title: Allergen induced gene expression of airway epithelial cells shows a possible role for TNF-α

status: Public on Oct 01 2007

city: Amsterdam

first: Aram

middle: Ben

last: Vroling

address: meibergdreef 9

institute: AMC

summary:
Response to allergen was studied in bronchial epithelial cell line H292. Cells were cultured and subsequently exposed to House dust mite or vessel (saline)
Microarray data was analysed using bioinformatics and biostastics. We find a strong response to allergen in epithelial cells
Keywords: cellular response to allergen

overall_design: Bronchial epithelial cell line was cultured and stimulated with house dust mite extract or diluent alone. Both conditions were performed in triplicate

middle: B

first: Dirk

last: Duinsbergen

first: Wytske

last: Fokkens

first: Cornelis

middle: M

last: van Drunen


title: The Induction of Senescence-Like Growth Arrest by Diterpene Esters in Solid Tumor Cells

status: Public on Oct 10 2007

city: Brisbane

first: Glen

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

country: Australia

institute: QIMR Berghofer Medical Research Insitute

summary:
We previously identified the induction of growth arrest with phenotypic characteristics of senescence in melanoma cell lines sensitive to diterpene esters, indicating a therapeutic potential.  Here we compared the cytostatic effects of two diterpene esters namely TPA (12-O-tetradecanoylphorbol-13-acetate) and PEP008 (20-O-acetyl-ingenol-3-angelate) in sensitive and resistant cell lines derived from melanoma, breast cancer and colon cancer.  We showed the diterpene esters to induce senescence-like growth arrest in the sensitive cells at 100-1000 ng/ml.  Use of the pan-PKC inhibitor bisindolylmaleimide-l demonstrated that activation of PKC was required for growth arrest.  Full genome expression profiling revealed that pivotal genes involved in DNA synthesis and cell cycle control were down-regulated by treatment in all three sensitive solid tumor models.  At the protein level, prolonged down-regulation of E2F-1 and proliferating cell nuclear antigen (PCNA), sustained expression of p21WAF1/CIP1 and dephosphorylation of retinoblastoma (Rb) occurred in the sensitive cells.  Although activation of extracellular signal-related kinase (ERK) 1/2 by the diterpene esters occurred in both sensitive and resistant cell lines, the HRASLS3 type II tumor suppressor, which appears to have a role in MAPK pathway suppression, was constitutively elevated in the resistant cell lines compared to their sensitive counterparts.  Together, these results demonstrate the ability of the PKC activating drugs TPA and PEP008 to induce growth arrest with characteristics of senescence in solid tumor cell lines derived from a variety of tissue types through a similar mechanism.  PKC-activating diterpene esters may therefore have therapeutic potential in a range of solid tumors.
Keywords: time course

overall_design: We analyzed the transcriptional profiles of the diterpene ester sensitive cell lines MCF7, COLO-205 and SK-MEL-5 following treatment with PEP008 using full genome expression profiling (Affymetrix, U133 Plus 2.0).  Cells were treated for 24 h and 24 h plus 72 h recovery with 1000 ng/ml of the drug, before harvesting RNA for analysis.  From the cell growth assays, all three cell lines demonstrated permanent growth arrest with diterpene ester treatments at the 1000 ng/ml dose.  Mock controls were treated with solvent alone for 24 h.  SK-MEL-5 cells were also treated with 1000 ng/ml TPA for 24 h.

first: Sharon

middle: A

last: Mason

first: Sarah-Jane

last: Cozzi

first: Sandra

middle: J

last: Pavey

first: Peter

middle: G

last: Parsons


title: Analysis of the in vitro transcriptional response of human pharyngeal epithelial cells to adherent pneumococci

city: Nijmegen

first: Hester

last: Bootsma

address: Kapittelweg 29

department: Pediatrics

country: Netherlands

institute: Radboud University Medical Centre

summary:
Infection of the human host by Streptococcus pneumoniae begins with colonization of the nasopharynx, which is mediated by adherence of bacteria to respiratory epithelium. Several studies have indicated an important role for the pneumococcal capsule in this process. Here, we used microarrays to characterize the in vitro transcriptional response of human nasopharyngeal epithelial Detroit 562 cells to adherence of serotype 2-encapsulated strain D39, serotype 19F-encapsulated strain G54, serotype 4-encapsulated strain TIGR4, and their nonencapsulated derivatives (Δcps). In total, 322 genes were found to be upregulated in response to adherent pneumococci. Twenty-two genes were commonly induced, including those encoding several cytokines (e.g., IL-1β, IL-6), chemokines (e.g., IL-8, CXCL1/2), and transcriptional regulators (e.g., FOS), consistent with an innate immune response mediated by Toll-like receptor signaling. Interestingly, 85% of genes was induced specifically by one or more encapsulated strains, suggestive of a capsule-dependent response. Importantly,  purified capsular polysaccharides alone had no effect. Over a third of these loci encoded products predicted to be involved in transcriptional regulation and signal transduction, in particular MAPK signaling pathways. Real-time PCR of a subset of ten genes confirmed microarray data and showed a time-dependent upregulation of especially innate immunity genes. Downregulation of epithelial genes was most pronounced upon adherent D39Δcps, as 68% of the 161 genes identified was only repressed using this nonencapsulated strain. In conclusion, we identified a subset of host genes specifically induced by encapsulated strains during in vitro adherence, and have demonstrated the complexity of interactions occurring during the initial stages of pneumococcal infection.
Keywords: Paired measurements

overall_design: We used three different pneumococcal strains and their isogenic nonencapsulated derivatives (Δcps): serotype 2-encapsulated strain D39, serotype 19F-encapsulated strain G54, and serotype 4-encapsulated strain TIGR4. All experiments were performed in triplicate (3 independent biological replicates) and compared to uninfected control Detroit 562 cells. Bacteria were allowed to adhere to the epithelial cells for 2 hours, after which the transcriptional response of the Detroit cells was analyzed using Affymetrix Human U133 Plus GeneChips. In addition to the 6 strains mentioned above, we included transcriptional analysis of the epithelial cell response to low-dose D39Δcps (giving adherence equivalent to wild-type D39) and purified type 2 capsular polysaccharides.

first: H

first: M

last: Egmont-Petersen

first: P

middle: W

last: Hermans


title: Full-term placenta, smokers and non-smokers

city: Kuopio

first: Markus

last: Storvik

address: University of Eastern Finland

department: Pharmacology

country: Finland

institute: University of Eastern Finland

summary:
Gene expression in placenta from 5 smoking and 5 non-smoking mothers analyzed by Affymetrix Hg133_plus2 microarrays.
Keywords: Toxic response

first: Pasi

last: Huuskonen

first: Mika

last: Reinisalo

first: Paavo

last: Honkakoski

first: Jaana

last: Rysä

first: Jukka

last: Hakkola

first: Markku

last: Pasanen


title: Transcriptional targets of p16INK4A in melanoma

city: Herston

first: Leisl

last: Packer

state: QLD

address: 300 Herston Rd

department: Cancer and Cell Biology

institute: Queensland Institute of Medical Research

summary:
Expression profiles of 17 melanoma cell lines were analysed to identify genes differentially expressed between cell lines harbouring wild-type or mutant p16INK4A. Relevant paper: Pavey et al. (2007). Note: all of these cell lines contained wild-type p14ARF, so that the transcriptional effects of p16INk4A could be determined without interference from p14ARF.
Keywords: Affymetrix Hu133_Plus microarrays

overall_design: The aim of this study was to identify genes which are transcriptional targets of p16INK4A in melanoma.

first: Nicholas

middle: K

last: Hayward

first: Mitchell

middle: S

last: Stark


title: Region specific gene expression profiling along the human epididymis

status: Public on Sep 25 2007

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

summary:
Analysis of the gene expression pattern in the caput, corpus and cauda epididymides of three donors of 26-50 years of age with no medical pathologies that could affect reproductive function. The data generated in this study demonstrate a region specific gene expression pattern along the human epididymis that seems to coincide with the morphological distinctive features of the excurrent duct.
Keywords: Tissue compartements comparison

overall_design: Epididymides were dissected in caput, corpus and cauda epididymidis from three donors: ages 26, 47, and 50 yrs. Expression profiles were generated on Affymetrix GeneChip U133 Plus 2.0 arrays (9 samples total).

first: Veronique

last: Thimon

first: Omedine

last: Koukoui

first: Robert

last: Sullivan


title: Molecular targets of proteasome inhibitor, bortezomib, on ATL cells

status: Public on Oct 09 2007

city: Tokyo

first: Junko

middle: H

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

country: Japan

institute: Tokyo Medical University

summary:
Adult T-cell leukemia (ATL) is a fatal neoplasia derived from HTLV-1 infected T lymphocytes exhibiting constitutive activation of NF-kB.  To elucidate the complex molecular mechanism of anti-tumor effect of the proteasome inhibitor, bortezomib in ATL cells, we attempted to perform gene expression profiling.
Keywords: dose response

overall_design: Four ATL cell lines were cultured with or without bortezomib, then analysed.


title: Differentially expressed genes in HEECs of eutopic endometrium of patients with endometriosis compared with control

status: Public on Oct 31 2007

city: BeiJing

first: Guihua

last: Sha

address: 1 Wangfujing, Shuaifuyuan

country: China

institute: Peking Union Medical College Hospital

summary:
The pathogenesis of endometriosis may result from aberrant angiogenesis that occurs in eutopic endometrium with retrograde menstruation. The difference in gene expression profile between human endometrial endothelial cells (HEECs) from eutopic endometria of patients with and without endometriosis would be determinant that affects the occurrence of endometriosis. To explore this kind of difference, we performed in vitro culture and identified their endothelial origin, as well as observed growth features of HEECs from the two different origins. Finally we identified the difference in gene expression profile when combined suppression subtractive hybridization(SSH) with genechip and confirmed the results by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The HEECs derived from endometriosis exhibited potent survival ability in vitro compared to that from non-endometriosis. We found that gremlin and fibronectin genes were up-regulated in HEECs derived from eutopic endometrium of patients with endometriosis when compared with that from patients without endometriosis. Our study implies that enhanced angiogenic capacity of eutopic HEECs may be an independent determinant in endometriotic aberrant angiogenesis in addition to the interaction of exfoliated endometrium and peritoneal environment elements such as activated macrophages and soluble cytokines.
Keywords: human endometrial endothelial cells (HEECs),endometriosis,differentially expressed genes

overall_design: We analyzed 5 arrays for HEECs derived from eutopic endometrium of patients with endometriosis and 5 arrays for HEECs derived from that of patients without endometriosis


title: Effects of Cimicfuga racemosa (black cohosh) in MCF-7 cells

status: Public on Sep 28 2007

city: Jena

first: Friedemann

last: Gaube

address: Semmelweisstr. 10

department: Pharmacy

country: Germany

institute: Friedrich-Schiller-University Jena

summary:
Extracts from the rhizome of Cimicifuga racemosa (black cohosh) are increasingly popular as herbal alternative to hormone replacement therapy (HRT) for the alleviation of postmenopausal disorders. However, the molecular mode of action and the active principles are presently not clear. Previously published data have been largely contradictory. We, therefore, investigated the effects of a lipophilic Cimicifuga rhizome extract on the ER+ breast cancer MCF-7 cells at transcriptional level in comparision to 17beta-estradiol and the ER antagonist tamoxifen. With the extract 431 genes were regulated more than 1.5 fold. The overall expression pattern differed from those of 17β-estradiol or the estrogen receptor antagonist tamoxifen. We observed an enrichment of genes in an anti-proliferative and apoptosis-sensitizing manner, together with an increase of mRNAs coding for gene products involved in several stress response pathways. Regulated genes of these functional groups were highly overrepresented among all regulated genes. Various transcripts coding for oxidoreductases were induced, as for example the cytochrome P450 family members 1A1 and 1B1. In addition, some transcripts associated with antitumor but also tumor-promoting activity were regulated.
Keywords: treatment with black cohosh

overall_design: MCF-7 cells were treated for 24 h with a lipophilic (dichloromethane) Cimicifuga rhizome extract, 17beta-estradiol, tamoxifen and the solvent control (DMSO 0,1%) in duplicate

first: Stefan

last: Wolfl

first: Larissa

last: Pusch

first: Torsten

middle: C

last: Kroll

first: Matthias

last: Hamburger


title: Resveratrol action on A549 lung cancer cells

status: Public on Sep 15 2007

city: Chicago

first: Lorna

last: Whyte

state: IL

address: 10 W 35th Street

department: Division of Carcinogenesis and Chemoprevention

country: USA

institute: IIT Research Institute

summary:
Resveratrol, a natural phytoestrogen found in red wine and a variety of plants, is reported to have protective effects against lung cancer, however there is very little work directed towards the understanding of the mechanism of action of resveratrol in lung cancer.  In this study we used an experimental approach to understand the biological activity and molecular mechanisms of resveratrol in A549 lung cancer cells. Gene expression profiles were compiled using an oligonucleotide microarray to determine altered expression levels in resveratrol treated cells.
Keywords: Genetic modification of A549 cells in response to resveratrol

overall_design:
A549 cells were treated with resveratrol (25microM) or with ethanol control for 48 h. 4 samples in all were hybridized to the affymetrix chip, one control sample and 3 replicates of the resveratrol treated sample.

Gene ontology-based gene lists are supplied in a supplementary file (Genelists.txt) at the foot of this record.

first: Ranjedra

last: Mehta


title: Death receptor O-glycosylation controls tumor-cell sensitivity to the proapoptotic ligand Apo2L/TRAIL

status: Public on Aug 31 2007

city: South San Francisco

first: Guy

last: Cavet

state: CA

address: 1 DNA Way MS93

institute: Genentech, Inc.

summary:
Apo2L/TRAIL stimulates cancer-cell death through the proapoptotic receptors DR4 and DR5, but the determinants of tumor susceptibility to this ligand are not fully defined. mRNA expression of the peptidyl O-glycosyl transferase GALNT14 correlated with Apo2L/TRAIL sensitivity in pancreatic carcinoma, non-small cell lung carcinoma and melanoma cell lines (P < 0.00009; n=83), and up to 30% of samples from various human malignancies displayed GALNT14 overexpression. RNA interference of GALNT14 reduced cellular Apo2L/TRAIL sensitivity, whereas overexpression increased responsiveness. Biochemical analysis of DR5 identified several ectodomain O-GalNAc-Gal-Sialic acid structures. Sequence comparison predicted conserved extracellular DR4 and DR5 O-glycosylation sites; progressive mutation of the DR5 sites attenuated apoptosis signaling. O-glycosylation promoted ligand-stimulated clustering of DR4 and DR5, which mediated recruitment and activation of the apoptosis-initiating protease caspase-8. These results uncover a novel link between death receptor O-glycosylation and apoptosis signaling, providing potential predictive biomarkers for Apo2L/TRAIL-based cancer therapy.
Keywords: cell type comparison

overall_design: Gene expression for untreated cell lines analyzed. Some cell lines have one replicate profile, some two (Samples with 2 CEL files). Normalized data for replicates was averaged. Analysis involved a regularized t-test to identify genes with expression differences between Apo2L sensitive and resistant lines.

first: Klaus

last: Wagner

first: Elizabeth

last: Punnoose

first: Thomas

last: Januario

first: David

last: Lawrence

last: Pitti

first: Kate

last: Lancaster

first: Dori

last: Lee

first: Melissa

middle: V

last: Goetz

first: Sharon

middle: F

last: Yee

first: Klara

last: Totpal

first: Ling

last: Huw

first: Viswanatham

last: Katta

first: Sarah

last: Hymowitz

first: Lukas

last: Amler

first: Avi

last: Ashkenazi


title: High risk HPV infection effect on expression profile mediated by tumor necrosis factor

status: Public on Aug 25 2007

city: Sao Paulo

first: Lara

last: Termini

state: SP

address: Rua Joao Juliao, 245 - 1th floor

country: Brazil

institute: Ludwig Institute for Cancer Research

summary:
Previous studies have shown that normal and HPV immortalized keratinocytes are sensitive to TNF anti-proliferative effect. Conversely, HPV18-immortalized keratinocytes are resistant to the cytostatic effect mediated by this cytokine. In this study we have compared gene expression patterns in primary cultures of human foreskin epidermal keratinocytes (PHK or NHFK) and HPV16 (HF698) and HPV18(HF18Nco)-immortalized cell lines, and profile the transcriptional changes 3 and 60 hours after TNF treatment.
Keywords: global expression profile, microarray, HPV, TNF

overall_design: In order to determine the effects of HPV infection and TNF treatment on global gene expression, were performed 2 independent experiment for each cell line, including the two periods of treatment with TNF. Furthermore, were performed 2 experiments for each control plate containing the non-treated cells.

first: Luiz

last: Reis

first: Luisa

last: Villa

first: Eduardo

last: Neves

first: Gustavo

last: Esteves

first: Waleska

last: Martins

first: Anna

middle: E

last: Coló

first: Roberto

last: Hirata


title: Primate blood signs of arenavirus hemorrhagic fever

status: Public on Sep 01 2007

city: Blacksburg

first: kommidi

middle: Reddy

last: Chaitanya

state: VA

address: Virginia Tech

institute: VBI

summary:
Lassa fever virus is a zoonotic pathogen that plagues the endemic areas of West Africa.  Rhesus macaques infected with a related arenavirus, LCMV-WE, serve as a model for Lassa-infection of human beings.  Using a dose similar to that expected from a needle-stick, monkeys experience an early pre-viremic phase (day 1-3), a viremic phase with febrile onset (day 4-7), and, like human beings who succumb, they die within two weeks.  Our goal was to monitor changes in gene expression that parallel disease progression in an effort to 1) identify genes with altered expression after infection, 2) identify genes that could discriminate between a virulent and non-virulent infection, and 3) identify genes encoding products that could serve as treatment targets for FDA-approved pharmaceuticals.  Genes related to all three of these categories have been identified and some have been given preliminary validation by quantitative PCR and proteomic studies.  These genes will be valuable candidates for future validation as prognostic biomarkers
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.
Keywords: time course

overall_design:
Rhesus macaques inoculated with a lethal dose of LCMV-WE were used to model human infection with Lassa fever virus (Lukashevich et al 2002, 2003; Rodas et al 2004).  To identify molecular events that occur during the first few days of virus exposure, we monitored gene expression in peripheral blood mononuclear cell (PBMC) samples by microarray analysis.  Approximately 150 samples from 23 different rhesus macaques (Table 1) were hybridized to Affymetrix U133 chips.

Affymetrix U133 arrays cover the entire human genome with approximately 54,000 gene fragments representing approximately 22,000 genes.  The use of these human arrays for macaque transcriptome analysis has been validated by other laboratories (Ace et al, 2004 Wang et al, 2004), i.e. 99.8% of the array elements for which human DNA gave a signal >1.4-fold over background were also >1.4 over background for macaque DNA (Rubins et al, 2004).  LCMV-infected blood samples were compared to uninfected controls and genes with over two-fold change in expression were designated “differentially expressed” (Fig. 1).  Thus, out of 54,000 elements, 8410 (16%) were differentially regulated with a >2-fold change in expression [supplementary Table 1 has these genes in order of the magnitude of their differential expression].

Virus was detectable in these monkeys at day 4 after infection by plaque assay and by RT-PCR of blood cDNA (Djavani et al 2005).  Although virus is replicating in monocytes, endothelial cells, liver, spleen, and peripheral lymphoid organs soon after inoculation (Rai et al, 1997; Lukashevich et al, 2002), virus is not detectable in the circulation for the first three days.  Thus we define the early, pre-viremic stage as days 1-3, and a later viremic stage as days 4-7.  Although the LCMV-Armstrong strain replicated as well in cell culture as LCMV-WE, the LCMV-Arm-infected monkeys did not experience viremia, i.e. viral nucleic acid were detected in tissues but virus loads were not high enough to be detected in the circulation.  The Arm-infected monkeys resisted a lethal challenge with LCMV-WE, further confirming that they had been productively infected (Rodas et al, 2004).  An overview of gene expression in monkeys shows a trend to down-regulate genes at the onset of viremia followed by a sharp increase in up-regulated genes.  Those monkeys that did not experience viremia (Armstrong-infected) showed no dramatic down-regulation trend (Fig. 1).  Over the entire study period of 7 days, the number of down-regulated genes in the WE-infected macaques was significantly more than the number seen in the Arm-infected monkeys (p < 0.005).

first: Mahmoud

last: Djavani

first: Oswald

last: Crasta

first: Juan

last: Zapata

first: Zhangjun

last: Fei

first: Otto

last: Folkerts

first: Bruno

last: Sobral

first: Mark

last: Swindells

first: Rick

last: Fagan

first: Joseph

last: Bryant

first: Harry

last: Davis

first: David

last: Pauza

first: Igor

last: Lukashevich

first: Rasha

last: Hammameieh

first: Marti

last: Jett

first: Maria

last: Salvato


title: Effect of oestrogen treatment on growth of human angiomyolipoma xenograft tumours

status: Public on Sep 19 2007

city: Nottingham

first: Simon

middle: R.

last: Johnson

address: Queen's Medical Centre

department: Therapeutics and Molecular Medicine

country: United Kingdom

institute: University of Nottingham

summary:
SV7tert AML cells were obtained from ATCC and cultured in Dulbecco's modified essential medium (DMEM), glutamine (4mmol) and 10% foetal bovine serum (FBS). Two million SV7tertAML  cells were subcutaneously injected into nude mice either with or without subcutaneous oestrogen pellets (n=4 per group); oestrogen was added using 0.36mg 60 day release oestrogen pellets implanted sub-cutaneously. Mice were housed in pathoflex isolators at 26°C, on 12 hour light / dark cycles. Irradiated RB2 diet and autoclaved water provided ad libertum.
All oestrogen treated mice inoculated with SV7tertAML cells developed subcutaneous tumours which required termination of the animals at six weeks due to tumour load. These primary tumours were removed and fragments placed subcutaneously in further nude mice which went on to develop tumours both in the presence and absence of oestrogen. Mice were weighed weekly and their clinical condition closely monitored by a trained observer. Mice were terminated individually when the tumour cross-sectional area reached 250mm2 or sooner, which has previously been seen to be below the limit of 10% of initial body weight set by the UKCCCR guidelines. Tumours were removed and a portion flash frozen in liquid nitrogen. RNA was extracted from five tumours from oestrogen treated and control animals. Equal quantities of RNA was pooled and quality checked by Agilent Bioanylyser.

Experimenter name = Simon Johnson
Experimenter institute = Queens Medical Centre
Keywords: estrogen treatment, angiomyolipoma xenograft tumors

overall_design: 2 samples were used in this experiment

first: Debbie

last: Clements

first: Henrik

last: Townsend

first: Zoe

last: Emmerson

first: Beatrice

last: Schildknecht


title: Escherichia coli strain 8624 and Escherichia coli strain VS94 with signaling molecules

status: Public on Sep 20 2007

city: Dallas

last: Rasko

state: TX

address: 6000 Harry Hines Blvd. NA6.138

department: Microbiology

institute: University of Texas Southwestern Medical Center at Dallas

summary:
These E. coli strains were grown with various signaling molecules and the expression profiles were determined.
Keywords: addition of quorum and host hormone signals

overall_design:
These E. coli strains were grown with various signaling molecules and the expression profiles were determined using the Affymetrix E. coli 2.0 Array.
Comparisons of the profiles were used to guide further examination using RT-PCR.

first: Melissa

last: Kendall

first: Vanessa

last: Sperandio


title: Domain-Wide Regulation of Gene Expression in the Human Genome

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

summary:
Transcription factor complexes bind to regulatory sequences of genes, providing a system of individual expression regulation. Targets of distinct transcription factors usually map throughout the genome, without clustering. Nevertheless, highly and weakly expressed genes do cluster in separate chromosomal domains with an average size of  80 to 90 genes. We therefore asked whether, besides transcription factors, an additional level of gene expression regulation exists that acts on chromosomal domains. Here we show that identical green fluorescent protein (GFP) reporter constructs integrated at 90 different chromosomal positions determined by sequencing, obtain expression levels that correspond to the activity of the domains of integration. These domains are about 80 genes long and can exert an effect of up to 8-fold on the expression of integrated genes. 3D-FISH shows that active domains of integration have a more open chromatin structure than integration domains with weak activity. These results reveal a novel domain-wide regulatory mechanism that, together with transcription factors, exerts a dual control over gene transcription.
Keywords: HEK293 cells

overall_design: The experiment was performed in duplo, whereby HEK293 cells were grown under standard conditions and RNA was isolated, labelled and hybridized separately. Data from the duplicate arraying experiment were then averaged and further analyzed.

first: Hinco

last: Gierman

first: Mireille

last: Indemans

first: Jan

last: Koster

first: Sandra

last: Goetze

first: Jurgen

last: Seppen

first: Dirk

last: Geerts

first: Roel

last: van Driel

first: Rogier

last: Versteeg


title: Genome-wide screen for promoter methylation in NSCLC identifies novel methylation markers for multiple malignancies

status: Public on Aug 28 2007

first: David

last: Shames

address: 1 DNA Way

department: Oncology Biomarker Development

institute: Genentech Inc

summary:
BACKGROUND: Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The "rules" governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor type-specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype would identify pathways important as therapeutic targets. METHODS AND FINDINGS: In an effort to identify new cancer-specific methylation markers, we employed a high-throughput global expression profiling approach in lung cancer cells. We identified 132 genes that have 5' CpG islands, are induced from undetectable levels by 5-aza-2'-deoxycytidine in multiple non-small cell lung cancer cell lines, and are expressed in immortalized human bronchial epithelial cells. As expected, these genes were also expressed in normal lung, but often not in companion primary lung cancers. Methylation analysis of a subset (45/132) of these promoter regions in primary lung cancer (n = 20) and adjacent nonmalignant tissue (n = 20) showed that 31 genes had acquired methylation in the tumors, but did not show methylation in normal lung or peripheral blood cells. We studied the eight most frequently and specifically methylated genes from our lung cancer dataset in breast cancer (n = 37), colon cancer (n = 24), and prostate cancer (n = 24) along with counterpart nonmalignant tissues. We found that seven loci were frequently methylated in both breast and lung cancers, with four showing extensive methylation in all four epithelial tumors. CONCLUSIONS: By using a systematic biological screen we identified multiple genes that are methylated with high penetrance in primary lung, breast, colon, and prostate cancers. The cross-tumor methylation pattern we observed for these novel markers suggests that we have identified a partial promoter hypermethylation signature for these common malignancies. These data suggest that while tumors in different tissues vary substantially with respect to gene expression, there may be commonalities in their promoter methylation profiles that represent targets for early detection screening or therapeutic intervention.
Keywords: Dose response, cell-type comparison,

overall_design: We compared the gene expression changes HBEC and NSCLC cells before and after treatment with 5-aza-2'deoxycytidine.

first: Luc

last: Girard

first: Boning

last: Gao

first: Mitsuo

last: Sato

first: Cheryl

last: Lewis

first: Narayan

last: Shivapurkar

first: Aixiang

last: Jiang

first: Charles

last: Perou

first: Young

last: Kim

first: Jon

middle: R

last: Pollack

first: Kwon

last: Fong

first: Chi-Leung

last: Lam

first: Maria

last: Wong

first: Yu

last: Shyr

first: Rita

last: Nanda

first: Olufunmilayo

middle: I

last: Olopade

first: William

last: Gerald

last: Euhus

first: Jerry

last: Shay

first: Adi

last: Gazdar

first: John

middle: D

last: Minna


title: Long Oligonucleotide Microarrays for African Green Monkey Gene Expression Profile Analysis

city: Paris cedex 15

first: Beatrice

last: JACQUELIN

address: 25 rue du Docteur Roux

department: Virologie

country: France

institute: Institut Pasteur

summary:
Nonhuman primates including African Green Monkey (AGM) are important models for biomedical research. The information on monkey genomes is still limited and no versatile gene expression screening tool is available. We tested human whole genome microarrays for cross-species reactivity with AGM transcripts using both long oligonucleotide arrays (60-mer probes, Applied Biosystems-ABI) and short oligonucleotide arrays (25-mer, Affymetrix). Using the long oligonucleotide arrays we detected four times more AGM transcripts than with the short oligonucleotide technology. The number of detected transcripts was comparable to that detected using human RNA, with 87% of the detected genes being shared between both species. The specificity of the signals obtained with the long oligonucleotide arrays was determined by analyzing the transcriptome of concanavalin A activated CD4+ T cells versus non-activated T cells of two monkey species AGM and macaque. For both species, the genes showing the most significant changes in expression, such as IL-2R, were those known to be also regulated in human CD4+ T cell activation. Finally, tissue-specificity of the signals was established by comparing the transcription profiles of AGM brain and tonsil cells. In conclusion, the ABI human microarray platform provides a highly valuable tool for the assessment of AGM gene expression profiles.
Keywords: Defining a microarray platform to study the AGM transcriptome by cross-species and cross-platform comparison

sample_organism:
Macaca mulatta
Homo sapiens
Chlorocebus sabaeus

overall_design:
5 healthy chinese rhesus macaques and 5 AGM (sabaeus, Senegal) were used in this study. PBMC were isolated from blood samples by Ficoll procedures and activated or not for 48H with concanavaline A. CD4+ cells were then sorted on miltenyi specific column. Total RNA from ConA
activated CD4+ cells from each animal was extracted, pooled to those of the same species and analyzed on both the ABI Human Whole Genome Arrays and Affymetrix U133 Plus 2.0 Arrays with two technical replicates per species. With the Affymetrix array protocol, 4μg of total RNA were used as starting material while 800ng were used with the ABI protocol to generate sufficient hybridization signal. For cross-species comparisons of the ABI platform, total RNA from non activated CD4+ cells isolated from macaques, AGM and human were analyzed. In order to determine optimal quantities of AGM RNA to use on the ABI platform, we tested 4 distinct RNA input quantities (0.5, 0.8, 1.2, and 2µg of RNA). We used a pool of total RNA from unstimulated CD4+ T cells isolated from 4 AGM. Tonsil and brain samples were obtained from chronically SIV-infected AGM. Total RNA was analyzed on ABI microarrays.

AGM_stim_1_AB and _2_AB stand for two ABI microarray technical replicates which were hybridized with RNA amplified from 0.8µg of AGM total RNA extracted from ConA activated CD4+ T cells as starting material.
AGM_stim_1_Affy and _2_Affy stand for two Affymetrix microarray technical replicates which were hybridized with RNA amplified from 4µg of AGM total RNA extracted from ConA activated CD4+ T cells as starting material.
The ABI microarrays AGM_unstim_1, _2, _3 and _4 were hybridized with RNA amplified from respectively, 0.5, 0.8, 1.2, and 2µg of AGM total RNA extracted from unstimulated CD4+ T cells.
MAC_stim_1 and _2 stand for two ABI microarray technical replicates which were hybridized with RNA amplified from 1.2µg of macaque total RNA extracted from ConA activated CD4+ T cells.
MAC_unstim_1 was hybridized with RNA amplified from 1.2µg of macaque total RNA extracted from unstimulated CD4+ T cells.
HUM_unstim_1 was hybridized with RNA amplified from 0.8µg of human total RNA extracted from unstimulated CD4+ T cells.
The ABI microarrays AGM_tonsil and _brain were hybridized with RNA amplified from 0.8µg of AGM total RNA extracted from tonsil and brain tissues, respectively.

last: Jacquelin

first: Veronique

last: Mayau

first: Guillaume

last: Brysbaert

last: Regnault

first: Ousmane

middle: M

last: Diop

first: Fernando

last: Arenzana-Seisdedos

first: Lars

last: Rogge

first: Jean-Yves

last: Coppee

first: Françoise

last: Barré-Sinoussi

first: Arndt

last: Benecke

first: Michaela

last: Müller-Trutwin


title: Gene expression analysis of  gamma-secretase inhibitor-sensitive and -resistant T-ALL cell lines

city: New York

first: Adolfo

middle: A

last: Ferrando

state: NY

address: 1130 St Nicholas Ave Irving Cancer Research Center 5-505A

department: Institute for Cancer Genetics

institute: Columbia University

summary:
Gain-of-function mutations in NOTCH1 are common in T-cell lymphoblastic leukemias making this receptor a promising target for drugs such as gamma-secretase inhibitors, which block a proteolytic cleavage required for NOTCH1 activation. However, the enthusiasm for these therapies has been tempered by tumor resistance and the paucity of information on the oncogenic programs regulated by oncogenic NOTCH1. Here we show that NOTCH1 regulates PTEN expression and the activity of the PI3K-AKT signaling pathway in normal and leukemic T cells.  Notch signaling and the PI3K-AKT pathway synergize in vivo in a Drosophila model of Notch-induced tumorigenesis, and mutational loss of PTEN is associated with increased glycolysis and resistance to NOTCH1 inhibition in human T-ALL. These findings identify the transcriptional regulation of PTEN and the control of cellular metabolism as key elements of the oncogenic program activated by NOTCH1 and provide the basis for the design of new therapeutic strategies for T-ALL.
Keywords: Drug sensitivity comparison

overall_design: Samples for microarray analysis were prepared and hybridized in Affymetrix Human U133 Plus 2.0 arrays according to the manufacturer’s instructions and as previously described. RNA was extracted from duplicate cultures of GSI-sensitive (ALL-SIL, CUTLL1, DND41, HPB-ALL, KOPTK1) and GSI-resistant (CCRF-CEM, MOLT3, P12 ICHIKAWA, PF382 and RPMI8402) T-ALL cell lines treated for 24 h with vehicle (DMSO) or 500 nM CompE.  Interarray intensity differences were normalized with Dchip

first: Teresa

last: Palomero

first: MariaLuisa

last: Sulis

first: Maria

last: Cortina

first: Pedro

middle: J

last: Real

first: Kelly

last: Barnes

last: Ciofani

first: Esther

last: Caparros

first: Jean

last: Buteau

first: Kristy

last: Brown

first: Sherrie

last: Perkins

first: Govind

last: Bhagat

first: Archana

last: Mishra

first: Mireia

last: Castillo

first: Giuseppe

last: Basso

first: Ramon

last: Parsons

first: Carlos

last: CordonCardo

first: JuanCarlos

last: Zúñiga-Pflücker

last: Dominguez


title: Hypoxia and lymphatic endothelial cells

status: Public on Aug 23 2007

city: Pamplona

first: Ana

last: Rouzaut

state: Navarra

address: Pio XII 55

department: Oncology

country: Spain

institute: University of Navarra/CIMA

summary:
Lymphatic endothelial cells were grown under normoxia, hypoxia (1% 0xygen) and conditioned medio from NSLCN growth under normoxia or hypoxia. Gene expression was measured and comparition between samples performed
Keywords: Comparative genomic hybridization

overall_design: RNA from different donnors where extracted, pooled to avoid interindividual differences and labelled. Microarrays hybridized and analyzed

first: Juan

last: Martinez Irujo

first: Marta

last: Irigoyen

first: Elena

last: Anso


title: Expression data from LNCaP cell line

city: Houston

first: Wei

last: Li

address: one baylor plaza, MS BCM305

institute: Baylor College of Medicine

summary:
Androgen receptor (AR) is a ligand-dependent transcription factor that plays a key role in the onset and progression of prostate cancer. Surprisingly little is known of AR binding sites and collaborating transcription factors in the human genome. Here we have identified the DNA sequence motifs that are significantly enriched within the authentic 90 AR target regions found on chromosomes 21 and 22 in human prostate cancer cells by combining chromatin immunoprecipitation for AR with chromosome-scale tiled oligonucleotide microarrays. By integrating the DNA sequence motif data with the gene expression profiles from human prostate cancers we identified the transcription factors that recognize each of these motifs. These factors form complexes with AR, bind to specific AR target regions and govern androgen-dependent transcription. Together with AR these collaborating transcription factors form a regulatory network that directs prostate cancer growth and survival and identify potential new opportunities for therapeutic intervention.
Keywords: time course

overall_design: The RNA samples are extracted from DHT 0, 4h and 16h treated LNCaP cells by using a RNeasy kit (Qiagen). The final RNAs submitted to Dana-Farber Cancer Institute (DFCI) Microarray Core Facility are all at 1.5ug/ul, A260/A280=2.1.

first: Qianben

last: Wang


title: Kaposi's Sarcoma-associated Herpesvirus Encodes an Ortholog of miR-155

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary:
MicroRNAs are small, non-coding RNAs that post-transcriptionally regulate gene expression by binding to 3’UTRs of target mRNAs. Kaposi’s sarcoma-associated herpesvirus (KSHV), a virus linked to malignancies including primary effusion lymphoma (PEL), encodes 12 miRNA genes, but only a few regulatory targets are known. We found that KSHV-miR-K12-11 shares 100% seed-sequence homology with hsa-miR-155, a miRNA frequently found up-regulated in lymphomas and critically important for B cell development. Based on this seed-sequence homology, we hypothesized that both miRNAs regulate a common set of target genes and as a result, could have similar biological activities.
Examination of five PEL lines showed that PELs do not express miR-155, but do express high levels of miR-K12-11. Bioinformatics tools predicted the transcriptional repressor BACH-1 to be targeted by both miRNAs and ectopic expression of either miR-155 or miR-K12-11 inhibited a BACH-1 3'UTR containing reporter. . Furthermore, BACH-1 protein levels are low in cells expressing either miRNA. Gene expression profiling of miRNA-expressing stable cell lines revealed 66 genes that were commonly down-regulated. For select genes, miRNA targeting was confirmed by reporter assays.
Thus, based on our in silico predictions, reporter assays, and expression profiling data, miR-K12-11 and miR-155 regulate a common set of cellular targets. Given the role of miR-155 during B cell maturation, we speculate that miR-K12-11 may contribute to the distinct developmental phenotype of PEL cells, which are blocked in a late stage of B cell development. Together, these findings indicate that KSHV miR-K12-11 is an ortholog of miR-155.
Keywords: comparison, experiemental versus control

overall_design: 12 samples, 4 experiemental (miR-155 ), 4 experimental (miR-K12-11) and 4 reference controls (pCDNA3.1)

first: Rebecca

last: Skalsky

first: Mark

last: Samols

first: Karlie

middle: B

last: Plaisance

first: Isaac

middle: W

last: Boss

first: Alberto

last: Riva

first: M

first: Henry

last: Baker

first: Rolf

last: Renne


title: Bone-marrow-derived mesenchymal stem cells promote breast cancer metastasis

status: Public on Oct 05 2007

city: Boston

first: Andrea

last: Richardson

state: MA

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

summary:
tumor microenviroment facilitates metastatic spread by eliciting reversible changes in the phenotypes of cancer cells
Keywords: expression analysis of breast tumor samples

overall_design: expression array of stromal samples prepared from 15 normal/DCIS and 7 IDC tumor specimans

first: A


title: Global transcriptional machinery engineering in E. coli in the presence and absence of ethanol

status: Public on Sep 23 2007

city: Cambridge

first: Joel

last: Moxley

address: 77 Massachusettes Ave

institute: MIT

summary:
We measured transcriptional changes in an effort to understand mechanisms of action resulting from the introduction of global transcriptional machinery engineering in E. coli in the presence and absence of ethanol.
Keywords: repeat

overall_design: We explored two types of experimental factors: genetic variation (mutated transcriptional machinery) and environmental variation (ethanol concentration).

first: Hal

middle: S

last: Alper

first: Greg

last: Stephanopoulos


title: Gene expression analysis of hormone treated MCF7 breast cancer cells in the presence or absence of cycloheximide

city: Montreal

first: David

last: Laperriere

state: QC

address: 2950, chemin de Polytechnique

department: IRIC - Institut de recherche en immunologie et en cancerologie

institute: Université de Montréal

summary:
Estrogen receptors (ERs), which mediate the proliferative action of estrogens in breast cancer cells, are ligand-dependent transcription factors that regulate expression of their primary target genes through several mechanisms. In addition to direct binding to cognate DNA sequences, ERs can be recruited to DNA through other transcription factors (tethering), or affect gene transcription through modulation of signaling cascades by non-genomic mechanisms of action. To better characterize the mechanisms of gene regulation by estrogens, we have identified more than 700 putative primary and more than 1500 putative secondary target genes of estradiol in MCF7 cells through microarray analysis performed in the presence or absence of the translation inhibitor cycloheximide.
Keywords: drug treatment

overall_design: RNA samples were collected 24 h after treatment of MCF7 cells with vehicle or 17{beta}-estradiol (25 nM). Cells were pre-treated 1 h before E2 stimulation with cycloheximide (CHX, 10 microg/ml). Microarray analysis was performed with four replicates for each condition.

first: Véronique

last: Bourdeau

first: Julie

last: Deschênes

last: Laperrière

first: John

last: White

first: Sylvie

last: Mader


title: Neutrophil and PBMC gene expression data from Job's Syndrome

status: Public on Sep 18 2007

city: Hamilton

first: Addie

last: Whitney

state: MT

address: 903 S 4th St

department: LHBP

institute: NIH/NIAID/RML

summary:
Hyper IgE Recurrent Infection Syndrome (HIES or Job’s syndrome), is a rare disorder of immunity and connective tissue, typically manifest with boils, cyst-forming pneumonias, and extremely elevated serum IgE as well as retained primary dentition and bone abnormalities. Inheritance can be autosomal dominant.
In order to identify a specific defect or gene of interest, we performed microarray expression analysis on samples from patients with Job's syndrome and from healthy control subjects.
Keywords: time course

overall_design: Polymorphonuclear leukocytes (PMNs) and peripheral blood mononuclear cells (PBMCs) were isolated from whole blood from patients with Job's syndrome and healthy control subjects.  PMNs and PBMCs were incubated with or without IgG- and C3bi-coated latex beads for 3 and 6 hours.

first: S

last: Holland

first: F

last: DeLeo

middle: P

last: Hsu

first: H

middle: Z

last: Elloumi

first: G

last: Uzel

first: N

last: Brodsky

last: Freeman

last: Demidowich

first: J

last: Davis

first: Maria

middle: L

last: Turner

first: Harry

last: Malech

last: Gallin

last: Kobayashi

last: Voyich

first: James

last: Musser

first: Christina

last: Woellner

last: Schaffer

last: Puck

first: B

last: Grimbacher


title: Leukotriene D4 induces gene expression in human monocytes through cysteinyl leukotriene type I receptor.

status: Public on Aug 30 2007

city: Bethesda

first: Grzegorz

last: Woszczek

state: MD

address: 9000 Rockville Pike

department: Critical Care Medicine Department

institute: NIH

summary:
Background: Cysteinyl leukotrienes (cysLTs) are important mediators of innate immune responsiveness and chronic inflammatory diseases. CysLTs acting through cysteinyl leukotriene receptors may influence the migration and activity of cells such as eosinophils, monocytes and dendritic cells.
Objective: To determine the gene expression signature of human monocytes in response to cysLTs and to elucidate the signaling pathways involved in monocyte activation.
Methods: Gene expression was analyzed using oligonucleotide microarrays. Responsiveness to cysLTs was assessed by real-time PCR, calcium flux, kinase activation and chemotaxis assays.
Results: Cysteinyl leukotriene type I receptor (CysLTR1) transcript 1 is predominantly expressed in human monocytes and cysLTs signal through CysLTR1 in these cells. Several immediate-early genes, including early growth response (Egr) -2, 3, FosB, activating transcription factor 3 and nuclear receptor subfamily 4 were significantly induced by LTD4. This effect was mediated by CysLTR1 coupled to Gαi/o, activation of phospholipase C, and inositol-1,4,5-triphosphate (IP3) and store operated calcium channels. LTD4 induced p38 MAP kinase phosphorylation, a pathway also involved in the regulation of immediate-early genes expression in monocytes. LTD4 stimulated monocyte chemotactic activity that was fully blocked by a selective CysLTR1 inhibitor MK571 and pertussis toxin, suggesting that CysLTR1 coupled to Gαi/o is a dominant functional pathway in human monocytes.
Conclusion: Our data show that cysLTs acting through CysLTR1 can significantly influence the activation and migration of human monocytes and that these effects can be fully inhibited by CysLTR1 antagonists.
Clinical implications: Antileukotriene therapies are likely to significantly block the proinflammatory functions of human monocytes.
Keywords: monocytes stimulated with LTD4

overall_design: 4 control sample, 4 LTD4 stimulated samples


title: miRNA34 expression in SW480 cells

status: Public on Aug 20 2007

city: Ann Arbor

first: Rork

last: Kuick

state: MI

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

institute: University of Michigan

summary:
SW480 were stably transfected with an episomal plasmid expressing GFP and miRNA34 from a bidirectional doxycyclin regulatable promoter (Bornkamm et al Nucleic Acids Res. 2005 Sep 7;33(16)). Polyclonal cell lines were obtained by selection with Hygromycin at 350ug/ml for 10 days. The cell llnes identified as GFP only express GFP, whereas the cell lines identified as miRNA34a express both GFP and miRNA34 under doxycyclin control. For the present experiment, cells were treated with 1ug/ml Docycyclin for 72h. Cells were harvested and total RNA was isolated using Trizol (Invitrogen). After RNA cleanup (RNeasy, Qiagen) Affymetrix 133 Plus 2.0 micorarrays were hybridized using standard techniques.
Keywords: Cell line transfection

overall_design:
2 cell lines with transfected miRNA34a with doxycyclin treatment, 2 cell lines with miRNA34a but without doxycyclin treatment, 2 cell lines with transfected GFP with doxycyclin treatment, and 2 cell lines with GFP but without doxycylin treatment.  One array for per sample.

The log-transformed probe-set values and the results of the statistical analysis for each probe-set, and the associated README file, are included as Supplementary files.

first: Guido

middle: T

last: Bommer

first: Ying

last: Feng

first: Andrew

last: Kacsorowski

first: Isabelle

last: Gerin

first: Thomas

last: Giordano

first: Ormond

last: MacDougald

first: Kathleen

last: Cho

first: Eric

last: Fearon


title: K562 Gene Expression Control vs 1R-Chl treatments

status: Public on Aug 22 2007

city: La Jolla

first: C. James

last: Chou

address: 10550 N. Torrey Pines Rd. MB-27

department: Molecular Biology

institute: The Scripps Research Institute

summary:
To determine whether the polyamide-Chl conjugate 1R-Chl would cause similar changes in global gene expression in K562 cells, affymetrix gene chip analysis was performed using 1R-Chl.  Through class comparison analysis, 1R-Chl affected the levels of transcription and genes of interest were determined.
Keywords: Treatment response

overall_design: K562 cells were incubated with 1R-Chl (at 250 nM) or in the absence of polyamide, in triplicate for 24 h before RNA purification and microarray analysis at The Scripps Research Institute microarray facility.  Affymetrix U133A Plus 2.0 GeneChips were hybridized in groups of three for each of the two groups.  The Affymetrix probe set data were imported into BRB Arraytools (3.5.0 Beta 2), selecting the U133 chips used in the experiment and leaving all filters off.

first: Joel

last: Gottesfeld

first: Peter

last: Dervan

middle: C

first: Michelle

last: Farkas

first: Sherry

last: Tsai

first: David

last: Alvarez


title: Genomic analyses of TF binding, histone acetylation and gene expression reveal classes of E2-regulated promoters

status: Public on Oct 19 2007

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary:
To explore the global mechanisms of estrogen-regulated transcription, we used chromatin immunoprecipitation coupled with DNA microarrays to determine the localization of RNA polymerase II (Pol II), estrogen receptor alpha (ERalpha), steroid receptor coactivator proteins (SRC), and acetylated histones H3/H4 (AcH) at estrogen-regulated promoters in MCF-7 cells with or without estradiol (E2) treatment. In addition, we correlated factor occupancy with gene expression and the presence of transcription factor binding elements. Using this integrative approach, we defined a set of 58 direct E2 target genes based on E2-regulated Pol II occupancy and classified their promoters based on factor binding, histone modification, and transcriptional output. Many of these direct E2 target genes exhibit interesting modes of regulation and biological activities, some of which may be relevant to the onset and proliferation of breast cancers. Our studies indicate that about one-third of these direct E2 target genes contain promoter-proximal ERalpha-binding sites, which is considerably more than previous estimates. Some of these genes represent possible novel targets for regulation through the ERalpha/AP-1 tethering pathway. Our studies have also revealed several previously uncharacterized global features of E2-regulated gene expression, including strong positive correlations between Pol II occupancy and AcH levels, as well as between the E2-dependent recruitment of ERalpha and SRC at the promoters of E2-stimulated genes. Furthermore, our studies have revealed new mechanistic insights into E2-regulated gene expression, including the absence of SRC binding at E2-repressed genes and the presence of constitutively bound, promoter-proximally paused Pol IIs at some E2-regulated promoters. These mechanistic insights are likely to be relevant for understanding gene regulation by a wide variety of nuclear receptors.
Keywords: MCF7 cells, E2, Estrogen, RNA, ER, RNA Polymerase II, SRC, Acetylated histones, ChIP-chip

overall_design: See Materials and Methods in the associated publication for more details

first: Miltiadis

last: Kininis

first: Benjamin

last: Chen

first: Adam

middle: G

last: Diehl

first: Gary

last: Isaacs

first: Tong

last: Zhang

last: Siepel

last: Clark

first: William


title: PPARg regulated gene expression in human dendritic cells

city: Debrecen

first: Istvan

last: Szatmari

address: Egyetem tér 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary:
In order to gain insights into how PPARg regulates different facets of dendritic cell (DC) differentiation, we sought to identify PPARg regulated genes and gene networks in monocyte-derived dendritic cells using global gene expression profiling. We employed an exogenous ligand activation approach using a selective PPARg ligand (rosiglitazone abbreviated as RSG). In addition, we have defined culture conditions in which human serum (HS) induces PPARg activation via a yet uncharacterized endogenous mechanism. We also compared the gene expression profile of developing dendritic cells obtained from patients harboring dominant negative mutations of the PPARg receptor (C114R and C131Y).
Keywords: ligand response

overall_design: Monocytes were cultured for 6, 24 hours or 5 days with 500 U/ml IL-4 and 800 U/ml GM-CSF; cytokine treatment was repeated at day 3. Cells were obtained from 12 healthy individuals (6 biological replicates; the 6 and 24 hours samples were obtained from a single individual but the 5 days samples from a different one). Ligands were added at the beginning of differentiation. The 6 and 24 hours cells were treated with vehicle (DC) or 1 uM rosiglitazone (DC RSG), in the case of 5 day cultured cells 2.5 uM RSG was used. Cells were cultured in RPMI plus 10% FBS, in the case of DC4-DC6 cells were also cultured in human AB serum (DC HS). Finally we also obtained cells from patients harboring point mutations of the PPARg receptor (C114R and C131Y)

first: Tibor

last: Nagy

first: Maura

last: Agostini

first: Krishna

last: Chatterjee

first: Laszlo


title: Host Susceptibility to H. ducreyi Infection is Associated with Unique Transcript Profiles in Tissue and Dendritic Cells

status: Public on Sep 13 2007

city: Indianapolis

first: Stanley

middle: M.

last: Spinola

state: IN

address: 545 Barnhill Dr.

department: Infectious Diseases

institute: Indiana University School of Medicine

summary:
Comparison of gene expression from subjects who resolved or formed pustules to H.ducreyi.
In human inoculation experiments, the cutaneous immune response to Haemophilus ducreyi consists of serum, PMN, macrophages, T cells and myeloid DC.  In reinfection experiments, some subjects form pustules twice (PP group) or resolve infection twice (RR group).  Although pustule formation is associated with serum resistance and phagocytic failure, there are no differences in the ability of isolated phagocytes or serum obtained from PP and RR subjects to ingest or kill H. ducreyi.  To identify the basis for differential host susceptibility to H. ducreyi, we used microarrays to profile gene expression in infected and uninfected tissue and monocyte-derived DC obtained from PP and RR subjects.  In infected tissue, both groups had a core response to H. ducreyi.  Many additional transcripts that signify active immune function were upregulated exclusively in RR tissue, while PP tissue exclusively contained differentially regulated transcripts consistent with immune dysregulation.  The core response of infected DC from both groups was typical of a DC1 response.  RR DC exclusively expressed many additional transcripts indicative of DC1 function, while PP DC uniquely expressed differentially regulated transcripts characteristic of both DC1 and DCreg.  The data suggest that DC from PP and RR subjects are prewired to respond differentially to H. ducreyi.
Keywords: comparison of two phenotypes, resolver and pustule former

overall_design: Six healthy adult volunteers (5 females, 1 male, 36 ± 13 yrs, mean age ± SD) who had been infected with H. ducreyi twice were inoculated a third time.  Each volunteer was inoculated at 3 sites on the upper arm with live H. ducreyi 35000HP (a human passaged isolate of strain 35000) and at 1 site with sterile PBS.  Forty-eight hours after inoculation, lesion size was measured and RNA was isolated from the infected site that had the largest diameter.  RNA was also obtained from the PBS control site (uninfected site).  We obtained peripheral blood 6 to 12 months after inoculation of the 6th subject and derived myeloid DC in vitro.  In brief, CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN).  The cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry.  The experiment was done in pairs so that DC from 1 RR subject were exposed to the same inoculum as DC from 1 PP subject.  DC were incubated with nonopsonized H. ducreyi for 90 minutes at an MOI of 30:1.  The DC were washed to remove non-associated bacteria, and incubated an additional 22.5 hours.  Cells were collected and used for microarray analysis.  Supernatants were collected and analyzed for cytokines using the Human Th1/Th2 II Cytometric Bead Array Kit per manufacturer’s instructions (BD Biosciences).

first: Tricia

last: Humphreys

first: Diane

last: Janowicz

first: Kate

last: Fortney

first: Xiaoman

last: Li

first: Lang

first: Barry

last: Katz

last: Wilkes

first: Howard

last: Edenberg


title: Effects of EPO and EST on erythroid maturation

first: Jeffery

middle: Lynn

last: Miller

address: 10 Center Drive

department: Molecular Medicine Branch

institute: NIH/NIDDK

summary: Transcriptional profiles of human CD34+ cells cultured in EPO and EST conditions.

overall_design: After obtaining informed consent, human CD34+ cells were isolated in high purity from the peripheral blood of normal human volunteers. The cells were cultured at a concentration of 104 - 105 cells/mL in medium supplemented with 4 U/mL Erythropoietin (EPO) versus  4 U/mL Erythropoietin + 50 ng/mL Stem Cell Factor + 1.25 ng/mL Transforming Growth Factor Beta (EST) as described previously. Cells were sampled on culture Day 7, culture Day 14, or both culture days and enumerated using an electronic cell counter (Coulter, Hialeah, FL). Adult and fetal hemoglobin was analysed by HPLC. RNA was extracted using QIAshredder and Rneasy Minikit.

first: Natarajan

middle: V

last: Bhanu

first: Toshihiko

last: Tanno

first: Terry

last: Lee


title: Dickkopf-1 is down-regulated by MYCN and inhibits neuroblastoma cell proliferation

status: Public on Aug 24 2007

city: Amsterdam

first: Richard

last: Volckmann

address: van der Boechorststraat 6a

institute: msterdam UMC and University of Amsterdam

summary:
Neuroblastomas are tumors of the developing peripheral sympathetic nervous system, which originates from the neural crest. Twenty percent of neuroblastomas show amplification of the MYCN oncogene, which correlates with poor prognosis. The MYCN transcription factor can activate and repress gene expression. To broaden our insight in the spectrum of genes down-regulated by MYCN, we generated gene expression profiles of the neuroblastoma cell lines SHEP-21N and SKNAS-NmycER, in which MYCN activity can be regulated. In this study, we show that MYCN suppresses the expression of Dickkopf-1 (DKK1) in both cell lines. DKK1 is a potent inhibitor of the wnt/beta-catenin signalling cascade, which is known to function in neural crest cell migration. We generated a DKK1 inducible cell line, IMR32-DKK1, which showed impaired proliferation upon DKK1 expression. Surprisingly, DKK1 expression did not inhibit the canonical wnt/beta-catenin signalling, suggesting a role of DKK1 in an alternative route of the wnt pathway. Gene expression profiling of two IMR32-DKK1 clones showed that only a few genes, amongst which SYNPO2, were up-regulated by DKK1. SYNPO2 encodes an actin-binding protein and was previously found to inhibit proliferation and invasiveness of prostate cancer cells. These results suggest that MYCN might stimulate cell proliferation by inhibiting the expression of DKK1. DKK1 might exert part of its growth suppressive effect by induction of SYNPO2 expression.
Keywords: DKK1, MYCN, neuroblastoma, Dickkopf

overall_design: Single time course experiment, including 4 time points

first: Arjen

last: Koppen

first: Rachida

last: Ait-Aissa

first: Saskia

last: Hopman

first: Jan

last: Koster

first: Franciska

last: Haneveld

first: Rogier

last: Versteeg

first: Linda

last: Valentijn


title: Effects of TGF-β1 on expression profile of human pulp and odontoblasts

status: Public on Aug 10 2007

city: Oulu

first: Virve

last: Pääkkönen

address: Aapistie 3

department: Institute of Dentistry

institute: University of Oulu

summary:
Transforming growth factor beta 1 (TGF-β1) is the most extensively studied growth factor in dentin-pulp complex, with pleiotropic effects on pulp response and healing. Our main objective was to analyze the expression profile of pulp tissue and odontoblasts, and the effects of TGF-β1 on these profiles in cultured human pulp and odontoblasts with a specific interest in the anti- and pro-inflammatory cytokines.
Keywords: Response to TGF-β1 treatment

overall_design: Pulp tissues and odontoblasts were cultured for different time periods, and microarray was performed to both cultured and native samples to detect the effects of TGF-β1. Expression of various interleukins (IL) were confirmed by RT-PCR, and in +/- TGF-β1 treated pulps also by antibody array.

first: Jussi

last: Vuoristo

first: Tuula

last: Salo

first: Leo

last: Tjäderhane


title: human peripheral blood derived monocytes, LPS stimulation time-series

city: Seattle

first: Jared

last: Roach

state: WA

address: 1441 North 34th St

institute: Institute for Systems Biology

summary:
To evaluate gene expression in human peripheral blood derived monocytes over the course of an LPS stimulation time-series.
Keywords: time course

overall_design: Blood samples from three individuals, each sample split into separate culture for each timepoint (0, 2, 4, 8, and 24 hours). RNA prepared from all, and analyzed with Bioanalyzer. Two best RNA samples from each timepoint analyzed by hybridization to a chip.


title: Hematopoietic stem cell mobilization with G-CSF (gene expression profiling)

status: Public on Aug 09 2007

city: Tampa

first: Matthew

last: Buzzeo

address: 12901 Bruce B. Downs Blvd

institute: University of South Florida College of Medicine

summary:
Granulocyte-colony stimulating factor (G-CSF) is used to boost granulocyte counts in immunocompromised patients, but its effects on the immune system may be counter productive. We tested the hypothesis that G-CSF mobilized peripheral blood stem cell (PBSC) products are immunologically down regulated based on gene microarray analysis.

Ten peripheral blood samples from normal donors for allogeneic PBSC transplantation were obtained before and after administration of G-CSF and tested on Affymetrix Human U133 Plus 2.0 GeneChip® microarrays. Significant changes in gene expression after G-CSF mobilization were reported by controlling the false discovery rate at 5%. Immune-related genes were isolated from the data set and categorized according to probe set annotations and a thorough, independent literature search.

We found that G-CSF up-regulated inflammatory and neutrophil activation pathway gene expression; however, adaptive immune-related gene expression, such as antigen presentation, co-stimulation, T cell activation and cytolytic effector pathways, were generally down-regulated.

Thus, despite significant increases in stem cells, lymphocytes and antigen presenting cells, G-CSF mobilized PBSC allografts exhibit a suppressive adaptive immune-related gene expression profile.  Our data provides an explanation for the potentially immunosuppressive effects observed after G-CSF administration.
Keywords: PBSCT, G-CSF, microarray, gene expression

overall_design: This study was approved by the University of Florida Institutional Review Board. Five healthy donors (A-E) for allogeneic PBSC transplantation consented and were mobilized with rHu G-CSF at 10µ/kg/day for five days. Approximately 4mL of venous blood was collected before (Pre-G-CSF) and after (Post-G-CSF) mobilization. Whole blood leukocyte RNA was purified from each sample and used to generate cRNAs which were subsequently hybridized onto Affymetrix Human U133 Plus 2.0 GeneChip® microarrays. Representative genes were successfully validated with quantitative RT-PCR.

first: Vijay

last: Reddy


title: Transformed Human Breast Epithelial Cell Types vs. Normal Cell-of-Origin

status: Public on Aug 15 2007

first: Tan

last: Ince

address: 9 Cambridge Center

institute: Whitehead Institute

summary:
The gene expression of two different tumorigenic human breast epithelial cell types (HMLER and BPLER) is compared with their immortalized parental cell-of-origin (HME and BPE).
Keywords: breast cancer, cell-of-origin, HMEC, BPEC,metastasis, tumor stem cells, tumor initiating cells, breast adenocarcinoma

overall_design: Two different normal primary human mammary epithelial cell populations (BPECs and HMECs) were isolated based on their differing in vitro growth requirements.  These cells were immortalized by hTERT giving rise to BPE and HME cells. These hTERT immortalized cells (BPE and HME) were transformed by SV40-early region (LT+st) and H-Ras giving rise to transformed tumorigenic derivatives BPLER and HMLER.  Biological replicates (4 - 6 samples) for each of 4 cell types were analyzed (untransformed hTERT immortalized cell populations (BPE&HME), and transformed tumorigenic derivatives (BPLER & HMLER).

first: Andrea

last: Richardson

first: Maki

last: Saitoh

first: James

last: Iglehart

first: George

last: Bell

first: Robert

last: Weinberg


title: The effects of chimeric EWS/ETS protein in human mesenchymal progenitor cells (MPCs).

status: Public on Aug 03 2007

city: Okura

first: Yoshitaka

last: Miyagawa

address: Setagaya-ku

institute: National Research Institute for Child Health and Development

summary:
We have examined the biological effect of EWS/ETS in human MPCs using UET-13 cells that are obtained by prolonging the lifespan of human bone marrow stromal cells using the retroviral transgenes hTERT and E7.  By exploiting tetracycline-inducible systems for expressing EWS/ETS (EWS/FLI1 and EWS/ERG), we investigated candidates for genes whose expression is regulated by EWS/ETS in human MPCs.
Keywords: Time course

overall_design: A change of expression profiles in the presence of EWS/ETS using Affymetrix HG-U133 Plus 2.0 (GPL570).

first: Hajime

last: Okita

first: Hideki

last: Nakaijima

first: Yasuomi

last: Horiuchi

first: Ban

last: Sato

first: Tomoko

last: Taguchi

first: Yohko

middle: U

last: Katagiri

first: Junichiro

last: Fujimoto

first: Jun-ichi

last: Hata

first: Akihiro

last: Umezawa

first: Nobutaka

last: Kiyokawa


title: Transcriptome profile of human colorectal adenomas.

city: Zurich

first: Giancarlo

last: Marra

address: Winterthurerstrasse 190

department: Molecular Cancer Research

country: Switzerland

institute: University of Zurich

summary:
Background: Colorectal cancers are believed to arise predominantly from adenomas. Although these precancerous lesions have been subjected to extensive clinical, pathological, and molecular analyses, little is currently known about the global gene expression changes accompanying their formation. Results: To characterize the molecular processes underlying the transformation of normal colonic epithelium, we compared the transcriptomes of 32 prospectively collected adenomas with those of normal mucosa from the same individuals. Important differences emerged not only between the expression profiles of normal and adenomatous tissues, but also between those of small and large adenomas. A key feature of the transformation process was the remodeling of the Wnt pathway reflected in patent over- and underexpression of 78 known components of this signaling cascade. Conclusions: Our transcriptomic profiles of normal colonic mucosa and colorectal adenomas shed new light on the early stages of colorectal tumorigenesis.
Keywords: tissue comparison

overall_design: Pedunculated, sporadic colorectal polyps and corresponding normal mucosa were obtained during colonoscopies. The tissues were collected prospectively with informed patient consent and the approval of the local Human Research Ethics Committee.

first: Jacob

last: Sabates

first: Hubert

last: Rehrauer


title: resting and IL2 activated human natural killer cells

status: Public on Aug 07 2007

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

summary:
The aim of the study was to investigate the activation of human NK cells by IL2 through analyzing the global gene expression at different time points (0, 2, 8 and 24 hours) after culture with the cytokine IL2 at 100 IU/ml. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected by immunomagnetic beads and re-examined by flow-cytometry to ensure greater than 90% purity .
Keywords: resting and IL2 activated NK cells(time series)

overall_design: RNA was extracted and pooled from 4 different donors, amplified and labled according to the manufacturer’s instruction (GeneChipU133plus2® , Affymetrix Inc, CA).

first: Karen

last: Dybkaer

first: Guimei

last: Zhou

first: Huimin

last: Geng

first: Li

last: Xiao

first: Alexander

last: Schmitz

first: Francesco

last: d’Amore

first: Wing

last: Chan


title: Effect on gene expression after administration of siRNA/siLNA targeting GFP

status: Public on Aug 01 2007

first: Olaf

last: Mook

address: Meibergdreef 9

department: Neurogenetics

institute: AMC

summary:
siRNA mediated gene knockdown has been shown to be extremely sequence specific. However, off-target gene regulation due to partial sequence homology has also been reported. Furthermore, sequence unrelated effects on gene regulation can occur when siRNA is applied in vivo. In this experiment we investigated off target gene regulation due to treatment of mice with siRNA and LNA modified siRNA targeting GFP. Off target gene regulation was observed and was markedly reduced upon introduction of LNA modifiecation in siRNA.
Keywords: comparison compound

overall_design: NMRI nu/nu mice were treated with saline (control), siRNA or siLNA for three weeks. Then the mice were sacrificed and tumor total RNA was isolated. The effect of siRNA/siLNA treatment was evaluated by comparing gene expression of saline treated animals with that of siRNA and siLNA treated animals respectively.


status: Public on Jul 27 2007

first: Yoshitaka

last: Miyagawa

summary:
For identification of candidate genes that is specifically expressed in Ewing family tumor (EFT) cells, we performed DNA microarray-based global expression profiling using Affymetrix Human Genome U133 Plus 2.0 Array and analyxed expression profiles from EFT cell lines (7 lines), neuroblastoma (NB) cell lines (3 lines), a Rhabdomyosarcoma (RMS) cell line, and a human immortalized mesenchymal progenitor cells UET-13 cells.
Keywords: Ewing family tumor

overall_design: Expression profiles of pediatric solid tumor cell lines were analyzed and compared using Affymetrix HG-U133 Plus 2.0 (GPL570).

first: Hajime

last: Okita

first: Hideki

last: Nakaijima

first: Yasuomi

last: Horiuchi

first: Ban

last: Sato

first: Tomoko

last: Taguchi

first: Yohko

last: Katagiri


title: Lymphocyte gene expression data from moderate stage HD patients and controls

first: Alexandre

last: Kuhn

address: 35 Convent Dr

department: NIA

summary:
Highly quantitative biomarkers of neurodegenerative disease remain an important need in the urgent quest for disease modifying therapies. For Huntington's disease (HD), a genetic test is available (trait marker), but necessary state markers are still in development. In this report, we describe a large battery of transcriptomic tests explored as state biomarker candidates. In an attempt to exploit the known neuroinflammatory and transcriptional perturbations of disease, we measured relevant mRNAs in peripheral blood cells. The performance of these potential markers was weak overall, with only one mRNA, immediate early response 3 (IER3), showing a modest but significant increase of 32% in HD samples compared to controls. No statistically significant differences were found for any other mRNAs tested, including a panel of 12 RNA biomarkers identified in a previous report [Borovecki F, Lovrecic L, Zhou J, Jeong H, Then F, Rosas HD, Hersch SM, Hogarth P, Bouzou B, Jensen RV et al. (2005) Proc Natl Acad Sci U S A 102: 11023-11028]. The present results may nonetheless inform the future design and testing of HD biomarker strategies.
Keywords: RNA biomarker screen

overall_design: Lymphocyte samples from 12 moderate stage HD patients (8 female and 4 male) and 10 age-matched controls (5 female and 5 male).

first: Heike

last: Runne

first: Edward

last: Wild

first: Wirahpati

last: Pratyaksha

first: Mark

last: Kristiansen

first: Jeremy

middle: D

last: Isaacs

first: Etienne

last: Régulier

first: Mauro

last: Delorenzi

first: Sarah

last: Tabrizi

first: Ruth

last: Luthi-Carter


title: Expression profiles of extremely low gestational age newborns as predictors of BPD

status: Public on Jul 26 2007

first: Jennifer

middle: N

last: Cohen

address: 75 Francis Street

department: Newborn Medicine

institute: Brigham and Women's Hospital

summary:
One third to one half of all infants born before the 28th wek of gestation develop BPD bronchopulmonary dysplasia.  Our objective is to evaluate the feasibility of using expression profiling in umbilical cord tissue to discover molecular signatures for developmental staging and for risk of BPD.
Keywords: disease state analysis

overall_design: 54 samples, no replicates

first: Isaac

last: Kohane


title: Comprehensive analysis of PPARα-dependent regulation of hepatic lipid metabolism by expression profiling - 5

status: Public on Jul 24 2007

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary:
PPARα is a ligand-activated transcription factor involved in the regulation of nutrient metabolism and inflammation. Although much is already known about the function of PPARα in hepatic lipid metabolism, many PPARα-dependent pathways and genes have yet to be discovered.  In order to obtain an overview of PPARα-regulated genes relevant to lipid metabolism, and to probe for novel candidate PPARα target genes, livers from several animal studies in which PPARα was activated and/or disabled were analyzed by Affymetrix GeneChips. Numerous novel PPARα-regulated genes relevant to lipid metabolism were identified. Out of this set of genes, eight genes were singled out for study of PPARα-dependent regulation in mouse liver and in mouse, rat, and human primary hepatocytes, including thioredoxin interacting protein (Txnip), electron-transferring-flavoprotein β polypeptide (Etfb), electron-transferring-flavoprotein dehydrogenase (Etfdh), phosphatidylcholine transfer protein (Pctp), endothelial lipase (EL, Lipg), adipose triglyceride lipase (Pnpla2), hormone-sensitive lipase (Lipe), and monoglyceride lipase (Mgll). Using an in silico screening approach, one or more PPAR response elements (PPREs) were identified in each of these genes.  Since Pnpla2, Lipe, and Mgll contribute to hepatic triglyceride hydrolysis, gene regulation was studied under conditions of elevated hepatic lipids. In wild-type mice fed a high fat diet, the decrease in hepatic lipids following treatment with the PPARα agonist Wy14643 was paralleled by significant up-regulation of Pnpla2, Lipe, and Mgll, suggesting that induction of triglyceride hydrolysis may contribute to the anti-steatotic role of PPARα. Our study illustrates the power of transcriptional profiling to uncover novel PPARα-regulated genes and pathways in liver.
Keywords: identification of target genes

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Primary rat and mouse hepatocytes were incubated in the presence (10 uM) or absence of the synthetic PPARα ligand Wy14643 for 24 hours. Primary human hepatocytes were incubated in the presence (50 uM) or absence of Wy14643 for 12 hours. Total RNA was pooled within groups and hybridized onto Rat Genome 230 2.0 Arrays, Mouse Genome 430 2.0 Arrays or Human Genome U133 Plus 2.0 Arrays.

first: Maryam

last: Rakhshandehroo

first: Linda

middle: M

last: Sanderson

first: Merja

last: Matilainen

first: Rinke

last: Stienstra

first: Carsten

last: Carlberg

first: Philip

last: de Groot

first: Michael

last: Muller

first: Sander

last: Kersten


title: The Hay Wells Syndrome-Derived TAp63alphaQ540L Mutant Has Impaired Transcriptional and Cell Growth Regulatory Activity

status: Public on Aug 02 2007

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary:
p63 mutations have been associated with several human hereditary disorders characterized by ectodermal dysplasia such as EEC syndrome, ADULT  syndrome and AEC  syndrome . The location and functional effects of the mutations that underlie these syndromes reveal a striking genotype-phenotype correlation. Unlike EEC and ADULT that result from missense mutations in the DNA-binding domain of p63, AEC is solely caused by missense mutations in the SAM domain of p63. We report a study on the TAp63a isoform, the first to be expressed during development of the embryonic epithelia, and on its naturally occurring Q540L mutant derived from an AEC patient. To assess the effects of the Q540L mutation, we generated stable cell lines expressing TAp63a wt, DeltaNp63 alpha or the TAp63 alpha-Q540L mutant protein and used them to systematically compare the cell growth regulatory activity of the mutant and wt p63 proteins and to generate, by microarray analysis, a comprehensive profile of differential gene expression. We found that the Q540L substitution impairs the transcriptional activity of TAp63a and causes misregulation of genes involved in the control of cell growth and epidermal differentiation.
Keywords: Hay Wells syndrome, TAp63alpha, genetic alteration, pp63 Q540L

overall_design: Three biological replicates of not induced TAp63 alpha wt, three biological replicates of induced TAp63 alpha wt, three biological replicates of not induced TAp63Q540L alpha mutant and two biological replicates of induced TAp63Q540L alpha mutant

first: Marco

last: Lo Iacono

first: Antonella

last: Di Costanzo

first: Gelsomina

last: Mansueto

first: Silvia

last: Savozzi

first: Stefania

last: Crispi

first: Alesandra

last: Pollice

first: Girolama

last: La Mantia

first: Viola

last: Calabrò


title: Gene expression profilie during cell cycle in T98G cells

status: Public on Jul 21 2007

city: Boston

first: Subhashini

last: Sadasivam

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Insitute

summary:
The mammalian Retinoblastoma (RB) family including pRB, p107, and p130 represses E2F target genes through mechanisms that are not fully understood. In D. melanogaster, RB-dependent repression is mediated in part by the multisubunit protein complex Drosophila RBF, E2F, and Myb (dREAM) that contains homologs of the C. elegans synthetic multivulva class B (synMuvB) gene products. Using an integrated approach combining proteomics, genomics, and bioinformatic analyses, we identified a p130 complex termed DP, RB-like, E2F, and MuvB (DREAM) that contains mammalian homologs of synMuvB proteins LIN-9, LIN-37, LIN-52, LIN-54, and LIN-53/RBBP4. DREAM bound to more than 800 human promoters in G0 and was required for repression of E2F target genes. In S phase, MuvB proteins dissociated from p130 and formed a distinct submodule that bound MYB. This work reveals an evolutionarily conserved multisubunit protein complex that contains p130 and E2F4, but not pRB, and mediates the repression of cell cycle-dependent genes in quiescence.
Keywords: Gene expression analysis during cell cycle

overall_design: Gene expression during the cell cycle in T98G cells. Cells were serum starved for 72 hours to induce G0 and then restimuated to enter cell cycle by serum addition. BrdU and FACS was done simultaneously to confirm their cell cycle phase.

first: Larisa

last: Litovchick

first: Xiaopeng

last: Zhu

first: Soundarapandian

last: Velmurugan

first: X

last: Liu

first: James

last: DeCaprio


title: Fetal cartilage selective genes identified in a genome-scale analysis

status: Public on Jul 06 2007

city: Los Angeles

first: Vincent

middle: Anthony

last: Funari

state: CA

address: 8700 Beverly Drive

department: Medical Genetics

institute: Cedars Sinai

summary:
Cartilage plays a fundamental role in the development of the human skeleton. Early in embryogenesis, mesenchymal cells condense and differentiate to chondrocytes to shape the early skeleton. Subsequently, the cartilage anlagen differentiate to form the growth plates, which are responsible for linear bone growth, and the articular chondrocytes, which facilitate joint function. However, despite the multiplicity of roles of cartilage during human fetal life, surprisingly little is known about its transcriptome. To address this, a whole genome microarray expression profile was generated using RNA isolated from 18-22 week human distal femur fetal cartilage and compared with a database of control normal human tissues aggregated at UCLA, termed CELSIUS. From the wealth of data, 161 cartilage-selective genes were identified, defined as genes significantly expressed in cartilage with low expression and little variation across a panel of 34 non-cartilage tissues. Among these 161 genes were cartilage-specific genes such as collagen genes and 25 genes which have been associated with skeletal phenotypes in humans and/or mice. Many of the other cartilage-selective genes do not have established roles in cartilage or are novel, unannotated genes. Quantitative RT-PCR confirmed the unique pattern of gene expression observed by microarray analysis. Defining the gene expression pattern for cartilage has identified new genes that may contribute to human skeletogenesis as well as provided further candidate genes for skeletal dysplasias. The data suggest that fetal cartilage is a complex and transcriptionally active tissue and demonstrate that the set of genes selectively expressed in the tissue has been greatly underestimated.
Keywords: Normal Tissue expression profile, tissue-selective Genes, tissue-specific genes

overall_design: RNA from 7 normal fetal cartilage samples was isolated. 5 samples were run in duplicate on U133 2.0 arrays, while 2 were run on U133A and U133B subsets. In brief, cartilage selective genes were identified by comparing 5 normal cartilage samples (GSM149638,GSM149639 ,GSM149640,GSM149641 ,GSM149642) to normal tissue expression profiles found on CELCIUS at UCLA. Genes which were found expressed at significantly higher levels were validated for their elevated and specific expression using the three platforms. The 9 validation arrays are: 5 U133 2.0 (GSM149643 ,GSM149644 ,GSM149645 ,GSM149646,GSM149647), 2 U133A (GSM149651, GSM149652), 2 U133B (GSM149653, GSM149654)

first: Allen

last: Day

first: Deborah

last: Krakow

first: Zachery

last: Cohn

first: Zugen

last: Chen

first: Stanley

middle: F

last: Nelson

first: Daniel

middle: H


title: An estrogen-dependent model of breast cancer created by transformation of normal human mammary epithelial cells

status: Public on Jun 22 2007

city: Bordeaux

first: Richard

last: Iggo

address: 229 cours de l'Argonne

department: Bergonie Cancer Institute

institute: University of Bordeaux

summary:
This study was performed to check that ESR1 and BMI1 are biologically active after lentiviral transduction of primary human mammary epithelial cells (HMECs) with lentiviral vectors expressing ESR1 and BMI1 from the human PGK promoter. ESR1 targets like PGR, PRLR and GREB1, but not TFF1 and XBP1, were induced by estradiol in the ESR1-expressing cells. BMI1 targets like BMI1, NEFL and CCND2 were repressed in the BMI1-expressing cells. BMI1 suppressed genes associated with squamous and neural differentiation in the ESR1 plus BMI1-expressing cells.
Keywords: Drug response

overall_design:
Infect with lentiviruses 24 hours after reduction mammmoplasty. Grow cells in human mammosphere medium: Hepes-buffered DMEM/F12 supplemented with 20 ng/ml EGF, 1x B-27 (GIBCO) plus 1 nM 17-β-estradiol  or 1 uM fulvestrant (ICI 182,780).
Lentiviral vectors: pSD-82, ESR1; pSD-84, BMI1; pSD-86, gusA.

first: Stephan

last: Duss

first: Sylvie

last: André

first: Anne-Laure

last: Nicoulaz

first: Maryse

last: Fiche

first: Hervé

last: Bonnefoi

first: Cathrin

last: Brisken


title: Genome wide analysis of placental malaria

status: Public on Jul 01 2007

first: Atis

last: Muehlenbachs

address: 307 Westlake Ave N

institute: Seattle Biomedical Research Institute

summary:
Chronic inflammation during placental malaria (PM) caused by Plasmodium falciparum is most frequent in first-time mothers and is associated with poor maternal and fetal outcomes. In the first genome wide analysis of the local human response to sequestered malaria parasites, we identified genes associated with chronic PM, then localized the corresponding proteins and immune cell subsets in placental cryosections.
Keywords: Disease state analysis

overall_design: Placental samples from twenty first-time mothers were selected based on placental malaria (PM) status and RNA quality. Ten had active PM-episodes, seven of which had inflammatory cells on histology. Of the ten PM-negative women, five had histological evidence of a past PM-episode, including one with inflammatory cells.

first: Patrick

middle: E

last: Duffy

first: Michal

last: Fried

first: Theonest

middle: K

last: Mutabingwa


title: Pediatric septic shock

status: Public on Jun 14 2007

city: Cincinnati

first: Hector

middle: R

last: Wong

state: OH

address: 3333 Burnet Ave

department: Division of Critical Care Medicine

institute: CIncinnati Children's Hospital Medical Center

summary:
In an ongoing translational research program involving microarray-based expression profiles in pediatric septic shock, we have now conducted longitudinal studies focused on the temporal expression profiles of canonical signaling pathways and gene networks. Genome-level expression profiles were generated from whole blood-derived RNA samples of children with septic shock (n = 30 individual patients) corresponding to days 1 and 3 of admission to the pediatric intensive care unit. Based on sequential statistical and expression filters, day 1 and day 3 of septic shock were characterized by differential regulation of 2,142 and 2,504 gene probes, respectively, relative to normal control patients. Venn analysis demonstrated 239 unique genes in the day 1 data set, 598 unique genes in the day 3 data set, and 1,906 genes common to both data sets. Analyses targeted toward derivation of biological function from these data sets demonstrated time-dependent, differential regulation of genes involved in multiple canonical signaling pathways and gene networks primarily related to immunity and inflammation. Notably, multiple and distinct gene networks involving T cell- and MHC antigen-related biological processes were persistently downregulated from day 1 to day 3. Further analyses demonstrated large scale and persistent downregulation of genes corresponding to functional annotations related to zinc homeostasis. These data represent the largest reported cohort of patients with septic shock, which has undergone longitudinal genome-level expression profiling. The data further advance our genome-level understanding of pediatric septic shock and support novel hypotheses that can be readily tested at both the experimental and translational levels.

Keywords: Inflammation; sepsis; innate immunity; T cells; MHC antigen
Keywords: to be updated

overall_design: To define the longitudinal, genome-level expression profile of children with septic shock.