title: Gene expression in rheumatoid arthritis synovial macrophages

status: Public on Feb 14 2008

first: Taras

last: Antoniv

address: 535 East 70th Street

department: Research

institute: Hospital for Special Surgery

summary:
Macrophages from RA synovial fluids were compared to primary human blood-derived macrophages.
Keywords: disease state analysis

overall_design:
Macrophages from synovial fluids of five RA patients were isolated by ficoll density gradient centrifugation, followed by positive selection of CD14+ cells using magnetic beads. The patients’ diagnoses were determined by their physicians, in each case a Board-certified rheumatologist at the Hospital for Special Surgery, and were definite RA according to American College of Rheumatology criteria. De-identified samples were processed in an anonymous manner using a protocol approved by the Institutional Review Board of the Hospital for Special Surgery.
Human peripheral blood mononuclear cells were isolated from venous blood of  independent healthy donors by centrifugation on a Ficoll density gradient. Monocytes were obtained from PBMCs using anti-CD14 magnetic beads, and were >96% pure as verified by flow cytometry. Monocytes were differentiated into macrophages by culturing  in RPMI 1640 medium supplemented with 10% fetal bovine serum and M-CSF (20 ng/ml). The viability and purity of macrophages was comparable in all conditions
Gene expression was analyzed using Affymetrix microarrays and protocols.

first: Lionel

middle: B

last: Ivashkiv

middle: T

first: Xiaoyu

last: Hu

first: Yarilina

last: Anna

first: Kyung-Hyun

last: Park-Min


title: 16 prostatic cancer cell lines and sensitivity to an anticancer tumor agent dasatinib

status: Public on Dec 01 2007

city: Princeton

first: Xi-De

last: Wang

state: NJ

country: USA

institute: Bristol-Myers Squibb

summary:
Transcriptional profiling was conducted on RNA from 16 prostatic cancer cell lines to identify genes whose expression level correlate with sensitivity of an anti-tumor agent (dasatinib).
Keywords: comparison of sensitive group versus resistant group of cell lines to agent

overall_design: Baseline gene expression profiling was performed using 16 prostatic cancer cell lines to identify expression signatures highly correlated with in vitro sensitivity to dasatinib.

first: X

middle: D

first: F

last: Huang


title: Early expression data of H69 xenograft tumors following PDT treatment.

status: Public on Nov 01 2007

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

summary:
The response of tumors to PDT treatment is expected to provide information on effects of oxygen depletion, induced apoptosis, induction of an inflammatory response and induction of an ani-tumor immune response.
Keywords: comparison of treatment vs control

overall_design: NCI-H69 human SCLC xenografts were induced in SCID mice.  Three pairs of xenograft tumors, PDT treated and untreated controls, were harvested four hours after PDT treatment. RNA was isolated and prepared for hybridization to human Affymetrix GeneChip arrays.

first: Jean

middle: R

last: Starkey

first: Alexsander

last: Rebane

first: Mikhail

middle: A

last: Drobizhev

first: Fanqing

last: Meng

first: Aijun

last: Gong

first: Aleisha

last: Elliott

first: Charles

middle: W

last: Spangler


title: Expression data from Annexin A1 Ac1-25 vs. Unstimulated human peripheral blood monocytes

status: Public on Sep 19 2007

city: Muenster

first: Carsten

last: Lange

state: NRW

address: Von-Esmarch-Str. 56

department: Medical Biochemistry

country: Germany

institute: ZMBE

summary:
We used microarrays to detail the global gene expression changes elicited by stimulation of human peripheral blood monocytes from buffy coats with 50µM Annexin A1 peptide Ac1-25 for 2h versus unstimulated control monocytes.
Keywords: comparative gene expression study

overall_design: three independent monocyte isolations each were used for stimulated and control cell RNA preparations and subsequent hybridization to arrays according to manufacturers protocols

first: Lange

last: Carsten

first: Starrett

last: Diane

first: Goetsch

last: Julia

first: Gerke

last: Volker

first: Rescher

last: Ursula


title: MoDCs grown with/without Etanercept TNF inhibitor

status: Public on Oct 06 2007

city: NYC

first: Lisa

middle: Caithleen

last: Zaba

state: NY

address: 1230 York Avenue

department: Dermatology

institute: Rockefeller University

summary:
The process for making monocyte derived DCs (moDCs) has been previously described (46).  All analysis was performed on “day 5” immature DCs.  Etanercept 10mg/mL was added to experimental wells on days 0, 2, and 4.  We chose this concentration of etanercept as it approximates the plasma concentration of drug when given 50mg BIW.
Keywords: Inhibition assay

overall_design: 6 totoal samples.  3 control replicates paired with 3 experimental replicates.

middle: C

first: James

middle: G

last: Krueger


title: The effect of erstressin and nostressin on cytokine-induced A172 human glioblastoma cells in culture.

status: Public on Sep 01 2007

city: San Diego

first: Sara

last: Dozier

state: CA

address: 10420 Wateridge Circle

institute: Kalypsys, Inc.

summary:
The unfolded protein response (UPR), a signaling pathway triggered by endoplasmic reticulum (ER) stress, is induced by a range of environmental factors. Here we describe the identification and characterization of a synthetic small molecule, erstressin, which activates the UPR.  Erstressin induced rapid phosphorylation of PERK and eIF2a and the alternative splicing of XBP-1, hallmark initiating events of the UPR.  Further, erstressin activated the transcription of multiple genes involved in the UPR.   Coincident with these effects, erstressin also downregulated the transcription of the inflammation-associated enzyme inducible nitric oxide synthase (iNOS) in cytokine-activated cells.  A close analog of erstressin that failed to induce the UPR did not attenuate expression of iNOS, suggesting that both biological effects of erstressin were mediated by a common mechanism.  Further, the structurally-distinct ER stressor thapsigargin also inhibited iNOS expression.  Together these chemical genetic studies reveal an unanticipated anti-inflammatory role for the UPR.
Keywords: Time course

overall_design: We utilized microarrays to understand the global effect of a novel compund, erstressin, on cytokine stimulated cells over time.

middle: J

first: Christian

last: Hassig

first: Mark

middle: E

last: Massari


title: Disruption of E-cadherin-mediated adhesion induces a functionally distinct pathway of dendritic cell maturation

city: Branford

middle: Andrew

last: Whitney

state: CT

address: 36 East Industrial Road

institute: CGI Pharmaceuticals Inc.

summary:
	The maturation of dendritic cells (DCs) after exposure to microbial products or inflammatory mediators plays a critical role in initiating the immune response.  We found that maturation can also occur under steady state conditions, triggered by alterations in E-cadherin-mediated DC-DC adhesion. Selective disruption of these interactions induced the typical features of DC maturation including the upregulation of costimulatory molecules, MHC class II, and chemokine receptors.  These events were triggered at least in part by activation of the b-catenin pathway.  However, unlike maturation induced by microbial products, E-cadherin-stimulated DCs failed to release immunostimulatory cytokines, exhibiting an entirely different transcriptional profile. As a result, E-cadherin-stimulated DCs elicited an entirely different T cell response in vivo, generating T cells with a regulatory as opposed to an effector phenotype. These DCs induced tolerance in vivo and may thus contribute to the elusive steady state “tolerogenic DCs”.
Keywords: time-course, dendritic cell maturation

overall_design: We performed a genome-wide microarray analysis to study the expression profiles of DCs matured by CD as opposed to a conventional TLR agonist (E. coli, which stimulates multiple TLRs).  RNA was isolated from human CD34+ DCs at various times after stimulation and used to probe Affymetrix U95Av2 chips.  A time course was followed after various stimuli, with single chips used per time point.  >700 genes were found differentially regulated upon maturation by either CD or bacterial stimulation.  Cluster analysis revealed that after an early phase (1-3 hr) of similarity, expression profiles exhibited by the two sets of DCs diverged dramatically at later time points (>6 hr).  A number of transcripts were markedly upregulated in the bacteria-stimulated set that remained relatively unchanged or actually decreased in the cluster-disrupted set.  There were some transcripts upregulated in cluster-disrupted cells, however, with at least some of these increases prevented by adding anti-E-cadherin mAb under conditions that blocked maturation. Clearly, the transcriptional events induced by alteration of E-cadherin-mediated adhesion were quite distinct from those induced by TLR activation.

first: Andrew

first: Aimin

last: Jiang

first: Shan

first: Satoru

last: Ono

first: Ira

last: Mellman


title: IL-1 treatment of human epidermal keratinocytes

status: Public on Sep 22 2007

city: New York

first: Miroslav

last: Blumenberg

address: 455 First Ave #874

institute: NYU School of Medicine

summary:
Interleukin-1 is a proinflammatory and immunomodulatory cytokine that plays a crucial role in inflammatory diseases of the skin, including bacterial infections, bullous diseases, UV damage and especially psoriasis. To characterize the molecular effects of IL-1 in epidermis, we defined the transcriptional changes in human epidermal keratinocytes 1, 4, 24, and 48 h after treatment with IL-1a. IL-1 significantly regulated 388 genes, including genes associated with proteolysis, adhesion, signal transduction, proliferation, and epidermal differentiation. IL-1 induces many genes that have antimicrobial function. Secreted cytokines, chemokines, growth factors, and their receptors are the prominent targets of IL-1 regulation, including IL-8, IL-19, elafin, C3, and S100A proteins, which implicates IL-1 in the pathogenesis of inflammatory diseases. IL-1 induced not only proliferation-associated genes but also differentiation marker genes such as transglutaminase-1 and involucrin, which suggests that IL-1 plays an important role in the aberrant proliferation and differentiation seen in psoriasis. Correlation of IL-1 regulated genes with the TNFa and IFNg regulated ones showed more similarities between IL-1 and TNFa than IL-1 and IFNg, whereas Oncostatin-M affected a largely unrelated set of genes. IL-1 regulates many genes previously shown to be specifically over-expressed in psoriasis. In summary, IL-1 regulates a characteristic set of genes that define its specific contribution to inflammation and aberrant differentiation in skin diseases.
Keywords: Time course

overall_design: keratinocytes were treated with 25 ng/ml IL-1 and transcriptomes compared to untreated controls at 1, 4, 24 and 48 h post treatment.

first: Shoichiro

last: Yano

first: Tomohiro

last: Banno

first: Rebecca

last: Walsh


title: Gemcitabine Drug resistance

status: Public on Aug 30 2007

city: Duarte

first: Xiyong

last: Liu

address: 1500 E Duarte Rd

department: Medical Oncology & Therapeutic Research

institute: City of Hope

summary:
KBwt is a KB parental cell
KBHURs is a hydroxyurea resistant KB clone
KBGem is a gemcitabine resistant KB clone
Keywords: HU95 V2

overall_design: We extracted the RNA from KBwt, KBHURs and KBGem clones, and conducted hybridization with HU95 v2 Chip.

first: Yun

last: Yen

first: Bingsen

last: zhou


title: Profiling Motility Signal-Induced Genes in Human Keratinocytes

status: Public on Aug 15 2007

city: LOS ANGELES

first: CHIEH-FANG

last: CHENG

address: 1303 N MISSION RD

department: DERMATOLOGY

institute: USC

summary:
In an acute skin wound, newly released serum growth factors in the wound bed drive lateral migration of human keratinocytes (HKs) to re-epithelialize the wound. However, profiling the migration signal-specific genes has long been challenged by pleiotropic effects of a given growth factor, including proliferation, migration and factor-specific responses. To overcome these technical problems, we 1)  took advantage of a unique response of HKs to transforming growth factor-beta (TGFbeta) to selectively suppress growth signal-responding genes and identify motility-specific genes and 2) employed dual stimulation of HKs with TGFalpha and insulin to identify the common genes and eliminate factor-specific genes. Under these conditions, DNA microarray analyses were utilized to study the profiles of both TGFalpha-regualted and insulin-regulated immediate early (IE, 30 min), early (E, 60 min) and delayed early (DE, 120 min) genes.
Keywords: time course, growth factor response

overall_design: HKs were seeded on collagen I pre-coated tissue culture plates (150 mm) around 45% confluence (~ 2.5 X 106 cells) in complete medium and incubated overnight. Next day, the cells (~ 4.5 X 106 cells) were deprived of any supplemental GFs and incubated in serum-free medium for 16 hours to rest the cells at G0/G1 phase. The cells were then washed with pre-warmed serum-free medium and incubated in fresh serum-free medium containing 20 ng/ml TGFbeta for 20 min at 37oC to block expression of growth signal-related genes. TGFalpha or insulin was added to separate plates (in the continued presence of TGFbeta) for 30 min, 60 min and 120 min. At the end of each stimulation time points, the cells were washed with ice-cold PBS to holt the stimulation and subjected to RNA isolation.

first: Chieh-Fang

last: Cheng

first: Jianhua

last: Fan

first: Balaji

last: Bandyopahdhay

first: Shengxi

last: Guan

first: Mei

last: Chen

first: David

last: Woodley

first: Wei

last: Li


title: Gene Profiling of Testosterone-Regulated Genes in the Skeletal Muscle of Hiv-Infected Men Experiencing Weight Loss

status: Public on Aug 29 2007

city: Boston

first: Monty

last: Montano

state: MA

address: 650 Albany Street, Bldg X, room 640

department: Medicine

institute: Boston Medical Center

summary:
Context: Although androgen treatment increases muscle mass in HIV-infected men, the underlying mechanisms are poorly understood. Analysis of genome-wide microarray data obtained from skeletal muscle biopsies can be used to profile androgen-regulated pathways.
Objective: To identify genes and pathways associated with testosterone treatment and myogenesis in the context of HIV-infected men using genome-wide microarray analysis of skeletal muscle biopsies.
Results: A significant weight gain was observed in subjects treated with testosterone compared to placebo (+2.05 kgs and –1.07 kgs, respectively; P = 0.003) as well as gains in DEXA lean
mass (2.93 kgs vs. 0.35 kgs, respectively; P = 0.003). Microarray expression profiles and RTPCR validation of RNA after 14 days of treatment indicated that several gene sets including
transcriptional control, myogenesis, adipogenesis, insulin signaling, apoptosis, cell cycle, chromatin remodeling, and stress response genes were differentially expressed with testosterone treatment. Protein expression analysis of myogenic differentiation and protein synthesis markers (MyoD, Myogenin, phosphorylated p38 MAPK and phosphorylated AKT) in muscle biopsies and skeletal muscle cells treated with DHT confirmed that testosterone engages
a network of pro-myogenic genes.
Conclusions: Testosterone-associated gain in muscle mass in HIV-infected men engaged a network of regulatory pathways involved in broad transcriptional control, myogenesis, insulin signaling, chromatin remodeling, and stress response. Further evaluation of precise signaling intermediates within androgen regulated pathways may help to better define improvements in muscle mass, both in healthy and HIV infected patients.
Keywords: Dose Response, Myogenesis

overall_design:
Design, Setting, and Participants: 44 HIV+ men with weight loss were randomized to receive either 300mg testosterone enanthate or placebo injections IM weekly for 16 weeks. Muscle
biopsies were obtained at baseline and on treatment day 14. A random subset of specimens was chosen for microarray analysis; changes in selected genes were confirmed by reverse transcriptase - polymerase chain reaction (RT-PCR), and western blot analysis. Human skeletal
myogenic precursor cells (SkMCs) were cultured in vitro in the presence of dihydrotestosterone (DHT) to evaluate activation of myogenic protein expression.
Main outcome measures: Relative RNA levels in skeletal muscle biopsies were measured by expression profiling with microarrays and expression levels were validated in samples using quantitative RT-PCR. Further confirmation of changes in key myogenic biomarkers was obtained in DHT treated SkMCs.

first: John

middle: N

last: Flanagan

first: Lan

last: Jiang

first: Paola

last: Sebastiani

first: Matthew

last: Rarick

first: Nathan

middle: K

last: LeBrasseur

first: Carl

last: Morris

first: Ravi

last: Jasuja

first: Shalender

last: Bhasin


title: Effect of INF-gamma and IL1-beta on thyroid cells

status: Public on Aug 24 2007

city: Ann Arbor

first: Rork

last: Kuick

state: MI

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

institute: University of Michigan

summary:
Normal primary thyroid cells were incubated with vehicle, 100 IU/ml IFN-gamma, 50 IU/ml IL1-beta, or a combination of both IFN-gamma and IL1-beta for 24 or 72 hours.  The experiment was repeated 5 times using thyroid cells from 5 different patients.   RNA expression was analyzed using Affymetrix HG_U133A arrays for 3 of the thyroids, and HG_U133A_2.0 (small version of HG_U133A)  arrays for 2 of the thyroids.
Keywords: cytokine treatments

overall_design:
Normal primary thyroid cells were incubated with vehicle, 100 IU/ml IFN-gamma, 50 IU/ml IL1-beta, or a combination of both IFN-gamma and IL1-beta for 24 or 72 hours.  The experiment was repeated 5 times using thyroid cells from 5 different patients.  One array was hybridized per sample (20 samples).

The probe-set intensities with accompanying statistical analysis (2-way ANOVA) and the associated README file are included as Supplementary files.

first: James

last: Baker

first: Su

middle: H

last: Wang

first: Mary

last: Van Antwerp

first: Paul

last: Gauger

first: Gerard

middle: M

last: Doherty


title: Synovial fibroblasts, RA versus OA

city: Dresden

first: Andreas

last: Beyer

address: Tatzberg. 47/49

institute: BIOTEC

summary:
mRNA expression levels in synovial fibroblasts in 6 rheumatoid arthritis patients versus 6 osteoarthritis patients.
Keywords: disease type comparison, mRNA expression study

overall_design:
Synovial tissue was obtained from open joint replacement surgery or
arthroscopic  synovectomy. Patients with RA or OA (n = 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.

first: Dirk

last: Pohlers

last: Koczan

first: Thomas

last: Wilhelm

first: Hans-Jürgen

last: Thiesen

first: Raimund

last: Kinne


title: Gene expression analysis of chronic inflamed and healthy human periodontal ligament cells in vivo

status: Public on Aug 01 2007

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
The periodontium are the tissues supporting and investing the tooth and consists of the periodontal ligament, the gingiva, the root cementum, and the alveolar bone. The functions of the cell populations in health and disease regarding the host-mediated tissue destruction are not well understood. To get a first idea, of which genes might play a distinct role in chronic periodontal disease in vivo, we compared the genom-wide gene expressions of chronic inflamed and healthy periodontal ligament cells by microarray analysis and validated the data by real-time RT-PCR. The expression rates of 14.239 genes were investigated and 3.018 of them were found differentially expressed by at least two-fold, the expression rates of 1.451 genes were significantly up-regulated and the expression rates of 1.567 genes were significantly down-regulated in inflamed PDL cells. We focused on mainly structural components, for example, laminins and integrins, as well as degrading enzymes, for example, MMPs and cathepsins. The molecular composition of the laminin network varies in chronic inflamed compared to healthy PDL cells in vivo. Furthermore, integrin alpha6beta4, together with laminin-332, might be involved in chronic periodontal inflammation. Findings that diverse keratins were upregulated in chronic disease indicate that the epithelial cell rests of Malassez might also be involved in chronic periodontal inflammation. Also cathepsin B and cathepsin C might participate in the connective tissue destruction. The microarray analysis has identified a profile of genes potentially involved in chronic periodontal inflammation in vivo. Further studies are needed to entirely understand cellular activities during chronic periodontal inflammation in vivo.
Keywords: expression analysis

overall_design: Periodontal tissue was collected from 32 patients at the Dental Medical School of the University of Goettingen (12 men, 20 women, aged between 18 and 72 years) from March 2005 to Dezember 2005. The tissue probes were taken from teeth, either extracted for orthodontic reasons (healthy periodontium) or because of chronic periodontal lesions. The differentiation between both collectives was performed using clinical and radiological parameters (clinical attachment loss, increase in probing depth, and radiographic bone loss). A detailed anamnesis of each patient was explored. All patients were without a medical history and were not on medication. In addition, the tissue samples used in our study were only taken from non-smokers. The extracted teeth were immediately frozen and stored at -80°C. All patients who participated in the study were informed about the nature and aim of this project and gave their written informed consent. The study was approved according to the regulations of the Ethics Committee of the Medical Faculty of the University of Goettingen.

first: R

first: N

last: Gersdorff

last: Miosge


title: Multiple sclerosis (oksen-affy-human-488680)

status: Public on Jul 26 2007

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Multiple sclerosis (MS) is a neuroinflammatory disease of the central nervous system (CNS) with a well documented genetic component. Significant advances in the identification of the genetic component of MS have yet to be realized.  The recent success that genetical genomics has shown in the identification of new QTL in plants and mice hold significant promise that this method can now be systematically applied in humans. Encouraging results indicate that even normal variation in gene expression could be genetically encoded. Characteristic patterns of gene expression have been already identified in PBMC from MS patients, and a high-resolution map of the human genome is readily available. We are combining these two powerful sources of information towards the identification of the long-time elusive genetic component of MS.  The study proposed herein of ten individuals is a pilot study to ensure that gene expression variation is detectable in selected samples from our lymphoblastoid cell line collection to warrart a larger genetical genomics study.
Pilot:  Verify that there is sufficient variation in lymphoblastoid cell lines to warrant a full study.
The full study will have the following specific aim:
To explore and identify genomic regions responsible for the gene expression signature characteristic of multiple sclerosis patients.
Gene expression patterns across lymphoblastoid cell lines from MS patients are sufficiently variable.
Following validation of the above hypothesis, the following hypothesis will be addressed in a full study:
Some of the genetic determinants of multiple sclerosis can be identified through the combination of studying gene expression and genomic mutations associated with this gene expression.
Ten human lymphoblastoid cell line samples from our repository have been selected for this pilot study.  Lymphoblastoid cell lines have been established by infection with the Epstein-Barr virus, and RNA has been isolated with the Rneasy kit (Qiagen, CA).  RNA was quantitated using the RibogreenTM reagent (Molecular Probes, Eugene, OR) and its integrity was evaluated by agarose gel electrophoresis.  BRB Arraytools, Bioconductor in R, and JMP Genomics (SAS Institute, Cary, NC) will be used to evaluate the expression variance of the samples by comparing them to already existing human microarray data.
Keywords: other

first: Jorge

last: Oksenberg


title: HMEC gene profile after stimulation with MRP8/MRP14

status: Public on Aug 08 2007

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

institute: Hannover Medical School

summary:
Generating the gene expression profile of MRP8/MRP14-stimulated HMEC monolayer.
Keywords: stress response

overall_design:
4 independent experiments
HMEC-1 monolayer were left untreated or stimulated for 6h with 200 µg/ml MRP8/MRP14.

first: Katarzyna

last: Barczyk

last: Vogl

first: Johannes

last: Roth


title: Expression data from ovarian cancer cells with time-course and concentration-profiles

status: Public on Jul 01 2007

city: Buffalo

first: Yseult

middle: F

last: Brun

address: Elm and Carlton St

department: Cancer prevention and epidemiology

institute: Roswell Park Cancer Institute

summary:
Time-course and concentration-effect experiments with multiple time points and drug concentrations provide far more valuable information than experiments with just two design-points (treated vs. control), as commonly performed in most microarray studies. Analysis of the data from such complex experiments, however, remains a challenge. Here we present a semi-automated method for fitting time profiles and concentration-effect patterns, simultaneously, to gene expression data. The submodels for time-course included exponential increase and decrease models with parameters such as initial expression level, maximum effect, and rate-constant (or half-time). The submodel for concentration-effect was a 4-parameter Hill model.
The method was applied to an Affymetrix HG-U95Av2 dataset consisting of 51 arrays. The specific study focused on the effects of two platinum drugs, cisplatin and oxaliplatin, on A2780 human ovarian carcinoma cells. Replicates were available at most time points and concentrations. Eighteen genes were selected; time-course and concentration-effect were modeled simultaneously. Comparisons of model parameters helped distinguish genes with different expression patterns between the two drug treatments. This overall paradigm can help in understanding the molecular mechanisms of the agents, and the timing of their actions.
Keywords: time course , dose response, cisplatin, oxaliplatin, Human ovarian carcinoma cells

overall_design: For the time-course experiments, samples were exposed to IC90 concentrations of oxaliplatin (32 μM) or cisplatin (25 μM) for 2 hours, and then allowed to grow in drug free medium. Cells were harvested and processed at the following times: before treatment, immediately after treatment (0 h), and at 2 h, 6 h, 16 h and 24 h after treatment. Control experiments were done following a similar design, but with exposure to drug-free medium. For the concentration-effect experiments, samples were treated with specific growth-inhibitory concentrations of cisplatin or oxaliplatin for 2 hours. The previously-estimated IC10, IC25, IC50, IC75 and IC90 concentrations (for 2 hr drug exposure; 72 hr total growth) for cisplatin and oxaliplatin growth inhibition of A2780 were 2.6, 4.0, 6.4, 12 and 25 μM and 2.8, 4.8, 8.5, 17 and 32 μM respectively. Cells were harvested and processed at 16 h after completion of treatment

first: Lakshmi

last: Pendyala

first: Suzanne

last: Hector

first: Ram

last: Varma

first: William

last: Greco

first: Ramakumar

last: Tummala


title: JAM-A Knockdown in HepG2 Cells

city: Charleston

first: Stephen

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

summary:
Hepatocytes are polarized epithelial cells whose function depends upon their ability to distinguish between the apical and basolateral surfaces that are located at intercellular tight junctions. It has been proposed that the signaling cascades that originate at these junctions influence cellular activity by controlling gene expression in the cell nucleus. To assess the validity of this proposal with regard to hepatocytes, we depleted expression of the tight junction protein junctional adhesion molecule-A (JAM-A) in the HepG2 human hepatocellular carcinoma cell line. Reduction of JAM-A resulted in a striking change in cell morphology, with cells forming single-layered sheets instead of the normal multi-layered clusters. In the absence of JAM-A, other tight junction proteins were mislocalized, and canaliculi, which form the apical face of the hepatocyte, were consequently absent. While most changes in gene expression were modest, there was a strong transcriptional induction of the adherens junction protein E-cadherin in cells with reduced levels of JAM-A. This increase in E-cadherin was partially responsible for the observed alterations in cell morphology and mislocalization of tight junction proteins. We therefore propose that we have uncovered a novel mechanism for crosstalk between specific components of tight and adherens junctions that can be utilized to regulate adhesion between hepatic cells and to maintain hepatocyte cell polarity.
Keywords: HepG2 cells

overall_design: HepG2 cells were transduced with lentiviruses and stably selected using puromycin.  Comparison of four controls and five JAM-A knockdown samples.

first: Genevieve

last: Konopka


title: PANC-1 cell differentiation

status: Public on May 15 2007

city: Bethesda

first: Margaret

last: Cam

state: MD

institute: NIH

summary:
Multiple commercial microarrays for measuring genome-wide gene expression levels are currently available, including oligonucleotide and cDNA, single- and two-channel formats. This study reports on the results of gene expression measurements generated from identical RNA preparations that were obtained using three commercially available microarray platforms. RNA was collected from PANC-1 cells grown in serum-rich medium and at 24 h following the removal of serum. Three biological replicates were prepared for each condition, and three experimental replicates were produced for the first biological replicate. RNA was labeled and hybridized to microarrays from three major suppliers according to manufacturers’ protocols, and gene expression measurements were obtained using each platform’s standard software. For each platform, gene targets from a subset of 2009 common genes were compared. Correlations in gene expression levels and comparisons for significant gene expression changes in this subset were calculated, and showed considerable divergence across the different platforms, suggesting the need for establishing industrial manufacturing standards, and further independent and thorough validation of the technology.

Keywords: Differentiation

overall_design: PANC-1 cells were grown in serum-containing media followed by exposure to serum-free media for 24 hours. In both groups, RNA extracted from the first biological replicate was derived from 3 culture dishes producing enough sample for three technical replicates, whereas RNA from the second and third biological replicates were derived from one culture dish each.

first: Marvin

last: Gershengorn


title: Gene expression profiling of testicular seminoma

status: Public on Jul 31 2007

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
Gene expression patterns of testicular seminoma were analysed applying oligonucleotide microarrays in 40 specimens of different tumour stages (pT1, pT2, pT3) and in 3 normal testes.
Keywords: ordered

overall_design: A total of 40 pure seminoma including 22 samples of tumour stage 1 (pT1), 14 samples of tumour stage 2 (pT2) and 4 of tumour stage 3 (pT3) as well as three normal testicular samples of high-quality mRNA were used for microarray analyses.

first: Isabella

last: Gashaw

first: Elke

last: Winterhager


title: Analysis of human cells response to benzene metabolites

status: Public on Apr 30 2007

city: Chicago

first: Zarema

last: Arbieva

state: IL

address: 835 S. Wolcott A301

department: RRC

institute: UIC

summary:
analyzed changes in cytokine/chemokine production and gene expression levels in, human peripheral blood mononuclear cells upon teratment with 15µM,2,4-benzenetriol
Keywords: treatment with chemical compound

overall_design: Two groups of PBMC samples treated (Bt5) and nontreated (med); each group was biologically replicated 8 times.Total number of samples 16.

first: Bellur

last: Prabhakar


title: Gene expression analysis of the human and chimpanzee brain

status: Public on Apr 26 2007

city: Barcelona

first: Mario

last: Cáceres

state: Barcelona

address: Dr. Aiguader 88

department: Genes and Disease Program

country: Spain

institute: Center for Genomic Regulation

summary:
The origin of humans was accompanied by the emergence of new behavioral and cognitive functions, including language and specialized forms of abstract representation. However, the molecular foundations of these human capabilities are poorly understood. Because of the extensive similarity between human and chimpanzee DNA sequences, it has been suggested that many of the key phenotypic differences between species result primarily from alterations in the regulation of genes rather than in their sequences.
To characterize gene expression patterns accross the brain and investigate the genetic basis of human specializations in brain organization and cognition, we used microarrays to quantify the transcript levels of thousands of genes in tissue samples from different brain regions of several human and chimpanzee individuals. Our results indicated that the human brain displays a distinctive pattern of gene expression relative to non-human primates, with higher expression levels for many genes belonging to a wide variety of functional classes. The increased expression of these genes could provide the basis for extensive modifications of cerebral physiology and function in humans, and suggests that the human brain is characterized by elevated levels of neuronal activity.
Keywords: Species comparative study

sample_organism:
Pan troglodytes
Homo sapiens

overall_design: Gene-expression profiling was performed on 32 tissue samples from different brain regions of a total of 7 humans and 4 chimpanzees. Most samples were hybridized to a single independent arrays, but in a few cases 2 replicates from the same sample were performed, totaling 37 different arrays.

first: Carrolee

last: Barlow


title: Activation-induced cytidine deaminase acts as a mutator in BCR-ABL1-transformed acute lymphoblastic leukemia cells

status: Public on Apr 03 2007

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

summary:
The Philadelphia chromosome (Ph) encoding the oncogenic BCR-ABL1 kinase defines a subset of ALL with a particularly unfavorable prognosis. Acute lymphoblastic leukemia (ALL) cells are derived from B cell precursors in most cases and typically carry rearranged immunglobulin heavy chain (IGH) variable (V) region genes devoid of somatic mutations. Somatic hypermutation is restricted to mature germinal center B cells and depends on activation-induced cytidine deaminase (AID). Studying AID expression in 108 cases of ALL, we detected AID mRNA in 24 of 28 Ph-positive ALLs as compared to 6 of 80 Ph-negative ALLs. Forced expression of BCR-ABL1 in Ph-negative ALL cells and inhibition of the BCR-ABL1-kinase showed that aberrant expression of AID depends on BCR-ABL1 kinase activity. Consistent with aberrant AID expression in Ph-positive ALL, IGH V region genes and BCL6 were mutated in many Ph-positive but unmutated in most Ph-negative cases. In addition, AID introduced DNA-single-strand breaks within the tumor suppressor gene CDKN2B in Ph-positive ALL cells, which was sensitive to BCR-ABL1 kinase inhibition and silencing of AID expression by RNA interference. These findings identify AID as a BCR-ABL1-induced mutator in Ph-positive ALL cells, which may be relevant with respect to the particularly unfavorable prognosis of this leukemia subset.
Keywords: gene expression array-based (RNA / in situ oligonucleotide)

overall_design: To study the gene expression profile of two Ph-positive ALL cell lines (BV173 and SUP-B15) in the presence or absence of 10 μmol/l STI571 for 16 hours

first: Niklas

last: Feldhahn

first: Nadine

last: Henke

first: Kai

last: Melchior

first: Cihangir

last: Duy

first: Bonaventure

last: Soh

first: Florian

last: Klein

first: Gregor

last: von Levetzow

first: Bernd

last: Giebel

first: Aihong

last: Li

first: Wolf-Karsten

last: Hofmann

first: Hassan

last: Jumaa


title: Pathway and single gene analysis of Caco-2 cell differentiation by ascorbate-stabilized quercetin

status: Public on Jun 01 2007

city: Zeist

first: Ashwin

last: Dihal

address: Utrechtseweg 48

department: Business Unit Physiologival Sciences

country: Netherlands

institute: TNO Quality of Life

summary:
The aim was to investigate mechanisms contributing to quercetin’s previously described effects on cell-proliferation and -differentiation, which contradicted its proposed anti-carcinogenic potency. In a 10-day experiment, 40 µM quercetin stabilized by 1mM ascorbate reduced Caco-2 differentiation up to 50% (P<0.001). Caco-2 RNA from days 5 and 10, hybridized on HG-U133A2.0 Affymetrix® GeneChips®, showed 1,743 affected genes on both days (P<0.01). All 14 Caco-2 differentiation-associated genes showed decreased expression (P<0.01), including intestinal alkaline phosphatase that was confirmed technically (qRT-PCR) and functionally (enzyme-activity).
The 1,743 genes contributed to 27 affected pathways (P<0.05) categorized under 6 gene ontology (GO) processes, including apoptosis and cell-cycle. Genes within these GO-processes showed fold changes that suggest increased cell-survival and -proliferation. Furthermore, quercetin downregulated expression of genes involved in tumor-suppression and phase II metabolism, and upregulated oncogenes.
Gene expression changes mediated by ascorbate-stabilized quercetin were concordant with those occurring in human colorectal carcinogenesis (≈ 80-90%), but were opposite to those previously described for Caco-2 cells exposed to quercetin in the absence of ascorbate (≈ 75-90%).
In conclusion, gene expression among Caco-2 cells exposed to ascorbate-stabilized quercetin showed mechanisms contrary to what is expected for a cancer-preventive agent. Whether this unexpected in vitro effect is relevant in vivo, remains to be elucidated.
Keywords: Colon cancer; Caco-2; quercetin; differentiation

overall_design: Caco-2 cells were harvested on days 5 and 10 post-confluency. Per day, fold changes were calculated as quercetin vs. control.

first: Chantal

last: Tilburgs

first: Marjan

last: van Erk

first: Ivonne

last: Rietjens

first: Ruud

last: Woutersen

first: Rob

last: Stierum


title: Microarray data from arsenite treated and non-treated G2-synchronized p53(+) and p53(-) fibroblasts

status: Public on Apr 07 2007

city: Louisville

first: Xiaoqiang

last: Xu

state: KY

address: University of Louisville

department: Department of Pharmacology & Toxicology

institute: University of Louisville

summary:
Microarray data from G2-synchronized p53(+) and p53(-) fibroblasts before and after 3 h release from cell cycle blockade in the presence of 5 µM sodium arsenite.
Keywords: Gene induction

overall_design: Cells expressing p53 from a tet-off regulated construct were synchronized in G2 with a two-step procedure using 24 h aphidicolin treatment for initial G1 synchronization and 12 h of Hoechst 33342 to effect a G2 blockade. During Hoechst treatment, tetracycline was added to suppress p53 in half the cultures. Cells were then released into media containing 5 µM sodium arsenite and the appropriate concentration of tetracycline to maintaining p53 expression. mRNAs were collected at 0 h and 3 h after release from G2 synchrony.

first: Samuel

last: McNeely

first: Ben

last: Taylor

first: Wolfgang

last: Zacharias

first: Michael

last: McCabe

first: Christopher

last: States


title: A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana

status: Public on Mar 07 2007

city: Lexington

first: Arthur

last: Hunt

address: 301A Plant Science Building

department: Dept. of Plant and Soil Sciences

institute: University of Kentucky

summary:
The oxt6 mutant is an oxidative stress-tolerant Arabidopsis mutant that is deficient in a polyadenylation factor subunit.  Expression analysis suggests that impaired poly(A) site choice is responsible for the stress-tolerant phenotype.
We used microarrays to understand the link between the polyadenylation defect and stress tolerance.
Keywords: mutant, wild-type, complemented line comparison

overall_design: Arabidopsis plants (the wild-type, oxt6 mutant, and two independent oxt6 transformants each carrying a gene encoding just the smaller of the two At1g30460-encoded proteins) were seeded and grown in soil.  Plants were harvested for RNA isolation after 30 days; for this, six samples derived from 10-15 plants were prepared for each line.  Ten samples were selected for study – three wild-type, three oxt6, and two from each of the complemented lines.  Analysis of independent complemented plants minimizes the possible effects that may arise due to T-DNA insertion.

first: Jingxian

last: Zhang

first: Balasubrahmanyam

last: Addepalli

first: Kil-Young

last: Yun

first: Ruqiang

first: Quinn

middle: Q

first: Suryadevara

last: Rao

first: Deane

last: Falcone


title: wheat expression level polymorphism study parental genotypes 2 biological reps

status: Public on Mar 25 2007

city: Winnipeg

first: Mark

last: Jordan

state: Manitoba

address: 195 Dafoe Rd.

department: Cereal research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

summary:
The use of statistical tools established for the genetic analysis of quantitative traits can be applied to gene expression data. Quantitative trait loci (QTL) analysis can associate expression of genes or groups of genes with particular genomic regions and thereby identify regions that play a role in the regulation of gene expression. A segregating population of 41 doubled haploid (DH) lines from the hard red spring wheat cross RL4452 x AC Domain was used.  This population had previously been mapped with microsatellites and includes a full QTL analysis for agronomic and seed quality traits. Expression analysis from 5 day post anthesis developing seed was conducted on 39 of the 41 DH lines using the Affymetrix wheat array.  Expression analysis of developing seeds from field grown material identified 1,327 sequences represented by Affymetrix probe sets whose expression varied significantly between genotypes of the population.  A sub-set of 378 transcripts were identified that each mapped to a single chromosome interval illustrating that major expression QTLs can be found in wheat. Genomic regions corresponding to multiple expression QTLs were identified that were coincident with previous identified seed quality trait QTL.  These regions may be important regulatory regions governing economically important traits. Comparison of expression mapping data with physical mapping for a sub-set of sequences showed that both cis and trans acting expression QTLs were present.
Keywords: genetic differences, expression QTL

overall_design: The two parental genotypes of mapping population RL4452 x AC Domain with 2 biological replicates per genotype. Grown in the field together with the mapping population.

first: Daryl

last: Somers


title: Wheat expression level polymorphism study parental genotypes 2 biological reps from SB location

summary:
The use of statistical tools established for the genetic analysis of quantitative traits can be applied to gene expression data. Quantitative trait loci (QTL) analysis can associate expression of genes or groups of genes with particular genomic regions and thereby identify regions that play a role in the regulation of gene expression. A segregating population of 41 doubled haploid (DH) lines from the hard red spring wheat cross RL4452 x AC Domain was used.  This population had previously been mapped with microsatellites and includes a full QTL analysis for agronomic and seed quality traits. Expression analysis from 5 day post anthesis developing seed was conducted on 36 of the 41 DH lines using the Affymetrix wheat array.  Expression analysis of developing seeds from field grown material in location 2 identified 10,280 sequences represented by Affymetrix probe sets whose expression varied significantly between genotypes of the population.  Of these 1,455 were identified in the point location as well. A sub-set of 542 transcripts were identified that each mapped to a single chromosome interval illustrating that major expression QTLs can be found in wheat. Genomic regions corresponding to multiple expression QTLs were identified that were coincident with previous identified seed quality trait QTL.  These regions may be important regulatory regions governing economically important traits. Comparison of expression mapping data with physical mapping for a sub-set of sequences showed that both cis and trans acting expression QTLs were present.
Keywords: genetic differences, expression QTL

overall_design: Parental genotypes of mapping population RL4452 x AC Domain with 2 biological replicates per genotype. Grown in the field in a lattice design at SB location with the 41 DH progeny lines.


title: Expression data from MCF10A cells subject to EGF stimulation

status: Public on Mar 01 2007

city: Rehovot

first: Tal

last: Shay

address: Herzel

department: Physics of Complex Systems

country: Israel

institute: Weizmann Institute of Science

summary:
MCF10A cells derived from spontaneously immortalized normal human mammary epithel were subjected to EGF/SERUM stimulation for 0,20,40,60,120,240 and 480 minutes.
We used microarrays to understand the temporal regulation of the cellular EGFR cascade.
Keywords: time course

overall_design: MCF10A cells were grown in DME:F12 medium supplemented with antibiotics, [10 mg/ml insulin, 0.1 mg/ml cholera toxin, 0.5 mg/ml hydrocortisone, heat-inactivated horse serum (5%); defined as 'serum' in the text] and 10ng/ml EGF. Cells were serum deprived for 24 hours. Following stimulation with EGF/SERUM for 0,20,40,60,120,240 and 480 minutes.

first: Amit

last: Ido

first: Citri

last: Ami

first: Shay

last: Tal

first: Domany

last: Eytan

first: Yarden

last: Yosef


title: wheat expression level polymorphism study 39 genotypes 2 biological reps

overall_design: 39 genotypes of mapping population RL4452 x AC Domain with 2 biological replicates per genotype. Grown in the field in a lattice design


title: Genome-wide gene expression differences between Crohn’s and ulcerative colitis from endoscopic pinch biopsies:

city: Baltimore

first: Shukti

last: Chakravarti

address: 720 Rutland Ave

institute: Johns Hopkins University School of Medicine

summary:
Ulcerative colitis (UC) and Crohn’s disease (CD) are inflammatory bowel diseases (IBD) with variable, overlapping clinical features and complex pathophysiologies. To identify pathogenic processes underlying these disease subtypes, using single endoscopic pinch biopsies to estabolish 36 expression profiles, we elucidated gene expression patterns of active and inactive areas of UC and CD, and compared these to infectious colitis and healthy controls.
Keywords: RNA

overall_design: To identify pathogenic processes underlying these disease subtypes, using single endoscopic pinch biopsies, we elucidated gene expression patterns of active and inactive areas of UC and CD, and compared these to infectious colitis and healthy controls. An unsupervised classification of a total of 36 samples yielded promising separation between IBD affected, unaffected, non-IBD colitis and normal controls, suggesting distinctive gene expression patterns for each sample type. The Significance Analysis of Microarays (SAM) software to select biologically significant changes in gene expression between groups. The criteria selected for SAM analysis are, a median false discovery rate (FDR) ≤ 0.00001%, fold change >2, and a Log2 mean expression index > 6.64.

first: Feng

last: Wu

first: Themistocles

last: Dassopoulos

first: Leslie

last: Cope

first: Anirban

last: Maitra

first: Steven

last: Brant

first: Mary

middle: L

last: Harris

first: Theodore

last: Bayless

first: Giovanni

last: Parmigiani


title: Wheat expression level polymorphism study 36 genotypes 2 biological reps from SB location

first: Mark

last: Jordan

overall_design: 36 genotypes of mapping population RL4452 x AC Domain with 2 biological replicates per genotype. Grown in the field in a lattice design at SB location


title: SCLC cell line profiling on HG-U133A arrays

status: Public on Apr 12 2007

city: Abbott Park

last: Anderson

address: 100 Abbott Park Road

institute: Abbott Laboratories

summary:
RNA expression analysis was performed to compare patterns to DNA copy number changes and sensitivity to BCL2 inhibitors.
Keywords: cell line comparison

overall_design: Naive cell lines were isolated in duplicate or triplicate (only a single for H69AR) to determine RNA expression pattern.

first: Tahir

last: Tahir


title: HeLa cells and MCF10A cells subject to EGF stimulation

first: Tal

last: Shay

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

overall_design: Refer to individual Series

first: Ido

last: Amit

first: Ami

last: Citri

first: Eytan

last: Domany

first: Yosef

last: Yarden


title: Wheat expression level polymorphism study parentals and progenies from SB location


title: Transcriptional Profiles of Human Epithelial Cells in Response to Heat

status: Public on Apr 10 2007

city: Boston

first: Jason

middle: Matthew

last: Laramie

address: 715 Albany Street

department: Bioinformatics

institute: Boston University

summary:
We hypothesized that broad-scale expression profiling would provide insight into the regulatory pathways that control gene expression in response to stress, and potentially identify novel heat-responsive genes. HEp2 cells were heated at 37 to 43 °C for 60 min to gauge the heat shock response, using as a proxy inducible HSP-70 quantified by western blot analysis.  Based on these results, microarray experiments were conducted at 37, 40, 41, 42 and 43°C (3 replicates/temperature x 5 groups = 15 U95Aver2 GeneChips).  Using linear modeling, we compared the sets of microarrays at 40, 41, 42 and 43°C with the 37°C baseline temperature and took the union of the genes exhibiting differential gene expression signal to create two sets of “heat shock response” genes, each set reflecting either increased or decreased RNA abundance.  Leveraging human and mouse orthologous alignments, we used the two lists of co-expressed genes to predict transcription factor binding sites in silico, including those for heat shock factor 1 (HSF1) and heat shock factor 2 (HSF2) transcription factors.  We discovered HSF1 and HSF2 binding sites in 15 genes not previously associated with the heat shock response.  We conclude that microarray experiments coupled with upstream promoter analysis can be used to identify novel genes that respond to heat shock.  Additional experiments are required to validate these putative heat shock proteins and facilitate a deeper understanding of the mechanisms involved during the stress response.
Keywords: stress response, temperature, human epithelial cells

overall_design:
Cell Culture:  HEp2 cells were acquired from American Type Culture Cell (Rockville, MD) and cultured in EMEM supplemented with 10% fetal bovine serum (Gibco Laboratories, Grand Island, NY), 1% nonessential amino acids (Gibco), and 1.5g/L sodium bicarbonate.  The cell cultures were maintained at 37°C in a humidified incubator in an atmosphere of 5% CO2 – 95% air and passaged at a 1:3 ratio with trypsin every 5-7 days.

Heat shock and RNA extraction:  After growing to confluency, cells were heated for 60 min in an incubator at 37, 38, 39, 40, 41, 42, or 43°C as measured by a sterile probe placed into each plate’s media.  After heating, media was removed and ice cold PBS was immediately added and cells were scraped from plates and put into 1.5mL centrifuge tubes and pelletted.  PBS was removed and replaced with 1 mL of TRIzol® and vortexed vigorously (Invitrogen, Carlsbad, CA) for 5min.  RNA was then extracted as per manufactures protocol.  RNA integrity was assessed by gel electrophoresis and the Agilent Bioanalyzer 2100 machine (Agilent Technologies, Waldbronn, Germany).

Affymetrix cRNA target generation: RNA purification (RNAeasy, Qiagen), cDNA synthesis (Invitrogen, Carlsbad, CA) and biotinylated cRNA (Invitrogen, Carlsbad, CA) were all performed in accordance with manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA).  Fragmented target cRNA was hybridized with U95v2 GeneChip using Affymetrix® equipment at the Alvin J. Siteman Cancer Center Genechip Facility.  Fluorescent signal was collected using an Affmetrix G2500A GeneArray Scanner (Hewlett-Packard, Inc., Cupertino, CA).

GeneChip microarray data were generated at cellular temperatures of 37, 40, 41, 42, and 43°C (U95Av2 GeneChips®, ~10,000 genes per microarray; 3 technical replicates per temperature = 15 GeneChips®).

first: Philip

last: Chung

first: Buddy

last: Brownstein

first: Gary

middle: D

last: Stormo

first: Perren

last: Cobb


title: Expression in Superior Frontal Gyrus of normal individuals or females of different ages affected by Rett syndrome

status: Public on Feb 05 2007

city: Beaverton

first: Valerie

last: Matagne

state: OR

address: 505 nw 185th Ave

department: Neuroscience

institute: OHSU

summary:
Rett syndrome (RTT, OMIM #312750) is a severe X-linked neurodevelopmental disorder linked to heterozygous de novo mutations in the MECP2 gene. MECP2 encodes methyl-CpG-binding protein 2 (MeCP2), which represses gene transcription by binding to 5-methylcytosine residues in symmetrically positioned CpG dinucleotides. The disorder is almost exclusively diagnosed in females, because males affected by the disease usually die perinatally due to severe encephalopathy.  Direct MeCP2 target genes underlying the neuropathogenesis of RTT remain largely unknown.
To identify genes involved in the neuropathogenesis of RTT we assessed the gene expression profile of postmortem brains affected by RTT and that of age-matched normal brains using Affymetrix arrays.
Keywords: comparison between Rettsyndrome  suffering  and non-suffering patients

overall_design: samples of the Superior Frontal Gyrus from normal and RTT patients of different ages were obtained from the Krieger Research Institute and the Harvard Brain Tissue Ressource Center. Samples from RTT-affected girls (2-4, 6 and 8 year-old) were compared with aged-matched normal brain tissue (2, 5 and 10 year-old). To ensure the quality of hybridization , labeled RNA was hybridized to a Test Array containing probe sets for all Affymetrix Expression Array controls. Background, noise, average Avg Diff, and ratio of Avg Diff values for probe sets representing the 5’ and 3’ ends of actin and GAPDH transcripts were used to determine target quality. Targets that did not meet empirically determined cut-off values within the project were remade. Quality tested samples were then hybridized to the HU_U95Av2 array. Quality-tested samples were then hybridized in the HU_U95Av2 array containing 12,625 human probes.

first: Vivianne

last: Deng

first: Sergio

middle: R

last: Ojeda


title: Expression data from rust or mock inoculated, fully expanded flag leaf halves

status: Public on Feb 01 2007

city: Manhattan

first: Jianfa

last: Bai

state: KS

address: 1800 Denison Ave

department: Diagnostic Medicine and Pathobiology

institute: Kansas State University

summary:
Two sets of wheat lines near-isogenic to Lr34 were used to compare gene expression profiles of wheat: 1. with and without Lr34 gene; 2. rust and mock inoculation; 3. distal and basal portion of the flag leaves.  The two sets of wheat near-isogenic lines were used to subtract genetic background variations and to enrich Lr34-regulated gene expression profiles.  The study is aimed to better understand the mechanisms of the well-known durable leaf rust resistance gene, Lr34, mediated resistance at the transcriptome level.
Keywords: Distal and basal leaf halves of near-isogenic lines

overall_design: Wheat near-isogenic lines, Jupateco with Lr34 (JUR), Jupateco without Lr34 (JUS), Thatcher with Lr34 (THR), and Thatcher without Lr34 (THS) were used.  Thatcher lines were rust (I) or mock (M) inoculated.  Jupateco lines were mock inoculated.  Distal (T) and basal (B) half of the leaves were harvested and processed separately.  Three biological replications were applied to each treatment.

first: Scot

last: Hulbert

first: John

middle: P

last: Fellers

first: Robert

last: Bowden


title: Expression data from Primary Prostate Tumor

status: Public on Jan 16 2007

city: Houston

first: Federico

middle: Alberto

last: Monzon

state: TX

address: 6565 Fannin St, MS205

department: Pathology

institute: The Methodist Hospital

summary:
Prostate cancer is characterized by heterogeneity in the clinical course that often does not to correlate with morphologic features of the tumor. Metastasis reflects the most adverse outcome of prostate cancer, and to date there are no reliable morphologic features or serum biomarkers that can reliably predict which patients are at higher risk of developing metastatic disease. Understanding the differences in the biology of metastatic and organ confined primary tumors is essential for developing new prognostic markers and therapeutic targets. Using Affymetrix oligonucleotide arrays, we analyzed gene expression profiles of 24 androgen-ablation resistant metastatic samples obtained from 4 patients and a previously published dataset of 64 primary prostate tumor samples. Differential gene expression was analyzed after removing potentially uninformative stromal genes, addressing the differences in cellular content between primary and metastatic tumors. The metastatic samples are highly heterogeneous in expression; however, differential expression analysis shows that 415 genes are upregulated and 364 genes are downregulated at least 2 fold in every patient with metastasis. The expression profile of metastatic samples reveals changes in expression of a unique set of genes representing both the androgen ablation related pathways and other metastasis related gene networks such as cell adhesion, bone remodeling and cell cycle. The differentially expressed genes include metabolic enzymes, transcription factors such as Forkhead Box M1 (FoxM1) and cell adhesion molecules such as Osteopontin (SPP1). We hypothesize that these genes have a role in the biology of metastatic disease and that they represent potential therapeutic targets for prostate cancer.
Keywords: disease state analysis

first: Uma

last: Chandran

first: Changqing

last: Ma

first: Rajiv

last: Dhir

first: Michelle

last: Bisceglia

first: Maureen

last: Lyons-Weiler

first: Wenjing

last: Liang

first: George

last: Michalopoulos

first: Michael

last: Becich

middle: A


title: Expression data from Normal Prostate Tissue Adjacent to Tumor

overall_design: Using Affymetrix oligonucleotide arrays, we analyzed gene expression profiles of 24 androgen-ablation resistant metastatic samples obtained from 4 patients and a previously published dataset of 64 primary prostate tumor samples. Differential gene expression was analyzed after removing potentially uninformative stromal genes, addressing the differences in cellular content between primary and metastatic tumors.


title: Expression data from head and neck squamous cell carcinoma

status: Public on Jan 20 2007

city: New York

first: Fang-An

last: Chen

address: 345E 24th Street

department: Oral and Maxillifacial surgery

institute: New York Univ. College of Dentistry

summary:
Forty-four paired (from the same patient) samples of head and neck squamous cell carcinoma (HNSCC) and normal tissue were studied with Affymetrix U95A chips. A stringent multi-test approach, combining 7 traditional and microarray-specific statistical tests, was used to analyze the resultant data. Candidate genes were assigned to tiers of significance based on the number of statistical tests that each gene satisfied. Representative genes (both up-regulated and down-regulated) from each of the 3 tiers would be quantified with RT-PCR on both microarray-tested and new samples of HNSCC.
The goal of this study is to identify reliable differentially-expressed genes on HNSCC and to testify our hypothesis whether or not a combinatorial approach (multi-tests) to analyzing microarray data can really identify differentially-expressed genes with fewer false-positives.
Keywords: disease state; tumor vs. normal

overall_design: Paired HNSCC tumor and normal samples from 22 patients were evaluated for differential gene expression on Affymetrix U95A chips.

first: M

last: Kuriakose

first: W

middle: T

first: Z

last: He

first: A

middle: G

last: Sikora

first: P

last: Zhang

middle: Y

last: Qiu

first: D

last: Hsu

first: C

last: McMunn-Coffran

first: S

last: Brown

first: E

last: Elongo

last: Delacure

first: F


title: Gene expression analysis of bronchial epithelial cells stimulated by different airway pathogens.

status: Public on Feb 27 2007

city: Munich

first: Joerg

last: Mages

address: Trogerstrasse 30

department: Institute of Medical Microbiology, Immunology and Hygiene

institute: Technical University Munich

summary:
Bronchial epithelial cells represent the first line of defense against invading airborne pathogens. They are important contributors to innate mucosal immunity and provide a variety of anti-microbial effectors. To investigate the role of epithelial cells upon infection of airway pathogens, we stimulated BEAS-2B cells for 4 h with UV-inactivated bronchial pathogens including Staphylococcus aureus, Pseudomonas aeruginosa and Respiratory Syncitial Virus (RSV) that among other receptors can strongly activate TLR2, TLR4 and TLR3, respectively.
Keywords: expression profiling, response to pathogens

overall_design: All conditions were done in triplicates except for Staphylococcus aureus, were two replicates were done. As a control, unstimulated BEAS-2B were used. Altogether 11 arrays were hybridized.

first: Anja

last: Mayer

first: Mario

last: Muehmer

first: Jörg

first: Katja

last: Gueinzius

first: Christian

last: Hess

first: Klaus

last: Heeg

first: Robert

last: Bals

first: Roland

last: Lang

first: Alexander

last: Dalpke


title: Expression Data from Normal and Prostate Tumor Tissues

status: Public on Jan 30 2007

first: Federico

last: Monzon


title: Expression data from Normal Prostate Tissue free of any pathological alteration

first: Uma

last: Chandran

first: Changqing

last: Ma

first: Rajiv

last: Dhir

first: Michelle

last: Bisceglia

first: Maureen

last: Lyons-Weiler

first: Wenjing

last: Liang

first: George

last: Michalopoulos

first: Michael

last: Becich


title: Expression data from primary human keratinocytes

status: Public on Jan 02 2007

city: Durham

first: Jennifer

middle: Yunyan

last: Zhang

state: NC

address: 3 Genome Ct, rm4130

department: Dermatology

institute: Duke University

summary:
Oncogenic Ras induces epidermal cell growth arrest. Induction of the JNK/Ap1 signaling cascade by expression of MKK7 overcomes Ras-induced cell growth arrest in a manner dependent on AP1 fucntion.
We used microarrays to detail the global programme of gene expression in response to MKK7, Ras  activation and AP1 inhibition
Keywords: response to specific genetic change

overall_design: To study the gene expression profile responsive to Ras and MKK7 expression. We used retroviral expression system to express LacZ, MKK7, Ras, DNc-Jun, MKK7+Ras, and MKK7+Ras +DNc-Jun in primary human keratinocytes, and then extract total RNA from the transduced cells for gene expression analysis.

first: Amy

last: Adams

first: Todd

middle: W

last: Ricky

first: Shiying

last: Tao

first: Paul

last: Khavari


title: Vanadium pentoxide induced gene expression in human lung fibroblasts

status: Public on Jan 01 2007

city: Research Triangle Park

first: James

middle: C

last: Bonner

address: 6 Davis Drive

department: Biological Sciences

institute: CIIT Centers for Health Research

summary:
Exposure to vanadium pentoxide (V2O5) is a cause of occupational bronchitis. We evaluated gene expression profiles in cultured human lung fibroblasts exposed to V2O5 in vitro in order to identify candidate genes that could play a role in airway remodeling associated with V2O5-induced bronchitis. Gene expression was measured at various time points over a 24 hr period using the Affymetrix Human Genome U133A 2.0 Array. Expression data were preprocessed using RMA with a log2 transformation. Statistical analysis was performed in R using the affylmGUI package using a linear model with contrasts between untreated control and V2O5-exposed fibroblasts. Genes identified as statistically significant were filtered by selecting only those genes that exhibited a > 2-fold change. Quantitative real-time RT-PCR was utilized to confirm expression of selected genes. More than 2000 genes were significantly changed in response to V2O5 over the time course of our experiment. Genes altered by V2O5 were involved in biologic processes related to cell growth and differentiation, oxidative stress responses, immune regulation, and interferon signaling and apoptosis. In particular, V2O5 induced genes that encode growth factors involved in epithelial repair (HB-EGF) or angiogenesis (VEGF), peroxide generating enzymes (SOD2), pro-inflammatory enzymes (PGHS2), while suppressing genes involved in growth arrest (GAS1, STAT-1) and cell cycle inhibition (CDKN1B). Our study also identified a variety of novel genes that could be used as biomarkers of V2O5-induced bronchitis or could serve as candidate genes for disease progression.
Keywords: time course, stress response

overall_design:
Experimental Design
Normal adult human lung fibroblasts (ATCC 16 Lu) were purchased from American Type Culture Collection (Rockville, MD). Fibroblasts were seeded into 175 cm2 plastic culture flasks and grown to confluence in 10% fetal bovine serum (FBS)/Dulbecco’s modified Eagle’s medium (DMEM), then trypsin-liberated, and seeded into 150 mm dishes. Confluent monolayers were rendered quiescent for 24 hrs in serum-free defined medium (SFDM) that consisted of Ham’s F-12 medium with 0.25% BSA with an insulin/transferrin/selenium supplement. Cells were treated with 10 µg/cm2 vanadium pentoxide, V2O5 (Aldrich Chemical, Milwaukee, WI) or SFDM and RNA was harvested from the fibroblast cultures at 1, 4, 8, 12 and 24 hrs post-treatment. RNA from an SFDM control was harvested at each of these time points to normalize the V2O5 treatment at the same corresponding time point. Three replicate chips were analyzed for SFDM and V2O5 treatment groups at each of the five time points tested.

Microarray Hybridizations and Data Analysis
Human lung fibroblast RNA was isolated using RNeasy columns (Qiagen, Valencia, CA). RNA quality was verified by spectrophotometry and gel electrophoresis using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  Probe preparation and hybridization to the microarray was performed in the CIIT Gene Expression Core Facility using standard Affymetrix procedures. Double-stranded cDNA was synthesized from RNA using an oligo-dT24-T7. Biotinylated cRNA was synthesized from an aliquot of the cDNA template using the T7 RNA Transcript Labeling Kit (ENZO Diagnostics, Farmingdale NY).  The labeled cRNA was then fragmented, hybridized to Affymetrix Human Genome U133A 2.0 arrays (Affymetrix, Santa Clara, CA), and stained using phycoerythrein-conjugated streptavidin (Molecular Probes, Eugene, OR).

Statistical Analysis and Data Processing
The microarray data were preprocessed using RMA with a log base 2 (log2) transformation. Statistical analysis of the data was performed in R using the affyImGUI package. To identify genes with significant changes in expression following V2O5 exposure, all treatment groups were analyzed using a linear model with contrasts between untreated fibroblasts and V2O5-exposed fibroblasts at each time point. Probability values were adjusted for multiple comparisons using a false discovery rate of 5% (FDR = 0.05). Genes identified as statistically significant were subject to an additional filter by selecting only those genes that exhibited  a > 2-fold change from the untreated fibroblasts.

last: Ingram

first: Aurita

last: Menezes

first: Elizabeth

last: Turpin

middle: B

last: Mangum

first: Linda

middle: J

last: Pluta

first: Russell

middle: S

last: Thomas


title: Expression data from Metastatic Prostate Tumor

first: Federico

last: Monzon

first: Uma

last: Chandran

first: Changqing

last: Ma

last: Dhir

last: Bisceglia


title: Acne lesion vs. normal skin. Also includes non-acne patients' normal skin samples.

status: Public on Dec 12 2006

city: Hershey

first: Wei

last: Zhao

state: PA

address: 600 Centerview Drive,  A210

institute: Penn State University

summary:
The pathogenesis of acne has been linked to multiple factors such as increased sebum production, inflammation, follicular hyperkeratinization, and the action of Propionibacterium acnes within the follicle. In an attempt to understand the specific genes involved in inflammatory acne, we performed gene expression profiling in acne patients. Skin biopsies were obtained from an inflammatory papule and from normal skin in six patients with acne. Biopsies were also taken from normal skin of six subjects without acne. Gene array expression profiling was conducted using Affymetrix HG-U133A 2.0 arrays comparing lesional to nonlesional skin in acne patients and comparing nonlesional skin from acne patients to skin from normal subjects. Within the acne patients, 211 genes are upregulated in lesional skin compared to nonlesional skin. A significant proportion of these genes are involved in pathways that regulate inflammation and extracellular matrix remodeling, and they include matrix metalloproteinases 1 and 3, IL-8, human beta-defensin 4, and granzyme B. These data indicate a prominent role of matrix metalloproteinases, inflammatory cytokines, and antimicrobial peptides in acne lesions. These studies are the first describing the comprehensive changes in gene expression in inflammatory acne lesions and are valuable in identifying potential therapeutic targets in inflammatory acne.
Keywords: acne lesion, normal skin

overall_design: total 18 chips. 6 for acne lesion samples, 6 for normal skin samples, 6 for non-acne patient normal skin samples

first: Diane

middle: M

last: Thiboutot


title: Comparative analysis of a CML cell line resistant to cyclophosphamide using oligonucleotide arrays and response to TKI

status: Public on Feb 24 2007

city: Shreveport

first: Reinhold

last: Munker

state: LA

address: 1501 Kings Highway

department: Medicine

institute: LSU Health Sciences Center

summary:
Acquired imatinib resistance in chronic myelogenous leukemia (CML) can be the consequence of mutations in the kinase domain of BCR-ABL or increased protein levels. However, as in other malignancies, acquired resistance to cytostatic drugs is a common reason for treatment failure or disease progression. As a model for drug resistance, we developed a CML cell line resistant to cyclophosphamide (CP). Using oligonucleotide arrays, we examined changes in global gene expression. Selected genes were also examined by real-time PCR and flow cytometry. Neither the parent nor the resistant lines had mutations in their ATP binding domain. Filtering genes with a low-base line expression, a total of 239 genes showed significant changes (162 up- and 77 down-regulated) in the resistant clone. Most of the up-regulated genes were associated with metabolism, signal transduction, or encoded enzymes. The gene for aldehyde dehydrogenase 1 was over-expressed more than 2000 fold in the resistant clone. BCR-ABL was expressed in both cell lines to a comparable extent. When exposed to the tyrosine kinase inhibitors imatinib and nilotinib, both lines were sensitive. In conclusion, we found multiple genetic changes in a CML cell line resistant to CP related to metabolism, signal transduction or apoptosis. Despite these changes, the resistant cells retained sensitivity to tyrosine kinase inhibitors.
Keywords: Cell type comparison

overall_design: A CML cell line and a CP resistant subline were compared by gene array. In addition other markers, the expression of BCR-ABL and the sensitivity to tyrosine kinase inhibitors were tested.

first: Fei

last: Bao

first: Paula

last: Polk

first: Mary

middle: L

last: Nordberg

first: Diana

last: Veillon

first: Amanda

last: Sun

last: Deininger

first: David

last: Murray

first: Borje

last: Andersson


title: MCF7 dose response

status: Public on Dec 09 2006

city: Yokohama

first: Mariko

last: Okada

address: W518, 1-7-22, Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN RCAI

summary:
ErbB receptor ligands, epidermal growth factor (EGF) and heregulin (HRG), induce dose-dependent transient and sustained intracellular signaling, proliferation and differentiation of MCF-7 breast cancer cells, respectively. In an effort to delineate the ligand-specific cell determination mechanism, we investigated time-course gene expressions induced by EGF and HRG that induce distinct cellular phenotypes in MCF-7 cells. To analyze the effects of ligand dosage and time for the gene expression independently, we developed a statistical method for decomposing the expression profiles into the two effects. Our results indicated that signal transduction pathways devotedly convey quantitative properties of the dose-dependent activation of ErbB receptor to early transcription. The results also implied that moderate changes in the expression levels of numbers of genes, not the predominant regulation of a few specific genes, might cooperatively work at the early stage of the transcription for determining the cell fate. However, the EGF- and HRG-induced distinct signal durations resulted in the ligand-oriented biphasic induction of proteins after 20 min. The selected gene list and HRG-induced prolonged signaling suggested that transcriptional feedback to the intracellular signaling results in a graded to biphasic response in the cell determination process, and that each ErbB receptor is inextricably responsible for the control of amplitude and duration of cellular biochemical reactions.
Keywords: time course, dose response

overall_design: MCF-7 human breast cancer cells were incubated from 5min to 90min after administration of different concentrations of the growth hormones (epidermal growth factor (EGF) and heregulin (HRG)). Control was set as growth hormone non-treated cells. For each growth hormone, one control was used.


title: Gene expression profiles of T-lymphocytes are sensitive to the influence of heavy smoking

status: Public on Dec 31 2006

city: Jena

first: Sandy

last: Mosig

address: Bachstrasse 18

department: Molecular Hemostaseology - Institute of Vascular Medicine

institute: University Hospital Jena

summary:
Cigarette smoke components have a proven negative influence on human health. Adverse metabolic effects have been observed in tissues and single cells. As T-lymphocytes get in contact with affected organs (e.g. lung) or cells (e.g.erythrocytes), as well as with smoke components and bioactive molecules, whose production is influenced by them, we compared the gene exression profiles in these cells of the adaptive immune system of three male heavy smokers and three male non-smokers We combined rapid immuno-precipitation and Affymetrix GeneChip® HG U133A2.0 microarray analysis to analyse the data set. 88 genes were found significantly (T-test) differentially expressed by a factor of 1.5-fold or larger between smokers and non-smokers. Using the gene function groups of the gene ontology consortium to categorize the functions of the differentially expressed genes the group termed “response to stimulus” was found most significantly affected by smoking. Our data indicate a prominent role of cytotoxic T-lymphocytes in response to smoking. Several genes that are typically found in these cells are found regulated although the ratio of cytotoxic and helper T-lymphocytes remained unchanged in smokers.
Keywords: gene expression changes in T-lymphocytes in response to smoking

overall_design: T-lymphocytes from three non-smokers (control group)and three smokers (case group) were immunoprecipitated from 4ml whole blood. Cells were lysed with Trizol, RNA was worked up using PLG Tubes and the RNeasy Kit. 1µg total RNA was processed according to the Affymetrix manual and hybridised on HG U133A 2.0 arrays. Data analysis was done with the GeneSpring software from Agilent. We performed a T-test to extract significantly altered genes from the data set.

first: Petra

last: Büttner

first: Harald

last: Funke


title: Gene Expression analyses in PBMCs and T-lymphocytes following acute exhausting exercise

summary:
White blood cells (WBCs) express tens of thousands of genes. Their expression levels are modified by genetic and external factors. In further study we found that gene expression profiles of these cellls can serve as surrogate markers for monitoring exercise and training load.The purpose of the present study was to investigate the effects of acute exercise on gene expression profiles (GEPs) of PBMCs and T-lymphocytes in order to re-detect the patterns in subpopulations. The use of WBC subpopulations is necessary because of the well known subpopulation shifts that occur during physical activities.
Three male probands performed an exhaustive treadmill test (ET) at 80% of their VO2max. PBMCs were isolated using BD Vacutainer CPT tubes containig Ficoll. T-lymphocytes were isolated from the PBMCs via rosetting technology. Gene expression profiles were measured using the Affymetrix GeneChip® technology. After scaling, normalisation, and filtering groupwise and pairwise comparisons of gene expression intensities were performed. We found that sorting increases the detection sensitivity and enables the researcher to observe regulation that is hidden in heterogenous populations. We therefore suggest not to work on mixed nbut instead on sorted cells when performing gene expression analyses.

Keywords: response of white blood cell sub populations to acute exercise

overall_design:
Three healthy male probands executed an exhaustive treadmill test (80% VO2max) until individual exhaustion. Blood samples (16ml) were drawn before and one hour past the tests. PBMCs were isolated using the Ficoll density centrifugation methode. T-lymphocytes were isolated by adding rosetting anibodies zo the cells before centrifugation. Cells were lysed using Trizol and worked up with Qiagen RNeasy Micro columns. RNA was processed and hybridised on U133A 2.0 Affymetrix GeneChips. Samples were grouped and gene expression changes were detected via multiple algorithms included in GeneSpring 7.2 (Agilent).
The four groups contained three samples related to the cell type "PBMC" or "T-cell" and "before exercise" or "1hour past exercise". TTest, GOs and KEGG classification, principal component analysis and hierarchical clstering were used to scan for gene expression profiles induced through the different exercise conditions.


title: Analysis of CD38+ and CD38- sub-clones derived from the same CLL patient

status: Public on Nov 23 2006

city: Cardiff

first: Chris

last: Pepper

state: Wales

address: Heath Park

department: Haematology

country: United Kingdom

institute: Cardiff University

summary:
CD38 expression is an important prognostic marker in CLL with high levels of CD38 associated with shorter overall survival. In this study, we used gene expression profiling and protein analysis of highly purified cell-sorted CD38+ and CD38- chronic lymphocytic leukemia cells to elucidate a molecular basis for the association between CD38 expression and inferior clinical outcome. Paired CD38+ and CD38- CLL cells derived from the same patient were shown to be monoclonal by VH gene sequencing but despite this, CD38+ CLL cells possessed a distinct gene expression profile when compared with their CD38- sub-clones.
Keywords: Sub-clonal analysis of CLL cells derived from the same leukemia sample

overall_design: These experiments compared the gene expression profile of CD38+ and CD38- sub-clones derived from 6 individual CLL patients.


title: Lentiviral gene delivery of vMIP-II

status: Public on Nov 11 2006

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary:
We engineered a lentiviral gene vector with vMIP-II, transduced both mature endothelial cells and endothelial cell progenitors, and transplanted these gene-modified cells in Matrigel templates as an in vivo angiogenesis model.  The results are the first demonstration in a cell transplantation setting that vMIP-II is proangiogenic in vivo and can deliver this function by vector-mediated gene delivery to both mature endothelial cells and progenitors.
Keywords: Comparative Genomic Hybridisations

overall_design: 5 samples in total, hybridised to Affymetrix HG-U133A 2.0 GeneChips, comprising 3 HUVEC control samples and 2 HUVEC experimental samples transduced with vMIP-II.

first: Stephanie

last: Cherqui

first: Camille

last: Thorpe

first: Daniel

last: Salomon


title: CTNNB1 mutations and overexpression of Wnt/beta-catenin target genes in WT1-mutant Wilms' tumors

status: Public on Oct 28 2006

first: Chi-Ming

last: Li

state: NY

address: 1130 St Nicholas Ave, rm607

department: ICG

institute: Columbia University

summary:
Gain-of-function mutations in exon 3 of beta-catenin (CTNNB1) are specific for Wilms' tumors that have lost WT1, but 50% of WT1-mutant cases lack such "hot spot" mutations. To ask whether stabilization of beta-catenin might be essential after WT1 loss, and to identify downstream target genes, we compared expression profiles in WT1-mutant versus WT1 wild-type Wilms' tumors. Supervised and nonsupervised hierarchical clustering of the expression data separated these two classes of Wilms' tumor. The WT1-mutant tumors overexpressed genes encoding myogenic and other transcription factors (MOX2, LBX1, SIM2), signaling molecules (TGFB2, FST, BMP2A), extracellular Wnt inhibitors (WIF1, SFRP4), and known beta-catenin/TCF targets (FST, CSPG2, CMYC). Beta-Catenin/TCF target genes were overexpressed in the WT1-mutant tumors even in the absence of CTNNB1 exon 3 mutations, and complete sequencing revealed gain-of-function mutations elsewhere in the CTNNB1 gene in some of these tumors, increasing the overall mutation frequency to 75%. Lastly, we identified and validated a novel direct beta-catenin target gene, GAD1, among the WT1-mutant signature genes. These data highlight two molecular classes of Wilms' tumor, and indicate strong selection for stabilization of beta-catenin in the WT1-mutant class. Beta-Catenin stabilization can initiate tumorigenesis in other systems, and this mechanism is likely critical in tumor formation after loss of WT1.
Keywords: single channel

overall_design: Identification of WNT/Beta-Catenin or WT1 target genes. 39 individual samples.

first: Benjamin

last: Tycko

first: Adam

last: Margolin


title: HGPC, in monolayer, 0.5 vs. 20% serum, complete

status: Public on Dec 03 2006

city: Jacksonville

first: Robert

middle: C.

last: Olney

state: FL

address: 807 Children's Way

department: Pediatrics

institute: Nemours Children's Clinic

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

overall_design: Refer to individual Series


title: A Gene Expression Signature Predicts Survival of Patients with Stage I Non-Small Cell Lung Cancer

status: Public on Nov 10 2006

city: st louis

first: Yan

last: Lu

state: MO

address: 660 s. euclid ave

institute: washington univ.

summary:
We applied a meta-analysis of datasets from seven different microarray studies on lung cancer for differentially expressed genes related to survival time (under 2 y and over 5 y). Systematic bias adjustment in the datasets was performed by distance-weighted discrimination (DWD). We identified a gene expression signature consisting of 64 genes that is highly predictive of which stage I lung cancer patients may benefit from more aggressive therapy.
Keywords: disease state analysis

overall_design: RNA was extracted from frozen tissue of primary stage I Non-Small Cell lung tumors for gene array analysis

first: Ming

last: You

first: Mark

last: Watson

first: Ramaswamy

last: Govindan

first: Zhifu

last: Sun

first: Ping

last: Yang


title: HeLa CD4+ transfection with epitope-tagged eTat or parental vector

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics


title: Docetaxel treatment of sensitve and resistant patients

first: Eric

last: Wooten

address: One Baylor Plaza

department: Breast Center

institute: Baylor College of Medicine


title: Cross-hybridization comparison between cRNA target and cDNA target

status: Public on Sep 08 2006

city: Lyngby

first: Aron

last: Eklund

address: Kemitorvet, Building 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: Technical University of Denmark

summary:
We used two RNA samples that differed only by a set of three hemoglobin transcripts to compare microarray cross-hybridization between two target preparation protocols.  We found widespread cross-hybridization using standard cRNA target but substantially less cross-hybridization using cDNA target.
Keywords: protocol comparison

overall_design: 2 protocols x 2 RNA samples x 3 replicates = 12 arrays.

first: Leah

last: Turner

first: Pengchin

last: Chen

first: Roderick

middle: V

last: Jensen

first: Gianfranco

last: deFeo

first: Anne

last: Kopf-Sill

first: Zoltan

last: Szallasi


title: Androgen-starved LNCaP cells treated with gedunin and androgen, androgen alone, or vehicle alone for 24h

status: Public on Sep 01 2006

city: CAMBRIDGE

first: Haley

last: Hieronymus

state: MA

address: 7 Cambridge Center

institute: Broad Institute of Harvard and MIT

summary:
Gedunin is a natural product that affects LNCaP androgen-signalling by 24h
We used microarrays to detail the androgen-responsive program of gene expression affected by gedunin treatment at 24h
Keywords: drug treatment

overall_design: LNCaP cells were grown to 50% confluency and deprived of androgen, and subsequently treated with gedunin plus androgen, androgen alone, or vehicle alone for 24h prior to direct Trizol lysis and RNA isolation

first: Todd

middle: R

last: Golub


title: Gene expression profiles in white blood cells in response to exercise

status: Public on Sep 06 2006

first: Sandy

last: Mosig

summary:
White blood cells (WBCs) express tens of thousands of genes. Their expression levels are modified by genetic and external factors. The purpose of the present study was to investigate the effects of acute exercise on gene expression profiles (GEPs) of WBCs and to identify suitable genes which may serve as surrogate markers for monitoring exercise and training load.
Five male probands performed an exhaustive treadmill test (ET) at 80% of their VO2max, and a moderate treadmill test (MT) at 60% VO2max for exactly the same time one to two week later. White blood cells (WBCs) were isolated by the erythrocyte lysis method. Gene expression profiles were measured using the Affymetrix GeneChip® technology. After scaling, normalisation, and filtering groupwise and pairwise comparisons of gene expression intensities were performed and validated by real-time PCR.
We found 450 genes up-regulated and 150 down-regulated (> 1.5-fold change; ANOVA with Benjamini-Hochberg correction for multiple testing, p<0.05) upon exhaustive exercise. Analysis of mean expression levels after MT showed that the extent of up- and down-regulation was workload dependent. The genes for the stress proteins HSPA1A, HSPH1 and the matrix metalloproteinase MMP-9 showed the most prominent increases whereas the mRNA concentrations of the YES1 oncogene (YES1), of CD160 (BY55), and of a member of the mitochondrial electron transport chain (ATP5s) were most strongly reduced. Remarkably, we could largely reproduce the data from a previous report by Connolly et al. (01) even though we used considerably different methodology. After acute exercise the genes with increased expression levels were highly significantly associated with the gene ontology terms heat-shock proteins, apoptosis and inflammation.
The results demonstrate that gene expression changes in WBCs can reflect intensity and duration of exercise. Further analysis is needed to confirm the applicability of expression fingerprints as useful tools for monitoring exercise and training loads in order to avoid training associated health risks.
Keywords: response to different loads of acute exercise

overall_design:
Five healthy male probands executed an exhaustive treadmill test (80% VO2max) until individual exhaustion. One week later they repeated the test at 60% VO2max for the same time (moderate test). Blood samples (9ml) were drawn before and one hour past the tests. Erythrocytes were lysed and RNA was isolated from the white blood cells. RNA was processed and hybridised on U133A 2.0 Affyetrix GeneChips. Samples were grouped and gene expression changes were detected via multiple algorithms included in GeneSpring 7.2 (Agilent).
Three groups were build from the twenty samples. All ten pre exercise samples were grouped together as the "pre test" group. The other two groups contained five samples related to the "exhaustive test" or the "moderate test". TTest in cobination with multiple testing corrections, principal component analysis and hierarchical clstering were used to scan for gene expression profiles induced through the different exercise conditions.


title: Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat

status: Public on Oct 14 2006

city: Adelaide

first: Jason

middle: Alan

last: Able

state: SA

address: Waite Main Building

department: School of Agriculture, Food & Wine

country: Australia

institute: The University of Adelaide

summary:
Our understanding of the mechanisms that govern the cellular process of meiosis is limited in higher plants with polyploid genomes. Bread wheat is an allohexaploid that behaves as a diploid during meiosis. Chromosome pairing is restricted to homologous chromosomes despite the presence of homoeologues in the nucleus. The importance of wheat as a crop and the extensive use of wild wheat relatives in breeding programs has prompted many years of cytogenetic and genetic research to develop an understanding of the control of chromosome pairing and recombination. The rapid advance of biochemical and molecular information on meiosis in model organisms such as yeast provides new opportunities to investigate the molecular basis of chromosome pairing control in wheat. However, building the link between the model and wheat requires points of data contact. We report here a large-scale transcriptomics study using the Affymetrix wheat GeneChip® aimed at providing this link between wheat and model systems and at identifying early meiotic genes. Analysis of the microarray data identified 1,350 transcripts temporally-regulated during the early stages of meiosis. Expression profiles with annotated transcript functions including chromatin condensation, synaptonemal complex formation,recombination and fertility were identified. From the 1,350 transcripts, 30 displayed at least an eight-fold expression change between and including pre-meiosis and telophase II, with more than 50% of these having no similarities to known sequences in NCBI and TIGR databases. This resource is now available to support research into the molecular basis of pairing and recombination control in the complex polyploid, wheat.
Keywords: Time course

overall_design:
 The seven stages collected were pre-meiosis (PM), leptotene to pachytene (LP), diplotene to anaphase I (DA), telophase I to telophase II (TT), tetrads (T), immature pollen (IP) and mature anthers (MAN). Immediately after determining the stage, the remaining two anthers from the floret were placed into liquid nitrogen. After collecting at least 25 staged anthers for each time point from several biological samples, anthers from the respective stages were pooled. Leaf material used in this study was collected from glasshouse-grown plants (six weeks) and total RNA isolated using Trizol® (Gibco BRL, Australia) according to the manufacturer’s protocol.
 Twenty micrograms of aRNA of from each of the seven samples were fragmented for hybridization to each microarray. In total three technical replicates were conducted for each of the seven stages examined. Affymetrix GeneChip® Wheat Genome Arrays were used for all samples. The arrays were hybridized and processed according to the manufacturer’s specifications.
 Normalization of the microarray data was conducted using RMA. The software package Acuity 4 (Molecular Devices, CA, USA) was then used to analyze the microarray data.

first: Wayne

last: Crismani

first: Ute

last: Baumann

first: Tim

last: Sutton

first: Neil

last: Shirley

first: Tracie

last: Webster

first: German

last: Spangenberg

first: Peter

last: Langridge


title: EBNA-2 target genes

status: Public on Oct 03 2006

first: Joerg

last: Mages

address: Trogerstrasse 30

institute: Technical University Munich

summary:
Two cell lines, BL41K3 and BJABK3, were chosen to perform a comprehensive screen for EBNA-2 target genes. Both cell lines are EBV negative B-cell lines and express a chimeric EBNA-2 protein fused to the hormone binding domain of the estrogen receptor (ER/EBNA-2). The cells are propagated in the absence of hormone 31,36. Estrogen stimulation activates ER/EBNA-2, which in turn activates well known EBNA-2 target genes like CD21. BL41K3 and BJABK3 were cultured in estrogen supplemented medium for 24h and gene expression profiles were established for unstimulated and stimulated cells.
Keywords: Transcription factor target identification

overall_design:
BJABK3: 3 biological replicates, for unstimulated and EBNA-2 induced cells, resp.
BL41K3: 2 biological replicates, for unstimulated and EBNA-2 induced cell, resp.

first: Sabine

last: Maier

first: Gabriele

last: Staffler

first: Andrea

last: Hartmann

first: Kristina

last: Grabusic

first: Julia

last: Höck

first: Reinhard

last: Hoffmann

first: Roland

last: Lang

first: Jörg

first: Bettina

last: Kempkes


title: Aplidin synergizes with cytosine arabinoside: functional relevance of mitochondria in Aplidin-induced cytotoxicity

status: Public on Sep 15 2006

city: New Brunswick

first: Pravin

last: Mishra

state: NJ

address: 195 Little Albany St.

department: Pharmacology

institute: UMDNJ

summary:
Aplidin (plitidepsin) is a novel marine-derived antitumor agent presently undergoing phase II clinical trials in hematological malignancies and solid tumors. Lack of bone marrow toxicity has encouraged further development of this drug for treatment of leukemia and lymphoma. Multiple signaling pathways have been shown to be involved in Aplidin-induced apoptosis and cell cycle arrest in G1 and G2 phase. However, the exact mechanism(s) of Aplidin action remains to be elucidated. Here we demonstrate that mitochondria-associated or -localized processes are the potential cellular targets of Aplidin. Whole genome gene-expression profiling (GEP) revealed that fatty acid metabolism, sterol biosynthesis and energy metabolism, including the tricarboxylic acid cycle and ATP synthesis are affected by Aplidin treatment. Moreover, mutant MOLT-4, human leukemia cells lacking functional mitochondria, were found to be resistant to Aplidin. Cytosine arabinoside (araC), which also generates oxidative stress but does not affect the ATP pool, showed synergism with Aplidin in our leukemia and lymphoma models in vitro and in vivo. These studies provide new insights into the mechanism of action of Aplidin. The efficacy of the combination of Aplidin and araC is currently being evaluated in clinical phase I/II program for the treatment of patients with relapsed leukemia and high-grade lymphoma.

Keywords: Aplidin, araC, drug combination, hematological malignancies

overall_design:
Overall goal of the experiment was to obtain molecular insight into the mechanism of action of Aplidin alone as well as its combination with AraC.
SKI-DLCL cells were treated in vitro with IC50 doses for Aplidin, AraC or Aplidin+AraC combination. Each samples was done in biological triplicates. Total number of samples was 12.
Alternatively, SKI-DLCL cells were injected into scid mice and when the tumor was pulpable animals were given a single dose of Aplidin 1mg/kg and AraC 50mg/kg in combination. On day eight after drugs administration tumors were harvested and total RNA was isolated. No replicates are available. Data was validated using semi-quantitative RT-PCR

first: Rita

last: Humeniuk

first: Lata

last: Menon

first: Guray

last: Saydam

first: Jose

last: Jimeno

first: Joseph

last: Bertino

first: Debabrata

last: Banerjee

first: Prasun