title: CTDG in non-activated Jurkat cells

status: Public on Jul 31 2008

city: Houston

middle: P.

last: Rice

state: TX

address: One Baylor Plaza

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

summary:
Cyclin T1-dependent genes in non-activated Jurkat cells.

HIV-1 is dependent upon cellular co-factors to mediate its replication cycle in CD4+ T cells and macrophages, the two major cell types infected by the virus in vivo.  One critical co-factor is Cyclin T1, a subunit of a general RNA polymerase II elongation factor known as P-TEFb.  Cyclin T1 is targeted directly by the viral Tat protein to activate proviral transcription.  Cyclin T1 is up-regulated when resting CD4+ T cells are activated and during macrophage differentiation or activation, conditions that are also necessary for high levels of HIV-1 replication.  Because Cyclin T1 is a subunit of a transcription factor, the up-regulation of Cyclin T1 in these cells results in the induction of cellular genes, some of which might be HIV-1 co-factors.  Using shRNA depletions of Cyclin T1 and transcriptional profiling, we identified 54 cellular mRNAs that are Cyclin T1-dependent for their induction in activated CD4+ T cells and during macrophage differentiation and activation.  The promoters for these Cyclin T1-dependent genes (CTDGs) are over-represented in two transcription factor binding sites, SREBP1 and ARP1.  Notably, 10 of these CTDGs have been reported to be involved in HIV-1 replication, a significant over-representation of such genes when compared to randomly generated lists of 54 genes (p value < 0.00021).  SiRNA depletions of two CTDGs identified here, CDK11 and Casein kinase1gamma1, suggest that these genes are also involved in HIV-1 replication.  It is therefore likely that the 54 CTDGs identified here include novel HIV-1 co-factors.  The presence of CTDGs in the protein space that was available for HIV-1 to sample during its evolution and acquisition of Tat function may provide an explanation for why CTDGs are enriched in viral co-factors.
Keywords: cyclin T1 knockdown

overall_design: Using shRNA knockdown of cyclin T1, cyclin T1-dependent genes were identified in non-activated Jurkat cells.

first: Wendong

last: Yu


title: LPS and PMA response in parental MM6 cells

first: Andrew

country: USA

summary:
Parental MM6 cells, as an additional control, were treated with LPS and PMA. Genes affected by the treatments were identified.

HIV-1 is dependent upon cellular co-factors to mediate its replication cycle in CD4+ T cells and macrophages, the two major cell types infected by the virus in vivo.  One critical co-factor is Cyclin T1, a subunit of a general RNA polymerase II elongation factor known as P-TEFb.  Cyclin T1 is targeted directly by the viral Tat protein to activate proviral transcription.  Cyclin T1 is up-regulated when resting CD4+ T cells are activated and during macrophage differentiation or activation, conditions that are also necessary for high levels of HIV-1 replication.  Because Cyclin T1 is a subunit of a transcription factor, the up-regulation of Cyclin T1 in these cells results in the induction of cellular genes, some of which might be HIV-1 co-factors.  Using shRNA depletions of Cyclin T1 and transcriptional profiling, we identified 54 cellular mRNAs that are Cyclin T1-dependent for their induction in activated CD4+ T cells and during macrophage differentiation and activation.  The promoters for these Cyclin T1-dependent genes (CTDGs) are over-represented in two transcription factor binding sites, SREBP1 and ARP1.  Notably, 10 of these CTDGs have been reported to be involved in HIV-1 replication, a significant over-representation of such genes when compared to randomly generated lists of 54 genes (p value < 0.00021).  SiRNA depletions of two CTDGs identified here, CDK11 and Casein kinase1gamma1, suggest that these genes are also involved in HIV-1 replication.  It is therefore likely that the 54 CTDGs identified here include novel HIV-1 co-factors.  The presence of CTDGs in the protein space that was available for HIV-1 to sample during its evolution and acquisition of Tat function may provide an explanation for why CTDGs are enriched in viral co-factors.
Keywords: knockdown

overall_design: This experiment is part of the big experiments to identify genes specifically affected by cyclin T1 in MM6 cells.

middle: P


title: CTDG in LPS-activated MM6 cells

summary:
Cyclin T1-dependent genes in LPS-activated MM6 cells.

HIV-1 is dependent upon cellular co-factors to mediate its replication cycle in CD4+ T cells and macrophages, the two major cell types infected by the virus in vivo.  One critical co-factor is Cyclin T1, a subunit of a general RNA polymerase II elongation factor known as P-TEFb.  Cyclin T1 is targeted directly by the viral Tat protein to activate proviral transcription.  Cyclin T1 is up-regulated when resting CD4+ T cells are activated and during macrophage differentiation or activation, conditions that are also necessary for high levels of HIV-1 replication.  Because Cyclin T1 is a subunit of a transcription factor, the up-regulation of Cyclin T1 in these cells results in the induction of cellular genes, some of which might be HIV-1 co-factors.  Using shRNA depletions of Cyclin T1 and transcriptional profiling, we identified 54 cellular mRNAs that are Cyclin T1-dependent for their induction in activated CD4+ T cells and during macrophage differentiation and activation.  The promoters for these Cyclin T1-dependent genes (CTDGs) are over-represented in two transcription factor binding sites, SREBP1 and ARP1.  Notably, 10 of these CTDGs have been reported to be involved in HIV-1 replication, a significant over-representation of such genes when compared to randomly generated lists of 54 genes (p value < 0.00021).  SiRNA depletions of two CTDGs identified here, CDK11 and Casein kinase1gamma1, suggest that these genes are also involved in HIV-1 replication.  It is therefore likely that the 54 CTDGs identified here include novel HIV-1 co-factors.  The presence of CTDGs in the protein space that was available for HIV-1 to sample during its evolution and acquisition of Tat function may provide an explanation for why CTDGs are enriched in viral co-factors.
Keywords: shrna knockdown

overall_design: Using shRNA knockdown of cyclin T1, cyclin T1-dependent genes were identified in LPS-activated MM6 cells.


title: CTDG in PMA-activated MM6 cells

summary:
Cyclin T1-dependent genes in PMA-activated MM6 cells.

HIV-1 is dependent upon cellular co-factors to mediate its replication cycle in CD4+ T cells and macrophages, the two major cell types infected by the virus in vivo.  One critical co-factor is Cyclin T1, a subunit of a general RNA polymerase II elongation factor known as P-TEFb.  Cyclin T1 is targeted directly by the viral Tat protein to activate proviral transcription.  Cyclin T1 is up-regulated when resting CD4+ T cells are activated and during macrophage differentiation or activation, conditions that are also necessary for high levels of HIV-1 replication.  Because Cyclin T1 is a subunit of a transcription factor, the up-regulation of Cyclin T1 in these cells results in the induction of cellular genes, some of which might be HIV-1 co-factors.  Using shRNA depletions of Cyclin T1 and transcriptional profiling, we identified 54 cellular mRNAs that are Cyclin T1-dependent for their induction in activated CD4+ T cells and during macrophage differentiation and activation.  The promoters for these Cyclin T1-dependent genes (CTDGs) are over-represented in two transcription factor binding sites, SREBP1 and ARP1.  Notably, 10 of these CTDGs have been reported to be involved in HIV-1 replication, a significant over-representation of such genes when compared to randomly generated lists of 54 genes (p value < 0.00021).  SiRNA depletions of two CTDGs identified here, CDK11 and Casein kinase1gamma1, suggest that these genes are also involved in HIV-1 replication.  It is therefore likely that the 54 CTDGs identified here include novel HIV-1 co-factors.  The presence of CTDGs in the protein space that was available for HIV-1 to sample during its evolution and acquisition of Tat function may provide an explanation for why CTDGs are enriched in viral co-factors.
Keywords: shrna knockdown

overall_design: Using shRNA knockdown of cyclin T1, cyclin T1-dependent genes were identified in PMA-activated MM6 cells.


title: Genome-wide expression profiling from formalin-fixed paraffin-embedded breast cancer core biopsies

status: Public on Aug 01 2008

city: Berlin

first: Jan

last: Budczies

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite - Universitaetsmedizin Berlin

summary:
The routine workflow for invasive cancer diagnostics is based on biopsy processing by formalin fixation and subsequent paraffin embedding. Formalin-fixed paraffin-embedded (FFPE) tissue samples are easy to handle, stable and particularly suitable for morphologic evaluation, immunohistochemistry and in situ hybridization. However, it has become a paradigm that these samples cannot be used for genome-wide expression analysis with microarrays. To oppose this view, we present a pilot microarray study using FFPE core needle biopsies from breast cancers as RNA source.  We found that microarray probes interrogating sequences near the poly-A-tail of the transcribed genes were well suitable to measure RNA levels in FFPE core needle biopsies. For the ER and the HER2 gene, we observed strong correlations between RNA levels measured in these probe sets and protein expression determined by immunohistochemistry (p = 0.000003 and p = 0.0022). Further, we have identified a signature of 364 genes that correlated with ER protein status and a signature of 528 genes that correlated with HER2 protein status. Many of these genes (ER: 60%) could be confirmed by analysis of an independent publicly available data set. Finally, a hierarchical clustering of the biopsies with respect to three recently reported gene expression grade signatures resulted in widely stable low and high expression grade clusters that correlated with the pathological tumor grade.  These findings support the notion that clinically relevant information can be gained from microarray based gene expression profiling of FFPE cancer biopsies. This opens new opportunities for the integration of gene expression analysis into the workflow of invasive cancer diagnostics as well as translational research in the setting of clinical studies.
Keywords: disease state analysis

overall_design: RNA from 24 breast cancer biopsies extracted with kit A, RNA from 6 breast cancer biopsies extracted with kit B

first: Wilko

last: Weichert

first: Carsten

last: Denkert

first: Volker

last: Gekler


title: CTDG in PMA-activated Jurkat cells

summary:
Cyclin T1-dependent genes in activated Jurkat cells.

HIV-1 is dependent upon cellular co-factors to mediate its replication cycle in CD4+ T cells and macrophages, the two major cell types infected by the virus in vivo.  One critical co-factor is Cyclin T1, a subunit of a general RNA polymerase II elongation factor known as P-TEFb.  Cyclin T1 is targeted directly by the viral Tat protein to activate proviral transcription.  Cyclin T1 is up-regulated when resting CD4+ T cells are activated and during macrophage differentiation or activation, conditions that are also necessary for high levels of HIV-1 replication.  Because Cyclin T1 is a subunit of a transcription factor, the up-regulation of Cyclin T1 in these cells results in the induction of cellular genes, some of which might be HIV-1 co-factors.  Using shRNA depletions of Cyclin T1 and transcriptional profiling, we identified 54 cellular mRNAs that are Cyclin T1-dependent for their induction in activated CD4+ T cells and during macrophage differentiation and activation.  The promoters for these Cyclin T1-dependent genes (CTDGs) are over-represented in two transcription factor binding sites, SREBP1 and ARP1.  Notably, 10 of these CTDGs have been reported to be involved in HIV-1 replication, a significant over-representation of such genes when compared to randomly generated lists of 54 genes (p value < 0.00021).  SiRNA depletions of two CTDGs identified here, CDK11 and Casein kinase1gamma1, suggest that these genes are also involved in HIV-1 replication.  It is therefore likely that the 54 CTDGs identified here include novel HIV-1 co-factors.  The presence of CTDGs in the protein space that was available for HIV-1 to sample during its evolution and acquisition of Tat function may provide an explanation for why CTDGs are enriched in viral co-factors.
Keywords: shrna knockdown

overall_design: Using shRNA knockdown of cyclin T1, cyclin T1-dependent genes were identified in activated Jurkat cells.


title: Transcriptional response of MM6 cells to cyclin T1

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

overall_design: Refer to individual Series


title: CTDG in non-activated MM6 cells

summary:
Cyclin T1-dependent genes in LPS-activated MM6 cells.

HIV-1 is dependent upon cellular co-factors to mediate its replication cycle in CD4+ T cells and macrophages, the two major cell types infected by the virus in vivo.  One critical co-factor is Cyclin T1, a subunit of a general RNA polymerase II elongation factor known as P-TEFb.  Cyclin T1 is targeted directly by the viral Tat protein to activate proviral transcription.  Cyclin T1 is up-regulated when resting CD4+ T cells are activated and during macrophage differentiation or activation, conditions that are also necessary for high levels of HIV-1 replication.  Because Cyclin T1 is a subunit of a transcription factor, the up-regulation of Cyclin T1 in these cells results in the induction of cellular genes, some of which might be HIV-1 co-factors.  Using shRNA depletions of Cyclin T1 and transcriptional profiling, we identified 54 cellular mRNAs that are Cyclin T1-dependent for their induction in activated CD4+ T cells and during macrophage differentiation and activation.  The promoters for these Cyclin T1-dependent genes (CTDGs) are over-represented in two transcription factor binding sites, SREBP1 and ARP1.  Notably, 10 of these CTDGs have been reported to be involved in HIV-1 replication, a significant over-representation of such genes when compared to randomly generated lists of 54 genes (p value < 0.00021).  SiRNA depletions of two CTDGs identified here, CDK11 and Casein kinase1gamma1, suggest that these genes are also involved in HIV-1 replication.  It is therefore likely that the 54 CTDGs identified here include novel HIV-1 co-factors.  The presence of CTDGs in the protein space that was available for HIV-1 to sample during its evolution and acquisition of Tat function may provide an explanation for why CTDGs are enriched in viral co-factors.
Keywords: cyclin T1 knockdown

overall_design: Using shRNA knockdown of cyclin T1, cyclin T1-dependent genes were identified in non-activated MM6 cells.


title: Common activation of RAS_MAPK pathway in serous LMP tumours

status: Public on Jul 30 2008

city: Melbourne

first: Prof David

last: Bowtell PhD.

state: VIC

address: Locked Bag 1 A' Beckett St

department: Research Division

country: Australia

institute: PeterMacCallum Cancer Centre

summary: Expression profile of 30 LMP tumours and 60 Serous tumours were compared to identify the biolgical pathways specific to these groups. Genotyping was done to identify the mutations potentially causing these phenotypes

overall_design: Expression profile of 30 LMP tumours and 60 Invasive srous tumours

first: Michael

middle: S

last: Anglesio

first: Jeremy

middle: M

last: Arnold

first: Joshy

last: George

first: Anna

middle: V

last: Tinker

first: Richard

last: Tothill

first: Nic

last: Wadell

first: Lisa

last: Simms

first: Bianca

last: Locandro

first: Sian

last: Fereday

first: Nadia

last: Traficante

first: Peter

last: Russell

first: Raghawa

last: Sharma

middle: J

last: Birrer

last: deFazio

first: Georgia

last: Chenevix-Trench

first: David

middle: D

last: Bowtell


title: Analysis of MYC in murine lymphoma cell lines

status: Public on Aug 12 2008

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: Regulation of mRNA expression of monocytic cells by stimulation with pro- abd anti-inflammatory eicosanoids

first: Hartmut

last: Kühn

state: Berlin

address: Monbijoustr. 2

summary:
Eicosanoids are potent regulators of gene expression of inflammatory cells. Pro- (leukotrienes B4 and C4) and anti-indflammatory (lipoxins A4 and B4) eicosanoids have been described in the literature but the detailed impact of these lipid mediators on the gene expression pattern of monocytic cells has not been studied in detail. We cultured the permanent monocytic cell line MonoMac 6 for 12 h in the absence (solvent control) and presence of these eicosanoids and quantified the differential gene expression patterns using the microarray technology.
Keywords: comparative expression studies after eicosanoid stimulation

overall_design: MonoMac6 cells were grown according to the recommendations of the German Tissue and Cell Culture Collection (Braunschweig) to near confluency. Then 100 nM of the eicosanoids (leukotriene B4, leukotriene C4, lipoxin A4, lipoxin B4) were added to the culture medium as DMSO stock solution and the cells were further cultured for 12 h with the stimuli. Then the cells were harvested, washed and total RNA was extracted according to the Qiagen protocol. Total RNA was used for microarray hybridization.

first: Dagmar

last: Heydeck

first: Ralf

last: Kuban

first: Ute

last: Ungetuem

last: Kuhn


title: Gene Expression Profile of Osteogenic Cells Derived from Human Bone Marrow and Trabecular Bone

status: Public on Jul 29 2008

city: Derio

first: Lourdes

last: Osaba

address: Parque Tecnologico de Bizkaia. Ed. 801

country: Spain

institute: Progenika Biopharma


title: Gene Expression Profile of Osteogenic Cells Derived from Human Bone Marrow and Trabecular Bone III

summary:
The aim of this study was to describe the gene expression patterns related to the differentiation and mineralization of bone-forming cells, including activation and/or repression of osteogenic or non-osteogenic pathways, remodeling of cell architecture, cell adhesion, cell communication, and assembly of extracellular matrix. The study implied patient selection, tissue collection, isolation and culture of human marrow stromal cells (hMSC) and osteoblasts (hOB), and characterization of bone-forming cells. RNA samples were collected at defined time points, in order to understand the regulation of gene expression during the processes of cell differentiation/mineralization that occur during bone repair. Transcriptome analysis was performed by using the Affymetrix GeneChip microarray technology platform and GeneChip® Human Genome U133 Plus 2.0 Array. Our results help to design a gene expression profile of bone-forming cells during specific steps of osteogenic differentiation. These findings offer an useful tool to monitor the behaviour of osteogenic precursors cultured in presence of exogenous stimuli, i.e. growth factors, or onto 3D scaffolds for bone engineering. Moreover, they can contribute to identify and clarify the role of new genes for a better understanding of the molecular mechanisms regulating osteogenesis.

Keywords: time course

overall_design: hMSC were obtained from bone marrow aspirates of four patients. hMSC cultures were maintained in mineralization medium containing β-glycerophosphate, and collected at different time points. The experimental protocol was specifically devised to mark three steps of hMSC mineralization (MM). The reference sample consisted in confluent hMSCs before the addition of mineralization medium (MD4).

first: Donatella

last: Granchi

first: Gabriela

last: Ciapetti


title: Expression data from breast cancer cell lines (MCF-7 and MDA-MB-231)

status: Public on Jul 22 2008

city: Aarhus

first: Jian

last: Li

address: The Bartholin Building

department: Institute of Human Genetics

country: Denmark

institute: University of Aarhus

summary:
We used microarrays to detail the global programme of gene expression for MCF-7 and MDA-MB-231 and revealed the correlation between the methylation state of various genomic components and gene expression level. The expression analyses of the two breast cancer cell lines are a part of the whole study. The summary of our study is as follows: We establish a technique, called modified methylation-specific digital karyotyping (MMSDK) based on methylation-specific digital karyotyping (MSDK) with a novel sequencing approach. Briefly, after a tandem digestion of genomic DNA with a methylation-sensitive mapping enzyme and a fragmenting enzyme, short sequence tags are obtained. These tags are amplified, followed by direct, massively parallel sequencing (Solexa 1G Genome Analyzer). This method allows high-throughput and low-cost genome-wide DNA methylation mapping. We applied this method to investigate global DNA methylation profiles for widely used breast cancer cell lines, MCF-7 and MDA-MB-231, which are representatives for luminal-like and mesenchymal-like cancer types, respectively. By comparison, a highly similar overall DNA methylation pattern was revealed for the two cell lines. However a cohort of individual genomic loci with significantly different DNA methylation profile between two cell lines was identified. Furthermore, we revealed a genome-wide significant correlation between gene expression and the methylation status of gene promoters with CpG islands (CGIs) in the two cancer cell lines, and a correlation of gene expression and the methylation status of promoters without CGIs in MCF-7 cells.

Keywords: genetic modification

overall_design: Breast cancer cell lines, MCF-7 and MDA-MB-231, were selected for the study of the impact of DNA methylation on gene expression regulation. Total RNA extraction was performed for both cell lines and hybridization was carried out using Affymetrix microarrays. We developed a modified methylation-specific digital karyotyping (MSDK) to obtain DNA methylation profiling genome wide. Then, we combined the analysis of DNA methylation data and gene expression data to reveal a correlation between epigenetic and transcriptional features genome wide.

first: Fei

last: Gao

first: Ning

first: Shengting

first: Kai

last: Wang

first: Geng

last: Tian

first: Shangang

last: Jia

first: Guangliang

last: Yin

first: Xiuqing

last: Zhang

first: Huanming

last: Yang

first: Anders

middle: L

last: Nielsen

last: Bolund


title: Gene Expression Profile of Osteogenic Cells Derived from Human Bone Marrow and Trabecular Bone II

overall_design: hMSC were derived from mononuclear cells (MNC) of bone marrow aspirates of four patients. MNC cultures were maintained in differentiation medium containing ascorbic acid-2 phosphate and dexamethasone, and hMSC were collected at different time points. The experimental protocol was specifically devised to mark five steps of hMSC differentiation (MD). The reference sample consisted in MNCs before the addition of differentiation medium (MD1).


title: Hepatic gene expression  after a hypocaloric, low-fat diet in obese women and controls

status: Public on Jul 23 2008

city: Oulu

first: Mirella

last: Hietaniemi

address: Aapistie 5A

department: Department of Internal Medicine, Biocenter Oulu

country: Finland

institute: University of Oulu

summary:
The prevalence of obesity has been increasing rapidly worldwide during the past two decades. This is alarming, since obesity has considerable effects on morbidity and mortality. The majority of gene expression studies about the effect of obesity and weight loss have been performed using the adipose tissue for mRNA extraction.  However, also the liver plays a central role in maintaining energy balance. To our knowledge, no overall analysis of hepatic gene expression in response to changes in nutritional status has been made in humans Therefore, it is important to investigate how a short-time hypocaloric diet affects overall hepatic gene expression and the metabolic profile in a group of overweight and obese women. The subjects (n=31) were middle-aged, overweight (BMI>25 kg/m2) women with gallstone disease scheduled for an elective gallbladder operation. The intervention subjects were placed on a hypocaloric AHA step I diet  with a recommended daily energy intake of 5.0 MJ. The objective was to reduce 0.5 kg of body weight per week.  The control subjects were instructed to continue their habitual diet and not to lose weight. Basic clinical measurements and laboratory analyses were performed twice at baseline and at two week intervals during the weight reduction period. Surgical liver biopsies were obtained at the end of the weight reduction period. RNA samples of 4 individuals from the intervention group and 4 individuals from the control group were selected for the microarray analysis. The results from the microarray analysis were fairly surprising. Only one gene was up-regulated and the rest 142 down-regulated in the diet intervention group compared to the control group when a minimum of 2-fold change was set as the limit. The global decrease in hepatic gene expression was unexpected but the results are interesting, with several genes not previously linked to weight reduction. The decrease in triglyceride and fasting plasma insulin concentrations observed in our study is in accordance with results from many previous weight-loss trials.
Keywords: Overall hepatic gene expression associated with obesity and moderate weight loss in a group of overweight and obese middle-aged women.

overall_design:
The subjects (n=31) were middle-aged, overweight (BMI>25 kg/m2) women with gallstone disease scheduled for an elective gallbladder operation in 4-8 weeks. Before the weight reduction period all the study subjects visited the laboratory twice. They consumed their habitual diets and seven-day food consumption records were collected and checked by an experienced dietitian. The weight reduction program was based on dietary counseling. The intervention subjects (n=12) were placed on a hypocaloric AHA step I diet with a recommended daily energy intake of 5.0 MJ. The objective was to reduce 0.5 kg of body weight per week.  The control subjects (n=19) were instructed to continue their habitual diet and not to lose weight. During the study period, the subjects visited the laboratory at two week intervals for a clinical follow-up, fasting blood sample collection and body weight recording on all occasions. At the end of the study, surgical liver biopsies were obtained during gallstone operation, flash-frozen in liquid nitrogen and kept at -70°C until RNA extraction.
Total RNA was extracted from liver tissue and RNA concentration and purity were assessed spectrophotometrically at wavelengths 260 and 280 nm. RNA integrity was checked by agarose gel electrophoresis. RNA samples of 4 individuals from the intervention group and 4 individuals from the control group were selected for the microarray analysis. The individuals from the diet intervention group were selected to represent the whole group, not just those who lost most weight. The microarray data was validated by performing relative quantitative real-time (RT) PCR using liver samples from 7 intervention subjects and 8 control subjects, including the samples used in the microarray analysis. 11 genes were selected on the basis of biological interest. The expression of these genes was concordant with the microarray data

first: Maire

last: Rantala

first: Maarit

last: Jokela

first: Olavi

last: Ukkola

first: Jussi

middle: T

last: Vuoristo

first: Mika

last: Ilves

first: Jaana

last: Rysä

first: Antero

last: Kesäniemi


title: Gene Expression Profile of Osteogenic Cells Derived from Human Bone Marrow and Trabecular Bone I

first: Lourdes

last: Osaba

overall_design: Differentiated osteoblasts (hOB) were obtained from trabecular bone fragments of four patients. hOB cultures were maintained in mineralization medium containing β-glycerophosphate, and collected at different time points. The experimental protocol was specifically devised to mark four steps of hOB mineralization (HM). The reference sample consisted in confluent hOBs before the addition of mineralization medium (HM1).

first: Donatella

last: Granchi

first: Gabriela

last: Ciapetti


title: Overcoming resistance to conventional drugs in Ewing’s sarcoma and identification of molecular predictors of outcome.

status: Public on Jul 15 2008

city: Bologna

first: Daniel

last: Remondini

address: Viale Berti Pichat 6/2

department: Physics and Astronomy - DIFA

country: Italy

institute: Bologna University

summary:
The improvement of Ewing's sarcoma (EWS) therapy is currently linked to find strategies to select patients with  poor and good prognosis at diagnosis and to generate modified treatment regimens. In this study, we analyze the molecular factors governing  EWS response  to chemotherapy  in order to identify genetic signatures that may be used for risk-adapted therapy.

Keywords: Gene Expression Analysis.

overall_design: Affimetrix platform was used for profiling 30 primary tumors of patients that were classified according to event-free survival and 7 metastasis.  NED: no evidence of diseaase (event-free); REL: relapse; MET: metastasis. For selected genes, Real-Time PCR was applied in 42 EWS primary tumors as validation assay. MTT test was used to evaluate in vitro drug sensitivity.

first: K

last: Scotlandi

first: D

first: G

last: Castellani

first: M

middle: C

last: Manara

first: F

last: Nardi

first: L

last: Cantiani

last: Francesconi

last: Mercuri

first: A

last: Caccuri

last: Serra

first: S

last: Knuutila

first: P

last: Picci


title: Expression of Escherichia coli treated with cefsulodin and mecillinam

city: University Park

first: Mary

middle: Elizabeth

last: Laubacher

state: PA

address: 317 S Frear

department: Biochemistry Microbiology and Molecular Biology

institute: Pennsylvania State University

summary:
Gram-negative bacteria possess stress responses to maintain the integrity of the cell envelope.  Stress sensors monitor outer membrane permeability, envelope protein folding, and energization of the inner membrane.  The systems used by Gram-negative bacteria to sense and combat stress resulting from disruption of the peptidoglycan layer are not well characterized.  The peptidoglycan layer is a single molecule that completely surrounds the cell and ensures its structural integrity.  During cell growth new peptidoglcyan subunits are incorporated into the peptidoglycan layer by a series of enzymes called the penicillin-binding proteins (PBPs).  To explore how Gram-negative bacteria respond to peptidoglycan stress, global gene expression analysis was used to identify Escherichia coli stress responses activated following inhibition of specific PBPs by the β-lactam antibiotics mecillinam and cefsulodin.  Inhibition of PBPs with different roles in peptidoglycan synthesis has different consequences for cell morphology and viability, suggesting that not all perturbations to the peptidoglycan layer generate equivalent stresses.  We demonstrate that inhibition of different PBPs resulted in both shared and unique stress responses.  The regulation of capsular synthesis (Rcs) phosphorelay was activated by inhibition of all of the PBPs tested.  Furthermore, we show that activation of the Rcs phosphorelay increased survival in the presence of these antibiotics, independently of capsule synthesis.  Both activation of the phosphorelay and survival required signal transduction via the outer membrane lipoprotein RcsF and the response regulator RcsB.  We propose that the Rcs pathway responds to peptidoglycan damage and contributes to the intrinsic resistance of E. coli to β-lactam antibiotics.

We used microarrays to identify changes in gene expression resulting from treatment of Escherichia coli with the β-lactam antibiotics cefsulodin, mecillinam, or the combination.

This SuperSeries is composed of the SubSeries listed below.

platform_organism:
Escherichia coli
Escherichia coli K-12


title: Ion transport and osmotic adjustment in E. coli in response to ionic and non-ionic osmotica

status: Public on Jul 25 2008

city: Hobart

first: John

middle: Phillip

last: Bowman

state: Tasmania

address: College Road, Sandy Bay

department: School of Agricultural Science

institute: University of Tasmania

summary: Bacteria respond to osmotic stress by a substantial increase in the intracellular osmolality, adjusting their cell turgor for altered growth conditions. Using E. coli as a model organism we demonstrate here that bacterial responses to hyperosmotic stress specifically depend on the nature of osmoticum used. We show that increasing acute hyperosmotic NaCl stress above ~1.0 Os kg-1 causes a dose-dependent K+ leak from the cell, resulting in a substantial decrease in cytosolic K+ content and a concurrent accumulation of Na+ in the cell. At the same time, isotonic sucrose or mannitol treatment (non-ionic osmotica) results in a gradual increase of the net K+ uptake. Ion flux data is consistent with growth experiments showing that bacterial growth is impaired by NaCl at the concentration resulting in a switch from net K+ uptake to efflux. Microarray experiments reveal that about 40% of up-regulated genes shared no similarity in their responses to NaCl and sucrose treatment, further suggesting specificity of osmotic adjustment in E. coli to ionic- and non-ionic osmotica The observed differences are explained by the specificity of the stress-induced changes in the membrane potential of bacterial cells highlighting the importance of voltage-gated K+ transporters for bacterial adaptation to hyperosmotic stress.

overall_design:
Two biological replicates per treatment with microarray analysis using the Affymetrix GeneChip E. coli Genome array. Treatments used included:
Control - E. coli Frag1, grown to early stationary growth phase in a mineral salts medium with 0.1% glucose at 25 C
Sucrose hyperosmotic treatment - 1.25 M sucrose added to control culture
for 10 min.
NaCl hyperosmotic treatment - 1.37 M NaCl added to control culture

For microarray data comparisons the sucrose and NaCl hyperosmotic treatment data was compared to the no treatment control data separately. The sucrose to control and NaCL to control comparison data tables are linked below.

first: Svetlana

last: Shabala

first: Janelle

last: Brown

first: Tom

last: Ross

middle: A

last: McMeekin

first: Sergey


title: MYC stimulates EZH2 expression by repression of its negative regulator miR-26a

first: Lars

last: Bullinger

summary: The MYC oncogene, which is commonly mutated/amplified in tumors, represents an important regulator of cell growth owing to its ability to induce both proliferation and apoptosis. Recent evidence links MYC to altered miRNA expression, thereby suggesting that MYC-regulated miRNAs might contribute to tumorigenesis. To further analyze the impact of MYC-regulated miRNAs we investigated a murine lymphoma model harboring the MYC transgene in a Tet-off system in order to control its expression. Microarray-based miRNA expression profiling revealed both known and novel MYC targets. Among the miRNAs repressed by MYC we identified the potential tumor suppressor miR-26a, which possessed the ability to attenuate proliferation in MYC-dependent cells. Interestingly, miR-26a was also found to be deregulated in primary human Burkitt lymphoma samples, thereby likely being of clinical relevance. While today only few miRNA targets have been identified in human disease, we could show that ectopic expression of miR-26a influenced cell cycle progression by targeting the bona fide oncogene EZH2, a Polycomb protein and global regulator of gene expression yet unknown to be regulated by miRNAs. Thus, in addition to directly targeting protein-coding genes, MYC modulates genes important to oncogenesis via deregulation of miRNAs, thereby vitally contributing to MYC-induced lymphomagenesis.

overall_design: Gene expression profiling (GEP) was performed in six cell line samples using Affymetrix microarray technology according to the manufacturer’s recommendations (Human Genome U133 Plus 2.0 Array, Affymetrix). Fluorescence ratios were normalized by applying the RMA algorithm using the BRB Array Tools software package. For subsequent analyses, we only included probe sets whose expression varied as previously determined.

first: Sandrine

last: Sander

first: Kay

last: Klapproth

first: Katja

last: Fiedler

first: Hans

last: Kestler

first: Thomas

middle: F

last: Barth

first: Peter

last: Möller

first: Stephan

last: Stilgenbauer

first: Jonathan

middle: R

last: Pollack

last: Wirth


title: Gene expression variation induced by loss of the CD146 mRNA in MDA-MB-231

status: Public on Jul 11 2008

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:
Metastasis is a complex process involving loss of adhesion, migration, invasion and proliferation of cancer cells. Cell adhesion molecules play a pivotal role in this phenomenon by regulating cell-cell and cell-matrix interactions. CD146 (MCAM) is associated with advanced tumor stage in melanoma, prostate and ovarian cancers.
For this study, the MDA-MB-231 cell line was used as a prototypic mesenchymal and invasive cell line, spontaneously expressing high levels of CD146. Using whole-genome DNA microarrays, we investigated genes for which expression was modified by CD146 down-regulation, obtained by siRNA or shRNA technology

overall_design: Expression profiles of two cell lines transfected by two differents ShRNA directed against CD146 were compared with expression profiles of 3 control cell lines (i.e. native cell line, empty plasmid and shRNA directed against GFP)

first: Gwladys

last: Zabouo

first: Anne-Marie

last: Imbert

first: Jocelyne

last: Jacquemier

last: Finetti

last: Moreau

first: Daniel

last: Birnbaum

first: François

last: Bertucci

first: Christian

last: Chabannon


title: Gene Expression Profiling Separates Chromophobe Renal Cell Carcinoma from Oncocytoma

status: Public on Jul 12 2008

city: NEW YORK

first: Piali

last: Mukherjee

state: New York

department: Medicine

institute: Weill Cornell Medicine

summary: This study aims to compare gene expression profiles of chromophobe renal cell carcinoma (RCC) and benign oncocytoma, aiming at identifying differentially expressed genes.

overall_design: Nine cases each of chromophobe RCC and oncocytoma were analyzed by oligonucleotide microarray.  Candidate genes that showed consistent differential expression were validated by RT-PCR using 25 fresh-frozen and 15 formalin-fixed paraffin-embedded tumor samples.  Immunohistochemical analysis was also performed for two selected gene products, Claudin 8 and MAL2.

first: Stephen

last: Rohan

first: Jiangling

last: Tu

first: Jean

last: Kao

first: Fabien

last: Campagne

first: Xi

middle: K

last: Zhou

first: Elizabeth

last: Hyjek

first: Miguel

last: Alonso

first: Yao-Tseng

last: Chen


title: Cellular Aging of Mesenchymal Stem Cells

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary:
To determine gene expression changes during in vitro senescence of MSC we have analyzed differential expression of the corresponding early passage (P2) and senescent passage (PX). There were global changes in the gene expression profile that were reproducible in three independent donor samples.
Keywords: Replicative senescence, time course

overall_design: Mesenchymal Stem Cells (MSC) were isolated from human bone marrow (BM) as described before  (Wagner et al., 2005, Exp Hematol, 33, 1402-1416; Wagner et al., Exp Hematol, 34, 536-548). Cells were always replated when grown to confluency. A sample for RNA isolation was taken at every passage until the cells finally became senescent: they became much larger with irregular and flat shape. The nucleus became more circumscribed in phase contrast microscopy. The cytoplasm began to be granular with many inclusions and there was more cell debris. Global gene expression profiles were analyzed to determine molecular changes between corresponding early passage (P2) and senescent passage (PX) in three donor samples. In addition we have analyzed different passages of donor 1 (P2, P3, P4, P5, P6, P7, P8, P10, and P11) to determine changes in the course of cellular aging. Data were median normalized and compared to P2 of the corresponding donor sample.

first: Patrick

last: Horn

first: Anke

last: Diehlmann

first: Simone

last: Bork

first: Vladimir

last: Benes

first: Jonathon

last: Blake

first: Anthony

last: Ho


title: Expression of Escherichia coli treated with cefsulodin and mecillinam, alone at the minimum inhibitory concentration

first: Mary

last: Laubacher

summary:
Gram-negative bacteria possess stress responses to maintain the integrity of the cell envelope.  Stress sensors monitor outer membrane permeability, envelope protein folding, and energization of the inner membrane.  The systems used by Gram-negative bacteria to sense and combat stress resulting from disruption of the peptidoglycan layer are not well characterized.  The peptidoglycan layer is a single molecule that completely surrounds the cell and ensures its structural integrity.  During cell growth new peptidoglcyan subunits are incorporated into the peptidoglycan layer by a series of enzymes called the penicillin-binding proteins (PBPs).  To explore how Gram-negative bacteria respond to peptidoglycan stress, global gene expression analysis was used to identify Escherichia coli stress responses activated following inhibition of specific PBPs by the β-lactam antibiotics mecillinam and cefsulodin.  Inhibition of PBPs with different roles in peptidoglycan synthesis has different consequences for cell morphology and viability, suggesting that not all perturbations to the peptidoglycan layer generate equivalent stresses.  We demonstrate that inhibition of different PBPs resulted in both shared and unique stress responses.  The regulation of capsular synthesis (Rcs) phosphorelay was activated by inhibition of all of the PBPs tested.  Furthermore, we show that activation of the Rcs phosphorelay increased survival in the presence of these antibiotics, independently of capsule synthesis.  Both activation of the phosphorelay and survival required signal transduction via the outer membrane lipoprotein RcsF and the response regulator RcsB.  We propose that the Rcs pathway responds to peptidoglycan damage and contributes to the intrinsic resistance of E. coli to β-lactam antibiotics.
We used microarrays to identify changes in gene expression resulting from treatment of Escherichia coli with the β-lactam antibiotics cefsulodin, mecillinam, or the combination.
Keywords: Dose response, stress response

overall_design: E. coli was treated with two b-lactam antibiotics, cefsulodin and mecillinam, alone at the minimum inhibitory concentration to identify the expression changes in response to antibiotic-induced peptidoglycan stress.  E. coli was grown to an OD of 0.2 at which time cefsulodin or mecillinam was added.  Samples of the bacteria were collected at 5 and 10 minutes after treatment with cefsulodin and 60 minutes after treatment with mecillinam.  Untreated cells were also collected at the same time points as controls.  Three biological replicates were collected for all time points and samples, however, only one of the 5 minute untreated samples was hybridized to the arrays.  In addition, a single sample from cells treated with the combination of cefsulodin and mecillinam was hybridized to allow for comparison with samples hybridized to Affymetrix antisense genechips.

middle: E

first: Sarah

last: Ades


title: Search for recessive retinitis pigmentosa genes using RNA expression analysis in lymphoblasts

status: Public on Jul 14 2008

city: Boston

first: Dyonne

middle: T.

last: Hartong

state: MA

address: 243 Charles Street

department: Massachusetts Eye and Ear Infirmary

institute: Harvard Medical School

summary:
Recessive retinitis pigmentosa (RP) is often caused by nonsense mutations that lead to low mRNA levels as a result of nonsense-mediated decay. Some RP genes are expressed at detectable levels in leukocytes as well as in the retina. We designed a microarray-based method to find recessive RP genes based on low lymphoblast mRNA expression levels

Keywords: Recessive mutations; mRNA expression; nonsense mediated-decay; retinitis pigmentosa; lymphocyte; Affymetrix genechip Human Genome U133Plus2.0.

overall_design: We established lymphoblast cell lines from 13 unrelated index patients with recessive RP as well all of their affected siblings (1 sibship with 4 affected members, 5 with 2 affected members, and 7 isolates) and 4 controls. RNA was isolated and hybridized on Affymetrix genechip Human Genome U133Plus2.0. After normalization, expression levels of the individual families were compared to the other samples; significance was tested using the Student t-test. The most significant suitable candidate genes were sequenced to screen for disease causing mutations and/or analyzed for segregation in the family.

first: Thaddeus

last: Dryja

first: Terri

last: McGee

first: Eliot

last: Berson

first: Mayura

last: Dange

first: Roberta

last: Colman


title: Oxygen downshift experiment with E.coli W3110

status: Public on Jul 08 2008

first: Jaakko

last: Soini

address: Erkki Koiso-Kanttilan katu 1

department: Process and Environmental Engineering

summary: Dynamical response to oxygen downshift under fermentation conditions was tested by taking sample before (S1) and after (S2, S3 and S4) the oxygen downshift. The dynamical changes relevant for ongoing research on physiology were applied.

overall_design:
Four microarray chips were analyzed:

S1 was taken 15 min before the oxygen downshift
S2, S3 and S4 were taken 15 min, 45 min and 75 min after the oxygen downshift, respectively


title: The transcriptome of human oocytes

status: Public on Jul 09 2008

city: East Lansing

first: Arif

middle: Murat

last: Kocabas

email: kocabas@msu.edu, hotu@bidmc.harvard.edu

state: MI

address: B270 Anthony Hall

department: Animal Science

institute: Michigan State University

summary: The identification of genes and deduced pathways from the mature human oocyte can help us better understand oogenesis, folliculogenesis, fertilization, and embryonic development. Human metaphase II oocytes were used within minutes after removal from the ovary, and its transcriptome was compared with a reference sample consisting of a mixture of total RNA from 10 different normal human tissues not including the ovary. RNA amplification was performed by using a unique protocol. Affymetrix Human Genome U133 Plus 2.0 GeneChip arrays were used for hybridizations. Compared with reference samples, there were 5,331 transcripts significantly up-regulated and 7,074 transcripts significantly down-regulated in the oocyte. Of the oocyte up-regulated probe sets, 1,430 have unknown function. A core group of 66 transcripts was identified by intersecting significantly up-regulated genes of the human oocyte with those from the mouse oocyte and from human and mouse embryonic stem cells. GeneChip array results were validated using RT-PCR in a selected set of oocyte-specific genes. Within the up-regulated probe sets, the top overrepresented categories were related to RNA and protein metabolism, followed by DNA metabolism and chromatin modification. This report provides a comprehensive expression baseline of genes expressed in in vivo matured human oocytes. Further understanding of the biological role of these genes may expand our knowledge on meiotic cell cycle, fertilization, chromatin remodeling, lineage commitment, pluripotency, tissue regeneration, and morphogenesis.

overall_design:
We generated a database of the human oocyte transcriptome by comparing the transcripts in the oocyte with the reference samples, which contain mRNA from several somatic tissues.

Human oocytes were obtained from three patients undergoing an assisted reproductive treatment (ART) at the Unit of Reproductive Medicine of Clinica Las Condes, Santiago, Chile. It is important to emphasize that the routine in vitro fertilization protocol at Clinica Las Condes calls for fertilizing only those oocytes that will be transferred into the uterus of the patient. Therefore, there is always a surplus of oocytes. We then had the opportunity to use specific criteria to select donors as follows: (i) <35 years old, (ii) reproductively healthy with regular ovulatory cycles, (iii) male factor as the only cause of infertility, and (iv) considerable number of developing follicles that assured spared oocytes. The experimental protocol was reviewed and approved by a local independent Ethics Review Board. All donors signed informed consent. At the time this manuscript was submitted, all three donors had already conceived; two of them got pregnant during the ART cycle in which our samples were collected, and the third one got pregnant after a spontaneous cycle with artificial insemination using donated sperm. Ovarian stimulation, oocyte retrieval, and cell lysis were performed as described in Supporting Materials and Methods, which is published as supporting information on the PNAS web site.

Three groups of 10 oocytes each were used. Reference RNA (100 μg) was prepared by mixing 10 μg of total RNA from each of 10 different normal human tissues, including skeletal muscle, kidney, lung, colon, liver, spleen, breast, brain, heart, and stomach (Ambion).

Transcriptional profile of each sample was probed by using Affymetrix Human Genome U133 Plus 2.0 GeneChips.

first: Javier

last: Crosby

first: Pablo

last: Ross

first: Hasan

middle: H

last: Otu

first: Zeki

last: Beyhan

first: Handan

last: Can

first: Wai-Leong

last: Tam

first: Guilherme

last: Rosa

first: Robert

middle: G

last: Halgren

first: Bing

last: Lim

first: Emilio

last: Fernandez

first: Jose

middle: B

last: Cibelli


title: Genomic Counter-Stress Changes Induced by Mind-Body Practice

status: Public on Jul 05 2008

first: Towia

last: Libermann

address: 99 Brookline Ave.

institute: Beth Israel Deaconess Medical Center

summary:
Mind-body practices that elicit the relaxation response (RR) have been used worldwide for millennia to prevent and treat disease. The RR is believed to be the counterpart to stress response and is characterized by decreased oxygen consumption, increased exhaled nitric oxide, and reduced psychological distress. Individuals experiencing chronic psychological stress have the opposite pattern of physiology and a characteristic transcriptional profile. We hypothesized that consistent, long-term practice of RR techniques results in characteristic changes in gene expression. We tested this hypothesis by assessing the transcriptional profile of whole blood in healthy, long-term practitioners of daily RR practice (group M) in comparison to healthy controls (group N1). The signature obtained has been validated on new subject data.
Keywords: time course

overall_design: In the study, the gene expression profiling was performed on individuals with a long-term RR practice (group M; n=19) or those with no prior RR experience; novice (group N1; n=19). Group N1 novices, furthermore, underwent 8-weeks of RR training (Group N2; n=20) for the prospective analysis.As a validation of results , we developed an independent validation sets that includes gene expression profiling on 4 N1, 4 N2 and 6 M subjects.

first: Jeffery

last: Dusek

last: Out

first: Ann

last: Wohlhueter

first: Manoj

last: Bhasin


status: Public on Jul 01 2008

city: London

first: Tim

last: Forshew

address: 4 Newark Street

department: Centre for Neuroscience

country: United Kingdom

institute: Queen Mary's School of Medicine and Dentistry

summary:
Expression profiling of MRC5, IFN gamma treated MRC5 and PGF cells.
Keywords: cell type comparison, IFN gamma treatment.

overall_design: MRC5 cells were treated for 24 hours with IFN gamma (200 IU/ml) and their expression profile was compared to untreated MRC5 and PGF cells.

first: Diego

last: Ottaviani


title: Effects of Prenatal Tobacco Exposure on Gene Expression Profiling in Umbilical Cord Tissue

status: Public on Jun 30 2008

city: Farmington

first: Winfried

last: Krueger

state: CT

address: 263 Farmington Aveneu

department: Genetics & Developmental Biology

institute: University of Connecticut Health Center

summary:
Maternal smoking doubles the risk of delivering a low birth weight infant. The purpose of this study was to analyze differential gene expression in umbilical cord tissue as a function of maternal smoking, with an emphasis on growth-related genes.  We recruited  15 pregnant smokers and 15 women  who never smoked during pregnancy to participate  RNA was isolated from umbilical cord tissue collected and snap frozen at the time of delivery.  Microarray analysis was performed using the Affymetrix GeneChip Scanner 3000.Six hundred seventy-eight probes corresponding to 545 genes were differentially expressed (i.e., an intensity ratio that exceeded +/-1.3 and a corrected significance value p < 0.005) in tissue obtained from smokers versus nonsmokers.  Genes important for fetal growth, angiogenesis, or development of connective tissue matrix were up-regulated among smokers. The most highly up-regulated gene was CSH1, a somatomammotropin gene.  Two other somatomammotropin genes (CSH2 and CSH-L1) were also up-regulated. The most highly down-regulated gene was APOBEC3A; other down-regulated genes included those that may be important in immune and barrier protection. PCR validation of the three somatomammotropin genes showed a high correlation between qPCR and microarray expression. Consequently, maternal smoking may be associated with altered gene expression in the offspring.

Keywords: substance exposure analysis

overall_design:
30 samples of two groups consiting of 15 smokers (smk) and 15 nonsmokers (nonsmk) were analyzed without replicates.

Note: Non-corrupt .CEL files are not available for the Samples in this study.

first: Naveed

last: Hussein

first: Jonathan

last: Covault

first: Steve

last: Walsh

first: Henry

last: Kranzler

first: Cheryl

last: Oncken


title: Effect of IL-17 on human vascular smooth muscle cells

status: Public on Jun 28 2008

city: New Haven

first: Raymond

middle: Emile

last: Eid

address: 10 Amistad Street

department: Surgery

institute: Yale University

summary:
Investigate the effect of recombinant human IL-17A on vascular smooth muscle cells cultured from human aortas.
Keywords: Dose response

overall_design: SMCs from the aortas of three different donors were cultured in M199 media supplemented with 20% FCS and used at passage 3. The cells were either not treated or treated with IL-17 at 100 ng/ml for 6 hr. The six samples were labeled as Untreated or IL-17-treated from three independent experiments labeled A, B, and C.

first: George

last: Tellides


title: Vitamin D sterol effects on coronary ASMC genes

city: Thousand Oaks

first: Lori

last: Twehues

state: CA

address: One Amgen Ctr

department: Computational Biology

institute: Amgen, Inc

summary:
Chondro/osteoblastic and cardiovascular-disease associated genes are modulated in human coronary artery smooth muscle cells that calcify in the presence of phosphate and vitamin D sterols.
Looking at the effect of media conditions with and without Vitamin D, paracalcitriol (a vitamin D analog), or R568 (a calcimimetic) vs. dose and time on calcification of human coronary smooth muscle cells.

overall_design: CASMCs were exposed to differentiation medium [beta glycerophosphate (10 mM), ascorbic acid (50 mg/ml), and dexamethasone (10-9 M) with and without calcitriol or paricalcitol (10-8 M) for 7 days, and total RNA was examined by microarray.

first: Vicki

last: Shalhoub


status: Public on Jun 26 2008

city: Sacramento

first: Jeffrey

last: Gregg

institute: University of California, Davis School of Medicine

summary:
Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD).
Keywords: autism analysis

middle: P

first: Lisa

last: Lit

first: Colin

last: Baron

first: Irva

last: Hertz-Picciotto

first: Wynn

last: Walker

first: Ryan

last: Davis

last: Croen

first: Sally

last: Ozonoff

first: Robin

last: Hansen

first: Isaac

middle: N

last: Pessah

first: Frank

last: Sharp


title: Prostate cancer fiber model

city: vancouver

first: Gang

last: Wang

state: BC

address: 675 W10th Ave.

department: Genome Sciences Centre

country: Canada

institute: BC Cancer Agenecy

summary:
hormonal progression in prostate cancer fiber model
Keywords: prostate cancer, hormonal progression, fiber model

overall_design: The LNCaP Hollow Fiber model of prostate cancer was appied. A total of 24 fibers were implanted in each animal, in bundles of eight fibers at three different regions in the animal. Castration of mice was performed At each time point, eight fibers from the same mouse were harvested and total RNA was isolated from LNCaP cells grown inside the fibers using Trizol

first: Marianne

middle: D

last: Sadar


title: Multiparameter Immune Profiling of Operational Tolerance in Liver Transplantation

status: Public on Jun 25 2008

city: Barcelona

first: Alberto

last: Sanchez-Fueyo

address: Villarroel 170

department: Liver Transplantation Unit

institute: Hospital Clinic Barcelona / IDIBAPS

summary: mmunosuppressive drugs can be completely withdrawn in up to 20% of liver transplant recipients, commonly referred to as ‘operationally’ tolerant. Immune characterization of these patients, however, has not been performed in detail, and we lack tests capable of identifying tolerant patients among recipients receiving maintenance immunosuppression. In the current study we have analyzed a variety of biological traits in peripheral blood of operationally tolerant liver recipients in an attempt to define a multiparameter ‘fingerprint’ of tolerance. Thus, we have performed peripheral blood gene expression profiling and extensive blood cell immunophenotyping on 16 operationally tolerant liver recipients, 16 recipients requiring on-going immunosuppressive therapy, and 10 healthy individuals. Microarray profiling identified a gene expression signature that could discriminate tolerant recipients from immunosuppression-dependent patients with high accuracy. This signature included genes encoding for ?d T-cell and NK receptors, and for proteins involved in cell proliferation arrest. In addition, tolerant recipients exhibited significantly greater numbers of circulating potentially regulatory T-cell subsets (CD4+CD25+ T-cells and Vd1+ T cells) than either non-tolerant patients or healthy individuals. Our data provide novel mechanistic insight on liver allograft operational tolerance, and constitute a first step in the search for a non-invasive diagnostic signature capable of predicting tolerance before undergoing drug weaning.

overall_design: The complete database comprised the expression measurements of 54 675 genes for nine operationally tolerant (TOL) and eight immunosuppression-dependent (ID) samples.


title: The MILE (Microarray Innovations In LEukemia) study pre-phase

status: Public on Jun 24 2008

city: Pleasanton

first: Rachel

last: Li

address: 4300 Hacienda Dr.

institute: Roche

summary:
An international standardization program towards the application of gene expression profiling in routine leukaemia diagnostics: The MILE study pre-phase.
A total of 11 laboratories from three continents performed 204 analyses using a whole-genome expression microarray.
In an effort to standardize the microarray procedure, each participating centre was equipped with identical hardware, software, and reagents. Designated study operators received intensive individual training on the sample preparation protocol.
Keywords: Standardization and reproducibility of microarray analysis

overall_design:
This study is part of the MILE Study (Microarray Innovations In LEukemia) program, headed by the European Leukaemia Network (ELN) and sponsored by Roche Molecular Systems, Inc.
Each laboratory prepared two separate cell line total RNA samples, as well as three replicate leukaemia patient lysates in two distinct project stages: (i) a five-day course of protocol training, and (ii) independent proficiency testing.
Using unsupervised, supervised, and r² correlation analyses we demonstrated that microarray analysis can be performed not only with remarkably high intra-laboratory reproducibility but also with comparable quality and reliability between eleven distinct laboratories.


title: Performance comparison of Affymetrix and Illumina microarray technologies_AffymetrixDataset

status: Public on Jun 27 2008

city: Paris

first: Francois

last: Cambien

state: France

address: 91 Bd de l'Hôpital

department: Cardiovascular Genomics

institute: INSERM

summary:
The present study was conducted to compare the ability of Affymetrix and Illumina microarray technologies to characterize the differential gene expression profiles of human monocytes and monocyte-derived-macrophages.
Keywords: Type Cross-platform comparison Summary

overall_design:
Blood samples were obtained from patients with symptoms of acute coronary syndrome who had undergone coronary angiography at the department of cardiology of the Pitié-Salpêtrière Hospital, Paris and who had one stenosis >50 % diagnosed in at least one major coronary artery.
RNA samples were extracted from monocyte and monocyte derived macrophage cells. Five biological replicates for each type of sample were hybridized in parallel to the Affymetrix HGU133 plus 2.0 and Illumina Bead Chip Human-6 v1 platforms. In addition, a reference list of differentially expressed genes was generated from a larger number of hybridizations (mRNA from 86 individuals) using a third technology (the academic RNG/MRC two-color chip) and was used as reference to assess the performance of the 2 platforms based on 10 samples. The internal consistency of each platform, the overlap in lists of genes identified as differentially expressed generated on each array type and the biological relevance of significant genes identified on each platform (Gene Ontology (GO) classes enrichments) were assessed.

first: Seraya

last: Maouche

first: Odette

last: Poirier

first: Tiphaine

last: Godefroy

first: Robert

last: Olaso

first: Ivo

last: Gut

first: Jean-Phillipe

last: Collet

first: Gilles

last: Montalescot

first: François


title: HEK293 cells overexpressing HNF4a2 wild type or mutant forms C106R or R154X

status: Public on Jun 20 2008

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
Identification of genes regulated by the transcription factor HNF4a2
Keywords: ordered

overall_design: We used microarrays to identify genes regulated by the transcription factor HNF4a2. HEK293 cell lines containing doxycyclin-inducible wilt type or mutant forms of HNF4a2m which were introduced by FRT/FLP mediated recombination into FLP-In T-REx 293 cells (Invitrogen) were treated for 24 hours with 1 µg/ml doxycyclin. Gene expression profiles of induced and noninduced cells were compared to identify HNF4 regulated targets.

first: Karen

last: Grigo

first: Andrea

last: Wirsing

first: Belen

last: Lucas

first: Gerhart

middle: U

last: Ryffel


title: E. coli K12 Bw25113/pCA24N-hha with 2 mM IPTG vs BW25113/pCA24N with 2 mM IPTG

status: Public on Jun 17 2008

city: State College

first: Thomas

middle: K.

last: Wood

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary:
gene expression profiles by overexpressing Hha from pCA24N-hha using 2 mM IPTG induction in BW25113 wild type suspension cells in LB medium at 37C relative to BW25113 carrying the empty vector plasmid in the same test conditions.
Keywords: overexpression, gene expression profiles

overall_design:
Strains: E. coli K12 BW25113/pCA24N, BW25113/pCA24N-hha
Growth conditions: grow culture in LB medium at 37C to OD600 0.1 and add 2 mM IPTG to induce, and grow to OD600 0.5 to collect cells. RNA was extraction, and gene expression profiles were evaluated.

first: Rodolfo

last: Garcia-Contreras

first: Xue-Song

last: Zhang

first: Younghoon

last: Kim


title: Variability in Small Airway Epithelial Gene Expression Among Normal Smokers

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Despite overwhelming data that cigarette smoking causes chronic obstructive pulmonary disease (COPD), only a minority of chronic smokers are affected, strongly suggesting that genetic factors modify susceptibility to this disease. We hypothesized that there are individual variations in the response to cigarette smoking, with variability among smokers in expression levels of protective / susceptibility genes. Affymetrix arrays and TaqMan PCR were used to assess the variability of gene expression in the small airway epithelium obtained by fiberoptic bronchoscopy of 18 normal non-smokers, 18 normal smokers and 18 smokers with COPD.
We identified 201 probesets representing 150 smoking-responsive genes that were significantly up- or down-regulated, and assessed the coefficient of variation in expression levels among the study population. Variation was a reproducible property of each gene as assessed by different microarray probesets and realtime PCR and was observed in both normal smokers and smokers with COPD. There was greater individual variability in smokers with COPD than in normal smokers. The majority of these highly variable smoking responsive genes were in the functional categories of signal transduction, xenobiotic degradation, metabolism, transport, oxidant-related and transcription. A similar pattern of the same highly variable genes was observed in an independent data set.We propose that there is likely genetic diversity within this subset of genes with highly variable individual to individual responses of the small airway epithelium to smoking, and this subset of genes represent putative candidates for assessment of susceptibility/protection from disease for future gene-based epidemiological studies for the risk of smokers for COPD.
Keywords: disease state analysis

first: Zeinab

last: Ammous

first: Neil

last: Hackett

first: Marcus

middle: W

last: Butler

first: Tina

last: Raman

first: Igor

last: Dolgalev

first: Tim

last: O'Connor

first: Ben-Gary

last: Harvey

first: Ronald

last: Crystal


title: Genomic alterations and gene expression in primary diffuse large B cell lymphomas of immune privileged sites

status: Public on Jun 19 2008

city: Groningen

first: Marije

last: Booman

department: Pathology

country: Netherlands

institute: University Medical Center Groningen

type: Genome variation profiling by genome tiling array

summary:
Primary diffuse large B cell lymphomas of different immune-privileged sites (IP-DLBCL) share many clinical and biological features, such as a relatively poor prognosis, preferential dissemination to other immune-privileged sites and deletion of the HLA region, which suggests that IP-DLBCL represents a separate entity. To further investigate the nature of IP-DLBCL, we investigated site-specific genomic aberrations in 16 testicular, 9 central nervous system (CNS) and 15 nodal DLBCL using array-CGH. We also determined minimal common regions of gain and loss. Using robust algorithms, the array-CGH data were combined with gene expression data to explore pathways deregulated by chromosomal aberrations.
Keywords: comparative genomic hybridisation, gene expression, tumor type comparison

overall_design: Whole tissue sections of 16 testicular, 9 central nervous system (CNS) and 15 nodal DLBCL were used for isolation of genomic DNA and total RNA.  Genomic aberrations were determined using an in house printed CGH array containing ~3700 large genomic insert clones. Gene expression was analyzed on Affymetrix HU133 plus 2.0 oligo arrays. Gene expression data and arrayCGH data were combined using the R program ACE-it.

first: Karoly

last: Szuhai

first: Andreas

last: Rosenwald

first: Elena

last: Hartmann

first: Hanneke

middle: C

last: Kluin-Nelemans

first: Daphne

last: de Jong

first: Ed

last: Schuuring

first: Philip

middle: M

last: Kluin


title: Rhesus Macaque gene expression data obtained using Rhesus Macaque Array or Human Genome U133 Plus 2.0 Array

status: Public on Jun 15 2008

city: Providence

first: Fenghai

last: Duan

state: RI

address: 121 S. Main Street

department: Biostatistics

institute: Brown University

summary:
The primary goal of this study was to compare the performances of Rhesus Macaque Genome Array and Human Genome U133 Plus 2.0 Array with respect to the detection of differential expressions when rhesus macaque RNA extracts were labeled and hybridized.
The secondary goal of this study was to investigate the effect of mismatch position on signal strength in Affymetrix GeneChips by examining naturally occurring mismatches between rhesus macaque transcripts and human probes from Human Genome U133 Plus 2.0 Array.
The primary goal of this study was to compare the performances of Rhesus Macaque Genome Array and Human Genome U133 Plus 2.0 Array with respect to the detection of differential expressions when rhesus macaque RNA extracts were labeled and hybridized.
The secondary goal of this study was to investigate the effect of mismatch position on signal strength in Affymetrix GeneChips by examining naturally occurring mismatches between rhesus macaque transcripts and human probes from Human Genome U133 Plus 2.0 Array.
Keywords: cross hybridization

platform_organism:
Macaca mulatta
Homo sapiens

overall_design:
Rhesus macaque RNA from five sources (immortalized fibroblasts, cerebral cortex, pancreas, testes and thymus) was divided into two sets of aliquots of equal amount.  Samples from each of the five sources were labeled and hybridized with either Rhesus Macaque Genome Array or two Human Genome U133 Plus 2.0 Array.
Rhesus macaque RNA from five sources (immortalized fibroblasts, cerebral cortex, pancreas, testes and thymus) was divided into two sets of aliquots of equal amount.  Samples from each of the five sources were labeled and hybridized with either Rhesus Macaque Genome Array or two Human Genome U133 Plus 2.0 Array.

first: Eliot

middle: R

last: Spindel

first: Robert

last: Norgren


title: Genome-wide analysis of gene expression patterns in human liver cancers

status: Public on Jul 11 2008

city: Taipei

first: Ann-Ping

last: Tsou

address: No. 155, Sec. 2, Li-Nong St., Beitou District

country: Taiwan

institute: National Yang-Ming University

summary:
To investigate the mechanisms of liver cancer progression and metastasis, we did expression profiling of human liver cancer and benign tissues.
Keywords: gene expression array-based (RNA / in situ oligonucleotide)

overall_design:
Total RNA was extracted from human liver cancer at
various stages (T1-1~4, T3-1~6), 2 normal human livers and HuH7 cell line. Genes showed differentially up- or downregulated
by two-fold with respect to the normal human livers
were identified using GeneSpring software version 7.2 (Silicon
Genetics, Agilent Technologies).

first: Yu

middle: L

last: Liao

first: Gar

middle: Y

last: Chau

first: Yat

first: Ann


title: Gene expression profiling in pediatric meningococcal sepsis reveals dynamic changes in NK-cell and cytotoxic molecules

status: Public on Jun 14 2008

city: Rotterdam

first: Marieke

last: Emonts

address: Dr Molewaterplein 50, room Ee15-02

institute: Erasmus MC

summary:
Objective. Meningococcal sepsis remains an important cause of childhood morbidity and mortality. Largely due to logistic complexities of research in young children with acute life-threatening disease, very little is known regarding differential expression kinetics and molecular regulation of immune response genes in leukocyte subsets.
Materials and methods. In this prospective case-control study, six children with meningococcal sepsis were included. Blood was drawn at four time points (t=0, t=8, t=24 and t=72 h after admission to the paediatric intensive care unit). Blood was also collected from matched controls. Detailed immunophenotyping of leukocytes was performed; RNA isolated from whole blood, lymphocytes, monocytes, and granulocytes was used to perform Affymetrix micro-array gene expression analysis.
Results and conclusion. There were no differences in total leukocyte count between patients and controls. In contrast to previous in vitro studies we observed an unexpected decrease in NK cell numbers, as well as downregulation of NK cell specific and cytotoxic T-cell related gene expression in patients with meningococcal septic shock. By contrast, expression of genes, involved in innate immunity and several other pathways, differed between the different leukocyte subpopulations in a dynamic fashion. Compared to previously reported gene expression profiles, it was possible to define a meningococcal sepsis specific expression profile.

overall_design:
In this prospective case-control study, six children with meningococcal sepsis were included. Blood was drawn at four time points (t=0, t=8, t=24 and t=72 h after admission to the paediatric intensive care unit). Blood was also collected from matched controls. Detailed immunophenotyping of leukocytes was performed; RNA isolated from whole blood, lymphocytes, monocytes, and granulocytes was used to perform Affymetrix micro-array gene expression analysis.
No replicates were performed.
Table 4. Results of between-subject analyses.

Source    Time (h) ca          co/ca at t=T
Blood     t0:  ca:2 3, co: a b c; t8:  2; t24 :ca:1 2 3; t72: ca:1 2.
Lym       t0: ca:2 3, co:a b c d;t8: ca:1 3 4;t24: ca:1 2 3 4 6; t72: ca: 1 2.
Mono      t0:ca: 1 3 4 6, co: a b d; t8: ca:1 2 3; t24:ca: 1 2 3; t72: ca:1.

Numbers represent the patient identification numbers.
Characters represent the individual controls.

first: Martine

last: Maat

first: Dick

last: de Ridder

first: Tom

last: Schonewille

first: Jan

last: Hazelzet

first: Jon

last: Laman

first: Jacques

last: van Dongen

first: Peter

last: Hermans

first: Frank

last: Staal

first: Ronald

last: de Groot


title: Carcinoma Associated Fibroblast Like Differentiation of Human Mesenchymal Stem Cells

status: Public on Jun 23 2008

city: New Brunswick

first: Pravin

last: Mishra

state: NJ

address: 195 Little Albany St.

department: Pharmacology

institute: UMDNJ

summary:
Carcinoma associated fibroblasts (CAFs) have recently been implicated in important aspects of epithelial solid tumor biology such as neoplastic progression, tumor growth, angiogenesis, and metastasis. However, neither the source of CAFs nor the differences between CAFs and fibroblasts from non-neoplastic tissue have been well defined. In this study we demonstrate that human bone marrow-derived mesenchymal stem cells (hMSCs) exposed to tumor-conditioned medium (TCM) over a prolonged period of time assume a CAF-like myofibroblastic phenotype. More importantly, these cells exhibit functional properties of CAFs including sustained expression of stromal derived factor 1 (SDF-1) and the ability to promote tumor cell growth both in vitro and in an in vivo co-implantation model and expression of myofibroblast markers including α-smooth muscle actin and fibroblast surface protein. hMSCs induced to differentiate to a myofibroblast-like phenotype using 5-azacytidine do not promote tumor cells growth as efficiently as hMSCs cultured in tumor-conditioned medium nor do they demonstrate increased SDF-1 expression. Furthermore, gene expression profiling revealed similarities between TCM exposed hMSCs and carcinoma associated fibroblasts. Taken together these data suggest that hMSCs are a source of carcinoma associated fibroblasts and can be used in the modeling of tumor-stroma interactions. To our knowledge this is the first report demonstrating that hMSCs become activated and resemble carcinoma associated myofibroblasts upon prolonged exposure to conditioned medium from MDAMB231 human breast cancer cells.
Keywords: differentiation

overall_design: The experiment was done to test the differentiation of hMSCs upon exposure to tumor condition media or epigenetic modifiers.

middle: J

first: Prasun

first: Rita

last: Humeniuk

first: Daniel

last: Medina

first: Gabriela

last: Alexe

first: Jill

last: Mesirov

first: Sridhar

last: Ganesan

first: John

last: Glod

first: Debabrata

last: Banerjee


title: Expression data from human mesenchymal stem cells (#4F1560)

status: Public on Jun 06 2008

city: Kawasaki

first: Shihori

last: Tanabe

state: Kanagawa

address: 3-25-26, Tonomachi, Kawasaki-ku

department: Division of Risk Assessment

country: Japan

institute: National Institute of Health Sciences

summary:
Human mesenchymal stem cells are expected to be a useful tool for cellular therapy. We used microarrays to detail the gene expression profiles and selected candidate biomarkers that indicate the culture stage of the cells.
Keywords: mesenchymal stem cells, passage numbers

overall_design: Human mesenchymal stem cells were cultured and subjected to RNA extraction and hybridization on microarrays. Cell cultures in passage numbers 5, 7, 9, 13, 14, 21, and 28 of lot#4F1560 were subjected to the microarray analysis.

first: Yoji

last: Sato

first: Takayoshi

last: Suzuki

first: Kazuhiro

first: Taku

last: Nagao

first: Teruhide

last: Yamaguchi


title: Expression data from Helicobacter positive and negative human gastritis samples

status: Public on Jun 04 2008

city: Budapest

first: Norbert

last: Solymosi

state: Budapest

address: István u. 2.

country: Hungary

institute: ATE

summary:
The whole-genome oligonucleotide microarray analysis gives an opportunity for studying the unidentified gene expression background of the idiopathic and H.pylori related gastric erosive alterations. Using microarrays we compared the whole genome gene expression profile of HP+ and HP- gastric erosions and normal adjacent mucosa to explain the possible role and response to HP infection and to get morphology related  mRNA expression patterns.
Keywords: whole genomic expression

overall_design: Total RNA was extracted from frozen gastric biopsy specimens of  patients with Helicobacter pylori positive (HP+) and Helicobacter pylori negative (HP-) antrum erosions (ER+), and the corresponding, adjacent normal mucosae (ER-) and hybridized on Affymetrix HGU133 Plus 2.0 microarrays

first: Orsolya

last: Galamb

first: Balázs

last: Győrffy

first: Zsolt

last: Tulassay

first: Béla

last: Molnár

first: Sándor

last: Spisák


title: Transcription profiling of biopsies from the descending colon of control subjects

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

institute: University of Copenhagen

summary: These samples were all taken from patients who underwent investigations including colonoscopy but where all tests were normal and the diagnosis of irritable bowel syndrome was reached. These observations have been used as references in studies of colonic gene expression in inflammatory bowel diseases

overall_design: 17 samples were analyzed each originating from an individual subject. No replicas.

first: Claudio

last: Csillag

first: Ole

last: Nielsen


title: Expression data from kidney and liver

status: Public on Jun 01 2008

city: Chicago

first: John

last: Marioni

state: IL

address: 920 East 58th Street

department: Human Genetics

institute: University of Chicago

summary:
mRNA expression differences between the liver and kidney of an adult male (homo sapien) were investigated using three technical replicates.
The purpose of the experiment was to compare array data generated using Affymetrix with measures of expression obtained using RNAseq (a sequencing approach for measuring expression that utilizes Solexa technology).
Keywords: kidney, liver

overall_design: RNA samples from the liver and kidney were extracted within 6 hours post mortem. Aliquots of mRNA were extracted and hybridized to three Affymetrix U133 Plus 2.0 arrays (three technical replicates). The purpose of the study was to compare the Affymetrix array data with expression results obtained from RNAseq (Solexa)

first: Yoav

last: Gilad


title: Performance comparison of Affymetrix and Illumina microarray technologies

first: Francois

last: Cambien

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

overall_design: Refer to individual Series


title: Gene expression data from non-malignant fallopian tube epithelium and high grade serous carcinoma.

status: Public on May 31 2008

city: Toronto

first: Patricia

middle: A

last: Shaw

state: Ontario

address: 200 Elizabeth St

department: Department of Pathology

institute: University Health Network

summary:
The purpose of this study was to identify molecular alterations potentially involved in predisposition to adnexal serous carcinoma (SerCa) in the non-malignant fallopian tube epithelium   (FTE) of BRCA1/2-mutation carriers, given recent evidence implicating the distal FTE as a common source for SerCa.
Keywords: disease state analysis

overall_design: We obtained and compared gene expression profiles of laser capture microdissected non-malignant distal FTE from 12 known BRCA1/2-mutation carriers (FTEb) and 12 control women  (FTEn) during the luteal and follicular phase, as well as 13 high grade tubal and ovarian SerCa.

first: Alicia

last: Tone

first: Heather

last: Begley

first: Monika

last: Sharma

first: Joan

last: Murphy

first: Barry

last: Rosen

first: Theodore

last: Brown


title: In vitro model of somitogenesis using human fibroblasts (kusum-affy-human-554575)

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Scoliosis is a common disorder, affecting one out of every twenty females.  Some forms of scoliosis are congenital, resulting from disruptions in early spinal development.  The spinal column is patterned during a cycling process called somitogenesis, and is the first musculoskeletal structure formed during development.  Genes in the notch signaling pathway regulate somitogenesis, and display oscillatory expression in synchrony with somite formation.  During somitogenesis, oscillatory expression of genes in the notch and wnt signaling pathways plays a key role in regulating segmentation. These oscillations in expression levels are elements of a species-specific developmental mechanism.  The periodicity and components of the human clock have recently been described by our group (William et al., Dev Biol, 2007). In that publication, we showed that a human mesenchymal stem/stromal cell (MSC) model can be induced to display oscillatory gene expression, including known cycling genes such as HES1 that displayed a period of 5 hours. We also observed cycling of Hes1 expression in mouse C2C12 myoblasts with a period of 2 hours, consistent with previous in vitro and embryonic studies. Furthermore, we used microarray and quantitative PCR (Q-PCR) analysis to identify additional genes that display oscillatory expression both in vitro and in mouse embryos. We confirmed oscillatory expression of the notch pathway gene Maml3 and the wnt pathway gene Nkd2 by whole mount in situ hybridization analysis and Q-PCR. Studies in mouse cell lines, including fibroblasts and PC12 neuronal cells, by R. Kageyema (Kyoto University, Hirata et al., Science, 2002) have shown that a number of mouse cell types can be synchronized to display oscillatory expression.  In this study, we extend our analysis of human cells to human primary fibroblasts.
Developing an in vitro model of somitogenesis using human mesenchymal stem cells and fibroblasts
a. Induce cycling gene expression in human mesenchymal stem cells (MSC) and fibroblasts and identify oscillatory genes (using Affymetrix U133 GeneChips®).  Compare lists of oscillatory genes identified in these two human cell types.
b. Characterize and validate mouse homologues of oscillatory genes for expression during somitogenesis.  Using notch and wnt pathway mutants and cultured half embryos, determine if these oscillatory genes also display cycling expression during somitogenesis.
We hypothesized that human fibroblasts could be synchronized to display oscillatory expression of notch and wnt pathway genes, including the marker gene HES1.  Preliminary quantitative analysis by Taqman-based Real-Time PCR for these samples confirms that HES1 expression displays oscillatory expression.
Homo sapiens fibroblasts were maintained in culture medium (DMEM high glucose with 10% fetal bovine serum, FBS), which was replaced twice weekly. The cells were then seeded at a density of 6,000-10,000 cells/cm2 and expanded in DMEM high glucose with 10% FBS. After 5-7 days of incubation at 37C in a humidified atmosphere containing 5% carbon dioxide, cells were detached with 0.05% trypsin for 2 minutes at confluency.
Cells were synchronized using low serum treatment, which has been described previously for Hes1 (Hirata et al., 2002). Cell culture synchronization is required to assay oscillatory expression levels, otherwise the oscillations of individual cells would be out of phase and cancel one another. Synchronized cells will gradually desynchronize, leading to diminished oscillatory amplitude. Briefly, synchronization was carried out as follows: T-25 cm flasks were set up in parallel. These cells were grown to 90% confluence in DMEM supplemented with 10% FBS (UCB-MSC), then incubated in DMEM with only 0.2% FBS for 24 hours, and returned to DMEM supplemented with FBS. Samples were collected at 1 hr. intervals from 0 to 12 hours. In addition, an unsynchronized cell culture was sampled. Total RNA was isolated from cells in culture using the RNeasy Mini Kit (Qiagen) and quantitated using a Nanodrop 2000.

Keywords: time-course

overall_design: A biological replicate of the submitted project (hCycle11) time-series was carried out in parallel has been collected (hCycle12). We have evaluated both biological replicates by Q-PCR. We have selected hCycle11 for HG-U133A Plus 2.0 analysis, and we reserve hCycle12 for possible future microarray analysis or comparison by Q-PCR.

first: Kenro

last: Kusumi


title: Hs 294T Cells Treated with Elesclomol Alone or in Combination with Paclitaxel Compared to DMSO Treated

status: Public on May 29 2008

city: Lexington

first: Jane

middle: Frances

last: Kepros

address: 45 Hartwell Ave

department: Biology

institute: Synta Pharmaceuticals Corp.

summary:
We used microarrays to detail gene expression changes in Hs 294T human melanoma cells after treatment with elesclomol alone, or in combination with paclitaxel, to aide in identifing the mechnism of action of elesclomol.

Keywords: treatment

overall_design: Hs 294T human melanoma cells were grown in vitro.  They were seeded at a low density and were left untreated, treated with the vehicle, treated with elesclomol, treated with paclitaxel, or treated in combination with both elesclomol and paclitaxel.  They were incubated for 6 hours before harvesting.

middle: F


title: Hs 294T Cells Treated with Elesclomol Alone or in Combination with NAC Compared to DMSO Treated

summary:
We used microarrays to detail gene expression changes in Hs 294T human melanoma cells after treatment with elesclomol alone, or in combination with NAC, to aide in identifing the mechnism of action of elesclomol.

Keywords: treatment

overall_design: Hs 294T human melanoma cells were grown in vitro.  They were seeded at a low density and were left untreated, treated with the vehicle, treated with elesclomol, treated with NAC, or treated in combination with both elesclomol and NAC.  The cells treated with NAC were given the NAC 30 minutes prior to additional treatments.  They were incubated for 6 hours before harvesting.


title: Gene Expression Patterns Involved in the Malignant Transformation and Progression of Metastatic Melanoma

status: Public on May 28 2008

city: Tampa

first: Sean

last: Yoder

state: FL

address: 12902 Magnolia Dr.

department: Molecular Genomics Core Facility

institute: Moffitt Cancer Center & Research Institute

summary:
Metastatic melanoma is a deadly disease while non-metastatic melanoma and other cutaneous tumor types are usually cured with surgical removal of the primary tumors.  This study evaluated gene expresion to determine if gene expression differences existed which would allow one to identify the metastatic tumors based on the expression of specific genes.
Keywords: multiple tissue comparison

overall_design: Tumor samples were collected from patients with various cutaneous tumors, flash frozen, and then processed for gene exprression analysis using microarrays.  The pool of tissues includes enough metastatic samples and non-metastatic samples to identify a gene expression signature associated with the outgrowth of the metastatic tumor.

first: Adam

middle: I

last: Riker

first: Steven

last: Enkemann

first: SuHu

last: Liu

first: Suping

last: Ren

first: Jon

last: Briggs

first: Yaguang

last: Xi

first: Paul

last: Howell

last: Eschrich

first: Adil

last: Daud

last: Messina

first: Matthew

last: D'Alessio

first: Vernon

middle: K

last: Sondak

first: Richard

last: Jove

first: Ralf

last: Beuttner

first: Rajeev

middle: S

last: Samant

first: Lalita

last: Shevde

first: Jingfang

last: Ju

first: Oystein

last: Fodstad

first: Jaime

last: Matta


title: The platelet transcriptome reveals changes in arginine metabolic pathways in patients with sickle cell disease

status: Public on May 22 2008

city: Bethesda

first: Xiuli

last: Xu

state: MD

address: Building 10-CRC, Room 5-5140

department: VMB,

institute: NHLBI, NIH

summary:
In sickle cell disease, ischemia-reperfusion injury and intravascular hemolysis produce endothelial dysfunction and vasculopathy characterized by reduced nitric oxide (NO) and arginine bioavailability. Recent functional studies of platelets in patients with sickle cell disease reveal a basally activated state, suggesting that pathological platelet activation may contribute to sickle cell disease vasculopathy. Studies were therefore undertaken to examine transcriptional signaling pathways in platelets that may be dysregulated in sickle cell disease. We demonstrate and validate here the feasibility of comparative platelet transcriptome studies on clinical samples from single donors, by the application of RNA amplification followed by microarray-based analysis of 54,000 probe sets. Data mining an existing microarray database, we identified 220 highly abundant genes in platelets and a subset of 72 relatively platelet-specific genes, defined by more than 10-fold increased expression compared to the median of other cell types in the database with amplified transcripts. The highly abundant platelet transcripts found in the current study included 82% or 70% of platelet abundant genes identified in two previous gene expression studies on non-amplified mRNA from pooled or apheresis samples, respectively. On comparing the platelet gene expression profiles in 18 patients with sickle cell disease in steady state to 12 African American controls, at a 3-fold cut-off and 5% false discovery rate, we identified ~100 differentially expressed genes, including multiple genes involved in arginine metabolism and redox homeostasis. Further characterization of these pathways using real time PCR and biochemical assays revealed increased arginase II expression and activity and decreased platelet polyamine levels. These studies suggest a potential pathogenic role for platelet arginase and altered arginine and polyamine metabolism in sickle cell disease and provide a novel framework for the study of disease-specific platelet biology.

Keywords: Platelets, genes, enzymes, metabolism, signal transduction, sickle cell disease

overall_design: There are 18 sickle cell samples and 12 control samples from healthy African American volunteers.

first: Nalini

last: Raghavachari


title: Taxonomy of placenta cells

status: Public on May 20 2008

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

summary:
The placenta is considered one of the candidate cell sources in cellular therapeutics because of a large number of cells and heterogenous cell population with myogenic potentials. We first analyzed myogenic potential of cells obtained from six parts of the placenta, i.e., umbilical cord, amniotic epithelium, amniotic mesoderm, chorionic plate, villous chorion (chorion frondosum), , and decidua basalis. Implantation of placenta-derived cells into dystrophic muscles of immunodeficient mdx mice restored sarcolemmal expression of human dystrophin. Co-existence of human and murine nuclei in one myotube and presence of human dystrophin in murine myotube suggests that human dystrophin expression is due to cell fusion between host murine myocytes and implanted human cells. In vitro analysis revealed that cells derived from amniotic mesoderm, chorionic plate, ,and villous chorion efficiently transdifferentiate into myotubes. These cells fused to C2C12 murine myoblasts by in vitro co-culturing, and murine myoblasts start to express human dystrophin after fusion. These results demonstrate that placenta-derived cells, especially extraembryonic mesodermal cells, have a myogenic potential and regenerative capacity of skeletal muscle. Determination of cell specification with the gene chip analysis revealed that each placental cell has a distinct expression pattern.

Keywords: Determination of cell specification

overall_design: To isolate chorionic villi cells, we used the explant culture method, in which the cells were outgrown from pieces of chorionic villi attached to dishes. Chorionic villi cells were harvested with 0.25% trypsin and 1 mM EDTA, and overlaid onto the cultured fetal cardiomyocytes at 7 x 103/cm2.  Every 2 days, the culture medium was replaced with fresh culture medium that was supplemented with 10% FBS and 1 ug/ml Amphotericin B (GIBCO).  The morphology of the beating chorionic villi cells was evaluated under a fluorescent microscope.

first: Yayoi

last: Kawamichi

first: Chang

middle: H

last: Cui

first: Masashi

last: Toyoda

first: Hatsune

last: Makino

first: Yoriko

last: Takahashi

first: Hiroaki

last: Ohta

first: Kayoko

last: Saito


title: Passage dependent gene expression in normal human dermal fibroblasts

status: Public on May 13 2008

city: Indianapolis

first: Tao

last: Wei

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary:
Human umbilical vein endothelial cells (HUVECs) formed capillary structures when co-cultured with normal human dermal fibroblasts (NHDFs). HUVEC competence and NHDF supportiveness of cord formation were found to be highly cell-passage dependent with the early passage cells forming more angiogenic cord structures.  We thus profiled gene expression in NHDFs with different passages to understand the molecular mechanisms underlying the in vitro angiogenesis control.
Keywords: Time course

overall_design: NHDFs cultured to various passages were assayed for their gene expression using the GeneChip technology.

first: Yuefeng

last: Chen

first: Lei

last: Yan

first: Frank

last: Lawrence

first: Hui-Rong

last: Qian

first: Jonathan

last: Yingling

first: Jianyong

last: Shou


title: Distinct gene-expression-defined classes of gastrointestinal stromal tumor (GIST).

city: Chuo

first: Umio

last: Yamaguchi

address: 5-1-1, Tsukiji

department: Chemotherapy

institute: NCCRI

summary:
GIST is considered to invariably arise through gain-of-function KIT or PDGFRA mutation of the interstitial cells of Cajal (ICC). However, the genetic basis of the malignant progression of GIST is poorly understood.
We analysed the expression levels of 54,613 probe sets in 32 surgical samples of untreated GIST of the stomach and small intestine with GeneChip Human Genome U133 Plus 2.0 arrays.
Keywords: gene expression array-based, count

overall_design: Total RNA was extracted from 32 fresh frozen tumour specimens. We analysed the global gene exprssion profiles of these GIST cases in order to clarify the genomic basis behind the malignant progression of this tumor