title: Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate

city: Griffin

first: Faith

last: Critzer

state: GA

address: 1109 Experiment St

department: Center for Food Safety/Food Science & Technology

institute: The University of Georgia

summary: Sodium benzoate is a widely used food antimicrobial in drinks and fruit juices. A microarray study was conducted to determine the transcriptional response of Escherichia coli O157:H7 to 0.5% (w/v) sodium benzoate.  Stationary phase E. coli O157:H7 grown in 150 ml Luria-Bertani broth (LB) was exposed to 0 (control) and 0.5% sodium benzoate. Each treatment was duplicated and sampled at 0 (immediately after exposure), 5, 15, 30, and 60 min. Total RNA was extracted and analyzed with E. coli 2.0 Gene Chips.

overall_design: Completely randomized design with 0% (control) and 0.5% (w/v) sodium benzoate treated cells were exposed for 0 (immediately after exposure), 5 min, 15 min, 30 min, and 60 min.  Each experiment was replicated once and total RNA was extracted and Affymetrix prokaryotic protocol was followed to hybridize cDNA onto E. coli Genome 2.0 Arrays.

last: Golden

first: Doris

last: D'Souza

first: Arnold

last: Saxton


title: Expression data using esophageal epithelia from 3 month old-mice lacking the transcription factor Klf4

status: Public on Oct 01 2009

city: Philadelphia

first: Jonathan

middle: P.

last: Katz

state: PA

address: 913 BRBII/III, 421 Curie Blvd.

department: Medicine/Gastroenterology

country: USA

institute: University of Pennsylvania

summary:
Using the ED-L2 promoter of Epstein-Barr virus to drive Cre, we obtained tissue specific ablation of Klf4 in the squamous epithelia of the esophagus.
Using a functional genomic approach, we showed decreased expression of critical late-stage differentiation factors and identified alterations of several genes important in cellular differentiation.

overall_design: For all experiments with ED-L2-Cre/Klf4loxp/loxp mice (mutant mice), sex-matched littermate Klf4loxp/loxp mice lacking the Cre transgene served as controls. 3 mutant mice and 3 controls were used.

middle: P

first: Marie

last: Tetreault


title: Expression data from ependymoma surgical samples

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

summary:
Ependymoma, the 3rd most common brain tumor in children, recurs in approximately 50% of patients. There is currently no robust marker that predicts for recurrence, which is a significant clinical problem
We used global gene expression profiling of 19 patient surgical samples obtained at initial diagnosis and with known clinical outcomes to discover novel prognostic markers.

overall_design: Gene expression profiles were generated from surgical tumor samples using Affymetrix HG-U133plus2 chips. Profiles were divided into recurrent and non-recurrent groups in order to identify differentially expressed genes that were associated with risk of recurrence. In addition, time to progression was correlated with gene expression as a continuous variable in the recurrent group.


title: Characterization of B- and T-lineage ALL by Integrated Analysis of microRNA and mRNA Expression Profiles

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

country: Italy

institute: Consiglio Nazionale delle Ricerche (CNR)

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Acute lymphoblastic leukemia (ALL) is an heterogeneous disease comprising several subentities that differ for both immunophenotypic and molecular characteristics. Over the years, the biologic understanding of this neoplasm has largely increased. Gene expression profiling has recently allowed to identify specific signatures for the different ALL subsets and permitted identification of pathways deregulated by a given lesion. MicroRNAs (miRNAs) are small non-coding RNAs which play a pivotal role in several cellular functions. In this study, we investigated miRNA and gene expression profiles in a series of adult ALL cases by microarray analysis and combined them by bioinformatic analysis. Interestingly, those miRNAs which are differentially expressed between the ALL classes accounted for a large proportion of miRNA/mRNA expression pairs identified by the above analysis. Moreover, the analysis highlighted several putative miRNA targets involved in apoptosis and cell-cycle regulation.

overall_design: We used microarrays to profile miRNA and gene expression in adult patients with newly diagnosed ALL of different subtypes. 20 microRNA samples, and 19 mRNA samples

first: Valerio

last: Fulci

first: Sabina

last: Chiaretti

first: Monica

last: Messina

first: Franca

last: Citarella

first: Simona

last: Tavolaro

first: Anna

last: Guarini

first: Robin

last: Foà

first: Giuseppe

last: Macino


title: Expression data of embryonal carcinoma (EC) cells derived pluripotent stem cells

status: Public on Oct 23 2009

city: Beijing

first: Vetto

last: Chang

address: No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing

country: China

institute: NIBS

summary:
EC cells derived pluripotent stem cells could prolong the development of tetraploid aggregated mice; and the increased pluripotecny of EC cells derived pluripotent stem cells coincided with the recovery of many critical genes. Therefore, EC cells derived pluripotent stem cells were really the intermediates between EC cells and ES cells. And they had specific molecular characteristics, which may account for the improved pluripotency observed.
We took use of microarray method to screen out the differentially expressed genes during the reprogarmming of EC cells; and the investigation of these genes may provide us with more about the transition between tumorigenesis and pluripotency.

overall_design: EC cells (P19), P19 cells derived pluripotent stem cells (N7P8) and ES cells (R1) were collected for total RNA extraction and hybridization on Affymetrix microarrays.In order to eliminate the varience, these kinds cells were all cultured in ES medium; and feeder cells were cleared out. And every sample had three biological repeats.

first: Gang

first: Shaorong

last: Gao


title: Identification of genes involved in CEACAM1-4S mediated lumen formation in a 3D model of mammary morphogenesis

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Identification of genes involved in lumen formation: gene chip analysis was performed on mRNA isolated from both wild type and T457A,S459A mutated CEACAM1-4S transfected MCF7 cells grown in Matrigel

overall_design: Microarray analysis of RNA isolated from MCF7 cells transfected with CEACAM1-S wild-type (SW) or CEACAM1-S double-A mutant T457A,S459A (DA) grown in Matrigel for 4 days

first: John

middle: E

last: Shively

first: Charng-Jui

last: Chen

first: Tung

last: Nguyen


title: Expression data from human livers shortly following partial hepatectomy (PHx)

city: Jerusalem

first: Galit

last: Tzur

address: Kiryat Hadassah

department: Gene Therapy

country: Israel

institute: Hadassah University Hospital

summary:
The liver has a remarkable ability to regenerate, with the best experimental model for regeneration being partial hepatectomy (PHx), in which up to two-thirds of the liver may be removed, and the residual lobes enlarge to make up for the missing mass in a few days’ time. Liver regeneration has been extensively studied, mainly in rodent models, and characterized in terms of transcriptional regulation of gene expression. However, little is known regarding regulation of gene expression in a human model of regeneration following PHx.
We used microarrays to follow gene expression changes shortly following PHx.

overall_design: Liver tissues were collected from patients undergoing a PHx surgery (1.5, 42 and 81 years) under an IRB approval, at the onset (T0) and shortly after PHx (0.5hr, 1hr and 1.5hrs) for RNA extraction and hybridization on Affymetrix microarrays.

first: Tzur

last: Galit

first: Galun

last: Eithan


title: Expression data of HUVEC and OVCA429 with recombinant MAGP2

status: Public on Oct 17 2009

city: Boston

first: Michael

last: Birrer

state: MA

address: 70 Blossom Street

department: Medicine

institute: MGH

summary: Identification of signaling events contributing to the effect of recombinant MAGP2 on HUVECs and OVCA429. We used microarrays to identify the signaling events and up-regulated genes associated with MAGP2.

overall_design:
To explore the consequences of recMAGP2-induced signaling in ovarian cancer, microarrays were completed for a series of recMAGP2-treated (n=3) and untreated (n=3) HUVEC and OVCA429 cells.

The supplementary files 'GSE18373_diff_exp_HUVEC.txt' and 'GSE18373_diff_exp_OVCA429.txt' contain differentially expressed genes for Samples GSM458345-GSM458350 and GSM458351-GSM458356, respectively.

middle: J


title: LOX-1-dependent transcriptional regulation after oxidized LDL (OxLDL) treatment of human aortic endothelial cells.

status: Public on Oct 07 2009

city: Cambridge

first: Andrew

last: Hill

address: 300 Technology Square

department: Research Business Technology

institute: Pfizer

summary: LOX-1 is the primary endothelial receptor for oxidized LDL in endothelial cells and plays a role in the development of atherosclerosis.  Expression profiling was carried out on samples from HAECT cells over-expressing either LOX-1 or GFP control and treated with or without OxLDL over a time course of  2, 6, 12 and 24 Hours.  The goal of the study was to identify genes expression changes activated by OxLDL binding to LOX-1 at several different time points.

overall_design: This series of samples is derived from HAECT cells, and for both GFP and LOX-1 overexpressing cells includes; 0 Hr untreated (n=3), 2 Hr untreated (n=3), 2Hr OxLDL treated (n=3), 6 Hr untreated (n=3), 6 Hr OxLDL treated (n=3), 12 Hr untreated (n=3), 12 Hr OxLDL treated (n=3), 24 Hr untreated (n=3), 24 Hr OxLDL treated (n=3).  For data analysis, it was assumed that 0 Hr oxLDL treatment condition (not measured) was equivalent to the 0 Hr untreated condition.

first: Mark

middle: D

last: Mattaliano

first: Christine

last: Huard

first: Wei

last: Cao

middle: A

first: Wenyan

last: Zhong

first: Robert

middle: V

last: Martinez

first: Doug

middle: C

last: Harnish

first: Janet

last: Paulsen

first: Heather

middle: H

last: Shih


title: Expression data from human embryonic (9-12w) and post-natal livers

summary:
The liver is a multifunctional organ, which undergoes rapid changes during the developmental period and relies on tightly-regulated gene expression. Little is known regarding the complex expression patterns of mRNAs during the early stages of human liver development in comparison to post-natal livers.
We used microarrays to detail the global programme of gene expression during liver development following specification, at the stage of proliferation and differentiation when compared to post-natal livers, and identified distinct classes of up-regulated and downregulated genes during this process.

overall_design: Liver tissues of aborted human embryos (9-12 weeks from last period) and adult patients (1.5, 42 and 81 years) were obtained under an IRB approval for RNA extraction and hybridization on Affymetrix microarrays. RNA extracted from tissues of a whole embryo without the liver tissue served as a control.


title: Genome-wide analysis of genes regulated transcriptionally and post-transcriptionally by HTLV-I p30

status: Public on Oct 13 2009

city: Kansas City

first: Christophe

last: Nicot

state: KS

address: 3901 Rainbow Blvd.

department: Pathology and Lab Medicine

institute: University of Kansas Medical Center

summary:
The Human T-cell Leukemia Virus (HTLV)-type-I non-structural protein p30 plays an important role in virus transmission and gene regulation. p30 has been documented to inhibit the export of certain viral mRNA transcripts from the nucleus to the cytoplasm. This nuclear retainment of RNA molecules essentially results in gene silencing, where protein products are not produced.
Considering this unique function of p30, we used microarray analysis to assess the ability of p30 to inhibit not only the regulation of transcription of cellular genes, but also the ability of p30 to regulate the export of cellular transcripts to the cytoplasm.

overall_design: Total or cytoplamsic RNA from peripheral blood mononuclear cells expressing HTLV-I p30 was isolated and analyzed by microarray analysis, in comparison with mock-transcuced cells.

first: Sofiane

last: Ghorbel

last: Taylor


title: Transcriptional Signature and Memory Retention of Human-induced Pluripotent Stem Cells

status: Public on Oct 20 2009

city: La Jolla

first: Alysson

middle: R

last: Muotri

address: 9500 Gilman Drive

department: Pediatrics/CMM

institute: University of California San Diego

summary:
Transient expression of two factors, or from Oct4 alone, resulted in efficient generation of human iPSCs. The reprogramming strategy described revealed a potential transcriptional signature for human iPSCs yet retaining the gene expression of donor cells in human reprogrammed cells free of viral and transgene interference.
Genetic reprogramming of somatic cells to a pluripotent state (induced pluripotent stem cells or iPSCs) by over-expression of specific genes has been accomplished using mouse and human cells. However, it is still unclear how similar human iPSCs are to human Embryonic Stem Cells (hESCs). Here, we describe the transcriptional profile of human iPSCs generated without viral vectors or genomic insertions, revealing that these cells are in general similar to hESCs but with significant differences. For the generation of human iPSCs without viral vectors or genomic insertions, pluripotent factors Oct4 and Nanog were cloned in episomal vectors and transfected into human fetal neural progenitor cells. The transient expression of these two factors, or from Oct4 alone, resulted in efficient generation of human iPSCs. The reprogramming strategy described here revealed a potential transcriptional signature for human iPSCs yet retaining the gene expression of donor cells in human reprogrammed cells free of viral and transgene interference. Moreover, the episomal reprogramming strategy represents a safe way to generate human iPSCs for clinical purposes and basic research.

overall_design: Gene expression profiles measured using human genome Affymetrix Gene Chip arrays were grouped by hierarchical clustering, and correlation coefficients were computed for all pair-wise comparisons

first: Muotri

last: Alysson

first: Yeo

last: Gene


title: Expression data from a malaria vaccine trial (HG-U133A2.0 and U133 Plus 2.0)

status: Public on Sep 30 2009

city: Rockville

first: Maryanne

last: Vahey

state: MD

address: 1600 East Gude Drive

institute: Walter Reed Army Institute of Research

summary:
Volunteers were assessed at study entry, the day of the third vaccination and 24, 72 hours, two weeks after vaccination, and 5 days after challenge. 13/39 vaccinees were protected and 26/39 were not protected. Eleven vaccinees exhibited delayed onset of parasitemia. All infectivity controls developed parasitemia. Prediction Analysis of Microarrays (PAM-R) identified genes corresponding with protection. Gene Set Enrichment Analysis (GSEA) identified sets of genes associated with protection after the third immunization, before challenge.
After the third immunization, prior to challenge, differential expression of genes in the immunoproteasome pathway distinguished protected and non protected persons

overall_design: Samples were collected at study entry, the day of third vaccination, 24 and 72 hours post the third vaccination and two weeks post the third vaccination as well as 5 days post challenge. Both longitudinal and cross-sectional analysis were carried out to investigate expression profiles associated with vaccine effects and vaccine efficacy. This dataset contains 215 samples from HG-U133 A 2.0 platform and 39 samples from HG Plus2.0 platform.


title: Expression data from +7 hNPCs and diploid hNPCs

city: Madison

first: Dhruv

last: Sareen

state: WI

address: 1111 Highland Ave, Rm 5031 WIMR

department: Neurology

institute: University of Wisconsin Madison

summary:
Human Neural progenitor cells have been found to have karyotypic abnormalities.  In this study we explored the gene changes between hNPCs that are karyotypically normal and hNPCs with a trisomy of chromosome 7.
We used Affymetrix GeneChips to study gene expression changes between karyotypically normal hNPCs and trisomy 7 hNPCs.

overall_design: Cells grown in culture for ~20 passages from diploid and + 7 hNPCs were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Clive

middle: N

last: Svendsen


title: Lymphatic endothelial cells (LEC) treated with a MAF-targeted siRNA

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building, Huntley Street

department: Cancer Institute

country: United Kingdom

institute: UCL

summary: Kaposi sarcoma is the most common cancer in AIDS patients and is typified by red skin lesions. The disease is caused by the KSHV virus (HHV8) and is recognisable by its distinctive red skin lesions. The lesions are KSHV-infected spindle cells, most commonly the lymphatic endothelial and blood vessel endothelial cells (LEC and BEC), plus surrounding stroma. The KSHV virus expresses multiple MAF-downregulating microRNA. Here we test the effects of MAF silencing by siRNA in LEC cells using Affymetrix hgu133plus2 chips.

overall_design: There are n=3 of  1. LEC control cells transfected with a non-targeting siRNA, 2. LEC transfected with a MAF-targeting siRNA

first: Amy

last: Hansen

first: Dimitrios

last: Lagos


title: Gene expression differences between adenocarcinoma and squamous cell carcinoma in human NSCLC

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

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

summary:
Non-small cell lung cancer (NSCLC) can be classified into the major subtypes adenocarcinoma (AC) and squamous cell carcinoma (SCC) subtypes. Although explicit molecular, histological and clinical characteristics have been reported for both subtypes, no specific therapy exists so far. However, the characterization of suitable molecular targets holds great promises to develop novel therapies in NSCLC. In the present study, global gene expression profiling of 58 human high grade NSCLC specimens revealed large transcriptomic differences between AC and SCC subtypes: More than 1.700 genes were found to be differentially expressed.
Keywords: disease subtype analysis

overall_design: The NSCLC patient collective was composed of the histological subtype adenocarcinoma (n=40) and squamous cell carcinoma (n=18). We subjected gene expression profiles of 40 AC and 18 SCC samples into further analysis. Unsupervised hierarchical clustering of all 58 NSCLC tumors using the 500 most variably expressed transcripts revealed two different clusters, which were strongly associated with the histological subtypes AC and SCC of NSCLC. Our result indicated that the major impact on global transcriptional changes was due to the NSCLC histology.

first: Holger

last: Sueltmann

first: Markus

last: Ruschhaupt

first: Andreas

last: Buness

first: Annemarie

last: Poustka

first: Hans

last: Hoffmann

first: Thomas

last: Muley

first: Michael

last: Meister

first: Phillipp

last: Schnabel

first: Arne

last: Warth


title: Antitumor efficacy of RAF inhibitor GDC-0879 involving BRAFV600E mutational status and ERK/MAPK pathway suppression

city: South San Francisco

first: Peter

last: Haverty

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
Unsupervised hierarchical clustering revealed a strong similarity in gene modulation resulting from either compound treatment or BRAF ablation mediated by RNA interference relative to DMSO-treated control samples .

Keywords: Expression Array

overall_design: We have generated melanoma A375 cells stably expressing a shRNA construct for doxycycline-inducible knockdown of B-Raf (2 mg/ml Dox, 48h). Small molecule treatment was at 1000nM R341787, 24h.

first: Zora

last: Modrusan

first: Klaus

last: Hoeflich


title: 11 Neuroblastoma cell lines under normoxic and hypoxic conditions

city: Genoa

first: Paolo

last: Fardin

address: Largo G. Gaslini 5

department: Molecular Biology

institute: Istiuto Giannina Gaslini

summary:
Hypoxia is a low oxygen condition that occurs in the developing tumor mass and that is associated with poor prognosis and resistance to chemo- and radio-therapy. The definition of the hypoxia gene signature is fundamental for the understanding of tumor biology, as in the case of neuroblastoma, the most common pediatric solid tumor. The issue of identifying a significant group of variables in microarray gene expression experiments is particularly difficult due to the typical high dimensional nature of the data and great effort has been spent in the development of feature selection techniques.
Our main goal is to define a robust hypoxia gene signature in neuroblastoma cell lines. A set of 11 neuroblastoma cell lines were cultured under normoxic and hypoxic conditions for 18 hours, and their gene expression profiles were measured with Affymetrix GeneChip HG-U133 Plus 2.0. We used the l1-l2 regularization framework in order to select the significant probesets defining hypoxic versus normoxic cell lines.

overall_design: The expression profiles of 11 neuroblastoma cell lines under normoxia vs hypoxia were studied.

first: Annalisa

last: Barla


title: Gene expression profile in human orthotopic liver transplantation

city: Napoli

first: Lucio

last: Nitsch

address: Via Pansini 5

department: Biologia e Patologia Cellulare e Molecolare

institute: Unversity of Naples Federico II

summary:
We have studied the genes activated in human liver transplantation to identify potential target genes for the prevention or treatment of related injuries.
In a first protocol, in order to evaluate the effect of Ischemia-Reperfusion Injury (IRI) on gene expression profile, we compared gene expression levels in transplanted-reperfused livers  versus basal values in donor livers, identifying 795 genes significantly modified in human liver after transplantation. Some genes are likely to be completely activated by IRI, as they are not expressed at all in basal livers.
In a second protocol, in order to identify gene dysregulations already present in donor livers, which might affect gene expression profile after transplantation, gene expression evaluated in the first study was compared to control livers (espression data retrieved from ArrayExpress database). About 900 genes in donor livers are dysregulated if compared to the control condition. At least 400 of them remain dysregulated or become more and more dysregulated after transplantation.

overall_design:
For the first protocol, two biopsies were collected from each liver: 1 biopsy before explantation from the donor, immediately after opening, before ice was applied, and 1 biopsy about 2-3 hours after liver reperfusion in the recipient organism. Gene expression of 5 transplanted livers was compared to that of 5 donor livers.
In the second protocol gene expression both of transplanted and donor livers was compared to gene expression data from 5 control livers retrieved from ArrayExpress repository SAMPLE ID: E-AFMX-11

first: Anna

last: Conti

first: Floriana

last: Fabbrini

first: Antonella

last: Izzo

first: Simona

last: Scala

first: Paola

last: D'Agostino

first: Elena

last: Alimenti

first: Daniele

last: Morelli

first: Angela

last: Tammaro

first: Fulvio

last: Calise

first: Antonio

last: Faiella

first: Maurizio

last: D'Esposito

last: Della Ragione

first: Vincenzo

last: Scuderi


title: Comparison of TCF hyper-activated and control Huh7 cells - microarray data

city: Istanbul

first: Ersen

last: Kavak

address: Bogazici Uni. North Campus, North otopark building, 212

department: Molecular Biology and Genetics

country: Turkey

institute: Bogazici University

summary: The Wnt signaling pathway is involved in many differentiation events during embryonic development and can lead to tumor formation after aberrant activation of its components. Β-catenin, a cytoplasmic component, plays a major role in the transduction of the canonical wnt/ β-catenin signaling. The aim of this study was to identify novel genes that are regulated by active β-catenin/TCF signaling in hepatocellular carcinoma. We selected and expanded isogenic clones from hepatocellular carcinoma-derived Huh7 cells with high and low β-catenin/TCF activities. We showed that, high TCF activity Huh7 cells lead to bigger and more aggressive tumors when xenografted into nude mice. We used SAGE (Serial Analysis of Gene Expression), genome-wide microarray and in silico promoter analysis in parallel, to compare gene expression between low (basal) and high (transfected) β-catenin/TCF activity clones, those had been xenografted into nude mice. We compared and contrasted SAGE and genome-wide microarray data, in parallel. Finally; after combined analysis, we identified BRI3 and HSF2 as novel targets of Wnt/β-catenin signaling in hepatocellular carcinoma.

overall_design: High TCF activity Huh7 cell line (Huh7-S33Y) was compared to control Huh7 cell line (Huh7-Vec) by using 10 ug of total RNA isolated from each sample (15 ug of labeled cRNA was hybridized to the arrays). Triplicates are coming from same total RNA extraction.

first: Adil

last: Duru

first: Ahmet

last: Koman


title: Effects of HHV8 infection in lymphatic endothelial cells

first: Stephen

last: Henderson

type:
Non-coding RNA profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series


title: Lymphatic endothelial cells (LEC) transfected with the KSHV microRNA cluster

summary: Kaposi sarcoma is the most common cancer in AIDS patients and is typified by red skin lesions. The disease is caused by the KSHV virus (HHV8) and is recognisable by its distinctive red skin lesions. The lesions are KSHV-infected spindle cells, most commonly the lymphatic endothelial and blood vessel endothelial cells (LEC and BEC), plus surrounding stroma. The KSHV virus expresses multiple microRNA in a single cluster. Here we test the effects of this KSHV microRNA cluster in LEC cells using Affymetrix hgu133plus2 chips.

overall_design: There are n=3 of: 1. LEC control with empty vector pSIN-MCS (LEC), 2. LEC transfected with the same vector containing the KSHV microRNA cluster.

first: Amy

last: Hansen

first: Dimitrios

last: Lagos


title: Infection of Lymphatic and Blood Vessel Endothelial Cells (LEC and BEC) with KSHV

summary: Kaposi sarcoma is the most common cancer in AIDS patients and is typified by red skin lesions. The disease is caused by the KSHV virus (HHV8) and is recognisable by its distinctive red skin lesions. The lesions are KSHV-infected spindle cells, most commonly the lymphatic endothelial and blood vessel endothelial cells (LEC and BEC), plus surrounding stroma. The effects of KSHV infection of both LEC and BEC were assayed using Affymetrix hgu133plus2 chips at 72 hours post infection.

overall_design: There are n=6 of: 1. LEC control (LEC), 2. KSHV-infected LEC (KLEC), 3. BEC control (BEC), and 4. KSHV-infected BEC (KBEC).


title: Comparison of TCF hyper-activated and control Huh7 cells

type:
Expression profiling by array
Expression profiling by SAGE


title: Expression data from HD-1 bri and HD-1 dim cells

city: Melbourne

first: Holger

last: Schlueter

state: Victoria

address: Locked Bag 1

department: Research

country: Australia

institute: Peter Mac Callum cancer Centre

summary: Pericytes derived from skin dermis can substantially enhance the short-term tissue-regenerative capacity of human epidermal cells already committed to differentiation; they also display both phenotypic and functional properties of mesenchymal stem cells. In this microarray analysis, we compared the gene expression profile of dermal pericytes to that of the remaining dermal cells of neonatal human foreskin.

overall_design: Human neonatal foreskin was digested overnight in dispase II at 4°C to separate the epidermis from the dermis. Subsequently the dermis was digested for 1-2 hours at 37°C in a mixed dispase and collagenase solution and then fractionated into two populations, i.e. pericytes (HD-1bri) and the remaining dermal cells (HD-1dim), on the basis of differential VLA-1 expression using fluorescence-activated cell sorting. Total RNA from 15,000 cells of each population was extracted from 4 independent replicate sorts. mRNAs were amplified using a T7-primer-based-2-round linear RNA amplification protocol (GeneChip Two-Cycle cDNA synthesis kit). Fragmented and biotin-labelled cRNA from each individual sample was hybridised to Affymetrix HG-U133 plus 2.0 arrays and scanned on a Affymetrix GeneChip scanner. Probe intensities were RMA normalized and log2-transformed expression values were compared using moderated t statistics to quantify differences between individual samples.

first: Sophie

last: Paquet-Fifield

first: Pritinder

last: Kaur


title: Generation of human induced pluripotent stem cells from mesenchymal cells of gut mesentery by Oct4/Sox2/Nanog

status: Public on Sep 26 2009

first: Yang

last: Li

address: Xueyuan Road 38

institute: Peking University

summary:
Background and aim: Human Induced pluripotent stem (iPS) cells have been derived from dermal ﬁbroblasts, keratinocytes and blood cells by ectopic expression of defined transcription factors.1–5 Application of this approach in human cells would have enormous potential and generate patient-specific pluripotent stem cells to accelerate the implementation of stem cells for clinical treatment of degenerative diseases. In the present study, we investigated whether genetically marked human mesenchymal cells of gut mesentery may give rise to iPS cells.
Methods: We used lentiviruses to express Oct4, Sox2, Nanog in mesenchymal cells of gut mesentery, then generated iPS cells were identified in many aspects including morphology, pluripotent markers, global gene expression profile, DNA methylation status at pluripotent cell-speciﬁc genes, embryoid bodies and terotomas formation.
Results: The resulting iPS cells from mesenchymal cells of gut mesentery were similar to human embryonic stem (ES) cells in morphology, proliferation, surface antigens, gene expression, and epigenetic status of pluripotent cell-speciﬁc genes. Furthermore, these cells could differentiate into cell types of the three germ layers in vitro and in teratomas. DNA ﬁngerprinting showed that the human iPS cells were derived from the donor cells and are not a result of contamination.

overall_design: one sample/variable

first: Lingsong

first: Feng

last: Lan


title: Half-life determination for human B-cells (BL41)

first: Lars

last: Dölken

state: Cambridgeshire

address: Addenbrookes Hospital, Hills Road

institute: University of Cambridge

summary:
RNA was labeled in BL41 cells by culturing cells for 60 min in media containing 100µM 4sU. Tc-RNA was separated into nt- and p-RNA. All three RNA subsets were subjected to microarray analysis. Only probe sets providing present calls in all RNA samples/subsets were included into the analysis
We used microarrays to determine half-lives of mRNAs expressed in BL41 cells
Keywords: Determination of mRNA half-life in human B-cells

first: Meister

last: Gunther


title: VEGF induction of HUVEC

city: Wien

first: Julia

last: Testori

address: Lazarettgasse 19

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Medical University Vienna

summary: Angiogenesis, the formation of new capillaries by sprouting from preexisting vessels, is mainly induced by VEGF-A. To identify genes which are induced by VEGF-A in endothelial cells, HUVEC were starved and induced by VEGF-A165 for 30, 60 and 150min. RNA of induced and uninduced cells was isolated and subjected to microarray analysis using Affymetrix microarray.

overall_design: Human umbilical vein endothelial cells were grown in complete EGM-2 medium in dense culture for four days without change of medium and before the stimulation in EGM-2 medium without growth factors over night. The cells were stimulated with 100ng/ml VEGF-A165 for 30, 60 and 150 min. RNA was isolated with Trizol according to the manufacturer's instructions.

first: Martin

last: Bilban

first: Erhard

last: Hofer


title: Expression data from JAK1 wild-type and JAK1 mutation-positive T cell acute lymphoblastic leukemia blasts

status: Public on Sep 24 2009

city: Brussels

first: Laurent

last: Knoops

address: Av Hippocrate, 74

country: Belgium

institute: de Duve Institute

summary:
Aberrant signal transduction contributes substantially to leukemogenesis. The Janus kinase 1 (JAK1) gene encodes a cytoplasmic tyrosine kinase that noncovalently associates with a variety of cytokine receptors and plays a nonredundant role in lymphoid cell precursor proliferation, survival, and differentiation. Somatic mutations in JAK1 occur in individuals with acute lymphoblastic leukemia (ALL). JAK1 mutations were more prevalent among adult subjects with the T cell precursor ALL, where they accounted for 18% of cases, and were associated with advanced age at diagnosis, poor response to therapy, and overall prognosis
We used microarray to compare the gene expression profile of JAK1 mutation positive or negative ALL blasts

overall_design: Thawed or freshly isolated T-ALL cells (>90% blasts) were homogenized, total RNA was extracted and hybridized on Affymetrix microarrays

first: Sabina

last: Chiaretti


title: Intratumoral injection of CpG1826

status: Public on Sep 23 2009

first: Michael

middle: Henry

last: Kershaw

address: 14 St. Andrews Place

institute: Peter MacCallum Cancer Centre

summary: To determine the effect on gene expression of intratumoral injection of the Toll-like receptor agonist CpG1826. MC38 colon cancer cells were injected subcutaneously into C57BL/6 mice and allowed to establish until ~40 mm2.

overall_design: 5 CpG1826-treated samples were analyzed and compared to 5 PBS-injected control tumors.


title: Endometrial receptivity

status: Public on Sep 22 2009

city: Brussel

first: Inge

last: Van Vaerenbergh

address: Laarbeeklaan 103

department: EXPA

institute: Vrije Universiteit Brussel

summary:
In GnRH-antagonist/rec-FSH stimulated cycles, advanced endometrial maturation on the day of oocyte retrieval correlates with altered gene expression

Keywords: gene expression analysis, advanced endometrial maturation

overall_design: Endometrial biopsies taken on the day of oocyte retrieval in stimulated IVF cycles with 1 or 2 embryos replaced on day 3 in the same cycle. Endometrial dating was performed according to Noyes' criteria. All endometria taken on the day of oocyte retrieval showed an advanced maturation, ranging from +d2 to +d4. The patients with a subsequent clinical pregnancy all showed a histological dating corresponding to +d2 or +d3. Gene expression of histologically more advanced endometria, as assessed by Noyes' criteria, (n=3, +d4) was compared with matched less advanced endometria (n=4,+d2-3).

first: Leentje

last: Van Lommel

first: Vanessa

last: Ghislain

first: Peter

last: In't Veld

first: Frans

last: Schuit

first: Human

last: Fatemi

first: Paul

last: Devroey

first: Claire

last: Bourgain


title: Identification of genes related to local aggressiveness and metastatical potential in mesenchymal tumors

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

summary: We analysed 102 sample of mesenchymal tumors of different histological type and biological behaviour. The aim of the study was to identify genes related to each characteristic analysed.

overall_design: We compared the gene expression profiles of 102 mesenchymal tumors with histological and clinical parameters. Total RNA was extracted, amplified and spotted on cDNA microarray slides. Experiments were performed in duplicate, using the dye-swap method.

first: Isabela

middle: W

last: Cunha

first: Waleska

middle: K

last: Martins

first: Alex

last: Fiorini

first: Luiz

middle: L

last: Reis


title: Genome-wide gene expression analysis of mucosal colonic biopsies and isolated colonocytes...

status: Public on Sep 16 2009

city: Copenhagen

first: Morten

last: Hansen

address: Blegdamsvej 3B

department: Department of Cellular and Melocular Medicine

country: Denmark

institute: Faculty of Health Sciences

summary:
Background & Aims: Genome-wide gene expression (GWGE) profiles of mucosal colonic biopsies have suggested the existence of a continuous inflammatory state in quiescent ulcerative colitis (UC). The aim of this study was to use DNA microarray-based GWGE profiling of mucosal colonic biopsies and isolated colonocytes from UC patients and controls in order to identify the cell types responsible for the continuous inflammatory state. Methods: Adjacent mucosal colonic biopsies were obtained endoscopically from the descending colon in patients with active UC (n=8), quiescent UC (n=9), and with irritable bowel syndrome (controls, n=10). After isolation of colonocytes and subsequent extraction of total RNA, GWGE data were acquired using Human Genome U133 Plus 2.0 GeneChip Array (Affymetrix, Santa Clara, CA). Data analysis was carried out by principal component analysis and projection to latent structure-discriminant analysis using the SIMCA-P11 software (Umetrics, Umeå, Sweden). Results: A clear separation between active UC, quiescent UC and control biopsies were found, whereas the model for the colonocytes was unable to distinguish between quiescent UC and controls. The differentiation between quiescent UC and control biopsies was governed by unique profiles containing gene expressions with significant fold changes. These primarily belonged to the family of homeostatic chemokines revealing a plausible explanation to the abnormal regulated innate immune response seen in patients with UC. Conclusion: This study has demonstrated the presence of a continuous inflammatory state in quiescent UC, which seems to reflect an altered gene expression profile of lamina propria cells.

Keywords: Colonocytes, continuous inflammation, mucosal colonic biopsies, gene expression profiles

overall_design: Adjacent mucosal colonic biopsies were attained endoscopically from the descending colon in patients with active UC (n=8), quiescent UC (n=9), and in controls (n=10). After extraction of total RNA, genome-wide gene expression data were acquired using Human Genome U133 Plus 2.0 GeneChip Array (Affymetrix, Santa Clara, CA). Amplification was required to obtain sufficient amounts of labelled complementary RNA (cRNA) target for analysis with arrays. Data analysis was carried out by principal component analysis and projection to latent structure-discriminant analysis using the SIMCA-P11 software (Umetrics, Umeå, Sweden).

first: Jacob

middle: T

last: Bjerrum

first: Jørgen

last: Olsen

first: Ole

last: Nielsen


title: Washing scaling of microarray expression

city: Leipzig

first: Knut

last: Krohn

address: Philipp-Rosenthal-Straße 55

department: Medizinische Fakultät

institute: University Leipzig

summary: Post-hybridization washing is an essential part of microarray experiments. Both, the quality of the experimental washing protocol and the adequate consideration of washing in intensity calibration ultimately affect the quality of the expression estimates extracted from the microarray intensities. We conducted experiments on GeneChip microarrays with altered protocols for washing, scanning and staining to study the probe-level intensity changes as a function of washing cycles. Particularly, three Affymetrix GeneChip HGU133plus2 arrays were hybridized and equilibrated for 16 hours in the hybridization oven. For one of the three arrays washing and staining was performed according to the manufacturer’s instructions. For another array the first scan was done immediately after low stringent wash and staining without intermitting stringent washing. Then, the array was stringently washed and scanned in alternating order three more times where each washing step consists of a definite number of washing cycles. The third array was low stringently washed followed by two stringent washing cycles and staining before the first scan. Subsequently it was analogously processed as array A. All three chips are repeatedly processed in a second series of alternating wash/scan-cycles which was performed using the same protocol for each chip as in the first series as described above. As in the first series the arrays were also stained a second time to compensate for any loss of bleached fluorescent dye. Analysis of the washing kinetics shows that the signal-to-noise ratio doubles roughly every ten stringent washing cycles. Washing can be characterized by time-dependent rate constants which reflect the heterogeneous character of target binding to microarray probes. We propose an empirical washing function which estimates the survival of probe bound targets. The washing function allows calibrating probe intensities for the effect of washing. On a relative scale, proper calibration for washing markedly increases expression measures especially in the limit of small and large values.

overall_design: The aim of the study was to understand the probe-level intensity changes as a function of washing cycles. For this experiment RNA was prepared from a cancer cell line and used for probe synthesis. Hybridisation to three Affymetrix microarrays was identically performed with aliquotes of one hybridization mix from a single RNA sample. The protocols for washing,  scanning and staining were altered.

first: Hans

last: Binder

first: Conrad

last: Burden


title: High resolution gene expression profiling for simultaneous analysis of RNA synthesis, abundance and decay

city: Cambridge

first: Lars

last: Dölken

department: Medicine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Zsolt

last: Ruzsics

first: Bernd

last: Rädle

first: Ulrich

last: Koszinowski

first: Caroline

last: Friedel

first: Ralf

last: Zimmer

first: Jörg

last: Mages

first: Reinhard

last: Hoffmann

last: Dickinson

first: Thorsten

last: Forster

first: Peter

last: Ghazal


title: Priming integrin alpha5 promotes human mesenchymal stromal cell osteoblast differentiation and osteogenesis

status: Public on Sep 10 2009

city: Berlin

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

institute: Charité

summary:
Human adult mesenchymal stromal cells (hMSC) have the potential to differentiate into chondrogenic, adipogenic or osteogenic lineages, providing a potential source for tissue regeneration. An important issue for efficient bone regeneration is to identify factors that can be targeted to promote the osteogenic potential of hMSCs. Using transcriptomic analysis, we found that integrin alpha5 (ITGA5) expression is upregulated during dexamethasone-induced hMSCs osteoblast differentiation. Gain-of-function studies showed that ITGA5 promotes the expression of osteoblast phenotypic markers as well as in vitro osteogenesis in hMSCs. Downregulation of endogenous ITGA5 using shRNA blunted osteoblast marker expression and osteogenic differentiation. Pharmacological and molecular analyses showed that the enhanced hMSCs osteoblast differentiation induced by ITGA5 was mediated by activation of FAK/ERK1/2-MAPKs and PI3K signaling pathways. Remarkably, activation of ITGA5 using a specific antibody that primes the integrin or a peptide that specifically activates ITGA5 was sufficient to enhance ERK1/2-MAPKs and PI3K signaling and to promote osteoblast differentiation and osteogenic capacity of hMSCs. We also demonstrate that hMSCs engineered to over-express ITGA5 exhibited a marked increase in their osteogenic potential in vivo. These findings not only reveal that ITGA5 is required for osteoblast differentiation of adult human MSCs but also provide a novel targeted strategy using ITGA5 agonists to promote the osteogenic capacity of hMSCs, which may be used for tissue regeneration in bone disorders where the recruitment or capacity of MSCs is compromised.

Keywords: Time course of osteogenic differentiation processes

overall_design: Gene expression profiles were generated from bone marrow MSC before and 1, 3 and 7 days after stimulation with 10E-7M dexamethasone to study the early molecular processes of osteogenic differentiation. 3 replicates per timepoint.

first: Zahia

last: Hamidouche

first: Olivia

last: Fromigué

first: Jochen

last: Ringe

first: Pascal

last: Vaudin

first: Samer

last: Srouji

first: Erella

last: Livne

first: Pierre

last: Marie


title: Effects of bevacizumab (avastin) in mouse model of endometrial cancer

city: Albuquerque

first: Gavin

last: Pickett

state: NM

address: 2325 Camino de Salud NE

department: Genomics

institute: UNM

summary:
Microarrays were used to determine the efficacy of bevacizumab (a monoclonal antibody against the vascular endothelial growth factor and its receptors.) on endometrial cancer cells.
Endometrial cancer is the most frequent gynecologic cancer in women. Long term outcomes for patients with advanced stage or recurrent disease are poor. Targeted molecular therapy against the vascular endothelial growth factor (VEGF) and its receptors constitute a new therapeutic option for these patients. The goal of our work was to assess the potential effectiveness of inhibition of VEGF/VEGFR signaling in a xenograft model of endometrial cancer using bevacizumab (Avastin, a humanized antibody against VEGFA). We also aimed to identify molecular markers of sensitivity or resistance to this agent. We show that bevacizumab retards tumor growth in athymic mice by inhibiting molecular components of signaling pathways that sustain cell survival and proliferation. We also demonstrate that resistance to bevacizumab may involve up-regulation of antiapoptotic genes and certain proto-oncogenes.

overall_design: Human xenografts produced from endometrial cell line, grown in athymic mice, were treated in vivo with bevacizumab.

first: Suzy

last: Davies

first: Kimberly

last: Leslie

first: Donghai

last: Dai


title: Bacterial Adrenergic signaling

status: Public on Sep 15 2009

city: Baltimore

first: David

last: Rasko

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

summary: The ability to respond to stress is at the core of an organism’s survival. The hormones epinephrine and norepinephrine play a central role in stress responses in mammals, which require the synchronized interaction of the whole neuroendocrine system. Bacteria also sense and respond to epinephrine and norepinephrine as a means to gauge the metabolic and immune state of the host. Mammalian adrenergic receptors are G-coupled protein receptors (GPCRs), bacteria, however, sense these hormones through histidine sensor kinases (HKs). HKs autophosphorylate in response to multiple signals and transfer this phosphate to response regulators (RRs). Two bacterial adrenergic receptors have been identified in EHEC, QseC and QseE, with QseE being downstream of QseC in this signaling cascade. We mapped the QseC signaling cascade in the deadly pathogen enterohemorrhagic E. coli (EHEC), which exploits this signaling system to promote disease. Through QseC, EHEC activates expression of metabolic, virulence and stress response genes, synchronizing the cell response to these stress hormones. Coordination of these responses is achieved by QseC phosphorylating three of the thirty two EHEC RRs. The QseB RR, which is QseC’s cognate RR, activates the flagella regulon which controls bacteria motility and chemotaxis. The QseF RR, which is phosphorylated by the QseE adrenergic sensor, coordinates expression of virulence genes involved in formation of lesions in the intestinal epithelia by EHEC, and the bacterial SOS stress response. The third RR, KdpE, controls potassium uptake, osmolarity response, and also the formation of lesions in the intestine. Adrenergic regulation of bacterial gene expression shares several parallels with mammalian adrenergic signaling having profound effects in the whole organism. Understanding adrenergic regulation of a bacterial cell is a powerful approach to study the underlying mechanisms of stress and cellular survival.

overall_design: Microarray comparisons reveal some trends with respect to signaling cascades. Comparative methods were used to identify networks.

last: Hughes

first: Vanessa

last: Sperandio


title: Effect of 10 Cigarette Smoke Condensates on Primary Human Airway Epithelial Cells

summary: Nine cigarette smoke condensates (CSCs) were produced under a standard ISO smoking machine regimen and one was produced by a more intense smoking machine regimen. These CSCs were used to treat primary normal human bronchial epithelial cells for 18 hours.

overall_design: Primary human bronchial/tracheal epithelial cells were grown in culture and treated with 10 different sources of cigarette smoke condensates.

first: Jean-Clare

last: Seagrave

first: Yohannes

last: Tesfaigzi

first: Susan

last: Boggs

first: Greg

last: Polzin

first: Patricia

last: Richter


title: Comparative analysis of gene regulation by the transcription factor PPARα_human

status: Public on Sep 21 2009

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
Studies in mice have shown that PPARα is an important regulator of hepatic lipid metabolism and the acute phase response. However, little information is available on the role of PPARα in human liver. Here we set out to compare the function of PPARα in mouse and human hepatocytes via analysis of target gene regulation. Primary hepatocytes from 6 human and 6 mouse donors were treated with PPARα agonist Wy14643 and gene expression profiling was performed using Affymetrix GeneChips followed by a systems biology analysis. Baseline PPARα expression was similar in human and mouse hepatocytes. Depending on  species and time of exposure, Wy14643 significantly induced the expression of 362-672 genes. Surprisingly minor overlap was observed between the Wy14643-regulated genes from mouse and human, although more substantial overlap was observed at the pathway level. Xenobiotics metabolism and apolipoprotein synthesis were specifically regulated by PPARα in human hepatocytes, whereas glycolysis-gluconeogenesis was regulated specifically in mouse hepatocytes. Most of the genes commonly regulated in mouse and human were involved in lipid metabolism and many represented known PPARα targets, including CPT1A, HMGCS2, FABP, ACSL, and ADFP. Several genes were identified that were specifically induced by PPARα in human (MBL2, ALAS1, CYP1A1, TSKU) or mouse (Fbp2, lgals4, Cd36, Ucp2, Pxmp4). Furthermore, several putative novel PPARα targets were identified that were commonly regulated in both species, including CREB3L3, KLF10, KLF11 and MAP3K8. Our results suggest that PPARα activation has a major impact on gene regulation in human hepatocytes. Importantly, the role of PPARα as master regulator of hepatic lipid metabolism is generally well-conserved between mouse and human. Overall, however, PPARα regulates a mostly divergent set of genes in mouse and human hepatocytes.

Keywords: Analysis of target gene regulation by using microarrays

overall_design: Primary hepatocytes from 6 human subjects were treated with the PPARα agonist Wy14643 for 6 and 24 hours, and gene expression profiling was performed using Affymetrix GeneChips.  Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.  Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate.  The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 microM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.

first: Maryam

last: Rakhshandehroo

first: Michael

last: Müller

first: Sander

last: Kersten


title: Conjugated and non-conjugated androgen differentially modulate gene expression in breast cancer cell lines.

status: Public on Sep 19 2009

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

country: Greece

institute: University of Crete

summary: The role of androgen in breast cancer development is not fully understood although androgen receptors (AR) have been identified in breast cancer clinical samples and cell lines. However the whole spectra of androgen actions cannot be accounted to the classic AR mode of action and the possible existence of a cell surface AR has been suggested. Indeed androgens like all steroids have been reported to trigger membrane initiated signaling activity and exert specific actions. Androgens acting on the membrane can rapidly activate kinase signaling pathways and ultimately could affect gene expression. However, the molecular nature of membrane androgen binding sites represents another major persisting question. In the present study, we investigated early transcriptional effects of testosterone and the impermeable testosterone-BSA conjugate, in two breast cancer cell lines, in an attempt to decipher specific genes modified in each case, providing evidences about specific membrane initiating actions. Our data indicate that the two agents tested affect the expression of several genes. A group of genes were commonly affected while others were uniquely modified by each agent. In MDA-MB-231 cells, that are AR negative, the majority of genes affected by testosterone were also affected by testosterone-BSA indicating a membrane action. Subsequent analysis revealed that the two agents trigger different molecular pathways and cellular/molecular functions, suggestive of a molecular heterogeneity of membrane and intracellular AR. In addition, the phenotypic interactions of membrane-acting androgen with growth factor were verified at the transcriptomic level. Finally an interesting interplay between membrane-acting androgen with inflammation-related molecules, with potential clinical implications was revealed.

overall_design:
Cell lines and culture conditions
The hormone-sensitive breast cancer cell line T47D (expressing ERα, ERβ and AR) and the hormone insensitive breast cancer cell line MDA-MB-231 (expressing only ERβ) were purchased from the European Collection of Cell Cultures (Salisbury, UK). T47D cells and MDA-MB-231 were cultured in RPMI-1640 medium, supplemented with 10% charcoal treated fetal bovine serum (FBS), in a humidified atmosphere of 5% CO2 in air, at 37°C. Culture media and serum were from Gibco BRL (Life Technologies, Paisley, UK).
Treatment- Gene expression assay
 Cells were serum starved for 6 hours and then treated with 10-7M Testosterone or charcoal-treated Testosterone-BSA, for 3 hours. Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Düren, Germany), labeled and hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), using the HGU133A plus 2 chip, analyzing a total of 54675 transcripts. Signals were detected by an Affymetrix microarray chip reader.

first: Vassiliki

last: Pelekanou

first: Elias

last: Castanas

first: Marilena

last: Kampa


title: Overexpression of USF1 in HEK293T cells

status: Public on Sep 14 2009

city: Seattle

first: Christopher

last: Plaisier

state: Washington

address: 401 Terry Avenue North

institute: Institute for Systems Biology

summary:
Overexpression of USF1 in HEK293T cells in vitro to ascertain the genes downstream of USF1. Will identify direct targets as well as indirect targets of USF1.

Keywords: Overexpression of transcription factor to determine downstream targets.

overall_design: Cloned USF1 from cDNA and transiently transfected into HEK293T cells. Total RNA collected 48 hours after transfection. Empty vector used as control. Expression of USF1 was validated using western blot, and qRT-PCR was used to validate differential expression.

first: Steve

last: Horvath

first: Adriana

last: Huertas-Vazquez

first: Ivette

last: Cruz-Bautista

first: Miguel

middle: F

last: Herrera

first: Teresa

last: Tusie-Luna

first: Carlos

last: Aguilar-Salinas

first: Paivi

last: Pajukanta


title: Gene expression comparison of drug-resistant Panc1/mock cells and Panc1 cells expressing wildtype syk

status: Public on Sep 09 2009

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary:
We recently identified the nonreceptor tyrosine kinase syk as a tumor suppressor in pancreatic ductal adenocarcinoma cells.  Reintroduction of syk into Panc1 cells promoted a more differentiated phenotype and retarded invasion and tumorigenic growth. Gene array analysis identified over 2,000 transcripts differentially expressed at FDR<0.01.  Among these were members of the MMP2 axis, which were subsequently shown to regulate Panc1 invasion.

Keywords: Genetic manipulation (stable transgene expression)

overall_design: Affymetrix global gene arrays were used to analyse differences in gene expression patterns in Panc1 cells stably reexpressing syk, or vector-only mock controls.  RNA was harvested from cells grown under identical conditions in standard culture.

first: Tracy

middle: M

last: Layton

last: Silletti


title: Whole blood transcript profiling of rheumatoid arthritis patients

first: Jadwiga

last: Bienkowska

address: 45 Fayette Str Apt 3

institute: BiogenIdec

summary: The whole blood was collected pre-treatment from rheumatoid arthritis patients starting the anti_TNF therapy. All patients were naïve to anti_TNFs. The disease activity was measured using the DAS28 score at the pre-treatment visit1 (DAS28_v1)  and 14 weeks after treatment visit3 (DAS28_v3). The response to the therapy was evaluated using the EULAR [European League Against Rheumatism] definition of the response. The objective of the data analysis was to identify gene expression coorelating with response as well as to identify genes that differentiate responders versus non-responders pre-treatment. The results of this investigation identified 8 trainscripts that predict responders vs. non-responders with 89% accuracy.

overall_design: Patients' response to anti-TNF was assessed using EULAR score and patients were classified as responders, moderate responders and non-responders. Genes correlating with the response status have been identified.

first: Peter

last: Gregersen

first: Franak

last: Batlivwalla

first: John

last: Carulli


title: Classical and/or alternative NF-kB pathway activation in multiple myeloma pathogenesis

status: Public on Sep 11 2009

city: Bethesda

first: Oleg

middle: Konstantin

last: Glebov

address: 8901 Wisconsin Ave., Bldg. 8, Rm. 5101

department: Genetics

institute: NCI

summary:
Mutations involving the NFKB pathway are present in at least 17% of multiple myeloma (MM) tumors and 40% of MM cell lines (MMCL). These mutations, which are thought to be progression events, enable MM tumors to become less dependent on extrinsic bone marrow signals that activate NFKB.  Studies on a panel of 50 MMCL provide some clarification of the mechanisms through which these mutations act and the significance of classical vs alternative activation of NFKB. First, only one mutation (NFKB2) selectively activates the alternative pathway, whereas several mutations (CYLD, NFKB1, TACI) selectively activate the classical pathway. However, most mutations affecting NIK level (NIK, TRAF2, TRAF3, cIAP1&2, CD40) activate the alternative but often both pathways.  Second, we confirm the critical role of TRAF2 in regulating NIK degradation, whereas TRAF3 enhances but is not essential for cIAP1/2-mediated proteosomal degradation of NIK in MM.
Third, using transfection to selectively activate the classical or alternative NFKB pathways, we show virtually identical changes in gene expression in one MMCL, whereas the changes are similar albeit non-identical in a second MMCL.  Together, our results suggest that MM tumors can achieve increased autonomy from the bone marrow microenvironment by mutations that activate either NFKB pathway.

overall_design: Total RNA was isolated from both H929 and SACHI cell lines at 3 consecutive time points after infection with retroviruses containing NIK-gene, IKKB-gene, or no gene of interest, providing 3 replicate RNA samples for each cell line and infection variant. These RNA samples were processed and hybridized according to Affymetrix protocols. In total, 2(cell lines) x 3 (infection variants) x 3(time points) = 18 arrays were hybridized and analyzed.

first: W

last: Kuehl

first: Yulia

last: Demchenko


title: Molecular analysis of ex-vivo CD133+ GBM cells revealed a common invasive and angiogenic profile but different proliferative signatures among high grade gliomas.

city: Salamanca

first: Fran

last: González

state: Salamanca

address: Plaza de España, 5-6

department: Discovery Information Systems

country: Spain

institute: OncoStem Pharma

summary:
Background: Gliomas are the most common type of primary brain tumours, and in this group glioblastomas (GBMs) are the higher-grade gliomas with fast progression and unfortunate prognosis. Two major aspects of glioma biology that contributes to its awful prognosis are the formation of new blood vessels through the process of angiogenesis and the invasion of glioma cells. Despite of advances, two-year survival for GBM patients with optimal therapy is less than 30%. Even in those patients with low-grade gliomas, that imply a moderately good prognosis, treatment is almost never curative. Recent studies have demonstrated the existence of a small fraction of glioma cells with characteristics of neural stem cells which are able to grow in vitro forming neurospheres and that can be isolated in vivo using surface markers such as CD133. The aim of this study was to define the molecular signature of GBM cells expressing CD133 in comparison with non expressing CD133 cells. This molecular classification could lead to the finding of new potential therapeutic targets for the rationale treatment of high grade GBM.
Methods: Eight fresh, primaries and non cultured GBMs were used in order to study the gene expression signatures from its CD133 positive and negative populations isolated by FACS-sorting. Dataset was generated with Affymetrix U133 Plus 2 arrays and analysed using the software of the Affymetrix Expression Console.  In addition, genomic analysis of these tumours was carried out by CGH arrays, FISH studies and MLPA.
Results: Gene expression analysis of CD133+ vs. CD133- cell population from each tumour showed that CD133+ cells presented common characteristics in all glioblastoma samples (up-regulation of genes involved in angiogenesis, permeability and down-regulation of genes implicated in cell assembly, neural cell organization and neurological disorders). Furthermore, unsupervised clustering of gene expression led us to distinguish between two groups of samples: those discriminated by tumour location and, the most importantly, the group discriminated by their proliferative potential.
Conclusions: Primary glioblastomas could be sub-classified according to the properties of their CD133+ cells. The molecular characterization of these potential stem cell populations could be critical to find new therapeutic targets and to develop an effective therapy for these tumours with very dismal prognosis.

overall_design: We studied a dataset generated with Affymetrix U133 Plus 2 arrays (Affymetrix, Santa Clara, CA, USA) in 8 gliomas. The collected cells (CD133+ and CD133- from each tumor) were sorted into separated vials containing RNA Later (Qiagen, Chatsworth, CA, USA), making a total of 16 samples (8 positives and 8 negatives).

first: Juan

last: García

first: María

last: Pérez-Caro

last: Gómez-Moreta

first: Francisco

middle: J

first: Javier

last: Ortiz

first: Oscar

last: Blanco

first: Magdalena

last: Sancho

first: Jesús

last: Hernández-Rivas

first: Rogelio

last: González-Sarmiento

first: Manuel

last: Sánchez-Martín


title: Networking of differentially expressed genes in human MDA-MB-468 breast cancer cells resistant to methotrexate

status: Public on Sep 08 2009

city: Barcelona

first: Carlos

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

institute: University of Barcelona

summary:
A summary of the work associated to these microarrays is the following:

The need for an integrated view of all data obtained from high-throughput technologies gave rise to network analyses. These are especially useful to rationalize phenomena in terms of how external perturbations propagate through the expression of genes. To address this issue in the case of drug resistance, we constructed Biological Association Networks of genes differentially expressed in cell lines resistant to methotrexate (MTX). Seven cell lines representative of different types of cancer including colon cancer (HT29 and Caco2), breast cancer (MCF7 and MDA-MB-468), pancreatic cancer (MIA PaCa-2), erythroblastic leukemia (K562) and osteosarcoma (Saos-2), were used. The differential expression pattern between sensitive and MTX-resistant cells was determined by microarrays covering the whole human genome and analyzed with the GeneSpring GX software package, v.7.3.1. Genes deregulated in common in the two colon cancer cell lines studied, were subject of Biological Association Networks construction. Dikkopf homolog-1 (DKK1) was a clear node of this network, and functional validations of this target using a siRNA showed a chemosensitization toward MTX. Members of the UDP-glucuronosyltransferase 1A (UGT1A) family formed a network of differentially expressed genes in the two breast cancer cell lines studied. siRNA treatment against UGT1A showed also an increase in MTX sensitivity. Eukaryotic translation elongation factor 1 alpha 1 (EEF1A1) was a gene overexpressed in common among the pancreatic cancer, leukemia and osteosarcoma cell lines, and siRNA treatment against EEF1A1 produced a chemosensitization toward MTX. Biological Association Networks identified DKK1, UGT1As and EEF1A1 as important gene nodes in MTX-resistance. Treatments using iRNA technology against these three genes show chemosensitization toward MTX.

overall_design: Two cell lines are compared, which are MDA-MB-468 breast cancer cells sensitive to methotrexate and MDA-MB-468 cells resistant to 10e-6M methotrexate. Six samples are provided which correspond to tripicates of each cell line. The sample provided were  analyzed using the specific software GeneSpring GX.

first: Elisabet

last: Selga

first: Carlota

last: Oleaga

last: de Almagro

first: Véronique

last: Noé


title: Networking of differentially expressed genes in CaCo2 human colon cancer cells resistant to methotrexate

overall_design: Two cell lines are compared, which are Caco2 colon cancer cells sensitive to methotrexate and Caco2 cells resistant to 10e-5M MTX. Six samples are provided, which correspond to triplicates of each cell line. The samples provided were analyzed using the specific software GeneSpring GX.


title: A systems genetics approach implicates USF1, FADS3 and other causal candidate genes for familial combined hyperlipidemia

first: Christopher

last: Plaisier

summary:
Assessment of mRNA expression levels in fat biopsies from subcutaneous adipose tissue from unrelated individuals.

Keywords: Subcutaneous adipose tissue.

overall_design: Subcutaneous adipose tissue from 70 unrelated individuals.

first: Steve

last: Horvath

first: Adriana

last: Huertas-Vazquez

first: Ivette

last: Cruz-Bautista

first: Miguel

last: Herrera

first: Teresa

last: Tusie-Luna

last: Aguilar-Salinas

first: Paivi

last: Pajukanta


title: Networking of differentially expressed genes in human K562 erythtoblastic leukemia cells resistant to methotrexate

overall_design: Two cell lines are compared, which are K562 erythroblastic leukemia cells sensitive to methotrexate and K562 cells resistant to 10e-5M methotrexate. Six samples are provided which correspond to triplicates of each cell line. The samples provided were  analyzed using the specific software GeneSpring GX.


title: Transcriptomic analysis of human lung development

city: Boston

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary:
We decompose the genome-wide expression patterns in 38 embryonic human lung (53-154 days post conception/dpc) into their independent, dominant directions of transcriptomic sample variation in order togain global insight of the developing human lung transcriptome.The characteristic genes and their corresponding bio–ontologic attribute profile for the latter were identified. We noted the over–representation of lung specific attributes (e.g., surfactant proteins) traditionally associated with later developmental stages, and highly ranked attributes (e.g., chemokine–immunologic processes) not previously reported nor immediately apparent in an early lung development context. We defined the 3,223–gene union of the characteristic genes of the 3 most dominant sources of variation as the developing lung characteristic sub–transcriptome (DLCS). It may be regarded as the minimal gene set describing the essential biology of this process. The developing lung series in this transcriptomic variation perspectiveform a contiguous trajectory with critical time points that both correlate with the 2 traditional morphologic stages overlapping -154 dpc and suggest the existence of 2 novel phases within the pseudoglandular stage. To demonstrate that this characterization is robust, we showed that the model could be used to estimate the gestational age of independent human lung tissue samples with a median absolute error of 5 days, based on the DLCS of their lung profile alone. Repeating this procedure on the homologous transcriptome profiles of developing mouse lung 14–19 dpc, we were able to recover their correct developmental chronology.
Whole human fetal lung gene expression profiling from estimated gestational ages 53 to 154 days post conception.

Keywords: Whole lung gene expression profiling, lung development, human fetus.

overall_design: Time series with biological replicates.

first: Soumyaroop

last: Bhattacharya

first: Kelan

middle: G

last: Tantisira


title: Novel treatment of human pancreatic cancer using masitinib combined with standard gemcitabine chemotherapy

status: Public on Sep 05 2009

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

summary: Masitinib is a tyrosine kinase inhibitor of c-Kit, PDGFRα and β, and to some extent Lyn of the Src kinase family. We evaluated the therapeutic potential of masitinib in vitro on human pancreatic tumour cell lines and in vivo in a mouse model of human pancreatic cancer.

overall_design: Expression patterns of masitinib tyrosine kinase targets including c-Kit, PDGFRα and PDGFRβ were determined in four pancreatic tumour cell lines by PCR. Proliferation assays were performed with masitinib alone or in combination with gemcitabine. To determine the in vivo effects of masitinib, Nog-SCID mice were injected subcutaneously with MiaPaca2 cells, randomised 28 days later and received one of the following treatments: vehicle control p.o., masitinib p.o., gemcitabine i.p., or a combination of masitinib plus gemcitabine. Additionally, the transcriptome of MiaPaca2 cells for each of these conditions was determined with Affymetrix arrays.

first: O

last: Hermine

first: A

last: Moussy

first: N

last: Castéran

first: S

last: Letard

first: J

last: Iovana

first: P

last: Finetti

first: F

last: Bertucci

first: T

last: Bader

first: M

last: Humbert

last: Dubreuil


title: Networking of differentially expressed genes in human MIA PaCa2 pancreatic cancer cells resistant to methotrexate

first: Carlos

last: Ciudad

overall_design: Two cell lines are compared, which are MIA PaCa2 pancreatic cancer cells sensitive to methotrexate and MIA PaCa2 cells resistant to 10e-6M MTX. Six samples are provided which correspond to triplicates of each cell line. The samples provided were  analyzed using the specific software GeneSpring GX.

first: Elisabet

last: Selga

first: Carlota

last: Oleaga

last: de Almagro

first: Véronique

last: Noé


title: Chondrogenic differentiation potential of OA chondrocytes and their use in autologous chondrocyte transplantation

status: Public on Sep 02 2009

first: Tilo

last: Dehne

state: Berlin

address: Tucholskystraße 2

department: Rheumatology and Clinical Immunology

institute: Charité - University Medicine Berlin

summary:
Autologous chondrocyte transplantation (ACT) is a routine technique to regenerate focal cartilage lesions. However, patients with osteoarthritis (OA) are lacking an appropriate long-lasting treatment alternative, partly since it is not known if chondrocytes from OA patients have the same chondrogenic differentiation potential as chondrocytes from donors not affected by OA. Articular chondrocytes from patients with OA undergoing total knee replacement (Mankin Score >3, Ahlbäck Score >2) and from patients undergoing ACT, here referred to as normal donors (ND), were isolated applying protocols used for ACT. Their chondrogenic differentiation potential was evaluated both in high-density pellet and scaffold (Hyaff-11) cultures by histological proteoglycan assessment (Bern Score) and immunohistochemistry for collagen types I and II. Chondrocytes cultured in monolayer and scaffolds were subjected to gene expression profiling using genome-wide oligonucleotide microarrays. Expression data were verified by using quantitative RT-PCR.   Chondrocytes from ND and OA donors demonstrated accumulation of comparable amounts of cartilage matrix components, including sulphated proteoglycans and collagen types I and II. The mRNA expression of cartilage markers (COL2A1, COMP, aggrecan, CRTL1, SOX9) and genes involved in matrix synthesis (biglycan, COL9A2, COL11A1, TIMP4, CILP2) was highly induced in 3D cultures of chondrocytes from both donor groups. Genes associated with hypertrophic or OA cartilage (COL10A1, RUNX2, periostin, ALP, PTHR1, MMP13, COL1A1, COL3A1) were not significantly regulated between the two groups of donors. The expression of 661 genes, including COMP, FN1, and SOX9, were differentially regulated between OA and ND chondrocytes cultured in monolayer. During scaffold culture, the differences diminished between the OA and ND chondrocytes, and only 184 genes were differentially regulated.   Only few genes were differentially expressed between OA and ND chondrocytes in Hyaff-11 culture. The risk of differentiation into hypertrophic cartilage does not seem to be increased for OA chondrocytes. Our findings suggest that the chondrogenic capacity is not significantly affected by OA and OA chondrocytes fulfill the requirements for matrix-associated ACT.

Keywords: time course, cell type comparison, tissue engineered cartilage; osteoarthritis; Hyaff-11 scaffold; human chondrocytes; gene expression profiling; regenerative medicine; differentiation potential

overall_design: Gene expression profiles of monolayer cultures (ML; passage 2) and Hyaff-11 scaffold cultures (3D; 14 days in vitro) of chondrocytes from 3 normal donors (ND; underwent ACT treatment) and 3 donors suffering from Osteoarthritis (OA; underwent knee replacement surgery) were determined. Comparative analyses between 3D and ML cultures (3D vs. ML) were performed to assess differentiation capacity of ND and OA chondrocytes. Furthermore, OA-related differences were determined comparing OA and ND monolayers as well as scaffold cultures (each OA vs. ND).

first: Camilla

last: Karlsson

first: Jochen

last: Ringe

first: Michael

last: Sittinger

first: Anders

last: Lindahl


title: Expression data in WT and Satb1-/- ES cells

status: Public on Sep 01 2009

city: Freiburg

first: Rudolf

last: Engelke

address: Stuebeweg 51

institute: Max Planck Institute of Immunobiology

summary:
Satb1 and Satb2 are regulators of higher order chromatin in T cells and osteoblasts repectively. We were interested if Satb1 and Satb2 play a role in the regulation of gene expression in ES cells.
In this experiment, we compared the transcriptome of wild type and Satb1-/- ES cells. Interestingly Satb1-/- ES cells display an impaired differentiation potential.

overall_design: WT and Satb1-/- ES cells were grown for 3 days in the presence of LIF and selected for Oct4-expression cells by the addition of hygromycin to the culture medium. Previously the cells had been engineered so that they contain a selectable HygroTK reporter in the the Oct4 locus. Total RNA was harvested and used for hybridization.

first: Fabio

last: Savarese

first: Robert

last: Nechanitzky

last: Grosschedl


title: Networking of differentially expressed genes in human MCF7 breast cancer cells resistant to methotrexate

overall_design: Two cell lines are compared, which are MCF7 breast cancer cells sensitive to methotrexate and MCF7 cells resistant to 10e-6M methotrexate. Six samples are provided which correspond to tripicates of each cell line. The samples provided were  analyzed using the specific software GeneSpring GX.


title: Networking of differentially expressed genes in human cancer cell lines resistant to methotrexate

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

overall_design: Refer to individual Series


title: Comparative profiling of mRNA expression in human mesenchymal stem cells derived from adult adipose and lipoma tissues

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
Human mesenchymal stem cells (MSCs) have been isolated from adult adipose tissues, and were shown to have ability to differentiate into multiple mesodermal lineages as well as non-mesodermal lineages. MSC had also been isolated from lipoma, and the lipoma-derived MSCs (LM6) showed very similar stem cell characteristics to adipose-derived MSCs (AM3). However, LM6 cells exhibited a higher cumulative population doubling levels as compared with AM3 cells. The expression profiles of both mRNAs and microRNAs (miRNAs) from AM3 and LM6 cells were compared to find considerable similarities except that miRNAs miR-99a and miR-152 were abundantly expressed in AM3, but absent in LM6 cells. The abundantly differentially expressed genes HAS2, VNN1, SLC16A6 and COL11A1 in LM6 cells were shown to be targets of miRNAs miR-99a and/or miR-152. Several additional genes were also found to be targets of miRNAs miR-99a and miR-152, as well as let-7g, let-7i, miR-199a, mir-134 and miR-374. The highly up-regulated expression of miRNA target genes such as SLC16A6, COL11A1 and TRHDE, as well as several other genes such as sushi domain containing 2, keratin associated proteins and tumor necrosis factor family, may explain the higher proliferation potential in LM6 cells compared with AM3 cells.

Keywords: genetic modification

overall_design: The expression profiles of both mRNAs and miRNAs from the same RNA samples of AM3 and LM6 cells were determined and compared in order to understand the genetic bases for their similarities and differences.

first: Li-Pin

last: Kao

first: Steven

middle: S

last: Li


title: Comparative analysis of gene regulation by the transcription factor PPARα between mouse and human

status: Public on Sep 04 2009

first: Guido

last: Hooiveld

summary:
Studies in mice have shown that PPARα is an important regulator of hepatic lipid metabolism and the acute phase response. However, little information is available on the role of PPARα in human liver. Here we set out to compare the function of PPARα in mouse and human hepatocytes via analysis of target gene regulation. Primary hepatocytes from 6 human and 6 mouse donors were treated with PPARα agonist Wy14643 and gene expression profiling was performed using Affymetrix GeneChips followed by a systems biology analysis. Baseline PPARα expression was similar in human and mouse hepatocytes. Depending on  species and time of exposure, Wy14643 significantly induced the expression of 362-672 genes. Surprisingly minor overlap was observed between the Wy14643-regulated genes from mouse and human, although more substantial overlap was observed at the pathway level. Xenobiotics metabolism and apolipoprotein synthesis were specifically regulated by PPARα in human hepatocytes, whereas glycolysis-gluconeogenesis was regulated specifically in mouse hepatocytes. Most of the genes commonly regulated in mouse and human were involved in lipid metabolism and many represented known PPARα targets, including CPT1A, HMGCS2, FABP, ACSL, and ADFP. Several genes were identified that were specifically induced by PPARα in human (MBL2, ALAS1, CYP1A1, TSKU) or mouse (Fbp2, lgals4, Cd36, Ucp2, Pxmp4). Furthermore, several putative novel PPARα targets were identified that were commonly regulated in both species, including CREB3L3, KLF10, KLF11 and MAP3K8. Our results suggest that PPARα activation has a major impact on gene regulation in human hepatocytes. Importantly, the role of PPARα as master regulator of hepatic lipid metabolism is generally well-conserved between mouse and human. Overall, however, PPARα regulates a mostly divergent set of genes in mouse and human hepatocytes.

This SuperSeries is composed of the SubSeries listed below.

first: Maryam

last: Rakhshandehroo

last: Müller

first: Sander

last: Kersten


title: Gene expression analysis of prostate cancer samples using Affymetrix U133Plus2 array

city: San Diego

first: Yipeng

last: Wang

country: USA

institute: Vaccine Research Institute of San Diego

summary:
Over one million prostate biopsies are performed in the U.S. every year. However, pathology examination is not definitive in a significant percentage of cases due limited diagnostic tumor. We have observed that the microenvironment of prostate tumor cells exhibits numerous differential gene expression changes and have asked whether such information can be used to distinguish “tumor” from “nontumor”. We initially compared expression analysis data (Affymetrix U133plus2) from 18 volunteer biopsy specimens to 17 specimens containing largely tumor-adjacent stroma and identified 964 significant (p_adj < 0.01 and B > 0) expression changes. These genes were filtered to eliminate possible aging-related genes and genes expressed in tumor cells > 10% of the stroma cell expression level leading to 23 candidate genes (28 Affymetrix probe sets). A classifier based on the 28 probe sets was tested on 289 independent cases, including 195 tumor-bearing cases, 99 nontumor cases (normal biopsies, normal autopsies, remote stroma as well as pure tumor adjacent stroma) all with accuracies >85%, sensitivities >90% and specificities >85%.  These results indicate that the prostate cancer microenvironment exhibits reproducible changes useful for categorization as “tumor” and “nontumor”.
For inquires please contact dmercola@uci.edu.

overall_design: Prostate cancer gene expression profiles were studied in this project. Total RNA from 154 prostate sample with various amount of different cell types were hybridized to Affymetrix U133Plus2 array. The percentage of different cell types were determined by a pathologist.


title: Role of Satb1 and Satb2 in embryonic stem cells

summary:
Satb1 and Satb2 are regulators of higher order chromatin in T cells and osteoblasts repectively. We were interested if Satb1 and Satb2 play a role in the regulation of gene expression in ES cells.

This SuperSeries is composed of the SubSeries listed below.


title: Gene expression during neuronal differentiation in two subtypes of SH-SY5Y

city: Yokohama

first: Tadayuki

last: Takeda

state: Kanagawa

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

department: Computatinal and Experimental Systems Biology Group

country: Japan

institute: RIKEN GSC

summary:
Background: SH-SY5Y cells exhibit a neuronal phenotype when treated with all-trans retinoic acid (RA), but the molecular mechanism of activation in the signaling pathway mediated by phosphatidylinositol 3-kinase (PI3K) is not sufficiently understood. To shed new light on the mechanism, we comprehensively compared the gene expression profiles between SK-N-SH cells and two subtypes of SH-SY5Y cells (SH-SY5Y-A and SH-SY5Y-E), each of which showed a different phenotype during RA-mediated differentiation. Results: SH-SY5Y-A cells differentiated in the presence of RA, whereas RA-treated SH-SY5Y-E cells required additional treatment with brain-derived neurotrophic factor (BDNF) for full differentiation. In combination with perturbation using a PI3K inhibitor, LY294002, we identified 386 genes and categorized them into two clusters dependent on the PI3K signaling pathway during RA-mediated differentiation in SH-SY5Y-A cells. Transcriptional regulation of the gene cluster was greatly reduced in SK-N-SH cells or partially impaired in SH-SY5Y-E cells in coincidence with a defect in the neuronal phenotype of these cell lines. Additional stimulation with BDNF induced a set of neural genes which were down-regulated in RA-treated SH-SY5Y-E cells but were abundant in the differentiated SH-SY5Y-A cells. Conclusions: We identified the gene clusters controlled by PI3K- and TRKB-mediated signaling pathways during differentiation in two subtypes of SH-SY5Y cells. TRKB-mediated bypass pathway compensates for the impaired neural functions generated by defects in several signaling pathways including PI3K in SH-SY5Y-E cells. The expression profiling data are useful for further studies to elucidate the signal transduction-transcriptional network including PI3K and/or TRKB.
Keywords: Cell type comparison, time course

overall_design: Human neuroblastomas, SK-N-SH (HTB-11) and SH-SY5Y-A cells (CRL-2266) were obtained from the American Type Culture Collection (ATCC). We also obtained SH-SY5Y-E cells (EC94030304) from the European Collection of Cell Cultures (ECACC). Tissue culture cells were maintained in D-MEM/F12 1:1 mixture supplemented with 15% FBS (Fetal Bovine Serum) and 1% NEAA (Non-essential amino acid) in a 5% CO2 humidified incubator at 37oC. The culture medium was changed twice a week. For the RA-inducible experiment, random culture cells from two clone subtypes of SH-SY5Y and SK-N-SH were seeded in laminin coated culture dishes (BioCoat Laminin Cellware; BD Biosciences, Billerica, MA, USA) for 1 day and then transferred to a medium containing 10 μM of RA in the presence or the absence of LY294002 (10μM) for five days. For BDNF-induced sequential differentiation of the SH-SY5Y-E strain, cells were washed with D-MEM/F12 twice after five days in the presence of RA and then incubated with 50 ng/ml of BDNF in D-MEM/F12 without serum for three days.

first: Yuichiro

last: Nishida

first: Naoki

last: Adati

first: Ritsuko

last: Ozawa

first: Aasami

last: Maeda


title: Analyses of heterogeneous renal allograft biopsies reveal conserved rejection signatures and molecular pathways I, partB

status: Public on Aug 28 2009

city: Kontiolahti

first: Andreas

last: Scherer

address: Pajutie 3A

country: Finland

institute: Spheromics

summary:
Specific early diagnosis of renal allograft rejection is gaining importance in the current trend to minimize and individualize immunosuppression. Gene expression analyses could contribute significantly by defining “molecular Banff” signatures. Several previous studies have applied transcriptomics to distinguish different classes of kidney biopsies. However, the heterogeneity of microarray platforms, clinical samples and data analysis methods complicates the identification of robust signatures for the different types and grades of rejection. To address these issues, a comparative meta-analysis was performed across five different microarray datasets of heterogeneous sample collections from two published clinical datasets and three own datasets including biopsies for clinical indications, protocol biopsies, as well as comparative samples from non-human primates (NHP). This work identified conserved gene expression signatures that can differentiate groups with different histopathological findings in both human and NHP, regardless of the technical platform used. The marker panels comprise genes that clearly support the biological changes known to be involved in allograft rejection. A characteristic dynamic expression change of genes associated with immune and kidney functions was observed across samples with different grades of CAN. In addition, differences between human and NHP rejection were essentially limited to genes reflecting interstitial fibrosis progression. This data set comprises all renal allograft biopsies for clinical indications from patients at Hôpital Tenon, Paris (February 2003 until September 2004) and few respective patients from Hôpital Bicêtre, Paris, Hôpital Pellegrin, Bordeaux, and Hôpital Dupuytren, Limoges, plus control normal kidney samples from Hôpital Tenon, Paris, France (first batch).
We used microarrays to identify different gene expression signatures of renal allograft biopsies that can classify them according to different types of allograft rejection or CAN.
Keywords: disease state analysis

Keywords: Expression profiling by array

overall_design: 16 renal allograft core biopsies for clinical indications with different histopathological diagnoses according to BANFF'97 criteria (additional samples associated with GSE9489)


title: Expression data in WT and ES cells overexpressing Satb2

last: Engelke

summary:
Satb1 and Satb2 are regulators of higher order chromatin in T cells and osteoblasts repectively. We were interested if Satb1 and Satb2 play a role in the regulation of gene expression in ES cells.
ES cells which can inducibly express Satb1 or Satb2 were generated using the tet-ON system. In this experiment, we compared gene expression in uninduced cells to that in cells which had been induced for 24h to express Satb2 ectopcially at very high levels.

overall_design: Cells were cultured, passaged every 3 days. After trypsinisation cells were grown for 1 day in the presence of LIF only, after 1 day a set of cultures was induced by the addition of DOX to the culture medium. Induction took place for 24h, RNA was generated 48h after passaging.

last: Savarese


title: Transcriptional profiling of CD16+ and CD16- peripheral blood monocytes from healthy individuals

status: Public on Aug 31 2009

city: Montreal

first: Petronela

last: ANCUTA

state: Quebec

address: 264, BVD Rene-Levesque East

department: Microbiology and Immunology

country: Canada

institute: Université de Montréal

summary:
Human peripheral blood monocytes (Mo) consist of subsets distinguished by expression of CD16 (FCGRIII) and chemokine receptors. Classical CD16- Mo express CCR2 and migrate in response to CCL2, while a minor CD16+ Mo subset expresses CX3CR1 and migrates into tissues expressing CX3CL1. CD16+ Mo produce pro-inflammatory cytokines and are expanded in certain inflammatory conditions including HIV infection.
To gain insight into the developmental relationship and functions of CD16+ and CD16- Mo, we examined transcriptional profiles of these Mo subsets in peripheral blood from healthy individuals. Of 16,328 expressed genes, 2,759 genes were differentially expressed and 228 and 250 were >2-fold upregulated and downregulated, respectively, in CD16+ compared to CD16- Mo. CD16+ Mo were distinguished by upregulation of dendritic cell (DC) (SIGLEC10, CD43, RARA) and macrophage (MF) (CSF1R/CD115, MafB, CD97, C3aR) markers together with transcripts relevant for DC-T cell interaction (CXCL16, ICAM-2, LFA-1), cell activation (LTB, TNFRSF8, LST1, IFITM1-3, HMOX1, SOD-1, WARS, MGLL), and negative regulation of the cell cycle (CDKN1C, MTSS1), whereas CD16- Mo were distinguished by upregulation of myeloid (CD14, MNDA, TREM1, CD1d, C1qR/CD93) and granulocyte markers (FPR1, GCSFR/CD114, S100A8-9/12). Differential gene expression in CD16+ and CD16- Mo was confirmed by quantitative real time RT-PCR (i.e., CD16, C3AR1, C1QR1, ICAM-2, CSF1R, CSF3R, CDKN1C, TNFRSF1, and LTB) and flow cytometry (i.e., CSF1R, CSF3R, C1QR1, C3AR1, CD1d, CD43, CXCL16, and CX3CR1). Furthermore, increased expression of RARA and KLF2 transcripts in CD16+ Mo coincided with absence of cutaneous lymphocyte associated antigen (CLA) expression, indicating potential imprinting for non-skin homing.
These results suggest that CD16+ and CD16- Mo originate from a common myeloid precursor, with CD16+ Mo having a more MF- and DC-like transcription program suggesting a more advanced stage of differentiation. Distinct transcriptional programs, together with their recruitment into tissues via different mechanisms, also suggest that CD16+ and CD16- Mo give rise to functionally distinct DC and MF in vivo.

overall_design: Total Mo were isolated by negative selection using magnetic immunobeads (Monocyte Isolation Kit II, Miltenyi). CD16+ and CD16- Mo fractions were further isolated using CD16 magnetic immunobeads (Miltenyi). Total RNA from Mo pellets was isolated by Trizol extraction and purified using RNeasy columns (Qiagen). The quality of RNA was assessed by visualization of intact bands corresponding to 18S and 28S rRNA on formaldehyde agarose gels. Total RNA (10 µg) from matched CD16+ and CD16- Mo samples isolated from 4 different healthy donors was quality tested using an Agilent 2100 Bioanalyzer chip, reverse transcribed, and hybridized on the GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix), which includes 54,000 probe sets on a single array (i.e., 47,000 transcripts and variants, including 38,500 well-characterized human genes). Primary data analysis performed using GeneSpring software (Biopolymer core facility, Harvard Medical School) generated Excel spreadsheets with relative gene expression values for the 4 matched CD16+ and CD16- Mo subsets.

last: Ancuta

first: Dana

last: Gabuzda


title: EGR4 is a master gene responsible for fertility in cryptorchidism

city: Basel

first: Edward

middle: James

last: Oakeley

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: RNA was isolated from testicular biopsies of cryptorchid boys. Gene expression profiles for these samples were investigated using Affymetrix arrays

overall_design: Whole testicular tissue was gained from cryptorchid boys aged 10 Months to 4.5 years as well as from controls of identical age. Each biopsy sample was collected for RNA isolation and GeneChip hybridization and was stored in cold 1x phosphate buffered saline (PBS). The tissue was then filtered through 100-nm nylon gauze. Fractions were collected, washed three times in 1x PBS, and snap-frozen in liquid nitrogen prior to storage at -80°C. An aliquot of each fraction was fixed in 1x PBS containing 1% formaldehyde (Polio, France) and 1% fetal calf serum (Eurabbie, France) and analyzed by DNA flow cytometry to determine its relative DNA content. Cell pellets and tissues were sheared in RLT buffer (Qiagen) supplemented with 1% β-Mercaptoethanol and further processed using a Qiashredder (Qiagen). The suspension was centrifuged for 2 min at maximum speed and the clarified lysate was stored at -80°C. Total RNA isolation was performed using RNeasy Mini-Spin columns (Qiagen) according to standard protocols. RNA quality was monitored using RNA Nano 6000 Chips and the 2100 BioAnalyzer (Agilent). cRNA synthesis, human U133 plus 2.0 GeneChip hybridization.

first: Faruk

last: Hadziselimovic

first: Nils

first: Michael

last: Primig

first: Gunthild

last: Krey

first: Philippe

last: Demougin

first: Burkhard

last: Hoecht


title: Expression data from hypoxia exposed normal human esophageal epithelial cells

city: Philadelphia

first: Hiroshi

last: Nakagawa

state: PA

address: 415 Curie Blvd.

department: Gastroenterology Division

institute: University of Pennsylvania

summary: To delineate the role of hypoxia in esophageal epithelial biology, we carried out gene array experiments using a non-transformed immortalized diploid human esophageal cell line, EPC2-hTERT (Mol Cancer Res. 2003;1:729-38). Unlike cancer cell lines, EPC2-hTERT has no genetic alterations at early passages that may affect the cellular response to hypoxia.

overall_design: EPC2-hTERT cells were exposed to moderate (1% O2) hypoxia in experiment 1 (Exp1) or severe (0.2% O2) hypoxia in experiment 2 (Exp2). Normoxia (21% O2) served as a control in both experiments.

first: Anil

last: Rustgi


title: Expression data from esophageal squamous cell carcinoma (ESCC)

summary: We used microarrays to determine global gene expression in primary tumor tissues (ESCC) and matched normal tissues (adjacent normal esophageal mucosa)

overall_design: Paired primary ESCC tumor and normal tissues were compared (n=5).