GSM94337, GSM94338, GSM94340, GSM94342, GSM94343, GSM94345, GSM94351, GSM94353, GSM94354, GSM94355, GSM94357, GSM94358, GSM94360, GSM94361, GSM94362, GSM94364, GSM94365, GSM94367, GSM94369, GSM94370, GSM94378
HIV seronegative samples:
GSM92590, GSM92788, GSM92789, GSM92790, GSM92791, GSM92792, GSM92793, GSM92794, GSM92795, GSM92796, GSM92797, GSM92798, GSM92799, GSM92800, GSM92801, GSM92802, GSM92803, GSM92804, GSM92805, GSM92806
HIV seropositive transmitter mothers:
GSM94333, GSM94334, GSM94335, GSM94336, GSM94337, GSM94338, GSM94340, GSM94342, GSM94343, GSM94345, GSM94378
HIV seropositive nontransmitter mothers:
GSM94351, GSM94353, GSM94354, GSM94355, GSM94357, GSM94358, GSM94360, GSM94361, GSM94362, GSM94364, GSM94365, GSM94367, GSM94369, GSM94370
Keywords: Cross-sectional, peripheral host response to HIV-1 infection, transmission associated gene expression.

overall_design: Total RNA was extracted from peripheral blood and processed for microarray hybridizations that were conducted using U133A 2.0 chips (Affymetrix, Santa Clara, CA). The 22,777 gene-probes were filtered based on presence/absence, resulting in data for 11,705 gene-probes. The array data sets were then analyzed for differential expression based on HIV status (seronegative, seropositive) and transmitter status (transmitter: TR, nontransmitter: NTR) using BADGE version 1.0, a computer program implementing a Bayesian approach to identify differentially expressed genes (Sebastiani et al, Nat.Gen, 2005). Once differentially expressed genes were identified by BADGE, the biologically enriched categories were identified, as recently described (Montano et al, Int Immunol, 2006), by implementing a stand-alone version of the EASE statistical software (Hosack et al, Genome Biol., 2003). Selected genes were validated using realtime reverse transcription PCR.

first: Matthew

last: Rarick

first: Paola

last: Sebastiani

first: Patrick

last: Brinkmann

last: Russell

first: Alison

last: Navis

first: Carolyn

last: Wester

first: Ibou

last: Thior

first: Max

last: Essex


title: torre-affy-human-217240

status: Public on May 02 2006

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
This project will help us to have a more accurate and useful explanation at molecular level, of the damage  caused by HIV when it infects the central nervous sythem (CNS) in Humans. CNS dysfunction is an important cause of morbidity and mortality in patients with human immunodeficiency virus-I (HIV-1) infection and the acquired immunodeficiency virus syndrome (AIDS).  Minor cognitive/motor dysfunction (MCMD) and HIV-1-associated dementia (HAD) develop in the absence of opportunistic infections and lymphoma, cerebrovascular disease and metabolic disorders. Patients with HAD may or may not present  an associated HIV encephalitis with viral replication limited to cells of monocyte origin. The inflammatory infiltrates of HIVE include activated microglia and perivascular and parenchymal monocytes, multinucleated giant cells and lymphocytes. In addition, HIVE may be accompanied by significant loss of neurons, presynaptic terminals and abnormal dendrites.
To determine if altered expression of neuronal growth factor, chemokine and cell death genes identified possible mechanisms of brain injury in AIDS patients with and without HIVE
Changes of gene expression occurring in brain of AIDS patients with and without HIVE, induce development of brain atrophy, mild gliosis, enhanced vascular permeability, along with alterations in neuronal HIV-1 chemokine coreceptors. In the cases of HIVE more remarkable gene expression changes result in significant loss of neurons, presynaptic terminals and abnormal dendrites. All these changes can be evaluated by microarray gene expression analysis and validated by Q-RT-PCR
The procedure includes 10 steps: 1-Frontal Cortex dissection from fresh frozen autopsy human brain samples (fragments of 0.8-1 cm3 are used) 2-totalRNA extraction using RNeasy Maxi Kit and following hand book protocol; Quiagen Inc., 3-RNA quantity determination using the NanoDrop ND-1000 UV-Vis Spectrophotometer: Nanodrop-Technologies 4-RNA quality analyzed by ribosomal fractions 28s/18s ratio, using  by Agilent RNA 6000 Assay Microchips: Agilent Technologies 5-mRNA suitability by RT-PCR test for housekeeping genes and genes of interest. 6-mRNA amplification and labeling in two steps: a-Generation of T7-conatining double stranded cDNA using T7-Poly-T Strategy (Invitrogen) b-mRNA amplification and labeling (aRNA) by in vitro transcription using T7 RNA polymerase, T7-cDNA as template and biotin-labeled ribonucleotides 7-Biotin-labeled aRNA quantity assess, as in step 3 8-Biotin-labeled aRNA  determination by amplified RNA electropherogram. Agilent RNA 6000 Assay Microchips: Agilent Technologies 9-Biotin-labeled aRNA fractionation, hybridization onto HG-95aVer2 oligonucleotide array and scanning, using Affymetrix platform: Affymetrix 10-Statistical gene expression analysis: Using GeneSpring Software (Slicon Gnetics) a-Normalization to the 50th percentile and per gene to specific control samples, using 'Disease vs. Normal' as the main parameter. b-Fold of expression filter (2 folds cutoff) using signal data in ratio mode interpretation c-Welch t-test, with p< 0.05 for significance, using log of ratio mode interpretation d-Differentially expressed genes clustering by K-means, experiment  and gene trees e-Differentially expressed genes analysis and  classes classification by  Gene Ontology and GeneMapp pathways
Keywords: other

first: Jorge

middle: E

last: Torres-Munoz


title: Gene expression profiles in white blood cell subgroups

status: Public on Jun 16 2006

city: Jena

first: Sandy

last: Mosig

address: Bachstrasse 18

department: Molecular Hemostaseology - Institute of Vascular Medicine

institute: University Hospital Jena

summary:
In recent years gene expression profiling with microarrays has become an important tool in genomic research. Its usefulness in diagnosis and disease classification is now well documented. In many cases routine access to tissues primarily involved in pathophysiological processes is not possible. Attempts have therefore been made to use gene expression patterns in white blood cells (WBCs) as surrogate markers. We investigated if the analysis of gene expression profiles in whole white blood cells is sufficient or if improvements in reliability and sensitivity can be obtained by the analysis of sorted subtypes of WBCs. Using Affymetrix U133A gene chips we have determined gene expression profiles in WBCs, PBMCs, and T-cells. Changes in gene expression were induced in these cells by oxygen-consumption controlled treadmill exercise of healthy volunteers. We found that gene expression changes in T-cells, which indicated the presence of cell activation and apoptosis after exercise, were masked when mixed cell populations were analyzed. Of 157 genes that were found significantly differently expressed in T-cells when before and after exercise samples were compared, only 50 showed significant differences when PBMCs were analyzed; in WBCs only 20 of these genes showed significant differences. In the latter cells, some genes actually showed a significant change in the opposite direction. We conclude that the threshold for the detection of gene expression changes is lowered when the analysis is done in leukocyte subpopulations. In addition, knowledge about the cellular origin of an observed expression shift facilitates the interpretation of the obtained results.
Keywords: T Lymphocytes, exercise, microarray analysis

overall_design: Genexpression profiles from 3 different probands before and after exhaustive exercise in White Blood Cells, Peripheral Blood Mononuclear Cells and T Lymphocytes, respectively, have been meassured on Affymetrix HG 133 A 2.0 GeneChips.

first: Petra

last: Buettner

first: Doreen

last: Glaeser

first: Thomas

last: Hilberg

first: Frank

middle: C

last: Mooren


title: Rotavirus activates B but impairs T lymphocytes

status: Public on Jun 01 2006

city: Atlanta

last: Wang

state: GA

institute: Centers for Diseases Control

summary:
Rotavirus infection is the single most important cause of severe diarrhea in young children worldwide. We used Affymetrix Human U95Av2 high density oligonucleotide arrays to compare gene expression profiles in peripheral blood mononuclear cells (PBMC) of 10 children with acute rotavirus diarrhea and 8 age-matched healthy children. We also examined patterns of gene expression in 5 convalescent-phase PBMC samples from rotavirus patients. For data analysis, we imported .cel files generated by Affymetrix MAS5.0 into Genetraffic 3.1 software (Iobion) and performed robust multi-chip analysis. We considered a gene in patients differentially expressed if its level of expression was at least 1.5-fold higher or lower than the baseline (arithmetic mean) of the corresponding gene in 8 controls and if its pattern of elevated or repressed expression was observed in at least 7 of the 10 patients. Using these criteria, we identified ~1% up- and ~2% down-regulated genes in acute-phase PBMC of patients. Up-regulated genes included those involved in the differentiation, maturation, activation, and survival of B cells, as well as an array of genes with function in inflammatory and antiviral activities. We observed a pattern of repressed expression of a number of genes involved in the various stages of T-cell development and activation. On the basis of these results, we conclude that rotavirus infection induces robust inflammatory response and B-cell activation but represses T-cell response.
Keywords: other

first: Yuhuan

first: Penelope

last: Dennehy

first: Harry

middle: L

last: Keyserling

first: Kevin

last: Tang

first: Jon

middle: R

last: Gentsch

first: Roger

middle: I

last: Glass

first: Baoming

last: Jiang


title: Treatment of heat shocked HeLa cells with siRNA (siHSF1#1)

status: Public on Feb 05 2006

city: RTP

first: Todd

last: Page

state: NC

address: 6 Davis Dr

institute: CIIT

summary:
Although HSF1 is known to play an important role in regulating the cellular response to proteotoxic stressors, little is known about the structure and function of the HSF1 signaling network under both stressed and unstressed conditions.  In this study, we used a combination of chromatin immunoprecipitation (ChIP) microarray analysis and time course gene expression microarray analysis with and without siRNA-mediated inhibition of HSF1 comprehensively identify genes directly and indirectly regulated by HSF1 and examine the structure of the extended HSF1 signaling network. Correlation between promoter binding and gene expression was not significant for all genes bound by HSF1 suggesting that HSF1 binding per se is not sufficient for expression.  However, the correlation with promoter binding was significant for genes identified as HSF1-regulated following siRNA knockdown allowing the identification of direct transcriptional targets of HSF1.  Among promoters bound by HSF1 following heat shock, a gene ontology (GO) analysis showed significant enrichment only in categories related to protein folding.  In contrast, analysis of the extended HSF1 signaling network showed enrichment in a variety of categories related to protein folding, anti-apoptosis, RNA splicing, ubiquitination and others, highlighting a complex transcriptional program directly and indirectly regulated by HSF1.
Keywords: Time Course, Heat Shock, siRNA

overall_design: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: Measles Virus-Infected Dendritic Cells

status: Public on Jan 19 2006

first: Michael

last: Zilliox

address: 1510 Clifton Road

department: Microbiology and Immunology

institute: Emory University School of Medicine

summary:
Human CD14+ monocytes were isolated and grown in GM-CSF and IL-4 for six days.  The cells were then infected with measles virus, Chicago-1 strain, and RNA was isolated at 3, 6, 12, and 24 hours post-infection.
Keywords: time-course

middle: J

first: Giovanni

last: Parmigiani

first: Diane

last: Griffin


title: SP600125 effect on keratinocytes

status: Public on May 16 2006

city: New York

first: Miroslav

last: Blumenberg

state: NY

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

summary:
In inflamed tissue, normal signal transduction pathways are altered by extracellular signals. For example, the JNK pathway is activated in psoriatic skin, which makes it an attractive target for treatment. To define comprehensively the JNK-regulated genes in human epidermal keratinocytes, we compared the transcriptional profiles of control and JNK inhibitor-treated keratinocytes, using DNA microarrays. We identified the differentially expressed genes 1, 4, 24 and 48 hrs after the treatment with SP600125. Surprisingly, the inhibition of JNK in keratinocyte cultures in vitro induces virtually all aspects of epidermal differentiation in vivo: transcription of cornification markers, inhibition of motility, withdrawal from the cell cycle, stratification and even production of cornified envelopes. The inhibition of JNK also induces the production of enzymes of lipid and steroid metabolism, proteins of the diacylglycerol and inositol-phosphate pathways, mitochondrial proteins, histones and DNA repair enzymes, which have not been associated with differentiation previously. Simultaneously, basal cell markers, including integrins, hemidesmosome and ECM components, are suppressed. Promoter analysis of regulated genes finds that the binding sites for the forkhead family of transcription factors are over-represented in the SP600125-induced genes, and c-Fos sites in the suppressed genes. The JNK-induced proliferation appears to be secondary to inhibition of differentiation. The results indicate that the inhibition of JNK in epidermal keratinocytes is sufficient to initiate their differentiation program, and suggest that augmenting JNK activity could be used to delay cornification and enhance wound healing, while attenuating it could be a differentiation therapy-based approach for treating psoriasis.
Keywords: Time course. Inhibitor

overall_design: Keratinocytes are grown to ~75% confluence and either treated with 5nM SP600125, or left untreated. Samples are harvested 1, 4, 24 and 48hrs post-treatment.

first: Alix

last: Gazel

first: Tomohiro

last: Banno

first: Rebecca

last: Walsh


title: Distinct gene expression in human Vd1 and Vd2 gd T cells following non-TCR agonist stimulation

status: Public on Feb 28 2006

city: Bozeman

first: Ellen

last: Kress

state: MT

department: Veterinary Molecular Biology

institute: Montana State University

summary:
The two major human gd T cell subsets, Vd1 and Vd2, display differences in tissue tropism and agonist responses, but we have little insight into global differences that may exist at the gene expression level.  This is due to the small numbers of these cells that can be obtained from healthy donors, which limit comprehensive, comparative gene expression analyses.   We established a culture method that expands Vd1 and Vd2 cells from the same PBL preparation to levels sufficient for sorting and microarray analysis.  Although the subsets were expanded identically (anti-TCR mAb, plus IL-15), 392 and 614 genes were identified, which were differentially expressed in the two subsets, from two donors, respectively.  Approximately 4,500 genes changed in both subsets following PMA/ionomycin treatment; about 50% of these genes were subset-specific.  Both subsets responded to a crude LPS preparation, but only 6% of the responsive genes were the same.  The differentially expressed genes were consistent with Vd2 cells being more inflammatory and Vd1 cells having more of a regulatory phenotype.  Both subsets expressed transcripts encoding an array of innate and NK cell receptors, supporting the relationship of gd?T cells to the innate immune system. Our results show that circulating Vd1 and Vd2 subsets in humans have considerable, inherent differences in gene expression following treatment with non-TCR agonists, supporting unique functional roles for these cells in vivo.
Keywords: cell type comparison

overall_design: To analyze global gene expression differences between Vd1 and Vd2 gd T cells, 12 Affymetrix Human Genome U133A 2.0 chips were run. 2 replicate sets of 6 chips from 2 donors were run; each set of six chips consisted of 3 chips for Vd1 cells and 3 chips for Vd2 cells.  The 3 chips for each subset consisted of cells treated with PBS, LPS, or PMA/ionomycin for 4 hours just prior to RNA extraction.

first: Jodi

middle: F

last: Hedges

first: Mark

middle: A

last: Jutila


title: Rectal Cancer Cells and Radiation-sensitivity

status: Public on Mar 29 2006

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

country: Japan

institute: University of Tokyo

summary:
Biopsy specimens were collected from rectal cancer before starting preoperative radiotherapy.The expression profiles were determined using Affymetrix Human Genome U95 version 2 arrays.Comparison between the sample groups allow to identify a set of discriminating genes that can be used for characterization of responders and nonresponders to preoperative radiotherapy in rectal cancer.
Keywords: repeat

overall_design: 35-training and 11-test samples were analyzed


title: Gene expression Profiling of Peripheral Blood Leukocytes after Endotoxin Challenge in Humans

status: Public on Jan 17 2006

city: Bethesda

first: Anthony

middle: F.

last: Suffredini

state: MD

address: Building 10, Rm 7D43, 10 Center Drive

department: Critical Care Medicine Department

institute: National Institutes of Health

summary:
Peripheral blood mononuclear cells were isolated 0, 30 min, 6 h, 24 h, and 7 day after intravenous endotoxin challenge.
Keywords: time course

overall_design: Peripheral blood mononuclear cells were isolated 0, 30 min, 6 h, 24 h, and 7 day after intravenous endotoxin challenge using cell preparation tubes (Vacutainer® CPT). The PBMC layer was lysed with RLT buffer, homogenized, and then stored at –80°C. Total RNA was extracted as per RNeasy‚ Midi protocol (Qiagen). Double stranded cDNA was synthesized from total RNA (5 to 20 µg) using 7-d(T)24  primer and SuperScript‰ Double-Stranded cDNA Synthesis Kit and purified by phase lock gel-phenol/chloroform extraction followed by ethanol precipitation. Biotin-labeled cRNA was prepared by in vitro transcription using HighYield‰ RNA Transcript Labeling Kit followed by fragmentation with 5X fragmentation buffer.  Fragmented cRNA (10 µg) was hybridized to Affymetrix Hu95Av2 oligonucleotide probe arrays for 16 h at 45∞C.  After removal of hybridization fluid, the arrays were washed, stained with streptavidin phycoerythrin (SAPE), and signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400.  Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix‚, Santa Clara, CA).

first: Shefali

last: Talwar

first: Peter

last: Munson

first: Jennifer

last: Barb

first: Carmen

last: Fiuza

first: Anadel

middle: P

last: Cintron

first: Carolea

last: Logun

first: Margaret

last: Tropun

first: Sameena

last: Khan

first: Debra

last: Reda

first: James

last: Shelhamer

first: Robert

last: Danner


title: Classification of neuroblastoma by integrating gene expression pattern with regional alterations in DNA copy number

status: Public on Jan 04 2006

city: Philadelphia

first: Jayanti

last: Jagannathan

state: PA

address: 34th & Civic center blvd

department: Oncology

institute: Childrens Hospital of Philadelphia

summary:
The specific genes that influence neuroblastoma biology and are targeted by genomic alterations remain largely unknown. We quantified mRNA expression in a highly annotated series of 101 prospectively collected diagnostic neuroblastoma primary tumors  and the expression profiles were determined using Affymetrix U95Av2 arrays.  Comparisons between the sample groups allow the identification of genes with localized expression patterns. This study demonstrates that the genomic data can be used to subcategorize the disease into molecular subsets and the regional copy number alterations are correlated with a broad number of transcriptional alterations genome wide. This data also suggests that multiple genes from several discrete regions of the human genome co-operate to supress neuroblastoma tumorigenesis and progression.
Keywords: Disease state analysis, genetic modification

overall_design: A highly annotated series of 101 prospectively collected diagnostic neuroblastoma primary tumors were selected to quantify mRNA expression using an oligonucleotide based microarray. Genomic copy number status at the prognostically relevant loci 1p36,2p24(MYCN), 11q23 and 17q23 was determined by PCR and was aberrant in 26, 20, 40 and 38 cases, respectively. Fetal brain RNA was used as a control sample.

first: Qun

last: Wang

first: Sharon

last: Diskin

first: Eric

last: Rappaport

first: Edward

last: Attiyeh

first: Yael

last: Mosse

first: Daniel

last: Shue

last: Seiser

first: Suzanne

last: Shusterman

first: Manisha

last: Bansal

first: Deepa

last: Khazi

first: Cynthia

last: Winter

first: Erin

last: Okowa

first: Gregory

last: Grant

first: Avital

last: Cnaan

first: Huaqing

last: Zhao

first: Nai-Kong

last: Cheung

first: William

last: Gerald

first: Wendy

last: London

first: Katherine

last: Matthay

first: Garrett

last: Brodeur

first: John

last: Maris


title: Lung tumors

status: Public on Dec 20 2005

city: Denver

first: Robert

middle: S

last: Stearman

state: CO

address: 4200 E Ninth Ave

department: Medicine/Pulmonary

institute: UCHSC

summary:
Lung tumors
Keywords: other

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Lori

last: Dwyer-Nield

first: Laura

last: Zerbe

first: Stacy

last: Blaine

first: Paul

last: Bunn

first: Gary

last: Johnson

first: Raphael

last: Nemenoff

first: Alvin

middle: M

last: Malinson

first: Mark

middle: W

last: Geraci


title: NIH/NIAID GM-CSF Modulates Global Changes in Neutrophil Gene Expression

status: Public on Oct 07 2005

city: Hamilton

first: Addie

last: Whitney

address: 903 S 4th St

department: LHBP

institute: NIH/NIAID/RML

summary:
PMNs were isolated from venous blood of healthy individuals in accordance with a protocol approved by the Institutional Review Board for Human Subjects, National Institute of Allergy and Infectious Diseases.  Human PMNs (107) were cultured in RPMI/H -/+ 100 ng/ml GM-CSF at 37oC and 5% CO2 for up to 24 h as indicated.  At the indicated time points, tissue culture medium was aspirated from each well and PMNs were lysed with RLT buffer (Qiagen).  Purification of PMN RNA and subsequent preparation of labeled cRNA target was performed as described in Methods.  Labeling of samples, GeneChip hybridization (Hu95Av2 oligonuceotide microarrays) and scanning were performed according to standard Affymetrix protocols (see http://www.affymetrix.com/support/technical/manual/expression_manual.affx).  Experiments were performed in triplicate, using PMNs from three healthy individuals for each treatment.  These analyses allowed comparison of global gene expression in human neutrophils during spontaneous apoptosis with that in cells cultured with human GM-CSF.
Keywords: time course

overall_design: 39 samples total:  9 time zero controls, -/+ GM-CSF at 5 time points in triplicate

first: Scott

middle: D

last: Kobayashi

first: Jovanka

last: Voyich

first: Adeline

first: Frank

last: DeLeo


title: Stable and Progressive B-CLL

status: Public on Sep 14 2005

city: Huddinge

first: Susann

last: Fält

country: Sweden

institute: Karolinska Institutet

summary:
Objective. B-cell chronic lymphocytic leukemia is a heterogeneous disease with a pronounced variation in the clinical course. With the purpose of identifying genes that could be related to disease progression, we have performed gene expression profiling on B-CLL patients with an indolent disease and patients with a progressive disease with need for therapy.
Materials and Methods. We applied the Affymetrix GeneChip technique to 11 B-CLL patients with stable and 10 patients with clinically progressive disease. Supervised and unsupervised clustering methods with different algorithms were used to identify genes that tend to give a distinction between stable and progressive disease.
Results. The supervised learning procedures identified groups of genes with a combined power to discriminate samples from progressive and stable disease with 70-90 % accuracy. The gene for protein phosphatase 2 regulatory subunit B’ (B56) gamma isoform (PPP2R5C) and the gene for retinoblastoma-like 2 (p130) (RBL2) were included among the best discriminators; both genes were down regulated in progressive as compared to stable B-CLL. In a hierarchical clustering analysis based on gene expression pattern three clinical sub-categories could be identified; one with a more severe clinical outcome, a second one with good prognosis and a third one that was intermediate between the other two groups.
Conclusions. Our application of microarray analysis on a clinically well defined material has identified a number of genes with combined expression patterns related to stable or progressive disease in general. Unsupervised clustering suggested the existence of subclasses of samples in the progressive group that may be identifiable through gene expression patterns.
Keywords: ordered

first: Mats

last: Merup

first: Gösta

last: Gahrton

first: Bo

last: Lambert

first: Anders

last: Wennborg


title: Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis

status: Public on Oct 22 2005

city: La Jolla

first: Jennifer

last: Hammond

state: CA

address: 10550 N. Torrey Pines Rd.

institute: The Scripps Research Institute

summary:
The neurodegenerative process in HIV encephalitis (HIVE) is associated with extensive damage to the dendritic and synaptic structure that often leads to cognitive impairment. Several mechanisms might be at play, including release of neurotoxins, oxidative stress and decreased activity of neurotrophic factors. Furthermore, HIV-mediated dysregulation of genes involved in neuronal maintenance might play an important role. For this purpose, cRNA was prepared from the brains of 17 AIDS patients for analysis with the Affymetrix Human U95Av2 GeneChip and analyzed with the GeneSpring Expression Analysis Software. Out of 12,625 genes analyzed, 74 were downregulated and 59 were upregulated compared to controls. Initial alternative analysis of RNA was performed by ribonuclease protection assay (RPA). In cases with HIVE, downregulated genes included neuronal molecules involved in synaptic plasticity and transmission (ion channels, synaptogyrin, synapsin II), cell cycle (p35, p39, CDC-L2, CDC42, PAK1) and signaling molecules (PI3K, Ras-Raf-MEK1), transcription factors and cytoskeletal components (MAP-1B, MAP-2, tubulin, adducin-2). Upregulated genes included those involved in neuroimmune (IgG, MHC, β2microglobulin) and anti-viral responses (interferon-inducible molecules), transcription (STAT1, OLIG2, Pax-6) and signaling modulation (MEK3, EphB1) of the cytoskeleton (myosin, aduccin-3, radixin, dystrobrevin). Taken together, this study suggests that HIV proteins released from infected macrophages might not only induce a neuroinflammatory response, but also may promote neurodegeneration by interfering with neuronal transcription of genes involved in regulating signaling and cytoskeletal molecules important in maintaining synapto-dendritic functioning and integrity.
Keywords: HIVE, HIV, AIDS, Microarray, neuroimmunity, neuroinflammatory, neurodegeneration

overall_design: RNA was obtained from brain slabs that are rapidly frozen after removal and stored at −80 °C for subsequent molecular and biochemical analysis. From each case, a frontal cortex (Broadmann area 46) block (1 mm3) was dissected from the frozen brain slabs. The underlying white matter was dissected out with a blade, thus most of the RNA obtained is isolated from a sample of gray matter. Total RNA (approximately 50 μg) was purified from 250 mg of this frozen tissue block with TRIzol Reagent (Invitrogen, Carlsbad, CA) following the manufacturer's protocol, with an additional centrifugation step to remove unwanted cellular debris. RNA was then further purified using the RNeasy mini kit (Qiagen, Valencia, CA) and the quantity of total RNA was assessed by 260-nm UV absorption, with quality analyzed by gel electrophoresis and analysis of the ribosomal RNA bands. This analysis confirmed that in the samples included for this study, the 18S and 28S bands were clearly identified, indicating that the RNA was well preserved (Fig. 1). For the protocol, 10 μg of total RNA was utilized per experiment. This was prepared to synthesize cDNA that was then used as a template to produce biotinylated cRNA. Affymetrix Test 2 chips were used to assess RNA quality by examining the 3′ to 5′ ratios for actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). A total of 15 μg cRNA was prepared in a hybridization cocktail of 300 ml total volume, of which 200 μl was placed on an Affymetrix Human U95Av2 GeneChip, containing 12,625 independent probe sets to analyze gene expression. After hybridization, this sample was returned to the original aliquot, which was then frozen. For the frontal lobe samples, a further 200 μl was sampled from the original cocktail and hybridized to a separate duplicate GeneChip within 30 days. Hybridization and subsequent washing and staining were carried out using the Affymetrix Fluidics Station 400 following supplied protocols. Chips were then double stained and scanned according to basic Affymetrix protocol to create GeneChip image files that were converted to text-bases files using Microarray Suite 5.0 software (Affymetrix, Santa Clara, CA). Experiments were repeated at least once to verify the specificity of the results.

first: Eliezer

last: Masiliah

first: Eleanor

last: Roberts

first: Dianne

last: Langford

first: Ian

last: Everall

first: Leslie

last: Crews

first: Anthony

last: Adame

first: Edward

last: Rockenstein

first: Howard

last: Fox


title: Interindividual Variability in LPS Responses

city: Seattle

first: Mark

last: Wurfel

state: WA

address: 300 9th Ave

department: Pulmonary & Critical Care Medicine

institute: University of Washington

summary:
We used an unbiased approach to identify differences in gene expression that may account for the high degree of interindividual variability in inflammatory responses to LPS in the normal human population. We measured LPS-induced cytokine production ex vivo in whole blood from 102 healthy human subjects and identified individuals who consistently showed either very high or very low responses to LPS. Comparison of gene expression profiles between the lpshigh and lpslow individuals revealed 80 genes that were differentially expressed in the presence of LPS and 21 genes that were differentially expressed in the absence of LPS (p < 0.005, ANOVA). Expression of a subset of these genes was confirmed using real-time RT-PCR. These data illustrate a novel approach to the identification of factors that determine interindividual variability in innate immune inflammatory responses.
Keywords: comparative response

overall_design: Six whole blood samples (three high and three low responders to LPS) were selected from a cohort of 102 healthy individuals, exposed to media or LPS for 4 hours. RNA was isolated and hybridized with an Affymetrix array.

first: William

middle: Y

last: Park

last: Radella II

first: John

last: Ruzinski

first: Andrew

last: Sandstrom

first: Jeanna

last: Strout

first: Roger

last: Bumgarner

first: Thomas

last: Martin


title: Variability in Microarray Labeling Methods

status: Public on Jan 01 2006

city: Houston

first: Federico

middle: Alberto

last: Monzon

state: TX

address: 6565 Fannin St, MS205

department: Pathology

institute: The Methodist Hospital

summary:
Considerable variation in gene expression data from different DNA microarray platforms has been demonstrated. However, no characterization of the source of variation arising from labeling protocols has been performed. To analyze the variation associated with T7-based RNA amplification/labeling methods, aliquots of the Stratagene Human Universal Reference RNA were labeled using 3 eukaryotic target preparation methods and hybridized to a single array type (Affymetrix U95Av2). Variability was measured in yield and size distribution of labeled products, as well as in the gene expression results. All methods showed a shift in cRNA size distribution, when compared to un-amplified mRNA, with a significant increase in short transcripts for methods with long IVT reactions. Intra-method reproducibility showed correlation coefficients >0.99, while inter-method comparisons showed coefficients ranging from 0.94 to 0.98 and a nearly two-fold increase in coefficient of variation. Fold amplification for each method was positively correlated with the number of present genes. Two factors that introduced significant bias in gene expression data were observed: a) number of labeled nucleotides that introduces sequence dependent bias, and b) the length of the IVT reaction that introduces a transcript size dependent bias. This study provides evidence of amplification method dependent biases in gene expression data.
Keywords: method validation study

overall_design: Universal Human Reference RNA were amplified with four T7 RNA polymerase based in vitro transcription RNA labeling methods--Affy, CodeLink, Enzo, Affy4h. 5 cRNA products amplified from each method were hybridized on Affymetrix HG-U95Av2 arrays. 20 hybridzations were performed in total.

first: Changqing

last: Ma

first: Maureen

last: Lyons-Weiler

first: Wenjing

last: Liang

last: LaFramboise

last: Gilbertson

first: Michael

last: Becich


title: Impact of cell division on the distribution of HIV integration.

status: Public on Nov 10 2005

city: philadelphia

first: Chris

last: Hoffmann

address: 3610 hamilton walk

institute: University of Pennsylvania

summary:
DNA integration is a defining step in the retroviral life cycle and the basis of stable gene transfer in retrovirus-based gene therapy.  Previous studies of integration by HIV-based vectors have shown that integration is not random, but favored in active transcription units.  Studies to date have focused on HIV integration in dividing cells, leaving open the question of whether integration target site selection might differ in nondividing cells.  According to one idea, division of the host cell might be required for favored integration in transcription units, possibly as a result of chromatin remodeling during DNA replication.  Here we have investigated this issue by comparing integration in dividing IMR-90 primary lung fibroblasts to integration in nondividing IMR-90 cells arrested in G1 by serum starvation and contact inhibition.  We identified several differences in integration site selection in arrested versus dividing cells, including the frequency of integration in transcription units and in gene-rich regions.  However, integration in nondividing cells was in fact more favored in transcription units, contrary to the idea that cell division was important for this bias.  These data provide the first view of lentiviral integration in nondividing cells and help constrain models for the mechanism of favored integration in genes.
Keywords: comparative genomic analysis, dividing versus non-dividing cells.

overall_design: IMR-90 cells (initially passaged 36 times) were cultured in DMEM with 10% FBS until the cells reached 100% confluence, at which point the medium was substituted to contain only 0.5% FBS. The cells were cultivated for 2 weeks prior to harvesting for RNA extraction. 2 arrays were hybridized, using RNA from 2 independent cell cultures. The data of these growth arrested cells was compared to dividing IMR90 cells (Mitchell et al. 2004. PLoS Biology. 2(8):E234).

first: Angela

last: Ciuffi

first: Richard

last: Mitchell

first: Christian

first: Jeremy

last: Leipzig

first: Paul

last: Shinn

first: Joseph

last: Ecker

first: Frederic

last: Bushman


title: Affected and unaffected skin of 4 psoriatic patients and normal skin of 3 psoriasis free individuals

status: Public on Oct 01 2005

city: Perth

first: William

middle: D.

last: Kenworthy

address: 90 South Street

department: Centre for Bioinformatics and Biological Computing

country: Australia

institute: Murdoch University

summary:
Gene expression profiling was performed on biopsies of affected and unaffected psoriatic skin and normal skin from seven Japanese patients to obtain insights into the pathways that control this disease. U95A Affymetrix DNA chips that contain oligonucleotide arrays of approximately 12,000 well-characterized human genes were used in the study. The statistical analysis of the Affymetrix data, based on the ranking of the Student-test statistic, revealed a complex regulation of molecular stress and immune gene responses. The majority of the 266 induced-genes in affected and unaffected psoriatic skin were involved with interferon mediation, immunity, cell-adhesion, cytoskeleton restructuring, protein trafficking and degradation, RNA regulation and degradation, signaling transduction, apoptosis and atypical epidermal cellular proliferation and differentiation. The disturbances in the normal protein degradation equilibrium of skin were reflected by the significant increase in the gene expression of various protease inhibitors and proteinases including the induced components of the ATP/ubiquitin-dependent non-lysosomal proteolytic pathway that is involved with peptide processing and presentation to T-cells. Some of the upregulated genes, such as TGM1, IVL, CSTA, FABP5 and SPRR, are well known psoriatic markers involved in atypical epidermal cellular organization and differentiation. In the comparison between the affected and unaffected psoriatic skin, the transcription factor JUNB was found at the top of the statistical rankings for the 51 significantly upregulated genes in affected skin, suggesting that it has an important but as yet undefined role in psoriasis. Our gene expression data and analysis suggest that psoriasis is a chronic IFN and T-cell-mediated immune disease of the skin where the imbalance in epidermal cellular structure, growth and differentiation arises from the molecular antiviral stress signals initiating inappropriate immune responses.
Keywords: Disease State Analysis

overall_design:
Analysis of the expression profile of skin samples for each of three conditions (states) of psoriasis activity
3 samples were from psoriasis negative individuals (biological replicates)
4 samples were from psorasis free skin areas of psoriasis active individuals (biological replicates)
4 samples were from psorasis active skin areas of psoriasis active individuals (biological replicates)

first: Jerzy

middle: K

last: Kulski

first: Matthew

last: Bellgard

first: Ross

last: Taplin

first: Koichi

last: Okamoto

first: Akira

last: Oka

first: Gen

last: Tamiya

first: Hidetoshi

last: Inoko


title: Transcriptional profiles of Th cells induced to polarize to Th1 or Th2 direction in the presence or absence of TGFbeta

status: Public on Sep 01 2005

city: Turku

first: Riikka

middle: Johanna

last: Lund

address: Tykistökatu 6 A

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku and Åbo Akademi University

summary:
Th1 and Th2 cells arise from a common precursor cell in response to triggering through the TCR and cytokine receptors for IL-12 or IL-4. This leads to activation of complex signaling pathways, which are not known in detail. Disturbances in the balance between type 1 and type 2 responses can lead to certain immune-mediated diseases. Thus, it is important to understand how Th1 and Th2 cells are generated. To clarify the mechanisms as to how IL-12 and IL-4 induce Th1 and Th2 differentiation and how TGF-beta can inhibit this process, we have used oligonucleotide arrays to examine the early polarization of Th1 and Th2 cells in the presence and absence of TGF-beta after 0, 2, 6 and 48 hours of polarization.
Keywords: time course, differentiation

overall_design: This study includes altoghether 34 samples. Six different types of treatments (Thp, Th0, Th1, Th2, Th1+TGFbeta, Th2+TGFbeta) were studied at 4 time points (0, 2, 6 and 48h). There are two biological replicates, for both time series, consisting of pooled samples derived from different individuals. The early time points (0, 2 and 6h) and late time point (0 and 48h) were done in separate experiments (cell from different individuals), because of the limited number of the cells obtained from each the cord blood.

first: Tero

last: Aittokallio

first: Olli

last: Nevalainen

first: Riitta

last: Lahesmaa

first: Essi

last: Kainonen

first: Anna-Maria

first: Craig

last: Dixon

first: Helena

last: Ahlfors

first: Outi

last: Melin

first: Miina

last: Miller


title: Breast Cancer Dataset

status: Public on Nov 07 2005

city: Durham

first: Joseph

middle: R.

last: Nevins

address: 2133 CIEMAS, 101 Science Dr.

department: IGSP

institute: Duke University

summary:
Signatures of Oncogenic Pathway Deregulation in Human Cancers.

The ability to define cancer subtypes, recurrence of disease, and response to specific therapies using DNA microarray-based gene expression signatures has been demonstrated in multiple studies. Such data is also of substantial importance to the analysis of cellular signaling pathways central to the oncogenic process. With this focus, we have developed a series of gene expression signatures that reliably reflect the activation status of several oncogenic pathways. When evaluated in several large collections of human cancers, these gene expression signatures identify patterns of pathway deregulation in tumors, and clinically relevant associations with disease outcomes. Combining signature-based predictions across several pathways identifies coordinated patterns of pathway deregulation that distinguish between specific cancers and tumor sub-types. Clustering tumors based on pathway signatures further defines prognosis in respective patient subsets, demonstrating that patterns of oncogenic pathway deregulation underlie the development of the oncogenic phenotype and reflect the biology and outcome of specific cancers. Furthermore, predictions of pathway deregulation in cancer cell lines are shown to coincide with sensitivity to therapeutic agents that target components of the pathway, underscoring the potential for such pathway prediction to guide the use of targeted therapeutics.
Keywords: other

overall_design: RNA was extracted from frozen tissue of primary breast tumors for gene array analysis.


title: Effect of BMP-2 on Pulmonary Artery Smooth Muscle Cells from Patients with Idiopathic Pulmonary Arterial Hypertension

status: Public on Oct 21 2005

first: Carmelle

middle: V

last: Remillard

institute: University of California San Diego

summary:
Bone morphogenetic proteins (BMP) inhibit proliferation and induce apoptosis in pulmonary artery smooth muscle cells (PASMC) from normal subjects. Dysfunction of BMP signaling due to mutations in and/or downregulation of BMP receptors has been implicated in idiopathic pulmonary arterial hypertension (IPAH). We examined whether BMP differentially regulates gene expression in PASMC from normal subjects and IPAH patients using the Affymetrix microarray analysis. BMP-2 treatment (200 nM for 24 hrs) altered expression levels of 6,206 genes in normal and IPAH PASMC. 1,063 of these genes were regulated oppositely by BMP-2: 523 genes were downregulated by BMP-2 in normal PASMC but upregulated in IPAH PASMC, whereas 540 genes were upregulated by BMP-2 in normal PASMC but downregulated in IPAH PASMC. The divergent effects of BMP-2 on gene expression profiles indicate that PASMC may undergo significant phenotypic changes in IPAH patients during development of the disease. The transition of the antiproliferative effect of BMP-2 in normal PASMC to its proliferative effect in IPAH patients is attributed potentially to its differential effect on expression patterns of various genes that are involved in cell proliferation and apoptosis. Among the 6206 BMP-2-sensitive genes, there are more than 1800 genes whose expression levels were negatively (with a correlation coefficient, r, < –0.9) or positively (with r > +0.9) correlated with the pulmonary arterial pressure. These results suggest that BMP-mediated gene regulation is significantly altered in PASMC from IPAH patients and mRNA expression changes in BMP-regulated genes may be involved in the development of IPAH.
Keywords = bone morphogenetic receptor protein
Keywords = idiopathic pulmonary arterial hypertension
Keywords = transcription factor
Keywords = gene expression profile
Keywords: other

first: Ivana

last: Fantozzi

first: Wei

last: Huang

first: Jifeng

last: Zhang

first: Shen

first: Oleksandr

last: Platoshyn

first: Patricia

last: Thistlethwaite

first: Jason

middle: X

last: Yuan


title: Differential Gene Expression on Human LNCaP Cells Following Treatment with DHEA versus DHT

status: Public on Nov 18 2005

city: Rockville

first: Vernon

middle: Eugene

last: Steele

address: 6130 Executive Blvd

department: DIvision of Cancer Prevention

institute: National Cancer Institute

summary:
ABSTRACT
The effects of DHEA were compared with those of DHT using gene expression array profiles in human LNCaP prostate cancer cells. LNCaP cells were exposed to DHEA (300 nM), DHT (300 nM), or vehicle for 48 hrs, and mRNA was isolated. mRNA expression was measured using Affymetrix HU-95 gene chips in 3 experiments performed on different dates. Gene expression values for the two treatment groups and control were sorted in ascending order on the p-values corresponding to a variance stabilized Hotelling test, which measured the extent of differential RNA expression between control and either hormone treatment.  The top four genes with significant differential expression were S100 calcium binding protein, neurotensin, 24-dehydrocholesterol reductase, and anterior-gradient 2 homologue. Corresponding per comparison p-values were less than 3 x 10 -5. Nested tests of differential expression between DHEA and DHT treatment revealed significant differences (p < 0.01) for two of the four genes: the S100 calcium binding protein and neurotensin.  The microarray findings were confirmed by quantitative RT-PCR. The top 83 genes found to exhibit differential expression were used in a pathway analysis. In general, DHT decreased expression of more genes involved in intercellular communication, signal transduction, nucleic acid binding and transport, and in structural components, such as myosin and golgin, than did DHEA. These data reveal consistent, measurable differences in gene expression patterns following treatment of LNCaP prostate cancer cells with DHEA versus DHT.  The mechanisms underlying these observations, and the possible pathophysiological significance of these differences, remain to be determined.
Keywords: differential gene expression between DHT and DHEA

overall_design: Three separate experiments were performed and labeled: 111502, 011403, and 022803. Three groups were run per experiment: Control, DHT or DHEA. Cells were exposed for 48 hr to 300 nM of DHT or DHEA. One Affymetrix HG_U95Av2 microarray chip per group was analyzed. The data was normalized by  the "dchip" process.

middle: E

first: Julia

middle: T

last: Arnold

first: Hahn

last: Le

first: Grant

last: Izmirlian

first: Marc

middle: R

last: Blackman


title: The Influence of Interferon Gamma on Gene Expression in Normal Human Bronchial Epithelial Cells

first: James

last: Shelhamer

institute: Clinical Center

summary:
RNA from cultured human bronchial epithelial cells treated for 8 hours or for 24 hours with medium alone, interferon gamma, dexamethasone or both interferon gamma and dexamethasone.
Keywords = interferon gamma
Keywords = dexamethasone
Keywords = human bronchial epithelial cells
Keywords: dose response

first: Rafal

last: Pawliczak

first: Carolea

last: Logun

last: Madara

first: Jennifer

middle: J

last: Barb

first: Anthony

last: Suffredini

first: Peter

last: Munson

first: Robert

middle: L

last: Danner

middle: H


title: Effects of allergen challenge on airway epithelial cell gene expression

status: Public on Aug 01 2005

city: Richmond

first: Larry

middle: A.

last: Sonna

state: VA

address: 2020-I Timbers Hill Road

institute: Gene Expression Consulting

summary:
Allergen exposure induces the airway epithelium to produce chemoattractants, proallergic interleukins, matrix-modifying proteins, and proteins that influence the growth and activation state of airway structural cells. These proteins, in turn, contribute to the influx of inflammatory cells and changes in structure that characterize the asthmatic airway. To use the response of the airway epithelium to allergen to identify genes not previously associated with allergic responses, we compared gene expression in cytokeratin-positive cells before and after segmental allergen challenge. After challenge with concentrations of allergen in the clinically relevant range, 755 (6%) of the detectable sequences had geometric mean fold-changes in expression, with 95% confidence intervals that excluded unity. Using a prospectively defined conservative filtering algorithm, we identified 141 sequences as upregulated and eight as downregulated, with confirmation by conventional polymerase chain reaction in all 10 sequences studied. Using this approach, we identified asthma-associated sequences including interleukin (IL-)-3, IL-4, and IL-5 receptor subunits, the p65 component of nuclear factor-kappaB, and lipocortin. The genomic response of the human airway to concentrations of allergen in the clinically relevant range involves a greater number of genes than previously recognized, including many not previously associated with asthma that are differentially expressed after airway allergen exposure.
Keywords: Before and after allergen challenge

overall_design: Five paired samples of total RNA extracted from bronchial epithelium biopsy samples from subjects before (pre-) and after (post-) undergoing a segmental endobronchial allergen challenge protocol.

first: Craig

middle: M

last: Lilly

first: Hiroki

last: Tateno

first: Tsuyoshi

last: Oguma

first: Elliot

last: Israel

middle: A


title: TNF time course study

status: Public on Jul 04 2005

city: Galveston

first: Allan

last: Brasier

address: 301 Univ. Blvd

institute: University Texas Medical Branch

summary:
TNF time course series of HelA tet off cells cultured in presence or absence of Dox

TNF is a pro-inflammatory cytokine that controls expression of inflammatory genetic networks.  Although the Nuclear Factor-kB (NF-kB) pathway is crucial for mediating cellular TNF responses, the complete spectrum of NF-kB dependent genes is unknown.  In this study, we used a tetracycline-regulated cell line expressing an NF-kB inhibitor to systematically identify NF-kB dependent genes.  A microarray data set generated from a time course of TNF stimulation in the presence or absence of NF-kB signaling was analyzed.

Methods:
Cell culture, treatment and transfection-The human cervical epithelioid carcinoma cell line HeLa expressing tTA (HeLa Tet-Off) pBI-EGFP- IkBa Mut was constructed earlier (23).  HeLa Tet-Off were grown in medium containing 90 % Dulbecco’s Modified Eagle’s Medium (DMEM), 10 % heat-inactivated fetal bovine serum (FBS), 4mM L-glutamine, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 100 mg/ml G418, 100 units /ml penicillin G sodium, and 100 mg/ml streptomycin sulfate in a humidified atmosphere of 5 % CO2.   For TNF stimulation, freshly isolated cells were split into two cultures, one group maintained in Dox, the other without for 7 d, a time at which IkBa Mut expression was maximal.  Thereafter, recombinant human (rh) TNFa (25 ng/ml, final concentration) was added directly to the culture medium for indicated times prior to harvest.

Oligonucleotide probe based microarray-Hu95Av2 GeneChip (Affymetrix Inc, Santa Clara, CA) containing 12,626 sequenced human genes were hybridized according to the manufacturer’s recommendations and washed using both non-stringent (1 M NaCl, 25 °C) and stringent (1 M NaCl, 50  °C) conditions prior to staining with phycoerythrin streptavidin (10 mg/ml final).  Arrays were scanned using a Gene Array Scanner (Hewlett Packard) and analyzed using the Gene Chip Analysis Suite 5 software (Affymetrix Inc).  For each gene, 16-20 probe pairs are immobilized as ~25-mer oligonucleotides that hybridize throughout the mRNA;  each probe pair is represented as a perfect match (PM) oligonucleotide and a mismatch (MM) oligonucleotide as hybridization control.  The the Absolute Call [e.g., the gene is detected (“present”) or not (“absent”)] and the Signal Intensity (measure of mRNA abundance) is determined.

Four independent experiments were performed identically including control (0 h ), 1, 3 and 6 h TNF stimulation (25 ng/ml) in the presence or absence of Doxycyline (2 mg/ml) in growth medium.
These are indicated as 180, 181, 220 and 266 series, and are considered replicates of each other.
Keywords: time-course

first: Bing

last: Tian


title: PBS vs. LPS stimulation of gd T cells

status: Public on Jul 20 2005

city: Bozeman

first: Jodi

middle: Fern

last: Hedges

address: 960 Technology Blvd.

institute: Montana State University

summary:
gd T cells recognize unprocessed or non-peptide antigens, respond rapidly to infection, and localize to mucosal surfaces.  We have hypothesized that the innate functions of gd T cells may be more similar to those of cells of the myeloid lineage than to other T cells.  To begin to test this assumption, we have analyzed the direct response of cultured human and peripheral blood bovine gd T cells to pathogen associated molecular patterns (PAMPs) in the absence of APCs using microarray, real time RT-PCR, proteome array, and chemotaxis assays.  Our results indicate that purified gd T cells respond directly to PAMPs by increasing expression of chemokine and activation related genes.  The response was distinct from that to known gd T cell antigens and different from the response of myeloid cells to PAMPs.  In addition, we have analyzed the expression of a variety of PAMP receptors in gd T cells.  Freshly purified bovine gd T cells responded more robustly to PAMPs than did cultured human cells and expressed measurable mRNA encoding a variety of PAMP receptors.  Our results suggest that rapid response to PAMPs through the expression of PAMP receptors may be another innate role of gd T cells.
Keywords: parallel sample

overall_design: Sorted cells from 4 human gd T cell cultures were treated with either PBS or phLPS for 4 hours, RNA was extracted with TRIzol® Reagent (Invitrogen Life Technologies) according to the manufacturer’s instructions, pooled and used to probe Affymetrix Genechip® Human Genome U133A 2.0 Arrays (Cat. # 900471 Affymetrix, Santa Clara, CA) that represent 14,500 human genes.  cDNA amplification and synthesis of biotin-labeled cRNA was performed with the Alternative One-cycle target labeling protocol with 10 micrograms total RNA as described in the GeneChip® Expression Analysis Technical Manual (March 2004).  Hybridization was performed with 10 micrograms biotin labeled cRNA.  Washing and staining was performed in the GeneChip® Fluidics Station 450 using the Midi_euk2v3 protocol.  Chip scans were performed on the Affymetrix GeneChip® Scanner 3000.  GeneChip® Operating Software (GCOS v.1.1, Affymetrix) was used for data collection.

middle: F

first: Kirk

last: Lubick

first: Mark

last: Jutila


title: Classical Hodgkin’s Lymphoma: Molecular evidence for specific alterations of circulating T lymphocytes

status: Public on Jul 13 2005

city: Braunschweig

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
Gene expression profiles were performed from CD3+ T cells isolated from peripheral blood samples of untreated patients with cHL versus 2 control groups consisting of healthy donors and patients with sarcoidosis.
Keywords = Hodgkin’s Lymphoma
Keywords = T cell
Keywords = immune regulation
Keywords: repeat sample

first: Christian

last: Koenecke

first: Anke

last: Franzke


title: Actions of tamoxifen in the uterus and its molecular effectors in endometrial carcinogenesis.

status: Public on Jul 29 2005

city: Beijing

first: Yongfeng

last: Shang

address: 38 Xue Yuan Road

department: Biochemistry and Molecular Biology

country: China

institute: Peking University

summary:
The molecular explanation for tamoxifen serving as a breast cancer treatment but displaying partial estrogenic in the uterus is not known. Previously, we reported that differential promoter context and cofactor recruitment contribute to the tissue specificity of tamoxifen. Here, we investigated the genomic basis for the partial oestrogenic activity of tamoxifen in the endometrium.  We showed that tamoxifen not only affects the rate of transcription of oestrogen target genes but also targets a unique set of genes.  Since oestrogen and tamoxifen are both able to bind to oestrogen receptors (ERs) and because both promote endometrial carcinogenesis, we hypothesized that the molecular effectors for ERs in endometrial carcinogenesis most likely reside in genes that are commonly targeted by oestrogen and tamoxifen. Among those target genes, we identified a paired-box gene PAX2 that is critically involved in cell proliferation and carcinogenesis in the endometrium.  Our experiments also demonstrated that PAX2 is activated by oestrogen and tamoxifen in endometrial carcinomas but not in normal endometrium, and this activation is associated with cancer-linked hypomethylation of the PAX2 promoter.
Keywords: actions of tamoxifen

overall_design: each experiment repeat 2 times.

first: yongfeng

last: shang


title: Ciprofibrate (PPAR-alpha agonist) in the monkey liver

status: Public on Aug 23 2005

city: Research Triangle Park

first: Neal

last: Cariello

address: 5 Moore Drive, Bldg 9, Rom 2011

department: Safety Assessment

institute: GlaxoSmithKline

summary:
Liver gene expression was examined in male cynomolgus monkeys treated with ciprofibrate (PPAR-alpha agonist) for 4 days at 400 mg/kg/day and treated for 15 days at 0, 3, 30, 150 or 400 mg/kg/day.  The untreated control group were given only the vehicle (0.5% hydroxypropyl methylcellulose).  Two animals per group were used for the 4 day treatment and four animals per group were used for the 15 day treatment (except the 15 day control group, which had three animals).  Selection of significantly changed probesets was done using Rosetta Resolver and the fold-change and p values as determined by Resolver are given below.  Affymetrix CEL files and MAS5-processed data have been made availabe for convenience.  Note that data processing reported in the Toxicological Sciences manuscript was done using Rosetta Resolver and the treated versus control group fold-change and p-value are appended to the Series entry.  An article has been published in Toxicological Sciences regarding this dataset; the data interpretation was based on the Rosetta Resolver data.
Keywords: repeat

overall_design: Groups consisted of (i) vehicle only for 4 days, (ii) 400 mg/kg/day ciprofibrate for 4 days, (iii) vehicle only for 15 days and (iv) 3, 30, 150, or 400 mg/kg/day ciprofibrate for 15 days.


title: Comparison between Control and POAG

status: Public on Sep 08 2005

city: Cleveland

first: Sanjoy

middle: K

last: Bhattacharya

state: OH

address: 9500 Euclid Avenue

department: Ophthalmic Research

institute: Cole Eye Institute, Cleveland Clinic Foundation

summary:
The total RNA from control and POAG optic nerve lamina cribrosa region was isolated and subjected to analysis on U133A 2.0 affymetrix microarray chip. The results from these two analysis was compared to determine whether PAD II  RNA level is altered.

Purpose of the study. This study was done to determine which RNA transcripts undergo significant changes in the optic nerve between normal and cadaver primary open-angle glaucoma donors. Using donor tissues from NDRI we have performed proteomic analyses (which will be published shortly), we intend a comparison between the proteomic and RNA changes for select proteins in our study.

Sample Collection and Preparation of Labeled Copy RNA

The total RNA from optic nerve was obtained using TRIZOL  (Invitrogen Inc., Carlsbad, CA) with modification of recommended protocols. The optic nerve from donor eyes were carefully excised and minced into small pieces first using a scissor and then a scalpel. Prior to use tissue was washed with DEPC water and all solutions were prepared in DEPC water. The minced tissue was placed in a glass homogenizer with 1 ml TRIZOL per 100 mg of tissue and homogenized in a glass homogenizer DUALL 20 (Kimble Kontes Glass Co, Vineland, NJ) with 10 strokes cycles each at room temperature and after freezing with liquid nitrogen for 1 min for 40 cycles. This RNA was extracted with chloroform, isoamylalcohol and precipitated with sodium citrate/sodium chloride and isopropanol. The final air-dried RNA precipitate was suspended in DEPC water and stored in –80oC prior to use.  RNA was prepared for hybridization according to the GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).  The hybridization was performed at Gene Expression Array Core Facility at Case Western Reserve University (www.geacf.net).  The RNA sample was cleaned using a column from a Qiagen RNeasy kit, (part # 74104 ) in accordance with the manufacturer’s instructions. The volume of DEPC water used to elute the RNA from the Qiagen column was dictated by the nominal mass of the loaded RNA sample. Samples were eluted in 100ml of water, precipitated with 0.5 volume of 7.5M Ammonium Acetate and 2.5 volumes of 100% ethanol at -20oC for 1 hr and centrifuged for 10 min at room temperature. The pellet was drained and washed twice in 500µl of 70% ethanol. Supernatant was aspirated. The pellet was dried briefly (less than 1 min) in a speeedvac (Savant) and re-suspended in a small volume (~ 12–15ml) of DEPC water. A small aliquot (2ml) of the sample was used for quantitation. Cleaned RNA samples were annotated as “clnRNA” and stored at -20oC.

cDNA Synthesis

The protocol recommended by Affymetrix Inc. for cDNA synthesis was used at all times. The reaction was primed by annealing an oligo-dT primer coupled to a T7 RNA polymerase promoter to the RNA sample. Whenever possible, 8 mg of clnRNA were reverse transcribed using Superscript II reverse transcriptase in a 20ml reaction at 42oC for 1 hr. Second strand synthesis was carried out immediately in a total reaction volume of 150ml in the presence of E. coli DNA polymerase I, RNAse H and DNA ligase. The reaction mixture incubated for 2 hrs at 16oC and for a further 5 min in the presence of T4 DNA pol.. The reaction was terminated by the addition of EDTA. The sample was cleaned with a Qiagen  cDNA clean-up column according to the manufacturers directions. The elution buffer volume was 14ml. The eluted samples were stored overnight at -20oC.

In-Vitro Transcription (IVT) reaction

In a 0.5ml microfuge tube, complementary RNA (cRNA) was generated in an IVT reaction using a BioArray High Yield ENZO kit (Affymetrix). The 40ml reaction contained 10ml of cDNA sample and was incubated at 37oC in the heating block for 4-5hrs. Samples were mixed by flicking, pulse-centrifuged and returned to the incubator once every 40 minutes. Upon completion of the reaction, IVT samples were adjusted to a volume of 100ml with DEPC-treated water and cleaned using Qiagen RNA clean-up columns. Samples were eluted in 45ml of DEPC-treated water. A 2ml-aliquot was used for quantitation.  Corrected concentrations of cRNA (minus the input clnRNA) were determined. A standard fragmentation reaction volume was 40ml in a 0.5 ml microfuge tube and used 20mg of overall IVT RNA in 1X fragmentation buffer (40mM Tris acetate, pH 8.1, 100mM KOAc, 30mM MgOAc). The reaction was incubated at 94oC for 35min in a heat block. After the 35 min incubation the fragmented samples were placed on ice.
The standard hybridization cocktail volume was 300ml. 150ml of 2X hybridization buffer was added (final concentrations : 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20) Herring sperm and acetylated BSA were added to a final concentration of 0.1 and 0.5mg/ml respectively. The amount of fragmentation reaction containing 15mg of cRNA was added to the cocktail and the remaining volume was made up with molecular biology grade water. A 15ml aliquot of a 20X mixture of in-vitro transcripts of bacterial genes BioB BioC BioD and cre as external controls (spikes) were added to the cocktail to give final concentrations of 1.5, 5, 25 and 100pM respectively. Control oligonucleotide (5ml) was added to a final concentration of 50pM.

Array Hybridization

Sample Hyridization cocktails (300ml) were removed from storage at –20oC and thawed in a 45oC temperature block. The samples were incubated at 45oC for 5 min, incubated at 45oC for 5 min and then centrifuged at 15,000g for 5 min. This study used commercially available Affymetrix HG U133A 2.0 arrays only. These are in situ synthesized, high density oligonucleotide arrays which can interrogate 22,777 gene entities. The part number is 900444 more detailed information may be found at www.affymetrix.com website.
Meanwhile, the affymetrix chip arrays were taken from their storage at 4oC and allowed to come to room temperature. The chamber was filled with 1X hybridization buffer (final concentrations : 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20). The chip was then preconditioned by incubation in the hybridization oven at 45oC for 10 min. The chip was removed and the chamber drained.  Sample cocktails (200ml) were then introduced into the chamber of the chips. The ports were sealed with tough-spots stickers and placed in the hybridization oven and incubated at 45oC with rotation overnight. Next day (16hr later), the incubation was terminated and the chips removed from the oven.  Samples were retrieved from the chips and stored again in a freezer at -20oC. The chips were filled with buffer A and placed in a module of Fluidics 400 wash station. The chips were subjected to the Affymetrix  “EuKws4 ver 2” programmed series of stringent post hybridization washes, staining and post-staining washes in accordance with Affy protocols. Upon completion of the wash series (approximately 2 hrs), the chips were removed from the Fluidics station. The chips were inspected. Chips were scanned using an Agilent Gene Array scanner 3000 driven by Affymetrix GCOS software.

Generation of Expression Values

Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver. 1.3.11; Corimbia Inc., Berkeley, CA) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates of gene expression for each probe set. The software identifies informative probe pairs, and down-weights the signal contribution of probe pairs that are subject to differential cross-hybridization effects or that consistently produce no signal. The software also detects and corrects for saturation artifacts, outliers, and chip defects. A probability statistic was generated for each probe set. The probability is associated with the null hypothesis that the expression level of the probe set is equal to zero (background). Genes not significantly expressed above background in any of the samples (P > 0.05) were
Keywords: ordered


title: Small Sample Amplification Technologies

status: Public on Jun 03 2005

city: Rochester

first: Chin-Yi

last: Chu

address: 75 Elmwood Avenue

department: Environmental Medicine

institute: University of Rochester

summary:
This sample is part of a study that compares small sample amplification technologies.  The analysis looks at differential gene expression when compared to one round of T7 amplification.  A tumor cell line was used in comparison to a human reference RNA in this study.
Keywords = amplification
Keywords = small sample
Keywords = Affymetrix
Keywords: other

first: Agnes

last: Viale

first: Juan

last: Li

first: Jay

last: Tiesman

first: Susan

last: Hester

first: Aldo

last: Massimi

first: Chandi

last: Griffin

first: George

last: Grills

first: Greg

last: Khitrov

first: Kathryn

last: Lilley

first: Kevin

last: Knudtson

first: Bill

last: Ward

first: Karl

last: Kornacker

first: Herbert

last: Auer

first: Andrew

middle: I

last: Brooks


title: Oncostatin experiment

status: Public on Jun 18 2005

city: New York

first: Miroslav

last: Blumenberg

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

summary:
Cultured epidermal keratinocytes treated with OsM 1, 4, 24 & 48hrs, and Skinethic epidermal substitutes treated 1, 4, 24, 48h & 7days, each with untreated control
Keywords: Time course

overall_design:
Each timepoint has treated/untreated matched control.
Skinethic 4h treated was replicated.
Note: OncostatinM treatment, GSM61488, is the 1h control!!

first: Alix

last: Gazel

first: Miki


title: Use of an Isothermal Linear Amplification Method with Small Samples on DNA Microarrays

status: Public on May 25 2005

city: San Francisco

first: Michael

middle: E.

last: Salazar

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

summary:
Experiment 1: U133A arrays (2) hybridized to duplicate sscDNA samples prepared from 20 ng Clontech UHR RNA
Experiment 2: Mu6500A arrays (6) hybridized to triplicate sscDNA samples prepared from 3 x 5 ng mouse liver RNA and 3 x 100 ng mouse liver RNA
Experiment 3: U95Av2 arrays (6) hybridized to triplicate sscDNA samples prepared from 3 x 10 ng K562 RNA and 3 x 10 ng Stratagene UHR RNA
Experiment 4: U95Av2 array (1) hybridized to sscDNA sample prepared from template minus reaction (negative control)
Keywords: parallel sample

sample_organism:
Homo sapiens
Mus musculus
unidentified

first: Christopher

middle: S

last: Barker

first: Gregory

last: Dolganov

first: Kristina

last: Hanspers

first: Jean

middle: Y

last: Yang

first: David

last: Erle


title: HIV-1 burden influences host response to co-infection with Neisseria gonorrhoeae in vitro

status: Public on Apr 09 2005

city: Boston

first: Monty

last: Montano

address: 650 Albany Street, Bldg X, room 640

department: Medicine

institute: Boston Medical Center

summary:
Gene networks involved in HIV-1 infection of human PBMCs were investigated by dose dependant infection with HIV-1 (Bal).  Perturbation of networks was evaluted using a co-infection with N. gonorrheae.  Hierarchical clustering, fold change analysis, and contour mapping of genes was used to identify gene groups that were then anlayzed for statisically significant associations using EASE.
Keywords: dose response

first: Matt

last: Rarick

first: Paola

last: Sebastiani

first: Patrick

last: Brinkmann

first: Russell

last: Ericksen

first: Jerry

last: Skefos


title: LIF-dependent gene expression in human neural stem cell cultures

status: Public on May 17 2005

city: Madison

first: Jiang

last: Li

state: WI

address: 777 Highland Ave.

department: School of Pharmacy

institute: University of Wisconsin Madison

summary:
Human cortical neural stem cells, provided by Dr. Clive Svendsen (Waisman Center, University of Wisconsin at Madison), were generated from human fetal cortex (9 weeks post conception) and grown as free-floating neurospheres as previously detailed (Wright, et al 2003. Journal of Neurochemistry 86, 179-195). At 15 weeks of growth, 10 ng/ml LIF was added to the cultures. In cases where LIF was withdrawn, neurospheres were collected, medium removed, and neurospheres washed three times with 1% N2 supplemented with 20 ng/ml EGF, and cultured into the same.
Total RNA was prepared from a single human neural progenitor cell grown long-term LIF collected at 3 time points: early passage (GSM51360-GSM51362), mid passage (GSM51363-GSM51365), and late passage (GSM51366-GSM51368).
Keywords: parallel sample

first: Lynda

last: Wright

first: Jeffrey

last: Johnson

first: Clive

middle: N

last: Svendsen


status: Public on Apr 13 2005

city: Washington

first: Timothy

last: McCaffrey

state: DC

address: 2300 I Street NW

department: Department of Biochemisty & Molecular Biology

institute: The George Washington University

summary:
Comparison of SMC resistant and sensitive to TGF and Fas ligation by CH11 antibody
Keywords: other


title: Expression data in patients with chronic myelogenous leukemia for response to imatinib

status: Public on Apr 18 2005

city: Portland

first: Tom

last: Shi

state: OR

institute: OHSU

summary:
This is a class prediction experiment, where the class is the response status to imatinib (also called Gleevec), a drug used to treat patients with chronic myelogenous leukemia (CML).  There are two data sets, a training set (from Leipzig, 8 Responders and 5 Non-Responders) and a validation set (from Mannheim, 8 Responders and 7 Non-Responders).  The objective is to identify differentially regulated genes between CML patients who respond and those who do not respond to imatinib and confirm the results in the validation data set.  The samples from blood or bone marrow of CML patients were hybridized to Affymetrix HG-U95Av2 chip and RMA was used to generate the normalized signal values.
Keywords = chronic myelogenous leukemia
Keywords = imatinib
Keywords = cytogenetic responses
Keywords = Gleevec
Keywords = Affymetrix
Keywords: other

first: Lucy

last: Crossman

first: Motomi

last: Mori

first: Yi-Ching

last: Hsieh

first: Byung

last: Park

first: Thoralf

last: Lange

first: Peter

last: Paschka

first: Christina

last: Harrington

first: Knut

last: Krohn

first: Dietger

middle: W

last: Niederwierser

first: Rudiger

last: Hehlmann

first: Andreas

last: Hochhuas

first: Brian

last: Druker

first: Michael

middle: WN

last: Deininger


title: TNF & Parthenolide treatment of keratinocytes

status: Public on Apr 06 2005

first: Miroslav

last: Blumenberg

summary:
Cultured keratinocytes treated with TNFa in the presence or absence of NFkB inhibitor; time course 1, 4, 24 & 48 hrs.
Keywords = Epidermis
Keywords = skin
Keywords = keratinocytes
Keywords = inflammation
Keywords = NFkB
Keywords = TNFa
Keywords: time-course

first: Miki

first: Tomohiro

last: Banno

first: Alix

last: Gazel


title: Hematopoietic stem cell subsets

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary:
Hematopoietic stem cell (HSC) subsets based on the CD34 expression and/or lineage markers expression
Keywords: parallel sample

first: Roberta

last: Zini

first: Simona

last: Salati

first: Michela

last: Siena

first: Elena

last: Tenedini

first: Enrico

last: Tagliafico

first: Monica

last: Montanari

first: Tommaso

last: Zanocco Marani

first: Claudia

last: Gemelli

first: Tatiana

last: Vignudelli

first: Alexis

last: Grande

first: Myriam

last: Fogli

first: Lara

last: Rossi

first: Maria

middle: E

last: Fagioli

first: Lucia

last: Catani

first: Roberto

last: Lemoli

first: Sergio

last: Ferrari


title: Expression patterns throughout disease progression and impact on neuroAIDS.

status: Public on Mar 10 2005

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary:
The virus/host interactions during the acute phase of human immunodeficiency virus (HIV) infection help determine the course of disease. During this time period, virus enters the brain. Here, we report clusters of genes whose transcripts are significantly upregulated in the frontal lobe of the brain during acute simian immunodeficiency virus (SIV) infection of rhesus monkeys. Many of these genes are involved in interferon (IFN) and/or interleukin (IL)-6 pathways. Although neither IFNa nor IFN? are elevated in the brain, IL6 is increased. Both IFNa and IL6 are elevated in plasma during this acute phase. The upregulation of STAT1, verified by immunohistochemical staining, can be due to both central nervous system (CNS) (SIV and IL6) and peripheral (IFNa and IL6) causes, and can itself drive the expression of many of these genes. Examination of the levels of expression of the upregulated genes in the post-acute and long-term phases of infection, as well as in SIV encephalitis, reveals increased expression throughout SIV infection, which may serve to protect the brain, but can have untoward long-term consequences.
Keywords = HIV dementia
Keywords = Gene array
Keywords = Cytokine
Keywords = Simian immunodeficiency virus
Keywords: other

middle: R

first: Eleanor

last: Roberts

first: E

last: Burudi

last: Flynn

first: Lisa

middle: J

last: Madden

first: Kelli

last: Roinick

first: Debbie

middle: D

last: Watry

first: Michelle

last: Zandonatti

first: Michael

last: Taffe

first: Howard

last: Fox

first: Stephen

last: Henriksen


title: AML1-ETO target genes

status: Public on Mar 01 2005

first: Agnes

last: Viale

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary:
human CD34 cells isolated from cord blood or peripheral blood transduced with AML1-ETO or Empty vector (MIGR1)
Keywords = AML1-ETO Leukemia
Keywords: repeat sample

last: Nimer

first: Jorg

last: Cammenga


title: pediatric AML and normal bone marrow

status: Public on Jan 28 2005

city: Tokyo

first: Hitoshi

last: Ichikawa

address: 5-1-1 Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

summary:
This series represents leukemic samples obtained from pediatric AML patients at diagnosis and control normal bone marrow samples.
Keywords: other


title: Induction of Pathogenic Sets of Genes in Macrophages and Neurons in NeuroAIDS

status: Public on Mar 08 2005

summary:
The etiology of the central nervous system (CNS) alterations after human immunodeficiency virus (HIV) infection, such as dementia and encephalitis, remains unknown. We have used microarray analysis in a monkey model of neuroAIDS to identify 98 genes, many previously unrecognized in lentiviral CNS pathogenesis, whose expression is significantly up-regulated in the frontal lobe of simian immunodeficiency virus-infected brains. Further, through immunohistochemical illumination, distinct classes of genes were found whose protein products localized to infiltrating macrophages, endothelial cells and resident glia, such as CD163, Glut5, and ISG15. In addition we found proteins induced in cortical neurons (ie, cyclin D3, tissue transglutaminase, 1-antichymotrypsin, and STAT1), which have not previously been described as participating in simian immunodeficiency virus or HIV-related CNS pathology. This molecular phenotyping in the infected brains revealed pathways promoting entry of macrophages into the brain and their subsequent detrimental effects on neurons. These data support the hypothesis that in HIV-induced CNS disease products of activated macrophages and astrocytes lead to CNS dysfunction by directly damaging neurons, as well as by induction of altered gene and protein expression profiles in neurons themselves which are deleterious to their function.
Keywords = HIV dementia
Keywords = Gene array
Keywords = Simian immunodeficiency virus
Keywords = rhesus macaque
Keywords: other


title: Hypopharyngeal_cancer_transcriptome

status: Public on Mar 09 2005

city: Illkirch

first: Annaïck

last: Carles

country: France

institute: IGBMC

summary:
Gene expression analysis of a unique HNSCC (Head and Neck Squamous Cell Carcinoma) localization, the hypopharynx. Four normal and 34 tumor samples were analysed using Affymetrix HG-U95A microarrays containing probe sets representing ~12650 distinct transcription features.
Keywords = HNSCC Hypopharynx
Keywords: ordered


title: Sarcoidosis + Follow-up study

status: Public on Jan 18 2005

city: Basel

first: Florent

last: Baty

address: Petersgraben 4

department: Pneumology

country: Switzerland

institute: Universitätsspital Basel

summary:
Sarcoidosis + Follow-up 6 month after
Keywords = sarcoidosis
Keywords = follow-up
Keywords: other

first: Michel

middle: P

last: Bihl

first: Martin

middle: H

last: Brutsche


title: B_Cell_Chronic_Lymphocytic_Leukemia

status: Public on Apr 01 2005

city: Vienna

first: Stratowa

last: Christian

address: Dr. Boehringergasse 5-11

department: Dept NCE Lead Discovery

country: Austria

institute: Boehringer Ingelheim Austria

summary:
We used high density oligonucleotide arrays to identify molecular correlates of genetically and clinically distinct subgroups of B-cell chronic lymphocytic leukemia (B-CLL). Gene expression profiling was used to profile the five most frequent genomic aberrations, namely deletions affecting chromosome bands 13q14, 11q22-q23, 17p13 and 6q21, and gains of genomic material affecting chromosome band 12q13. A strikingly high degree of correlation between loss or gain of genomic material and the amount of transcripts from the affected regions leads to the hypothesis of gene dosage as a significant pathogenic factor. Furthermore, the influence of the immunoglobulin variable heavy chain (VH) mutation status was determined. A clear distinction in the expression profiles of unmutated and mutated VH samples exists, which can be discovered using unsupervised learning methods. However, when samples were separated by gender, this separation could only be detected in samples from male patients.
Since the samples were either hybridized onto HG-U95A arrays or onto HG-U95Av2 arrays, only genes common to both arrays were used for further analysis.
This study is described in more detail in Haslinger C, et al. 2004. J Clin Oncol. 22:3937-3949
Series _keyword: CLL, chronic lymphocytic leukemia, immunoglobulin somatic hypermutation, genomic aberrations
Keywords: other

first: C

last: Haslinger

first: N

last: Schweifer

first: S

last: Stilgenbauer

first: H

last: Doehner

first: P

last: Lichter

last: Kraut

last: Stratowa

first: R

last: Abseher


title: A549 lung pneumocytes cell line infected with wildtype and deletion mutation PAK strain Pseudomonas aeruginosa

status: Public on Dec 10 2004

first: Atul

last: Butte

state: MA

address: 300 Longwood Avenue

institute: Children's Hospital, Boston

summary:
The bacterial type III secretion system (TTSS) is dedicated to directly effect host cell pathways by pathogens. In order to identify the key host responses of the various parts of the TTSS, we utilized expression profiling of a lung pneumocytes cell line, A549, exposed to various isogenic mutant strains of Pseudomonas aeruginosa PAK. We have devised a novel filtering method to isolate the key responses to the effector proteins as well as the translocation machinery. Individually, the effector proteins elicited host responses that were consistent with the known function of each, many of which either regulated, or are regulated by the cell cycle. However, our analysis has shown that the effector proteins elicit a distinct host expression pattern when present in combination, suggesting that these proteins function in synergy. Furthermore, the host transcriptional response to the translocation complex involved genes that are involved in remodeling of the plasma membrane, suggesting that the host cell is able to sense the protrusion of the TTSS machinery. This study shows that the individual components of the TTSS define an integrated system and that a systems biology approach is required to fully understand the complex interplay between pathogen and host.
Keywords = Pseudomonas aeruginosa
Keywords = A549 human lung carcinoma cell line
Keywords = cystic fibrosis
Keywords: repeat sample

first: Jeffrey

first: Sangeeta

middle: B

last: English

first: Matthew

middle: C

last: Wolfgang

last: Lory


title: Gene expression in Cryptosporidium parvum-infected human ileocecal adenocarcinoma cells (HCT-8)

status: Public on Feb 15 2005

city: Saint Paul

first: Mingqi

last: Deng

state: MN

address: 1988 Fitch Avenue

department: Veterinary and Biomedical Sciences

institute: University of Minnesota

summary:
• The origin of biological samples (In vitro infection of HCT-8 cells with Cryptosporidium parvum)

Monolayers of the HCT-8 cells (ATCC CCL-244, American Type Culture Collection) were cultured in RPMI 1640 medium containing 10% fetal bovine serum and additional nutritional supplements. Cells in log phase were plated at 2×106 cells per 150 mm tissue culture dish and infected with sterilised Cryptosporidium parvum oocysts (Iowa strain). Purified oocysts were suspended in phosphate buffered saline, sterilised in 33% bleach for 7 min on ice, washed in Hank's buffered saline solution, and added to HCT-8 cultures at a ratio of one oocyst per cell. Following a 2 h excystation period at 37 °C, cells were washed with warm Hank's buffered saline solution, and cells were incubated in fresh supplemented media. Mock-infected cultures were treated identically, with the exception that oocysts were not added to the cultures.

Three independent mock- and C. parvum-infected cultures were prepared for analysis.

•  The origin of mRNA samples

At 6, 12, 24, 48, and 72h post-inoculation, cell culture media were removed and cultures were immediately lysed by the addition of 3.5 ml of Trizol® reagent (GIBCO BRL Life Technologies) directly to the culture plate. Total RNA was prepared as described by the manufacturer, and poly(A) mRNA was isolated using oligo-dT cellulose columns (Amersham Pharmacia Biotech). The qualities of total RNA and poly(A) mRNA preparations were assessed by Northern blot.

•  Protocols for conducting microarray hybridization

Poly(A) mRNA was converted into ‘target’ suitable for hybridisation to Affymetrix microarray chips according to protocols provided by Affymetrix Inc. (Santa Clara, CA). Briefly, 2.0  g of poly(A) mRNA was reverse-transcribed to prepare double-stranded cDNA using T7-(dT)24 primer (GENSET Corp., La Jolla, CA) and Superscript II reverse transcriptase (GIBCO). Approximately 1  g of cDNA was used for in vitro transcription in the presence of biotinylated UTP and CTP using the Enzo BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, Inc). This labelled cRNA was fragmented in 40 mM Tris–acetate (pH 8.1), 100 mM potassium acetate, and 30 mM magnesium acetate at 94 °C for 35 min. The integrity of cRNA and the efficiency of fragmentation were monitored by Northern blot analysis (not shown).
Fragmented biotinylated cRNA targets were hybridised to HG-U95Av2 chips (Affymetrix) that contain probe sets for 12,600 human gene/transcripts. Fifteen micrograms of fragmented cRNA and appropriate controls were hybridised to the chips at 45 °C for 16 h with constant rotation at 60 rev./min. The chips were subsequently washed and stained with streptavidin–phycoerythrin conjugate using the GeneChip Fluidics station protocol EukGE_WS2 (Affymetrix). Following washing and staining, microarray chips were scanned twice at 3  m resolution using a Hewlett-Packard confocal scanner and hybridisation intensities for each of the genes/transcripts were collected from scanned images.

•  Analysis of microarray data

Gene expression data were initially analysed with the GeneChip® expression analysis software (Affymetrix Microarray Suite, version 5.0). The fluorescence intensity of the genes/transcripts was measured for each probe array and, to minimise discrepancies due to non-biological variations, normalised by global scaling to 1000.

Further data analyses were performed using GeneSpring software (version 6.0; Silicon Genetics, Redwood City, CA). Per gene normalisation was applied in which the expression signal of each gene in C. parvum-infected cells (raw data) was normalised to the median of its measurements in the mock-infected samples (control); and the ratio of expression levels between mock and infected samples was calculated as the mean value of normalised signal vs. control signal among three replicates. To identify genes with significantly altered expression, a series of statistical analyses (filtering) were performed: cut-off values for ratio of expression levels 1.80 and 0.55 were used to filter genes with expression level fold changes greater than ±1.8 in all three independent samples. Genes with fold change variations >1.5 across the three samples were excluded. Furthermore, a ‘statistical group comparison’ using Student's t-test/ANOVA was conducted to compare mean expression levels between mock-infected and infected samples, and the genes with significant differential expression (P<0.05) were selected. Identified differentially expressed genes were then annotated using GeneSpring's ‘Build Simplified Ontology’ constructor which hierarchically groups genes into meaningful biological categories (gene lists) based on the Gene Ontology Consortium Classifications. Various lists of regulated genes were created by cross-referencing annotated gene lists and applying assorted statistical and visualisation methods.
Keywords: time-course

first: Mitchell

last: Abrahamsen


title: Adenovirus-mediated E2F-1 gene transfer in melanoma cell line

status: Public on Jan 01 2005

city: Louisville

first: Kelly

middle: M

last: McMasters

state: KY

address: 580 South Preston, Room# 326

department: Surgery

institute: University Of Louisville

summary:
E2F-1 gene expression profiling by adenovirus-mediated gene transfer in SKMEL-2 melanoma cell line.
Keywords: other

first: Azemat

last: Jamshidi-Parsian

first: YanBin

last: Dong

first: Heshan Sam

last: Zhou


city: Lexington

first: David

middle: Murray

last: Kaetzel

address: 800 Rose Street

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky College of Medicine

summary:
Overall study: Identification of PDGF-dependent patterns of gene expression in U87 glioblastoma cells.

RNA was obtained from triplicate dishes of 5 different groups of U87 cells, each (total 15) analyzed with one U95 microarray chip.

Three different comparisons were made:
1) Clone 3.1 (34580-34582) vs. clone 3.3 (34583-34585) vs. parent U87 (34592-34594).

Purpose: demonstrate that the gene expression profiles between these 3 cell lines are not different, so they could be pooled as a single untreated group.

2)  Pooled control group (34580-34585, 34592-34594) vs. clone 8.1 (34586-34588).

Purpose:  identify genes specifically controlled by autocrine PDGF activity.

3)  Clone 8.1 (34586-34588)
vs. clone 8.1 treated with PDGF (34589-34591)

Purpose:  Identify genes specifically induced by exogenous PDGF.
Keywords = platelet-derived growth factor
Keywords = glioblastoma
Keywords = brain cancer
Keywords = sterol regulatory element binding protein
Keywords = SREBP
Keywords: ordered

first: Deqin

last: Ma

first: Catherine

last: Nutt

first: Piam

last: Shanehsaz

first: Xuejun

last: Peng

last: Louis