title: Survival Related Profile, Pathways and Transcription Factors in Ovarian Cancer

city: Groningen

first: Rudolf

middle: Stephan Nicolaas

last: Fehrmann

state: Groningen

department: Gynecologic Oncology

institute: University Medical Center Groningen

summary:
To date, a variety of studies have employed gene expression profiling to classify ovarian carcinomas in clinically relevant subtypes. These studies provided valuable first clues to molecular changes in ovarian cancer that might be exploited in new treatment strategies. However, most studies were of relatively limited size and the number of overlapping genes in the identified profiles was minimal. Although identification of gene expression profiles associated with clinically relevant subtypes in ovarian cancer is important, knowledge is now emerging rapidly on how genes interact in pathways, networks and complexes; this allows us to unravel those cellular pathways determining the biological behavior of ovarian cancer, that might be successfully targeted with drugs. The aim of our study was: 1) To develop a gene expression profile associated with overall survival in advanced stage serous ovarian cancer, 2) to assess the association of pathways and transcription factors with overall survival, and 3) to validate our identified profile and pathways/transcription factors in an independent set of ovarian cancers. According to a randomized design, profiling of 157 advanced stage serous ovarian cancers was performed in duplicate using ~35K 70-mer oligonucleotide microarrays. A continuous predictor of overall survival was built taking into account well-known issues in microarray analysis, such as multiple testing and overfitting. A functional class scoring analysis was utilized to assess pathways/transcription factors for their association with overall survival. The prognostic value of genes that constitute our overall survival profile was validated on a fully independent, publicly available data set of 118 well-defined primary serous ovarian cancers. Furthermore, functional class scoring analysis was also performed on this independent data set to assess the similarities with results from our own data set. An 86-gene overall survival profile discriminated between patients with unfavorable and favorable prognosis (median survival, 19 vs. 41 months, respectively; permutation p-value of log-rank statistic = 0.015) and maintained its independent prognostic value in multivariate analysis. Genes that comprised the overall survival profile were also able to discriminate between the two risk groups in the independent data set. In our dataset 17/167 pathways and 13/111 transcription factors were associated with overall survival of which 16 and 12 respectively were confirmed in the independent dataset. Our study provides new clues to genes, pathways and transcription factors which contribute to the clinical outcome of serous ovarian cancer and might be exploited in designing new treatment strategies.

Keywords: Oncology/Gynecological Cancers, Genetics and Genomics/Cancer Genetics, Genetics and Genomics/Gene Expression, Genetics and Genomics/Genomics

overall_design: According to a randomized design, profiling of 157 advanced stage serous ovarian cancers was performed in duplicate using ~35K 70-mer oligonucleotide microarrays. Two randomly selected samples were hybridized together on the arrays for intensity-based instead of ratio-based analysis of the microarray data.

first: Ate

last: van der Zee


title: E-cadherin and EMT regulation by E47 transcription represor

status: Public on Dec 21 2008

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

summary:
Expression profile analysis in MDCK-E47 cells in comparisom with MDCK CMV control cells
Keywords: Genetic Modification (overexpression of E-cadherin repressors)

overall_design: The Oncochip microarray platform v1.1 contains 9,726 clones corresponding to 6,386 different genes, and it includes 2,489 duplicate clones. Duplicate samples (different extrations of RNA)  were labeled with dUTP-Cy5 and hybridized against dUTP-Cy3-MDCK control cells. In addittion, one RNA extraction was labelled with dUTP-Cy3 and was hybridized againts dUTP-Cy5- CMV control cells

first: VERONICA

middle: R

last: SOBRADO

first: LIAM

last: HOLT

first: GEMA

last: MORENO-BUENO

first: ANGELA

last: NIETO

first: FRANCISCO

last: PORTILLO

first: AMPARO

last: CANO


title: Liver tissue from the "Four Core Genotype" treated group C57BL/6J mice versus pool C57BL/6J mice of chow diet Liver

status: Public on Dec 08 2008

city: Los Angeles

first: Leslie

last: Ingram-drake

state: CA

department: Medicine/MIMG/Human Genetics

country: USA

institute: UCLA

summary: The purpose of this experiment was to determine the expression traits in Liver tissue from the Four Core Genotype treated group. Keywords: Sry transgene Four Core Genotype Mouse liver Tissue

overall_design: Liver tissue from the "Four Core Genotype" treated group consists of 20 female and male C57BL/6J mice fed a chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were gonadectomized at 8 weeks of life.  In mice of the "four core genotypes" (FCG), the Y chromosome is deleted for the testis-determining gene Sry, producing the Y- chromosome.  The Sry transgene is inserted onto an autosome, so that testis determination is independent of the complement of sex chromosomes.  XY-Sry gonadal males are bred with XX gonadal females, producing progeny with four different genotypes: two types of gonadal males (XX.Sry and XY-Sry) and two types of gonadal females (XX and XY-).  At 12 weeks mice were sacrificed, after a 12-hour fast, Liver tissue were dissected and flash frozen in LN2 and stored at -80°C.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.


title: A 50-Gene Predictor of Recurrence as a Guide to Therapy in Early-Stage Colon Cancer.

status: Public on Dec 03 2008

city: Durham

first: Chaitanya

last: Acharya

state: NC

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

department: Dept. of Surgery

institute: Duke University

summary:
Gene expression profiles reflect unique aspects of individual biologic phenotypes and may characterize the heterogeneity of solid tumors. Using previously-described methodologies that employ DNA microarray data, a 50-gene expression profile (metagene) that predicts risk of recurrence in early stage colon carcinoma was identified. This analysis used an initial discovery cohort of 52 patients. The performance of the 50-gene predictor was evaluated in an independent validation cohort of 73 patients. Using a connectivity map analysis of the 50-gene model, we identified candidate agents and then tested the in vitro efficacy of these compounds in colon cancer cell lines.
73 samples that had patient recurrence data with stage information were used in the analysis.
Keywords: Disease state analysis

overall_design: A total of 73 samples were spotted on microarray slides. No replicates are included in the study.

first: Katherine

middle: S

last: Garman

first: Marian

last: Grade

first: Shivani

last: Sud

first: Kelli

last: Walters

first: Sayan

last: Mukerjee

first: Geoffrey

last: Ginsburg

first: William

middle: T

last: Barry

first: David

last: Hsu

first: Joseph

last: Nevins

first: Thomas

last: Ried

first: Anil

last: Potti


title: In vivo endothelial transcriptomic responses to diesel engine exhaust are potentiated by hypercholesterolemia

status: Public on Dec 15 2008

city: Honolulu

first: John

last: Maresh

state: HI

address: 651 Ilalo

department: Medicine

institute: University of Hawaii

summary: By means of Operon V3 microarrrays, the in vivo, aortic endothelial transcriptomic responses to chronic (30 day) whole body exposure to diesel exhaust were assessed in wild type and Apo E (-/-) mice.  The in vitro response of cultured Svec 4-10 cells exposed  to a soluble extract extract of diesel engine particulate were similarly assessed.

overall_design:
Mice of the Tie 2 GFP strain as well as a stable hybrid strain derived by cross of Tie 2 GFP with the Apo E (-/-) strain were bred in suffficient quantities for these experiments.  Male mice at 4 months of age at the initiation of the exposure to 30 days of dilute diesel engine 94 hours/day, 5 days/week) at either 0 (control), 300 or 1000 ug/ cubic meter exhaust particulate.   Following exposure, three pooled aortae of each experimental and ceach c age-matched control group were dissected from the aortic arch to the iliac bifurcation, minced and collagenolytically digested prior to FACS into Trizol.  Purification yielded aortic endothelial RNA subjected to amplification with Nugen isothermal linear amplification to produce amplified cDNA.  Microarrays were performed with a single dye reversal to compare the transcriptome of exposed mice to age-matched control mice.
In addition, identical cultures of Svec 4-10 cells were exposed for 24 hours to a methanol extract of forklift diesel engine particulate at 50 ug/ml.  Following extraction of RNA and amplification to cDNA as described above, duplicate arrays with a single dye reversal were performed.

middle: G

first: Ralph

middle: V

last: Shohet

first: Matthew

last: Reed

last: Campen


title: Modulation of gene expression in U251 glioblastoma cells by binding of mutant p53 to intronic and intergenic sequences

status: Public on Dec 18 2008

city: Hamburg

first: Genrich

last: Tolstonog

department: Department of Tumor Virology

country: Germany

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

summary: Missense point mutations in the TP53 gene are frequent genetic alterations in human tumor tissue and cell lines derived thereof. Mutant p53 (mutp53) proteins have lost sequence-specific DNA binding, but have retained the ability to interact in a structure-selective manner with non-B DNA and to act as regulators of transcription. To identify functional binding sites of mutp53, we established a small library of genomic sequences bound by p53R273H in U251 human glioblastoma cells using chromatin immunoprecipitation (ChIP). Mutp53 binding to isolated DNA fragments confirmed the specificity of the ChIP. The mutp53 bound DNA sequences are rich in repetitive DNA elements, which are dispersed over non-coding DNA regions. Stable down-regulation of mutp53 expression strongly suggested that mutp53 binding to genomic DNA is functional. We identified the PPARGC1A and FRMD5 genes as p53R273H targets regulated by binding to intronic and intra-genic sequences. We propose a model that attributes the oncogenic functions of mutp53 to its ability to interact with intronic and intergenic non-B DNA sequences and modulate gene transcription via re-organization of chromatin.

overall_design: For the study of the consequences of mutant p53 (R273H) knockdown on gene expression, total RNA from parental U251 glioblastoma cells and UsiA12 clone was prepared from two independent cell culture experiments (biological replicates) and processed for microarray-based profiling of gene expression. UsiA12 clone was derived from the U251 cells transfected with the pSuper-p53 and pCI-neo vectors.

first: Wolfgang

last: Deppert


title: Identification of candidate genes involved in SOD1G93A glial toxicity

status: Public on Dec 04 2008

city: Cambridge

first: Gabriella

middle: Lutz

last: Boulting

state: MA

address: 7 Divinity Ave. rm 423

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: To better understand how the expression of a mutant gene that causes ALS can perturb the normal phenotype of astrocytes, and to identify genes that may have a role in their toxic effect on motor neurons, we used oligonucleotide arrays to compare the global gene expression profiles of glia overexpressing the mutant SOD1G93A protein with two different sets of controls: non-transgenic glia and glia overexpressing the wild type form of the human SOD1 protein (P<0.001) .

overall_design: Glia were derived from P1-P3 mouse pups transgenic for SOD1G93A (G93A), SOD1WT (WT) or non-transgenic pups (NT). Once the cells reached confluence, total RNA was isolated using Trizol (Invitrogen) from three different biological replicates for each type of glia. RNA was amplified by one round of T7 transcription using the Illumina TotalPrep RNA Amplification Kit. Illumina Bead Array Reader. Analysis was done using the Illumina Bead Studio Program.

first: Francesco

middle: P

last: Di Giorgio

middle: L

first: Samuel

last: Bobrowicz

first: Kevin

middle: C

last: Eggan


title: Primary and ras keratinocytes plus TGFbeta1

status: Public on Dec 02 2008

city: Washington

first: DONG-SOON

last: BAE

state: DC

address: 2300 I Street, NW

department: Pharmacology & Physiology

institute: George Washinton Uni.

summary:
We have compared the response to TGFbeta1 in normal and v-rasHa transduced primary mouse keratinocytes using NCI cDNA microarrays. This analysis reveals that Ha-ras alters global TGFbeta1 mediated gene expression in a gene specific manner. The expression pattern of TGFbeta1 immediate early response genes and down regulation of cell cycle control genes is not altered by Ha-ras but the induction of most extracellular matrix genes is blocked. Using Smad3 null keratinocytes, we find that the majority of TGFbeta1 responsive genes in primary keratinocytes are Smad3 dependent, but patterns of transcriptional responses suggest that the ability of Ha-ras to block TGFbeta1 mediated gene expression is not dependent on Smad3. However, the combination of oncogenic ras and loss of Smad3 prevents the TGFbeta1 dependent suppression of genes associated with cell cycle progression and apoptosis observed with either genotype alone. In addition several extracellular matrix genes are super-repressed by TGFbeta1 in the Ha-ras Smad3 null keratinocytes. These data provide a genomic framework for understanding how disruptions of TGFbeta signaling and oncogenic ras cooperate to promote premalignant progression of primary keratinocytes.
Keywords: time series design

overall_design: RNA from Balb/c primary and ras keratinocytes treated for 1, 6, 24, and 48 hours with TGFbeta1 at 1ng/ml was compared to RNA from the corresponding untreated controls. For each timepoint sample from primary and ras cells, multiple arrays (including dye swaps) were analyzed. There are 6, 7, 6, and 5 arrays analyzed for RNA from primary keratinocytes treated for 1, 6, 24, and 48 hours as compared to RNA from untreated primary cells, respectively. There are 6, 8, 7, and 5 arrays analyzed for RNA from ras keratinocytes treated for 1, 6, 24, and 48 hours as compared to RNA from untreated ras cells, respectively. There are 50 arrays analyzed for the Balb/c time-course dataset. RNA from Smad3 WT and KO primary and ras keratinocytes treated 48 hours with TGFbeta1 were compared to RNA from its untreated corresponding controls. There are 6 arrays analyzed for the Smad3 WT/KO data set. There are 56 arrays in this series.


title: Prostate Cancer Gene Expression Changes after Treatment with Neoadjuvant Dutasteride

status: Public on Dec 01 2008

city: Seattle

first: Denise

last: Mauldin

state: WA

address: 1100 Fairview Ave N D4-100

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

summary:
To identify molecular changes underlying the chemopreventive or tumor promoting effects of SRD5A inhibition, we profiled gene expression changes in benign prostate epithelium from patients with PCa treated with dutasteride, a dual SRD5A inhibitor. Subjects were aged 45-80 years with clinically localized PCa (T1C to T2b), Gleason score <7, and serum PSA 2.5-10 ng/dL. 81 men were randomized to immediate RP  (n=25) or to dutasterdie at 0.5 mg (n=26) or 3.5 mg (n=24) orally per day for four months prior to RP. Prostate samples embedded in OCT were used for laser capture microdissection (LCM).
Keywords: clinical trial, Dutasteride, PEDB, dose response, prostate cancer, microarray

overall_design: Subjects were aged 45-80 years with clinically localized PCa (T1C to T2b), Gleason score <7, and serum PSA 2.5-10 ng/dL. 81 men were randomized to immediate RP (n=25) or to dutasterdie at 0.5 mg (n=26) or 3.5 mg (n=24) orally per day for four months prior to RP. Prostate samples embedded in OCT were used for laser capture microdissection (LCM). Approximately 2000-3000 epithelial cells per sample were collected from 8µm sections using the Arcturus Veritas™ Laser Capture Microdissection System according to the Arcturus HistoGene LCM Frozen Section Staining Kit Protocol (Mountain View, CA). Total RNA was isolated using the Arcturus Picopure™ Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNase Set (Qiagen Inc, Valencia, CA). Total RNA was subjected to two rounds of linear amplification using the Ambion MessageAmpII Kit (Ambion Inc, Austin, TX), quantitated in a Gene-Spec III spectrophotometer (Hitachi, Tokyo) and aRNA integrity evaluated using gel electrophoresis.  40 Human Prostate (PEDB) Microarrays were run with sample on the Cy3 channel against a Human Gold Standard (v5) on the Cy5 channel.

first: Elahe

middle: A

last: Mostaghel

first: Ilsa

middle: M

last: Coleman

middle: E

last: Abbott

first: Peter

last: Nelson


title: Transcriptional response of Candida albicans to endothelial cells

city: Torrance

first: Hyunsook

last: Park

address: 1124 W carson st

department: Infectious Diseases

institute: Los Angeles Biomedical Research Institute at Harbor-UCLA medical center

summary:
Candida albicans is exposed to a different host environment during different site of infection. Thus, different virulence factors may be active during differenttypes of infection. However,little is known about the C. albicans genes that are required for the initiation and maintenance of candidiasis. To identify potential virulence factors relevant to hematogenously disseminated candidiasis, we determined the transcriptional response of C. albicans to human umbilical vein endothelial cells (HUVECs) in vitro.
Keywords: cell interaction

overall_design: Two different Candida albicans strains, CAI4-URA and a clinical isolate 36082, were used to identify the transcriptional response of C. albicans to HUVECs. The strains were incubated with either the HUVECs or bare plastic for 45, 90, and 180 min. C. albicans RNA was extracted and the transcriptional profile of these organisms was analyzed using the C. albicans oligonucleotide microarray. The transcriptional response to HUVECs was compared to that to bare plastic as a control condition. Each time point contains six biological replicates, three of which are from each C. albicans strain.

first: Scott

last: Filler

first: Haoping

last: Liu

first: Norma

last: Solis


title: Prostate Cancer Gene Expression Changes with Neoadjuvant Hormone Therapy

summary:
Men with clinically localized prostate cancer were treated with 0 to 9 months of neoadjuvant hormone suppression prior to prostatectomy.
Keywords: microarray, hormone,

overall_design: 9 men with prostate cancer were assigned to neoadjuvant hormone suppression therapy for 3-6, 6, or 0 months.


title: Involvement of JunD in the antiproliferative effect of 9-tetrahydrocannabinol on human breast cancer cells 1

first: Hector

last: Hernandez-Vargas

summary:
THC induces an activation of JunD, by upregulation and translocation to the nuclear compartment, which is accompanied by a decrease in cell proliferation
Keywords: THC, JUND

overall_design: Total RNA was isolated from cells treated with vehicle (DMSO), 3 or 5 uM THC for 8 or 24h, and non-treated cells at the time of drug addition (t=0, reference) using RNeasy Mini Kit (Qiagen, Hilden, Germany). Double strand cDNA was amplify with Superscript Choice System and T7-(deoxythymidine)24 oligo-primers (Life Technologies, Inc., Gaithersburg, MD) and in vitro transcription was carried out with MegascriptTM T7 (Ambion, Austin, TX). For each condition, half of the replicates were labeled with Cy5-dUTP fluorochrome (Amersham, Uppsala, Sweden) and the reference with Cy3-dUTP fluorochrome (Amersham), and the other half were dye swapped. Hybridization was performed on a new version of the Spanish National Cancer Research Center (CNIO) Oncochip manufactured by the CNIO Genomic Unit (http://bioinfo.cnio.es/data/oncochip), which contains 9.726 clones corresponding to 6,386 different genes. Slides were scanned in a Scanarray 5000 XL scanner (GSI Lumonics Kanata, Ontario, Canada) and quantified using the GenePix Pro 6.0 program (Axon Instruments Inc., Union City, CA).

first: Maria

last: Caffarel

first: Gema

last: Moreno-Bueno

first: Jose

last: Palacios

first: Manuel

last: Guzman

first: Cristina

last: Sánchez


title: Gene expression in C57BL/6 mouse lungs after exposure to aerosolized NTHi lysate

status: Public on Nov 26 2008

city: Houston

last: Evans

state: TX

address: 1400 Holcombe Blvd

department: Pulmonary Medicine - Unit 1462

institute: University of Texas-M.D. Anderson Cancer Center

summary:
Pneumonia is a serious problem worldwide.  We recently demonstrated that innate defense mechanisms of the lung are highly inducible against pneumococcal pneumonia.  To determine the breadth of protection conferred by stimulation of lung mucosal innate immunity, and to identify cells and signaling pathways activated by this treatment, mice were treated with an aerosolized bacterial lysate, then challenged with lethal doses of bacterial and fungal pathogens.  Mice were highly protected against a broad array of Gram-positive, Gram-negative, and Class A bioterror bacterial pathogens, and Aspergillus fumigatus.  Protection was associated with rapid pathogen killing within the lungs, and this effect was recapitulated in vitro using a respiratory epithelial cell line.  Gene expression analysis of lung tissue showed marked activation of NF-kappaB, Type I and II interferon, and antifungal Card9-Bcl10-Malt1 pathways.  Cytokines were the most strongly induced genes, but the inflammatory cytokines TNF and IL-6 were not required for protection.  Lung-expressed antimicrobial peptides were also highly upregulated.  Taken together, stimulated innate resistance (StIR) appears to occur through the activation of multiple host defense signaling pathways in lung epithelial cells, inducing rapid pathogen killing, and conferring broad protection against virulent bacterial and fungal pathogens.  Augmentation of innate antimicrobial defenses of the lungs might have therapeutic value for protection of patients with neutropenia or impaired adaptive immunity against opportunistic pneumonia, and for defense of immunocompetent subjects against a bioterror threat or epidemic respiratory infection.

Keywords: differential gene expression; time course; innate immunity; pneumonia; immunocompromised host; lung epithelium

overall_design: Gene expression patterns in mouse lung homogenates were analyzed 2h after exposure to aerosolized PBS (Sham treatment), 2h after exposure to aerosolized NTHi lysate or 4h after exposure to aerosolized NTHi lysate.  Each group consisted of six mice.


title: Gene expression in respiratory epithelial cells treated to induce StIR

status: Public on Nov 21 2008

summary:
Pneumonia is a serious problem worldwide.  We recently demonstrated that innate defense mechanisms of the lung are highly inducible against pneumococcal pneumonia.  To determine the breadth of protection conferred by stimulation of lung mucosal innate immunity, and to identify cells and signaling pathways activated by this treatment, mice were treated with an aerosolized bacterial lysate, then challenged with lethal doses of bacterial and fungal pathogens.  Mice were highly protected against a broad array of Gram-positive, Gram-negative, and Class A bioterror bacterial pathogens, and Aspergillus fumigatus.  Protection was associated with rapid pathogen killing within the lungs, and this effect was recapitulated in vitro using a respiratory epithelial cell line.  Gene expression analysis of lung tissue showed marked activation of NF-kappa-B, Type I and II interferon, and antifungal Card9-Bcl10-Malt1 pathways.  Cytokines were the most strongly induced genes, but the inflammatory cytokines TNF and IL-6 were not required for protection.  Lung-expressed antimicrobial peptides were also highly upregulated.  Taken together, stimulated innate resistance (StIR) appears to occur through the activation of multiple host defense signaling pathways in lung epithelial cells, inducing rapid pathogen killing, and conferring broad protection against virulent bacterial and fungal pathogens.  Augmentation of innate antimicrobial defenses of the lungs might have therapeutic value for protection of patients with neutropenia or impaired adaptive immunity against opportunistic pneumonia, and for defense of immunocompetent subjects against a bioterror threat or epidemic respiratory infection.

Keywords: Differential expression, innate immunity, pneumonia, immunocompromised host; lung epithelium, in vitro,

overall_design: MLE-15 cells were treated with sham (PBS), NTHi lysate (100 ug/ml) or EF2505-III (40 ug/ml).  4 unique samples per group. Treated for 2 hours. Hybridized to Illumina Sentrix Mouse-6 v1.1 Beadhips.


title: Gene expression in the human mammary epithelium during lactation: the milk fat globule transcriptome

status: Public on Nov 25 2008

first: Patricia

last: Maningat

address: 1100 Bates St

department: CNRC

institute: Baylor College of Medicine

summary:
The 24h gene expression profile in the lactating mammary gland was demonstrated using the Human Ref-8 BeadChip array (Illumina, Inc).  Of the 22,184 gene transcripts on the array, 14,070 genes were consistently expressed and represented the milk fat globule transcriptome.  Milk protein genes were among the most highly expressed along with genes involved in the milk syntesis processes.

Keywords: time course analysis

overall_design: Serial milk samples were collected every 3h for 24h from 5 normal, lactating women.  RNA was isolated from the milk fat globules and utilized for microarray analyses.

first: Partha

last: Sen

first: Agneta

last: Sunehag

first: Darryl

last: Hadsell

first: Molly

last: Bray

first: Morey

last: Haymond


title: Parity and the genomic signature in the Human Breast

status: Public on Nov 04 2008

city: Philadelphia

first: Julia

last: Santucci-Pereira

state: PA

address: 333 Cottman Ave, P2051

institute: Fox Chase Cancer Center

summary:
Case-control study for the analysis of the gene expression profile of epithelial cells microdissected from normal breast tissues obtained from 17 parous and 7 nulliparous women free of breast pathology (controls),
and 39 parous and 8 nulliparous women with history of breast cancer (cases).

Keywords: genetic modifications

overall_design:
Four-condition experiment: nulliparous case, nulliparous control, parous case and parous control labeled with Cy5 and Universal human reference used as a common reference labeled with Cy3. Moderated t statistic was used as the basic statistic for significance analysis; it was computed for each probe and for each contrast. False discovery rate was controlled using the Benjamini and Hochberg. All genes with P value below a threshold of 0.05 were selected as differentially expressed, maintaining the proportion of false discoveries in the selected group below the threshold value, in this case 5%.

Breast 11 parous control HuII, Breast 28 parous case HuII, and Breast 62 nulliparous control HuIII excluded: raw data is missing

last: Russo

first: Gabriela

last: Balogh

first: Irma

middle: H

first: Daniel

last: Mailo


title: Low-Fat, Low-Glycemic Load Diet, Surgical Manipulation and Prostate Gene Expression

first: Denise

last: Mauldin

summary:
Prostate Microarrays for two studies on Low-Fat, Low-Glycemic Load Diet intervention in prostate cancer and the effect of Surgical Manipulation on Prostate Gene Expression.

Influence of Surgical Manipulation on Prostate Gene Expression: Implications for Molecular Correlates of Treatment Effects and Disease Prognosis
"Measurements of tissue gene expression are increasingly used for disease stratification, clinical trial eligibility, and assessment of neoadjuvant therapy response. However, the method of tissue acquisition alone could significantly influence the expression of specific transcripts or proteins. This study examines whether there are transcript alterations associated with surgical resection of the prostate gland by radical retropubic prostatectomy."

Low-Fat, Low-Glycemic Load Diet and Gene Expression in Human Prostate Epithelium: A Feasibility Study of Using cDNA Microarrays to Assess the Response to Dietary Intervention in Target Tissues
"We examined the feasibility of using gene expression changes in human prostate epithelium as a measure of response to a dietary intervention."
Keywords: Low-fat, Low-Glycemic Load, Prostate Cancer, Radical Prostatectomy, Ischemia

overall_design:
Participants were 12 men with clinically localized prostate cancer, who elected to undergo radical prostatectomy and received no neoadjuvant therapy. Study activities began within 2 weeks of diagnosis.  Participants were randomly assigned to one of three groups: group I received instructions to follow a low-fat/low-glycemic load diet (<20% energy from fat and total daily glycemic load <100) and group II was instructed to follow a ‘‘standard American’’ diet (35% energy from fat
and total daily glycemic load >200) and group III received no dietary intervention.  No participant received previous hormonal ablation, chemotherapy, or radiotherapy.  At time of radical prostatectomy and after induction of anesthesia,we obtained four in situ prostate biopsy cores using an 18-gauge prostate needle biopsy gun (Bard Inc, Murray Hill, NJ), and immediately embedded and froze them. Radical prostatectomy was performed as follows: The prostate was mobilized from surrounding tissue, and the dorsal venous complex was divided and oversewn. After dissecting the adjacent neurovascular bundle(s), where appropriate, the urethra was incised, the prostate was dissected free of
the rectum, and the vascular pedicles were ligated. The seminal vesicles were then mobilized from the surrounding tissue, and the prostate was dissected free of the bladder neck and removed. We immediately obtained four ex vivo biopsy cores following the same protocol just described. The time interval from ligation of vascular pedicles to ex vivo biopsy was defined as the ischemia time.  Biopsy cores were embedded individually in polyethylene glycol freezing media (Tissue-Tek OCT
Compound, Sakura Finetek), placed in isopentane that was precooled in liquid nitrogen, and stored at 80C. We used laser capture microdissection to collect 5,000 epithelial cells from histologically benign epithelial glands and extracted RNA using a standardized protocol.  We prepared and hybridized spotted cDNA microarrays as previously described (10), using RNA from a single batch of reference standards for each hybridization. Fluorescent array images were collected for both
Cy3and Cy5 using a GenePix 4000B fluorescent scanner (Axon Instruments), and GenePix Pro 4.1 software was used to grid and extract image intensity data. Spots of poor quality, as determined by visual inspection, were removed from further analysis. To normalize log ratio data, a print tip–specific Lowess curve was fit to the log-intensity versus log-ratio plot, using 20.0% of the data to calculate the fit at each point. This curve was used to center the log-ratio for each spot. Data were filtered to exclude poorly hybridized cDNAs by removing values
with average foreground minus background intensity levels less than 300. We used the average of the two duplicate cDNA spots on each microarray chip in subsequent analyses.

middle: W

last: Lin

first: Ilsa

last: Coleman

first: Sarah

last: Hawley

first: Ruth

last: Dumpit

first: David

last: Gifford

first: Philip

last: Kezele

first: Hau

last: Hung

last: Abbott

first: Marian

last: Neuhouser

first: Jeannette

last: Schenk

first: Beatrice

last: Knudsen

first: Alan

last: Kristal

first: Peter

last: Nelson


title: Transcriptional response of Candida albicans to oral epithelial cells

first: Hyunsook

last: Park

summary:
Candida albicans is exposed to a different host environment during oropharyngeal candidiasis (OPC) compared to hematogenously disseminated candidiasis.  Thus, different virulence factors may be active during these two types of infection.  However,little is known about the C. albicans genes that are required for the initiation and maintenance of OPC.  To identify potential virulence factors relevant to this disease, we determined the transcriptional response of C. albicans to oral epithelial cells in vitro.
Keywords: cell interaction

overall_design: Two different Candida albicans strains, CAI4-URA and a clinical isolate 7392,  were used to identify the transcriptional response of C. albicans to oral epithelial cells. The strains were incubated with either the FaDu oral epithelial cell line or bare plastic for 45, 90, and 180 min. C. albicans RNA was extracted and the transcriptional profile of these organisms was analyzed using the C. albicans oligonucleotide microarray. The transcriptional response to Fadu cells was compared to that to bare plastic as a control condition. Each time point contains six biological replicates, three of which are from each C. albicans strain.

first: Scott

last: Filler

first: Haoping

last: Liu

first: Norma

last: Solis


title: 129, AJ and Balb CGH against C57 reference on Agilent whole genome and custom mouse long oligonucleotide arrays

status: Public on Nov 20 2008

city: Manchester

first: Catriona

last: Rennie

address: Oxford Rd

department: Faculty of Life Sciences

country: United Kingdom

institute: The University of Manchester

type: Genome variation profiling by genome tiling array

summary:
CGH comparing 3 inbred mouse strains to a C57BL/6 reference.
The 3 inbred strains used have known trypanotolerance phenotypes, and these data were originally acquired as part of a study investigating the genetic mechanisms underlying trypanotolerance.
These data have also been used in conjunction with the Perlegen 8 million SNP dataset to examine the effect of sequence mismatches on the log2 signal ratios acquired by these long oligonucleotide arrays.
Keywords: comparative genomic hybridisation

overall_design:
2 separate array platforms were used - the standard Agilent mouse whole genome 244K CGH array, and a custom Agilent mouse 56K CGH array.
There were twelve hybridisations in total, as for each of the two array platforms, six competitive 2-colour hybridisations were carried out.
129 vs C57BL/6
C57BL/6 vs 129 - dye-flip of the above
AJ vs C57BL/6
C57BL/6 vs AJ - dye-flip of the above
Balb vs C57BL/6
C57BL/6 vs Balb - dye-flip of the above

first: Harry

last: Noyes

first: Stephen

middle: J

last: Kemp

first: Helen

last: Hulme

last: Hoyle

first: Andrew

last: Brass


title: Specific, Durable and Accurate Gene Expression Signatures of Radiation Response in Mice and Humans

status: Public on Nov 29 2008

first: Holly

middle: Kloos

last: Dressman

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University Medical Center

summary:
Previous work has demonstrated the potential for peripheral blood (PB) gene expression profiling for the detection of disease or environmental exposures.    We have sought to determine the impact of several variables on the PB gene expression profile of an environmental exposure, ionizing radiation, and to determine the specificity of the PB signature of radiation versus other genotoxic stresses.
Keywords: peripheral blood, gene expression study, radiation reponse

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We have sought to determine the impact of several variables on the PB gene expression profile of an environmental exposure, ionizing radiation, and to determine the specificity of the PB signature of radiation versus other genotoxic stresses.  Neither genotype differences nor the time of PB sampling caused any lessening of the accuracy of PB signatures to predict radiation exposure, but sex difference did influence the accuracy of the prediction of radiation exposure at the lowest level (50 cGy).   A PB signature of sepsis was also generated and both the PB signature of radiation and the PB signature of sepsis were found to be 100% specific at distinguishing irradiated from septic animals.  We also identified human PB signatures of radiation exposure and chemotherapy treatment which distinguished irradiated patients and chemotherapy-treated individuals within a heterogeneous population with accuracies of 90% and 81%, respectively.
Human and Murine samples used in models
Peripheral blood was collected from patients prior to and 6 hrs following total body irradiation with 150 to 200 cGy as part of their pre-transplantation conditioning.  For additional comparison, peripheral blood was obtained from healthy volunteers and an additional cohort of patients prior to and 6 hrs following the initiation of alkylator-based chemotherapy alone (without radiotherapy).

first: Sarah

middle: K

last: Meadows

first: Garrett

last: Muramoto

first: Heather

last: Himburg

first: Alice

last: Salter

first: Zheng

middle: Z

last: Wei

first: Geoff

last: Ginsburg

first: Nelson

last: Chao

first: Joseph

last: Nevins

first: John

last: Chute


title: Differential gene expression analysis in the larval heart of Drosophila

status: Public on Oct 29 2008

city: MARSEILLE Cedex 9

first: Bruno

last: ZEITOUNI

address: Campus de Luminy Case 907

institute: CNRS

summary:
The abstract of the manuscript titled "Identification of co-regulated genes and cis-regulatory modules in Drosophila contractile cardiomyocytes" is given below:
"Understanding how sets of genes are co-regulated to generate cell diversity during metazoan development is a major challenge. This requires the identification of tightly co-expressed genes in a given developmental process, of the responsible cis-regulatory modules, and of the combination of trans-acting transcription factors. We chose the Drosophila cardiac tube to address this issue. The cardiac tube is composed of a rostral aorta and a caudal heart, with distinct morphologies and functions and its development is controlled by conserved transcription factors.
Our goal was to identify heart specific expressed genes and to use a combination of genetic and bioinformatic tools to identify and characterize their heart cis-regulatory modules (CRMs). By combined candidate gene approach and microarray experiments, we found 15 different genes that are specifically co-expressed in the contractile cardiomyocytes of the heart. Potential heart-specific CRMs were retrieved from evolutionary conserved non-coding sequences that were ranked according to an integrated score based on combinations of conserved occurrences of potential binding sites for transcription factors known to be expressed in the cardiovascular system, namely Abd-A, Tin, GATA, Mef2, Hand, and T-box factors. Candidate CRMs were then tested in vivo by generating nGFP reporter construct transgenic flies, allowing the identification of three heart enhancers precisely reproducing endogenous gene expression in the heart.
We identified 15 genes that are tightly co-regulated in the contractile cardiomyocytes of the heart and for three of them found the responsible enhancer through computational predictions. A computational post-analysis suggests that different combinations of heart transcription factors may regulate these enhancers and permits to further refine the in silico identification of heart-specific CRMs."

overall_design:
In the present study, we described two distinct whole-genome microarray experiments to identify differentially expressed genes in the drosophila larval heart (or dorsal vessel) :
1) comparison of the transcriptome of heart (posterior part) versus aorta (anterior part) from the third instar larval cardiac organ,
2) comparison of the transcriptome of the entire larval dorsal vessel to that of sibling whole larvae.
For each microarray experiment, 4 biological replicates were used through a dye-switch (or biological dye-swap) microarray experimental design in which they were labelled so that each of two conditions has half the samples tagged with Cy3 dyes (2 with Cy3) and the other half with Cy5 dyes (2 with Cy5), then independently hybridized in a reverse and balanced way on dual-channel microarrays (4 arrays). A graphical representation of the design used on this study is showed in the associated manuscript.

first: Maria

middle: F

last: Tevy

last: Zeitouni

first: Stein

last: Aerts

first: Delphine

last: Potier

first: Elisabetta

last: Tosi

first: Francesca

last: Buontempo

first: Bassem

last: Hassem

first: Michel

last: Sémériva

last: Capovilla

first: Laurent

last: Perrin


title: Transcriptional profiles of Ad-F3 and Ad-F7 transduced macrophages

status: Public on Nov 30 2008

city: Montreal

first: Eduardo

last: Hernandez

state: Quebec

address: 3755 Cote-Sainte-Catherine Road

department: Molecular Oncology Group

country: Canada

institute: Lady Davis Institute for Medical Research (JGH)

summary: To identify genes that may regulate distinct or overlapping functions of IRF-3 and IRF-7, primary human macrophage preparations were transduced with adenoviral vectors: Ad-GFP (control), Ad-F3 (expressing the active form of IRF-3, IRF-3 5D), or Ad-F7 (expressing the active form of IRF-7, IRF-7 D247-467) and evaluated by microarray analysis.

overall_design: RNA was collected 24 hours post-transduction with Ad-GFP, Ad-F3 and Ad-F7  and subjected to microarray analysis. Submited tables show the average of 7 donors.

last: Goubau

last: Hiscott


title: Gene expression profiling in cardiac AngII-overexpressing mice (TG1306/1R)

status: Public on Oct 25 2008

city: Chicago

first: Andrea

middle: A.

last: Domenighetti

state: IL

address: 345 East Superior St

institute: Northwestern University & Rehabilitation Institute of Chicago

summary: Agonist-induced cardiac hypertrophy in TG1306/1R transgenic mice with cardiac angiotensin II overproduction leads to a gradual transition from a compensatory hypertrophic state to heart failure. To gain insight into the molecular mechanisms that play a role in maintaining cardiac integrity in the diseased heart, we performed a comparative study of gene expression between wild-type (WT) and transgenic (TG) hearts using microarray analysis. TG1306/1R transgenics were separated into two phenotypic groups (hypertrophic and dilated) based on morphological parameters (cardiac weight index and histology) and either a moderate (hypertrophic) or a high (dilated) upregulation of molecular markers for hypertrophy and failure, and compared to age and sex-matched wild-types.

overall_design:
In this series, twelve 60 week old male TG1306/1R mice were separated into 3 groups:

WT1-4= Four Wild-types TG1306/1R littermates genetically negative for the transgene (-/-)

Hyp1-4= Four TG1306/1R mice heterozygote for the transgene (-/+) and developing a concentric hypertrophic phenotype*

Dil1-4 = Four TG1306/1R mice heterozygote for the transgene (-/+) and developing a dilated cardiac phenotype*

This series contains 4 biological replicates for the following triangulation: WT is compared to Hyp, WT is compared to Dil, and Hyp is compared to Dil.

* For further information read:
Domenighetti AA, Wang Q, Egger M, Richards SM, Pedrazzini T, Delbridge LM. Angiotensin II-mediated phenotypic cardiomyocyte remodeling leads to age-dependent cardiac dysfunction and failure. Hypertension. 2005 Aug;46(2):426-32. [PMID: 15998712]

first: Thierry

last: Pedrazzini


title: Gene expression profiling of rat endometrial cancer

status: Public on Oct 02 2008

city: Skövde

first: Sandra

last: Karlsson

address: Högskolevägen 1

department: School of Life Sciences

country: Sweden

institute: University of Skövde

summary:
Transcriptional profiling of rat EAC - comparison of non-/pre-malignant endometrium with endometrial tumors
Endometrial cancer develops from the endometrium of the uterus and is the most common pelvic malignancy diagnosed in women in the western countries. Similar to all cancer diseases, endometrial cancer is a genetic disorder that results from complex patterns of genetic and epigenetic alterations involved in the malignant transformation. The genetic heterogeneity inherent in the human population, differences in the environment and life styles poses enormous difficulties when analyzing the complex patterns of genetic alterations contributing to cancer etiology. Inbred animal models constitute unique experimental genetic tools as the genetic heterogeneity and the influence of environmental factors can be readily reduced. The BDII/Han rat model is unique for spontaneous hormonal carcinogenesis since more than 90% of the female virgins spontaneously develop endometrial cancer during their life span. The possibility to perform global gene expression profiling of tumor cells would likely provide important information of the genes and pathways that are involved in EAC susceptibility and carcinogenesis.

Keywords: Endometrial tumors developed in crosses with the BDII inbred rat strain (from backcrosses, NUT, and intercrosses, RUT) and Sprague Dawley curley-3 and Brown Norway

overall_design: Common reference design - Universal rat reference (Stratagene) hybridized to all arrays. Biological replicates and technical replicates (3) of each clone printed at random positions on the array.

first: Karin

last: Levan


title: Erythropoietin use in kidney transplants

status: Public on Oct 21 2008

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Background and objectives: This report describes an unusual presentation of severe hypertension (HTN) in a subset of pediatric kidney recipients treated with a steroid avoidance pediatric renal transplantation protocol. The HTN was secondary to atypical, reno-vascular abnormalities (RVA) of the transplanted vasculature, temporally associated with erythropoietin (EPO) use. Design, setting, participants, and measurements: To investigate the clinical significance underlying this event, a retrospective clinical study of 100 pediatric renal transplants was undertaken (50 steroid-free and 50 matched steroid-based controls), with peripheral blood transcriptional analysis of four RVA patients and controls. Results: Regardless of a higher observed incidence of anemia (p < 0.001) and greater overall EPO usage in the first post-transplant year in steroid-free patients, the incidence of new-onset HTN at one yr was significantly less in the steroid-free cohort (p = 0.03). Nevertheless, early EPO (first week post-transplant) was significantly associated with the combinatory findings of new-onset HTN (p = 0.03) and RVA (p = 0.007). Molecular mechanisms of RVA injury were investigated further by peripheral blood cDNA microarray gene expression profiling. A panel of 42 transcripts differentiated patients with RVA and HTN from three sets of matched controls, with and without HTN and EPO use, with 100% concordance (p < 0.001). The biological processes governed by these significant genes suggest a role for EPO regulation of growth factor receptor ubiquitination as a putative mechanism for renal vascular injury. Conclusion: This study cautions against the use early post-transplant use of EPO in immunosuppression regimens with steroid minimization/avoidance, which may have an increased incidence of post-transplant anemia.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Disease State: patient with high blood pressure

Keywords: Logical Set

overall_design: Using regression correlation

first: Minnie

last: Sarwal


title: Comparison of the transcriptome of the ethanol adapted yeast and control at 10% ethanol

city: Osaka

first: Thai

middle: Nho

last: Dinh

state: Osaka

address: 2-1 Yamadaoka, Suita

department: Biotechnology

country: Japan

institute: Osaka University

summary: In this study, using DNA microarray analysis, we compared the comprehensive expression profiles of two yeast trains, i.e, the previously obtained ethanol-adapted yeast strain and the parental strain as control (FY834), under the ethanol stress condition (YPD medium contained 10% ethanol). As a result, we identified certain genes and functional categories of the genes that are possible involved in growth under the ethanol stress condition.

overall_design: The ethanol adapted and FY834 yeasts were cultivated in YPD medium containing 10% ethanol. For the control, FY834 strain was cultivated in YPD medium. Cells were harvested in the logarithmic growth phase and then immediately frozen in liquid nitrogen. Total RNA was extracted by the hot phenol method and purified into mRNA using an Oligo dT30<Super> mRNA purification kit. Cy3-labelled cDNA targets were prepared from 1.5 µg of mRNA samples of yeasts grown in the ethanol stress condition. Cy5-labelled cDNA targets were prepared from 1.5 µg of mRNA samples of yeast grown in YPD. Cy3-and Cy5-labelled cDNA targets were mixed and then hybridized with probes on the DNA microarray, Yeast gene chip ver.2. (DNA Chip Research Inc.,Japan). The preparation of fluorescent-dye-labeled cDNA targets, hybridization, and washing were carried out as described in instruction manuals supplied by the manufacturer of the DNA microarray.

middle: N

first: Keisuke

last: Nagahisa

first: Katsunori

last: Yoshikawa

first: Takashi

last: Hirasawa

first: Chikara

last: Furusawa

first: Hiroshi

last: Shimizu


title: Analysis of Genes in the Hypothalamus Controlling Feed Intake and Energy Metabolism in Neonatal Chicks

status: Public on Oct 18 2008

city: College Park

first: Tom

middle: E.

last: Porter

state: MD

address: Building 142

department: Animal and Avian Sciences

institute: University of Maryland

summary:
Delayed access to feed following hatching has been associated with reduction in growth performance in chicks. However, the gene networks within the hypothalamus that regulate feed intake and metabolism, and the effects of fasting on those pathways are not well understood. The present experiment evaluated global hypothalamic gene expression in neonatal chicks using the Arizona Gallus gallus 20.7K Oligo Array v1.0 to elucidate genes and pathways regulated by feeding, fasting, and refeeding. Ten groups of chicks were sampled over four days post-hatch, including: control (at hatch), 24h fed, 24h fasted, 48h fed, 48h fasted, 48h fasted then 4h refed, 72h fed, 48h fasted then 24h refed, 96h fed, and 48h fasted then 48h refed. Non-esterified fatty acids were elevated, and triglycerides were decreased in fasted chicks at 24 and 48h, indicating that fasting induced physiological changes. Hypothalamic samples were collected from 16 chicks per group, and total RNA was extracted and pooled for hybridization (n=4). Expression patterns of selected genes were confirmed by quantitative real-time PCR.  Two-fold differences in gene expression were detected in 1,272 genes between treatment groups, and of those, 119 genes were significantly (P<0.05) different. Assignment of gene ontology terms to the significant genes resulted in 34 different categories of biological processes, with 24% of genes participating in signal transduction, transport, or metabolic processes. Genes that were upregulated during fasting (and confirmed by qPCR) include FK506BP51, which is involved in the formation of steroid receptor complexes, and deiodinase type II, which is responsible for converting the thyroid hormone T4 into T3. Confirmed genes, downregulated due to fasting, included proopiomelanocortin and fatty acid binding protein 7. Other regulated genes were identified that play a role in feeding and obesity in other species, such as relaxin 3 and adrenergic receptor-β2. Further analysis of differentially regulated genes could provide new information regarding the role of the hypothalamus in feed intake and metabolism.

Keywords: Metabolic perturbation

overall_design: Ten experimental groups with 4 replicates each were analyzed.  A reference RNA design was used for this microarray.  Equal amounts of amplified RNA (aRNA) from all samples were pooled and labeled with the Alexa 647 to create the reference pool.  Each individual sample was labeled with Alexa 555.  Each slide was hybridized with both the reference pool and one sample.

first: T

first: S

last: Higgins


title: Liver tissue from hormone treated C57BL/6J mice versus pool C57BL/6J mice of chow diet Liver

status: Public on Dec 08 2008

city: Los Angeles

first: Leslie

last: Ingram-drake

department: Medicine/MIMG/Human Genetics

institute: UCLA

summary: The purpose of this experiment was to determine the expression traits in animals of inbred strain C57BL/6J, treated with gonadal hormones. (N=40, 20 males and 20 females).

overall_design: Liver tissue from the hormone treated group consists of 40 female and male C57BL/6J mice fed a chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were gonadectomized at 8 weeks of life, implanted with hormone pellets at 12 weeks, and sacrificed at 14 weeks.  Male and female mice of the hormone treated groups received subcutaneous implants of either 0.5 mg estradiol (E2) pellet (plasma yield of 300 picogram/ml) or a 5 mg dihydrotestosterone (DHT) pellet (plasma yield of 1-2 nanogram/ml), designed to release over 21 days, (Innovative Research of America, 17B-estradiol: Cat. No. E-121 0.5mg/pellet, 5a-dihydrotestosterone: Cat. No. A-16).  Control mice were treated with the placebo pellet (Innovative Research of America, placebo: Cat. No. C-111).  At 14 weeks mice were sacrificed, after a 12-hour fast, Liver tissue were dissected and flash frozen in LN2 and stored at -80°C.  All sample were compared to a common pool created from equal portions of RNA from each of the samples. Keywords=hormone treated Mouse liver Tissue


title: The transcriptomic signature of hungry murine liver

status: Public on Oct 23 2008

city: Amsterdam

first: Milka

last: Sokolovic

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: AMC

summary:
Background
In the postabsorptive state, the portal-drained viscera are a major energy consumer, but a comprehensive overview of the adaptive fasting response in the liver is lacking. Hence, gene-expression profiling, pathway, network and gene-set enrichment analysis and immunohistochemistry were carried out on mouse liver after 0, 12, 24, and 72 hours of fasting.
Results
Liver weight has fallen to 50% of control after three days of fasting, hepatocyte size was reduced with no apparent increase in apoptosis, while the basic liver structure and metabolic zonnation were preserved.
Expression profiling and pathway analysis depicted four master processes, all with response peaking at 24 hours, and all but one decreasing towards 72h. Changes in gene expression were compatible with cellular energy deficiency, and metabolic adaptations were directed at enhanced glucose production, stimulation of lipid catabolism and ketone body synthesis, and strongly augmented ATP production. Consequently, the expression of genes involved in oxidative and endoplasmic reticulum stress response was increased. In addition, urea cycle genes were strongly upregulated during whole duration of fasting, in spite no obvious increase in amino-acid catabolism. Major physiological change upon continued fasting was restoration of glycogen reserves, but with reverse localization, demonstrating utilization of different glycogenic precursor compared to the fed controls.
Conclusion
The changes in liver gene expression indicate a rapid onset of generating glucose and ketone bodies during short, and a return to near normal situation in prolonged fasting. The reason apparently lies in glycogen repletion, due to late fasting glucose production by (gut and) kidney.
Keywords: fasting response, time course

overall_design: Male FVB mice (Charles River, Maastricht, The Netherlands) were housed at 20-22°C, 50-60% humidity, a 12 hours light/dark cycle, and food and water ad libitum. At 6 weeks of age, mice were fasted by removing chow for up to 72 hours before sacrifice (n = 6 per group). All animals were sacrificed between 9:00 and 10:00 a.m. by cervical dislocation. The liver was removed quickly, weighed, snap-frozen in liquid N2, and stored at -80°C. Total intestinal RNA was extracted from frozen tissue using TRIzol (Invitrogen), followed by a cleanup through a RNeasy column (Qiagen). The quality of RNA was assessed with the RNA 6000 Nano LabChip® Kit in an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA). The 60-mer Mouse Development (22K) Oligo Microarray G4120A (Agilent) was used. Three arrays per experimental condition were used. Per microarray, 20 μg mRNA, pooled from 2 livers, was reverse transcribed with Cy3-labelled dCTP (Perkin Elmer, Boston, USA), using the Agilent Fluorescent Direct Label Kit. Cy5-labeled cDNA produced from RNA pooled from livers of 6 fed animals served as the common reference across all arrays. Hybridized cDNAs were detected with Agilent’s dual-laser microarray slide scanner. The data were retrieved with Agilent’s Feature Extraction software 6.1.1.

first: Aleksandar

first: Diederik

last: Wehkamp

first: Emiel

last: Ver Loren van Themaat

first: Dirk

middle: R

last: de Waart

first: Lisa

last: Gilhuijs-Pederson

first: Yuri

last: Nikolsky

first: Antoine

last: van Kampen

first: Theodorus

middle: B

last: Hakvoort

first: Wouter

last: Lamers


title: Determining the impact of alternative splicing events on transcriptome dynamics

city: Bures-sur-Yvette

first: Arndt

last: Benecke

address: 35 route des Chartres

department: Integrative Biology

institute: Institut des Hautes Etudes Scientifiques & I.R.I.-CNRS

summary:
Background
The complete sequencing of the human genome and its subsequent analysis revealed a predominant role for alternative splicing in the generation of proteome diversity. Splice switching oligonucleotides (SSOs) are a powerful and specific tool to experimentally control alternative splicing of endogenous messenger RNAs in living cells. SSOs also have therapeutic potential to treat diseases that are caused by aberrant splicing. The assignment of biological roles to alternative splicing events of currently unknown function promises to provide a largely untapped source of potential new therapeutic targets. Here we have developed a protocol that combines high sensitivity microarrays with the transfection of SSOs to monitor global changes in gene expression downstream of alternate, endogenous splice events.

Findings
When applied to a well-characterized splicing event in the Bcl-x gene, the application of high sensitivity microarrays revealed a link between the induction of the Bcl-xS isoform and the repression of genes involved in protein synthesis.

Conclusions
The strategy introduced herein provides a useful approach to define the biological impact of any given alternative splicing event on global gene expression patterns. Furthermore, our data provide the first link between Bcl-xS expression and the repression of ribosomal protein gene expression.

overall_design: Biological triplicates, 2 conditions: control oligonucleotide,  Bcl-x oligonucleotide

first: Emmanuelle

last: Wilhelm

first: Francois-Xavier

last: Pellay

first: Brendan

last: Bell


title: Primary human leucocyte RNA expression of unrelated celiac disease cases and unrelated healthy controls.

status: Public on Oct 01 2008

city: London

first: Graham

last: Heap

address: 4 Newark Street

institute: QMUL

summary:
The goal of this study was to study the effect of genetic variation on gene expression of untouched primary leucocytes. This expression data is used in conjunction with genome-wide association genotype data that is available for the celiac disease samples, typed on the Illumina Infinium HumanHap300 platform.

All genotype data are available upon request.

overall_design: Gene expression data was determined of untouched primary leucocytes (n=132) from unrelated UK individuals with celiac disease (n=110) - a common condition with multiple risk variants identified and unrelated UK controls (n=22).

first: Gosia

last: Trynka

first: Ritsert

middle: C

last: Jansen

first: Marcel

last: Bruinenberg

first: Lotte

last: Dinesen

first: Karen

last: Hunt

first: Cisca

last: Wijmenga

first: David

last: van Heel

first: Lude

last: Franke


title: Macgoren-Abnornal karyotype

city: Seoul

first: Su

last: Hong

department: Life Science Institute

country: South Korea

institute: Macrogen Inc.

summary:
Recently, several reports described chromosomal abnormalities in cultured human embryonic stem cell (hESC) lines may be prone to specific genetic changes involving addition of the whole or parts of chromosome 12, 17, or X. However, why these chromosomes seem to be involved more often in genetic aberrations is not yet fully clear. In this study, it is of interest that the specific chromosome 12 and X change observed.
Keywords: Human embryonic stem cell, trisomy, chromosome abnormality

overall_design: We analyzed the gene expression profiling in two normal (SNUhES3: S3 and SNUhES4: S4), two variants of SNUhES3 (trisomy 12: S3v12 and XXY: S3vX), and variant of SNUhES4 (trisomy 12: S4v12). Gene expression pattern was profiled using the Illumina HumanRef-6 BeadChip, which included 48,095 probe sets. From these analyses, 55 up-regulated genes and 28 down-regulated genes were identified in S3v12 versus S3. In S3vX, 98 up-regulated genes and 75 down-regulated genes were identified. In S4v12, 87 up-regulated genes and 61 down-regulated genes were identified.

first: Hye-Won

last: Seol

first: Jae-Ku

last: Kang

first: Hee-Sun

last: Kim

first: Jung-Jun

last: Park

first: Eun-Sook

last: Ryu

first: Jin-Ah

last: Baek

first: Sun-Kyung

last: Oh

first: Woong-Yang

first: Jong-Ho

last: Lee

first: Shin-Yong

last: Moon

first: Jeong-Sun

last: Seo

first: Young-Min

last: Choi


status: Public on Sep 30 2008

city: Toronto

first: Irene

middle: L

last: Andrulis

state: ON

address: 600 University Avenue

department: Research

institute: Mount Sinai Hospital

summary:
Molecular Profiling of BRCA1-and BRCA2-associated Breast Cancers Identifies FGFR2 as a Gene More Highly Expressed in BRCA2-associated Tumors

BRCA1- and BRCA2-associated tumors have many morphologic characteristics in common, but appear to have distinct molecular signatures. BRCA1-associated tumors are predominantly basal-like cancers, whereas BRCA2-associated tumors have a predominant luminal-like phenotype. These two molecular signatures reflect in part the two cell types, basal/myoepithelial and luminal, found in the terminal duct lobular unit of the breast. To elucidate novel genes involved in these two spectra of breast cancer tumorigenesis we performed global gene expression analysis on breast tumors from germline BRCA1 and BRCA2 mutation carriers.  Breast tumor RNAs from 7 germline BRCA1 and 6 germline BRCA2 carriers were profiled using UHN human 19K cDNA microarrays.  Supervised univariate analyses were conducted to identify genes differentially expressed between BRCA1 and BRCA2-associated tumors. Selected discriminatory genes were validated using real time reverse transcription polymerase chain reaction (RT-PCR) in the tumor RNAs, and/or by immunohistochemistry (IHC) or by in situ hybridization (ISH) on tissue microarrays (TMAs) containing an independent set of 58 BRCA1 and 64 BRCA2-associated tumors.  Genes more highly expressed in BRCA1-associated tumors included stathmin/oncoprotein 18, osteopontin, TGFß2 and Jagged 1 in addition to genes previously identified as characteristic of basal-like breast cancers. Genes more highly expressed in BRCA2-associated tumors had functions related to transcription, signal transduction (particularly MAPK signaling), cell proliferation, cell adhesion and extracellular matrix remodeling. BRCA2-associated cancers were characterized by the higher relative expression of amongst others, FGF1 and FGFR2. Tissue microarrays were used to validate the expression of FGFR2 protein by immunohistochemistry and Jagged 1 expression by in situ hybridization. BRCA2-associated cancers expressed higher levels of FGFR2 protein than BRCA1-associated cancers (p=0.004); whereas BRCA1-associated tumors exhibited elevated levels of Jagged1 mRNA compared to BRCA2-associated cancers (p=0.02).  FGFR2 and FGF1 were more highly expressed in BRCA2-associated cancers compared with BRCA1-associated breast cancers, suggesting the existence of an autocrine or paracrine stimulatory loop. In addition to corroborating the basal-like signature of BRCA1-associated tumors, we identified osteopontin, stathmin/oncoprotein 18, TGFβ2, and Jagged 1 as being more highly expressed in BRCA1-associated tumors.
Keywords: Gene expression profiling, genetic comparison

overall_design: 13 tumor samples: 7 BRCA1 and 6 BRCA2, no replicates, there is a reference sample, 2 dye-swaps for the tumor samples 1693-BRCA1 and  4324-BRCA2)

first: Anita

last: Bane

first: Dushanthi

last: Pinnaduwage

first: Sarah

last: Colby

first: Shelley

last: Bull

first: Frances

middle: P

last: O'Malley


title: Validation of the Swine Protein-Annotated Oligonucleotide Microarray.

city: East Lansing

first: Catherine

middle: W.

last: Ernst

state: MI

address: 3330 Anthony Hall

department: Animal Science

institute: Michigan State University

summary: In this study we evaluate the Swine Protein-Annotated Oligonucleotide Microarray by profiling the expression of transcripts in four porcine tissues. We validate the hybridization results by comparative analysis of expression in human orthologs, confirm expression patterns for a subset of genes by QPCR, and assess the usefulness of designed control oligonucleotides. Simple descriptive diagnostic analyses of PM/MM probe sets introduced in this paper are useful to detect non-specific hybridization. Using comparative transcriptional profiling, we found that the microarray data correlate to QPCR data for most genes detected as differentially expressed using the microarray platform. Moreover, comparison to human ortholog expression confirmed the utility of experiments based on this array in swine species as a biomedical model for human tissue specific expression.

overall_design: Arrays for this study contained 20,400 70-mer oligonucleotides (http://www.pigoligoarray.org/). Hybridization stringency controls included six mismatch probes (1, 2, 3, 5, 7, and 10 mismatches) designed against each of 60 contigs with the highest EST count in the database. Sixty negative controls oligonucleotides corresponded to scrambled sequence without presumed representation in either the pig or bovine genome or pig EST databases. The samples used in this study included liver, brain stem, longissimus muscle and uterine endothelium that were collected from 4 pigs (gilts at approximately 165 d of age). Tissues samples from the four gilts were evaluated in a loop design experiment. Four loops were used, one for each animal, such that loop and animal were confounded. However, the tissue sequence between loops was altered such that all tissue pairs were represented in at least one array, and tissue and dye levels were balanced.

first: Juan

last: Steibel

first: Michal

last: Wysocki

first: Joan

last: Lunney

first: Antonio

middle: M

last: Ramos

first: Zhiliang

last: Hu

first: Max

last: Rothschild


title: Constitutively active RhoA (RhoAV14) expression and regulation of acqeous humor outflow dynamics

status: Public on Sep 25 2008

city: Durham

first: Vasantha

last: Rao

address: 2351 Erwin Rd

department: Ophthalmology

summary:
Impaired drainage of aqueous humor through the trabecular meshwork (TM) culminating in increased intraocular pressure is a major risk factor for glaucoma, a leading cause of blindness worldwide. Regulation of aqueous humor drainage through the TM, however, is poorly understood. The role of RhoA GTPase-mediated contractile activity, cell adhesive interactions, and gene expression in regulation of aqueous humor outflow was investigated using adenoviral vector-driven expression of constitutively active RhoA (RhoAV14). Organ cultured anterior segments from porcine eyes expressing RhoAV14 exhibited significant reduction of aqueous humor outflow. Cultured TM cells expressing RhoAV14 revealed strong contractile cell morphology, increased actin stress fibers and focal adhesions, along with increased levels of phosphorylated myosin II, and collagen IV, fibronectin and laminin. cDNA microarray analysis of RNA extracted from RhoAV14 expressing human TM cells revealed a significant increase in the expression of genes encoding extracellular matrix (ECM) proteins, cytokines, integrins, cytoskeletal proteins and signaling proteins. Conversely, various ECM proteins stimulated robust increases in phosphorylation of myosin II, paxillin and focal adhesion kinase, and activated Rho GTPase and actin stress fiber formation in TM cells, indicating a potential regulatory feedback interaction between ECM-induced mechanical strain and Rho GTPase-induced isometric tension in TM cells. Collectively, these data demonstrate that sustained activation of Rho GTPase signaling in the aqueous humor outflow pathway increases resistance to aqueous humor outflow through the trabecular pathway by influencing the contractile force, cell adhesive interactions, and the expression of ECM proteins and cytokines in TM cells.
Keywords: Gene Expression

overall_design: Two condition experiment: Human trabecular mesh work cells infected with  Adenivirus expressing GFP Vs Adenovirus expressing GFP and constitutively active RhoAV14

first: Vasanth


title: Chicken family BC1 1940: transcriptome profiling used for QTL/eQTL detection

status: Public on Sep 20 2008

city: Rennes

first: Sandrine

last: Lagarrigue

address: 65 rue de St Brieuc

institute: Agrocampus Rennes/ INRA

summary: The family concerns 46 offspring of the sire BC1 n°1940 (produced from an F1 male obtained by-intercrossing two fat (FL) and lean (LL) meat-type chicken lines that divergently selected on fatness [Leclercq et al. 1980]) mated with 8 LL females. Hepatic transcriptomic profiles were obtained using the chicken 20K oligochip (ARK-genomics). The 46 chickens were fed ad libitum using a conventional starter diet (0-3 weeks: 12.8 MJ of metabolizable energy) and then a growing broiler diet (4-9 weeks: 13.0 Mj of metabolizable energy). Light/dark periods were 24h light for the first 2 days, then 14h light/10h night up to slaughtering. At 4 weeks of age, blood samples were collected for DNA extraction and genotyping. At 9 weeks of age, the birds were fed ad libitum for 4 hours minimum after overnight fasting and then weighed and sacrificed by electrical stunning in the experimental processing plant (Station de Recherches Avicoles, Inra, Nouzilly, France). Following sacrifice, livers were collected, quickly frozen in liquid nitrogen and stored at −80°C until RNA extraction for transcriptome analyses.

overall_design: Five micrograms of total RNA from each sample were labeled with Cy5 and then hybridized to the microarray with a same Cy3-labeled reference probe. The reference RNA pool was made from an equal amount of RNA derived from all liver samples.

first: Guillaume

last: Le Mignon


title: Hela cells treated with or without IFNgamma at different time points

status: Public on Jan 15 2009

first: Zhaodong

last: Xu

state: Ontario

address: Mc6-424, 399 Bathurst Street

department: Genetics & Development Division

institute: TWRI, UHN

summary:
The purpose of this study is to define which genes are IFNgamma sensitive, resistant, or irrelevant in our desired 16MB Human genome. Different ISGs(Interferon sensitive genes) were categorized based on this expression array data and can be visulized in our 16MB IFNgamma genes DB.
Keywords: treated/untreated different time point comparison

overall_design:
HeLa cells left untreated or 6, 24 and 48 hours after IFNgamma treatment were collected for RNA isolation as previously described (Pattenden et al., EMBO (2002) 21: 1978).  Briefly, cells were washed with cold PBS, scraped and spun down at 1200 rpm for 5 min.  Cell pellet was suspended in Trizol (invitrogen), left for 5 minutes at room temperature and was chloroform extracted.  RNA was precipitated with isoprpanol and s8spendeed in RNAse-free water.  RNA was Dnase treated (Ambion).  Microarray whole genome analysis was performed on Illumina HumanRef-6 Expression Beadchip. Raw intensities from three independent biological replicates was processed by Illumina BeadStudio  software (Illumina, Toronto, ON).

Compared to data normalized by various procedures, the data submitted (average raw value) provides the best validation by real-time PCR.

first: Rod

last: Bremner

first: Mohamed

last: Abou EL Hassan


title: Overexpression of Musashi1 (Msi1) in HEK293T cells.

status: Public on Oct 30 2008

city: San Antonio

first: Luiz

last: Penalva

address: 8403 Floyd Curl Drive

department: GCCRI

institute: UTHSCSA

summary: Gene expression analysis of the Msi1 overexpression in HEK 293T cells.

overall_design: There were two biological replicates of Msi1 and GFP (Green Fluorescent Protein) as control, used in the experiment. Each slide includes 4 microarrays with one biological sample versus control. Samples were hybridized with dye-swap replica.

first: Jennifer

last: Rebeles

first: Suzanne

last: Burns

first: Tarea

last: Burton

first: Raquel

last: Abreu


title: Segmentation-based detection of allelic imbalance and LOH in cancer cells using whole genome SNP arrays

status: Public on Sep 18 2008

city: Lund

first: Johan

last: Staaf

address: Medicon Village

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

summary:
High-resolution microarray-based whole genome genotyping (WGG) techniques based on SNP analysis have successfully been applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Problems in data interpretation arise when WGG is applied on tumor tissue specimens, in which normal cell components and tumor subpopulations frequently exist. Such heterogeneity may lead to reduced detection of cancer cell specific genomic alterations.

To circumvent problems with sample heterogeneity, we propose using a segmentation strategy derived from DNA copy number analysis for detection of LOH and allelic imbalance. We generated an experimental dilution series of a tumor cell line mixed with its paired normal cell line and simulated data for such dilutions to test the strategy. We also used data sets generated on both Affymetrix and Illumina WGG platforms, including paired tumor-normal samples and tumors previously characterized by FISH. We tested the segmentation strategy against several reported algorithms. We demonstrate high sensitivity and specificity of the segmentation strategy for detecting both minute and gross allelic imbalances originating from DNA copy number gain, loss, and neutral events in tumor specimens. For example, hemizygous copy number loss can be detected in samples containing only 20-25% tumor cells. Furthermore, the strategy can identify cell subpopulation specific events and accurately estimate the fraction of cells affected by an allelic imbalance.

Thus, the segmentation strategy extends the usefulness of WGG platforms for
investigation of allelic imbalances in heterogeneous tumor genomes.

overall_design: The proposed segmentation strategy detects allelic imbalance originating from DNA copy number gain, loss or copy neutral events. Here we use Illumina 317K, 370K and 550K and Affymetrix 250K whole-genome single-nucleotide polymorphism arrays hybridized with tumor samples (breast, colon, leukemia, and urothelial) to evaluate the segmentation strategy against several other reported methods. The data sets include a simulated dilution series, an experimental dilution series of a breast cancer cell line as well as paired tumor-normal samples. This GEO series include the 12 sample experimental dilution series of the HCC1395 breast cancer cell line (CRL-2324: www.atcc.org) and 4 paired urothelial tumor-normal samples, all hybridized on Illumina HumanCNV 370k BeadChips.

first: David

last: Lindgren

last: Vallon-Christersson

first: Anders

last: Isaksson

first: Hanna

last: Göransson

first: Gunnar

last: Juliusson

first: Richard

last: Rosenquist

first: Mattias

last: Höglund

first: Ake

last: Borg

first: Markus

last: Ringner


title: Effect of short- and long-term morphine treatment on gene expression in the hypothalamus and pituitary

city: Santa Monica

first: Adrian

last: Anghel

address: 2825 Santa Monica Blvd. Suite 200

department: Medicine

institute: University of California, Los Angeles (UCLA)

summary:
Addictive drugs including opioids activate signal transduction pathways that regulate gene expression in the brain. However, changes in CNS gene expression following morphine exposure are poorly understood. We studied the effect of short- and long-term morphine treatment on gene expression in the hypothalamus and pituitary using genome-wide DNA microarray and real-time reverse transcriptase polymerase chain reaction (RT-PCR) analyses. In the hypothalamus, we found that short-term morphine administration up-regulated (at least 2-fold) 39 genes and down-regulated six genes. Long-term morphine administration up-regulated 35 genes and down-regulated 51 hypothalamic genes. In the pituitary, we found that short-term morphine administration up-regulated (at least 2-fold) 110 genes and down-regulated 29 genes. Long-term morphine administration up-regulated 85 genes and down-regulated 37 pituitary genes. Strikingly, microarray analysis uncovered several genes involved in food intake (neuropeptide Y, agouti-related protein, and cocaine and amphetamine-regulated transcript) whose expression was strongly altered by morphine exposure in either the hypothalamus or pituitary. Subsequent RT-PCR analysis confirmed similar gene regulation of noteworthy genes in these regions. Finally, we found functional correlation between morphine-induced alterations in food intake and regulations of genes involved in this process. Changes in genes related to food intake may uncover new pathways related to some of the physiological effects of opioids.
Keywords: Comparative treatment versus placebo

overall_design:
8 samples analyzed: 4 from hypothalamus (2 biological replicates and 2 dye swaps) and 4 from pituitary (2 biological replicates and 2 dye swaps)
8 samples analyzed: 4 from hypothalamus short term treatment (2 biological replicates and 2 dye swaps) and 4 hypothalamus long term treatment (2 biological replicates and 2 dye swaps)


title: Gene expression changes in LPS-induced neuroinflammation

status: Public on Nov 01 2008

city: Bethesda

first: Robert

middle: H

last: Bonow

address: 9 Memorial Drive, Building 9

department: Brain Physiology and Metabolism Section

institute: National Institute on Aging / NIH

summary: Neuroinflammation plays a role in the progression of several neurodegenerative disorders. We used a lipolysaccharide (LPS) model of neuroinflammation to characterize the gene expression changes underlying the inflammatory and behavioral effects of neuroinflammation. A single intracerebroventricular injection of LPS (5 ug) was administered into the lateral ventricle of mice and, 24 hours later, we examined gene expression in the cerebral cortex and hippocampus using microarray technology. Gene Ontology (GO) terms for inflammation and the ribosome were significantly enriched by LPS, whereas GO terms associated with learning and memory had decreased expression. We detected 224 changed transcripts in the cerebral cortex and 170 in the hippocampus. Expression of Egr1 (also known as Zif268) and Arc, two genes associated with learning and memory, was significantly lower in the cortex, but not hippocampus, of LPS-treated animals. Overall, altered expression of these genes may underlie some of the inflammatory and behavioral effects of neuroinflammation.

overall_design: Mice were given intracerebroventricular injections of saline vehicle (n = 4) or lipopolysaccharide (n = 4).  Twenty-four hours later, we dissected the hippocampus and cerebral cortex and processed the tissue for microarray analysis.  Gene expression changes observed in the microaray data were validated with quantitative real-time PCR.

first: Saba

last: Aid

first: Yonqing

last: Zhang

first: Kevin

middle: G

last: Becker

first: Francesca

last: Bosetti


title: Karyotype analysis of S. cerevisiae chromosome replacement lines - a-type cells

status: Public on Sep 16 2008

city: Taipei

first: Jun-Yi

last: Leu

address: 128 Academia Road, Section 2, Nankang

department: Insititute of Molecular Biolody

country: Taiwan

institute: Academia Sinica

summary: The S. cerevisiae hybrid karyotypes were analyzed by array-CGH to identify small regions of duplication or homeologous chromosomal exchange occurring during the strain construction.

sample_organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

overall_design: a-type cells. S. cerevisiae vs. Chromosome replacement lines. Biological replicates: 1 control (S. bayanus), 11 Chromosome replacement lines, independently grown and harvested. Two replicate per array.

first: J

middle: Y


title: Karyotype analysis of S. cerevisiae chromosome replacement lines - alpha-type cells

overall_design: alpha-type cells. S. cerevisiae vs. Chromosome replacement lines. Biological replicates: 1 control (S. bayanus), 11 Chromosome replacement lines, independently grown and harvested. Two replicate per array.


title: Pancreatic Tumor vs Various Tissue Normals

status: Public on Sep 15 2008

city: Phoenix

first: Yoga

last: Balagurunathan

state: AZ

address: 445 N. Fifth street

institute: TGEN

summary:
Pancreatic Tumor samples from biopsy collected at different stages along with normal tissue samples from various organ sites including commercial normals arrayed on 2channel Agilent 60mer Oligo arrays (human v1 & v2), median normalized for cross comparison. Some normal samples temporarily removed to public due to Intelectual property conflict.

Keywords: Pancreatic tumor comparison to normals for multimetric study

overall_design: Single channel array expression from two Agilent versions (V1:18k,V2: 22k) (i.e: GPL885,GPL887) combined based on matching probes, remove repeating control substituted with median values, final probe down to ~17k.

first: Yoganand

last: Morse

first: Galen

last: Hostetter

first: Vijayalakshmi

last: Shanmugam

first: Phillip

last: Stafford

first: Sonsoles

last: Shack

first: John

last: Pearson

first: Maria

last: Trissal

first: Micheal

middle: J

last: Demeure

first: Daniel

middle: D

last: VonHoff

first: Victor

last: Hruby

last: Gillies

first: Michael

last: Bittner

first: Haiyong

last: Han


title: The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers

status: Public on Sep 09 2008

first: Dong-Yu

last: Wang

address: 610 University Ave

institute: UHN-PMH-OCI

summary:
Paired fine needle aspiration biopsies (FNABs) of breast cancers were taken before (PRE) and after (POST) surgeries from 16 patients and compared the cDNA microarray data to determine the genes that were differentially expressed between the FNABs taken at the two time points.
The timing of fine needle aspiration biopsies can be a confounding factor in microarray data analyses in breast cancer. FOS-related genes, which have been implicated in early hypoxia as well as the development of breast cancers, were differentially expressed before and after surgery. Therefore, it is important that future studies take timing of tissue acquisition into account.

Keywords: Breast cancer, fine needle, biopsy timing, microarray standardization, early hypoxic genes

overall_design: Dye-swap technical replicates were included both in PRE and POST FNABs for every patient, then the two replicated array data were combined for analysis.

first: Dong

first: Vietty

last: Wong

first: Wey

last: Leong


title: Differential expression of MEN2 versus VHL human Pheochromocytomas

first: Christopher

last: Pan

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

summary: This study utilized oligonucleotide microarrays to examine gene expression profiles in pheochromocytomas from 23 patients; 11 VHL tumors and 12 MEN2 tumors. RNA was extracted and linearly amplified once, then dye-labeled and co-hybridized to a microarray with over 34,000 oligos representing more than 25,000 unique human genes.  In validation of our strategy, many genes known to have elevated expression in MEN2 tumors (e.g., CALM1, CHGB, CABP1and NPY) and several genes known to be specific to VHL (e.g., AQP1) were independently identified by this approach.  In addition to known genes, our method has identified several hundred of previously uncharacterized genes that are enriched in the MEN2 or VHL tumors.

overall_design: A 34k expression arrays were generated by printing Oligo nucleotides from the Qiagen HV3 set onto epoxy coated slides (Corning, Inc). Total RNA from pheochrmocytoma tumors or normal adrenals was amplified using an Ambion kit (Cat#1753), labeled with Cy5 and cy3 dyes respectively and hybridized overnight to the oligo chip in a MAUI chamber.


title: Mechanisms underlying hypoxia tolerance in Drosophila melanogaster: hairy as a metabolic switch

city: La Jolla

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

summary:
Hypoxia-induced cell injury has been related to multiple pathological conditions. In order to render hypoxia-sensitive cells and tissues resistant to low O2 environment, in this current study, we used Drosophila melanogaster as a model to dissect the mechanisms underlying hypoxia-tolerance. A D. melanogaster strain that lives perpetually in an extremely low-oxygen environment (4% O2, an oxygen level that is equivalent to that over about 4,000 m above Mt. Everest) was generated through laboratory selection pressure using a continuing reduction of O2 over many generations. This phenotype is genetically stable since selected flies, after several generations in room air, survive at this low O2 level. Gene expression profiling showed striking differences between tolerant and naïve flies, in larvae and adults, both quantitatively and qualitatively. Up-regulated genes in the tolerant flies included signal transduction pathways (e.g., Notch and Toll/Imd pathways), but metabolic genes were remarkably down-regulated in the larvae. Furthermore, a different allelic frequency and enzymatic activity of the triose phosphate isomerase (TPI) was present in the tolerant versus naïve flies. The transcriptional suppressor, hairy, was up-regulated in the microarrays and its binding elements were present in the regulatory region of the specifically down-regulated metabolic genes but not others, and mutations in hairy significantly reduced hypoxia tolerance. We conclude that, the hypoxia-selected flies: (a) altered their gene expression and genetic code, and (b) coordinated their metabolic suppression, especially during development, with hairy acting as a metabolic switch, thus playing a crucial role in hypoxia-tolerance.

Keywords: genetic bases of hypoxia adaptation

overall_design: 27 isogenic D. melanogaster Lines were pooled and following long-term selection over generations with decreased oxygen level in the culture environment. The differences in gene expression were compared between adapted flies and generation matched naive controls by microarray. Pooled RNA samples from 3rd instar larvae of 27 parental lines were used as common reference.

first: Jin

last: Xue

first: James

last: Lai

first: Nicholas

last: Schork

first: Kevin

last: White

first: Gabriel

last: Haddad


status: Public on Sep 08 2008

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

summary:
To identify mRNAs associated with human PUM2 protein, we used a modified Ribonucleoprotein-ImmunoPrecipitation Microarray (RIP-Chip) approach on HeLa S3 cancer cells that express PUM2. PUM ribonucleoprotein (RNP) complexes were captured from cell-free extracts with specific anti PUM2 antibody coupled to protein A sepharose beads, and then eluted with SDS-EDTA. To control for non-specifically enriched RNAs, the same procedure was performed with beads that were not coupled with immunoprecipitating antibodies (mock samples). Total RNA was isolated from cell extracts and immunopurified samples with the mirVanaTM PARISTM kit (Ambion). RNA was quantified with a NanoDrop device (Witeg AG). Poly-adenylated RNAs were amplified in the presence of aminoallyl-UTP with Amino Allyl MessageAmp II aRNA kit (Ambion). For this purpose, 500 ng total RNA from extracts and half (50-100 ng) of the immunopurified RNAs were used for amplification. 8 ug of the amplified RNAs (aaRNA) were fluorescently labeled with NHS-monoester Cy3 and Cy5 dyes (GE HealthSciences), except for mock RNA samples, where an aaRNA amount proportional to the yield obtained from corresponding PUM affinity isolates was used.For PUM2 RIPs, we performed four biological replicates but omitted the dye swaps due to the lower aaRNA obtained after amplification (~10 ug aaRNA from PUM2 RIPs, 9 ug aaRNA from mock RIPs). The Cy3- and Cy5-labeled aaRNA samples were mixed and hybridized to human cDNA microarrays. Detailed methods for microarray experiments are available at http://cmgm.stanford.edu/pbrown/protocols/index.html. cDNA microarrays were produced by the Stanford Functional Genomic Facility and contained 43,197 human probes representing 26,524 Unigene cluster IDs (12,466 ENSEMBL annotated genes) spotted on Corning Ultra GAPS slides. Spotted cDNAs were cross-linked with 65 mJ of UV irradiation on slides, which were then post-processed for 1 hour at 42°C in pre-hybridization solution (5x SSC, 0.1% SDS, 0.1 mg/ml BSA), washed twice in 400 ml of 0.1x SSC for 5 min, dunked in 400 ml ultrapure water for 30 sec, and dried by centrifugation at 550 rpm for 5 min. Slides were used the same day.  Cy3- and Cy5-labeled aaRNA probes were mixed and applied to arrays in hybridization solution (3x SSC, 20 ug poly(A) RNA [Invitrogen], 20 ug yeast tRNA [Invitrogen], 20 ug Human Cot-1 DNA [Invitrogen], 20 mM HEPES [pH 7.0] and 0.3% SDS) for 18 h at 65°C. The arrays were then washed sequentially in 400 ml of 2x SSC with 0.1% SDS, 1x SSC, and 0.2x SSC. The first wash was performed for 5 min at 65°C, the subsequent washes were performed for 5 min at RT. The arrays were dried by centrifugation and immediately scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). Arrays were normalized computationally by the Stanford Microarray Database (SMD). The data were filtered for signal over background of greater than 1.5 in the channel measuring aaRNA from extract, and only features that met these criteria in > 50% of the arrays were included for further analysis. Log2 median ratios were retrieved and exported into Microsoft Excel.  To identify transcripts that were specifically enriched by association with PUM2, we performed two class Significance Analysis of Microarrays (SAM) on median centered arrays.
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
Antibody used in IP: 50 ug rabbit anti-PUMILIO 2 (Bethyl Laboratories, #300-202A)

Keywords: replicate_design

overall_design: Computed

first: Alessia

last: Galgano


title: The effect of prohibitin overexpression in Caco2-BBE intestinal epithelial cells

status: Public on Sep 05 2008

city: Atlanta

first: Arianne

last: Theiss

state: GA

address: 615 Michael St

institute: Emory University

summary: To determine the effect of prohibitin overexpression on global gene expression in Caco2-BBE intestinal epithelial cells.

overall_design: 4 individual wells of Caco2-BBE cells, passage 41, were transfected with either empty vector (pcDNA4) or prohibitin/pcDNA4 for 72 hours.  Total RNA isolated from 4 wells of cells/per treatment were pooled together for labeling and hybridization purposes.

first: Matam

last: Vijay-Kumar

first: Tracy

middle: S

last: Obertone

first: Jason

last: Hansen

first: Dean

last: Jones

first: Andrew

middle: T

last: Gewirtz

first: Didier

last: Merlin

first: Shanthi

middle: V

last: Sitaraman


title: Chromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip.

status: Public on Sep 06 2008

city: Muenster

first: Carsten

last: Müller-Tidow

address: Domagkstrasse 3

institute: University Hopital Muenster

type: Genome binding/occupancy profiling by genome tiling array

summary:
A global view of PML-RARα transcriptional functions was obtained by genome-wide binding and chromatin modification analyses, combined with genome wide expression data.

Complete Abstract:
The translocation t(15;17) generates the chimeric PML-RARα transcription factor that is the initiating event of acute promyelocytic leukemia. A global view of PML-RARα transcriptional functions was obtained by genome-wide binding and chromatin modification analyses, combined with genome wide expression data. ChIP-chip experiments identified 372 direct genomic PML-RARα targets. A subset of these was confirmed in primary acute promyelocytic leukemia. Direct PML-RARá targets include regulators of global transcriptional programs as well as critical regulatory genes for basic cellular functions such as cell cycle control and apoptosis. PML-RARα binding universally led to HDAC1 recruitment, loss of histone H3 acetylation, increased tri-methylation of histone H3 lysine 9 and unexpectedly increased tri-methylation of histone H3 lysine 4. The binding of PMLRARα to target promoters and the resulting histone modifications resulted in mRNA repression of functionally relevant genes. Taken together our results reveal that the transcription factor PML-RARα regulates key cancer related genes and pathways by inducing a repressed chromatin formation on its direct genomic target genes.

Keywords: ChIP on Chip

overall_design: U937 transfected with an inducible PML-RARα/empty vecor were induced, harvested and Chromatin-Ips for PML, AcH3 followed by microarray hybridasation were carried out. For detailed procedures see Hoemme et al. "Chromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip"

first: Claudia

last: Hoemme

first: A

last: Peerzada

first: Gerhard

last: Behre

first: Yipeng

last: Wang

first: M

last: McClelland

first: Kay

last: Nieselt

first: Matthias

last: Zschunke

first: Christine

last: Disselhoff

first: Shuchi

last: Agrawal

first: Fabienne

last: Isken

first: Nicola

last: Tidow

first: Wolfgang

middle: E

last: Berdel

first: Hubert

last: Serve