title: Drosha knockdown in human cells reduces viability but does not affect snRNA or rRNA synthesis or processing

status: Public on Jan 01 2008

first: John

last: Newman

address: 1959 NE Pacific St.

department: Biochemistry

summary:
We asked whether the human drosha protein, an RNase III homolog known to process microRNAs (miRNAs), might also be a small nuclear RNA (snRNA) 3' processing factor.  Using retroviral siRNA silencing constructs, we stably knocked down drosha protein to nearly undetectable levels.  Knockdown cells exhibited reduced growth rates and viability compared to controls, but no accumulation of unprocessed U2 snRNA precursors.  In fungi, RNase III homologs process rRNA precursors and certain mRNAs.  Although rRNA processing appears to be normal in the drosha knockdown cells, expression microarray analysis revealed misregulation of several mRNAs involved in cell growth and proliferation.  Curiously, drosha knockdown appeared to downregulate the predicted mRNA targets of several miRNAs
Keywords: siRNA knockdown

overall_design: The experimental goal was to evaluate gene expression changes induced by siRNA knockdown of drosha. Four samples of HeLa cells were transfected with retroviral siRNA expression vectors: two replicates of an anti-GFP siRNA vector (siGFP) and two different anti-drosha siRNA vectors (sidroshaB and sidroshaC). Cells were selected with puromycin 24 hours after transfection and harvested 72 hours after transfection. Trizol-harvested RNA was processed with standard Affymetrix protocols and hybridized to U133Plus2.0 GeneChips. Signals were scaled to an arbitrary global mean value of 800.

first: Erica

middle: Y

last: Jacobs

first: Alan

last: Weiner


title: Primary Sjogren's syndrome and control whole saliva

status: Public on Dec 31 2007

city: Los  Angeles

first: david

last: wong

state: CA

address: 10833 Le Conte ave.

country: USA

institute: UCLA

summary:
10 saliva samples from patients with primary Sojgren's syndrome and 10 saliva samples from control subjects
Keywords: Biomarker development

overall_design: Gene profilling from 10 saliva samples from patients with primary Sojgren's syndrome and 10 saliva samples from control subjects using Affymetrix HGu133+2 microarray.

first: Jianghua

last: Wang

first: Shen

last: Hu

first: David

last: Wong


title: Expression data for NMD inhibition in Mantle Cell Lymphoma

city: Barcelona

first: Pedro

last: Jares

state: Barcelona

address: c/ Villarroel 170

department: Genomics Unit

country: Spain

institute: IDIBAPS

summary:
Identification of potential tumor suppressor genes using the GINI strategy in Mantle Cell Lymphoma cell lines
Keywords: response to drug treatment

overall_design: Inhibition of the NMD pathway was performed in Mantle Cell Lymphoma cell lines according to a modified protocol previously described (Noensie EN et al Nat Biotechnol 2001;19:434-439; Huusko P et al, Nat Gentet 2004; 36:979-983). The cells were treated with emetine or with emetine followed by incubation with actinomycin D during a time course. Mock treated cells were used as reference.

first: Magda

last: Pinyol

first: Silvia

last: Bea

first: Laura

last: Plà

first: Andreas

last: Rosenwald

first: Elías

last: Campo


title: Expression profiles of peripheral blood monocytes in periodontal therapy

city: Vancouver

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

country: Canada

institute: University of British Columbia

summary:
Periodontal infections have been associated with systemic inflammation and risk for atherosclerosis and vascular disease. We investigated the effects of comprehensive periodontal therapy on gene expression of peripheral blood monocytes. Approximately 1/3 of the patients showed substantial changes in expression in genes relevant to innate immunity, apoptosis, and cell signaling. We concluded that periodontal therapy may alter monocytic gene expression in a manner consistent with a systemic anti-inflammatory effect.
Keywords: time course,disease state analysis

overall_design: Fifteen patients with periodontitis contributed with blood samples at four time points: 1 week prior to periodontal treatment (#1), at treatment initiation (baseline, #2), 6 weeks (#3) and 10 weeks post-baseline (#4). At baseline and 10 weeks, periodontal status was recorded and subgingival plaque samples were collected and processed by checkerboard DNA-DNA hybridization. Periodontal therapy, including periodontal surgery and extractions but no adjunctive antibiotics, was completed within 6 weeks. At each of the four time points, serum concentrations of 19 biomarkers were determined using multiplex assays for Luminex technology. Peripheral blood monocytes were purified, RNA was extracted, reverse-transcribed, labeled, and hybridized with Affymetrix U133 Plus 2.0 chips. Expression profiles were analyzed using linear random effects models. Further analysis of Gene Ontology (GO) terms summarized the expression patterns into biologically relevant categories. Treatment resulted in substantial improvement in clinical periodontal status and reduction in levels of several periodontal pathogens. Expression profiling over time revealed more than 11,000 probes sets differentially expressed at a false discovery rate of <0.05.

first: Panos

middle: N

last: Papapanou

first: Ryan

last: Demmer


title: Lung metastatic derivative LM2 cells with and without miR-335

city: new york

first: sohail

middle: f.

last: tavazoie

state: NY

address: 1275 york avenue

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Institute

summary:
the LM2 breast cancer cell line is an in vivo derived line from the MDA-MB-231 parental line.  this LM2 line has been transduced either with a short hairpin control or miR-335 expression vector.
Keywords: breast cancer, metastasis, miRNA

overall_design: the LM2 cell line is transduced either with a short hairpin control vector or miR-335 expression vector.

middle: f

first: Joan

last: Massague


title: gene expression profiles of healthy male participants in rest

city: Jena

first: Sandy

last: Mosig

address: Bachstrasse 18

department: Molecular Hemostaseology - Institute of Vascular Medicine

country: Germany

institute: University Hospital Jena

summary:
These gene expression profiles were measured to create a broad and balanced control for any project that examines gene expression changes in men exposed to a defined stimulus (see series 5105).
Keywords: gene expression profiles of healthy males

overall_design: 9 healthy men (aged 21 to 44) gave written agreement to participate to this study. At the time of blood withdrawal all participants were non-smokers, with normal BMI and did not obtain any medicamentation. We collected 12ml of whole blood and isolated T-lymphocytes out of 4ml and monocytes out of 8ml whole blood.

first: Petra

last: Büttner

first: Stefan

last: Vogt

first: Lothar

last: Heinrich

last: Schmid

first: York

middle: O

last: Schubert

first: Hans-Hermann

last: Dickhuth

first: Arnd

last: Brandenburg

first: Ernst

last: Jakob

first: Manfred

last: Baumstark

first: Harald

last: Funke


title: The DExH-box RNA helicase RHAU is a Nuclear Protein Involved in Transcription and mRNA Decay

city: Basel

first: Fumiko

last: Iwamoto

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

summary:
RHAU (RNA helicase-associated with AU-rich element) is a DExH protein that was originally identified as a factor accelerating AU-rich element-mediated mRNA degradation. The finding that RHAU is predominantly localized in the nucleus, despite that mRNA degradation occurs in cytoplasm, prompted us to consider nuclear functions of RHAU. In HeLa cells, RHAU was localized throughout the nucleoplasm with some concentration in nuclear speckles in a manner dependent on ATPase activity. Transcriptional arrest altered its localization to nucleolar caps where it was colocalized with other RNA helicases, p68 and p72, suggesting that RHAU is involved in transcription-related RNA metabolism in the nucleus. To see whether RHAU affects global gene expression either transcriptionally or posttranscriptionally, we performed microarray analysis using total RNA prepared from RHAU-depleted HeLa cell lines, measuring both steady-state mRNA levels and mRNA half-lives by ActinomycinD-chase. We found that most transcripts whose steady-state levels were affected by RHAU knockdown did not show changes in their half-lives, suggesting the involvement of transcriptional regulation for these transcripts. We propose that RHAU has dual functions involved in synthesis and degradation of mRNA in different subcellular compartments.
Keywords: mRNA decay study using HeLa cells expressing shRNA

overall_design:
HeLa-shRHAU and HeLa-shLuc cells were treated with doxycycline (1 μg/ml) for 6 days. At the 4th day of dox-treatment, 4 clones of each cell line were pooled and total 2×106 cells were reseeded in 10 cm dishes. For the starvation experiment; medium was replaced with serum-free DMEM on the 5th day, 24 h before the collection of RNA. The ActD-chase experiment was done on the 6th day of doxycycline treatment. For the mRNA decay experiment; ActD was added to the medium at 5 μg/ml and total RNA was collected at 0, 30, 60, 90, and 120 min after the addition of ActD. Samples for time 0, representing the total amount RNA in the normal condition, and samples from starved cells were analyzed in triplicates, whereas ActD-treated samples for the mRNA decay study were analyzed in duplicates. Total RNA was isolated using the RNeasy kit from QIAGEN (Hombrechtikon, Switzerland).
Total RNA  (5 μg) from each replicate was reverse transcribed and labelled using the Affymetrix 1-cycle labelling kit according to manufacturer’s instructions. Biotinylated cRNA (20 μg) was fragmented by heating with magnesium (as per Affymetrix’s instructions) and 15 μg of this fragmentated cRNA was hybridized to Human U133 plus 2.0 GeneChipsTM. GC-RMA expression values and detection P-values were estimated using Refiner 4.0 from Genedata AG (Basel, Switzerland). Data analysis was performed using Analyst 4.0 from Genedata AG (Basel, Switzerland). The chip distributions were standardized by quantile normalization and they were scaled to make the median expression value, of genes with a detection P-value < 0.04, equal to 500. For the analysis of steady-state RNA levels, genes were required to have a detection P-value < 0.04 (Affymetrix default) in at least two replicates of at least one condition. The objective was to exclude genes that are not expressed in any condition. They were then subjected to a student t-test (P<0.05) and have a median fold change of 1.5 or 2 greater between samples dox+ and dox- or with and without starvation. Multiple testing errors were dealt with using a Benjamini and Hochberg false discovery correction.

first: Michael

last: Stadler

first: Edward

last: Oakeley

first: Yoshikuni

last: Nagamine


title: Gene expression profiles after lentiviral transduction

city: Cleveland

first: Fangjing

last: Wang

state: OH

address: Bishop building, Room s731, UH

department: Biomedical Engineering

institute: case Western Reserve University

summary:
Human mesenchymal stem cells (hMSCs) were transduced using lentivirus containing the  the triple fusion reporter gene fluc-mrfp-ttk. Microarray studies of hMSCs after transduction with the triple reporter genes using lentivirus were performed to study the effects of transduction on stem cell properties using an oligonucleotide human microarray. Transduced cells were sorted by FACS. Cells with high and low signals were ftacrtionated, and gene expression profiles were determined.
Keywords: comparative study

overall_design: In this study, 8 samples were experimentally evaluated. 2 samples were used as the control without undergoing any transduction. 2 samples were transduced with the virus containing only the backbone. 2 samples were transduced with the lentivirus containing the triple reporter and has high MGFP (>10^3), while 2 samples <10^3.

first: Luis

last: Solchaga

first: Zhenghong

last: Lee


title: IL-13 involvement in eosinophilic esophagitis: transcriptome analysis

status: Public on Dec 21 2007

city: cincinnati

first: Marc

middle: E.

last: Rothenberg

address: 3333 burnet avenue

department: Allergy and Immunology

institute: Cincinnati Children's Hospital Medical Center

summary:
3 eosinophilic esophagitis biopsies, cultured and stimulated with IL-13 : each of them was either left unstimulated or stimulated (100ng for 48h)
We used microarray to uncover the IL-13-induced genes in esophageal epithelial cells of the esophagus
Keywords: treated vs non treated

overall_design: 3 biopsies from EE patients were obtained and primary epithelial cell  were cultured and  either left unstimulated or stimulated with IL-13 followed by RNA extraction and hybridization on Affymetrix microarrays.

first: Carine

last: Blanchard

first: Melissa

middle: K

last: Mingler

first: Maria

last: Vicario

first: Pablo

last: Abonia

first: Yi

last: Ying Wu

first: Thomas

middle: X

last: Lu

first: Margaret

middle: H

last: Collins

first: Philip

middle: E

last: Putnam

first: Susanne

middle: I

last: Wells


title: AML1-ETO transduced human cord blood cells, CD34 selected, compared to normal cord blood cells, CD34 selected

status: Public on Dec 20 2007

city: Cincinnati

first: James

last: Mulloy

address: 3333 Burnet Ave

department: Experimental Hematology

institute: Cincinnati Children's Hospital Research Foundation

summary:
AML1-ETO expression in normal human umbilical cord blood CD34+ cells leads to long-term proliferation of an early self-renewing primitive progenitor cell with multilineage potential and stem cell ability, but these cells do not induce leukemia in immunodeficient mice. This comparative microarray study was initiated to determine the differences in the transcriptome of AML-ETO-expressing CD34+ cells after extended culture in vitro, using normal cord blood cells expanded for 6-8 weeks in vitro and subsequently purified for the CD34+ population as the control comparison.
Keywords: Disease state analysis; comparison of changes in transcriptome due to long-term AML1-ETO expression in normal human hematopoietic CD34+ progenitor cells

overall_design: We have established a culture system whereby we retrovirally transduce human CD34+ cells, obtained from cord blood, with the leukemia fusion gene AML1-ETO. Cells expressing this fusion protein are able to proliferate long-term in vitro in a cytokine dependent manner.  AML1-ETO-expressing cord blood cells have a large population of primitive self-renewing CD34+ cells with continued abnormal differentiation. We grow these cells in serum-free conditions using the BIT supplement from Stem Cell Technologies. For the current experiments we used cell cultures that had been proliferating in vitro for 8-12 weeks, in a cytokine cocktail of SCF, TPO, FLT3L, IL-6 all at 20 ng/mL and IL-3 at 10 ng/mL. Control cord blood samples that were CD34 purified were expanded for 5-8 weeks in the same culture media as used for AML1-ETO cells. All samples were magnetically selected for the CD34+ population, returned to culture, and one week later again selected for CD34+ cells and then lysed for RNA isolation.

first: Ondrej

last: Krejci

first: Mark

last: Wunderlich

middle: C

last: Jansen

first: David

last: Schleimer

first: Hartmut

last: Geiger

first: Paul

last: Andreassen


title: Zonal Heterogeneity for Gene Expression in Human Pancreatic Carcinoma Growing in the Pancreas of Nude Mice

city: Columbus

first: Kevin

middle: R

last: Coombes

state: Ohio

address: 340E Lincoln Tower, 1800 Cannon Drive

department: Biomedical Informatics

institute: Ohio State University Wexner Medical Center

summary:
Using Affymetrix HG-U133-Plus 2.0 array and Laser Capture Microdissection techniques, we determined whether growth in different zones of the same tumor affected expression of genes by human pancreatic cancer cells.  Human L3.6pl pancreatic cancer cells were implanted into the pancreas of nude mice.  Gene expression patterns in tumor cells within the central and peripheral zones were compared and statistical differences were determined for 1222 genes.  Bioinformatic functional prediction analysis revealed that 346 upregulated genes in the peripheral zone were related to cytoskeleton organization and biogenesis, cell cycle, cell adhesion, cell motility, DNA replication, localization, integrin-mediated signaling pathway, development, morphogenesis, and IkB kinase/NF-kB cascade; and 876 upregulated genes in the central zone were related with regulation of cell proliferation, regulation of transcription, transmembrane receptor protein tyrosine kinase signaling pathway, response to stress, small GTPase mediated signal transduction, hexose metabolism, cell death, response to external stimulus, carbohydrate metabolism, and response to wounding.  Results from the microarray were confirmed for reliability by in situ hybridization analysis.  Collectively, these data demonstrate zonal heterogeneity for gene expression profiles in tumors and suggest that characterization of zonal gene expression profiles are essential to obtain reproducible data, to predict disease prognosis, and to design specific therapeutics.
Keywords: cell type comparison

overall_design: Three paired samples

first: Toru

last: Nakamura

first: Toshio

last: Kumai

first: Yasuhiko

last: Kitadai

first: Takumitsu

last: Sasaki

first: Dominic

last: Fan

first: Sun-jin

last: Kim

first: Isaiah

middle: J

last: Fidler


title: A Mathematical Model for Affymetrix GeneChip Probe Level Data

city: Hiroshima

first: Eiso

last: Hiyama

state: Hiroshima

address: 1-2-3, Kasumi, Minami-ku

department: Natural Science Center for Basic Research and Deve

country: Japan

institute: Hiroshima University

summary:
Affymetrix GeneChip PM-MM probe pair is designed with the intension of measuring non-specific binding. Though the rationale behind the design id that a PM probe is expected to have a larger value than that of the MM probe, there are many exceptions in actual data.  We gave an explanation for this inconsistency based on the assumption of functional states of a gene ‘ON/OFF’. Our hypothesis on PM-MM probe pairs is that the logarithmic of PM and MM values have the same distribution when gene is in OFF state. It means that the probability of MM > PM is expected to be equal to that of MM < PM for OFF genes. The validity of the hypothesis was given by inter-platform comparisons using common targets among three different types of platforms.
Keywords: Affymetrix Gene Chip; Binomial distribution; Mathematical modeling; Oligonucleotide microarray; ON/OFF genes

overall_design: Three commercially available single-color oligonucleotide microarray platforms for profiling gene expression - CodeLinkTM Human Whole Genome Bioarray (~55,000 transcripts, GE Healthcare, Tokyo, Japan), Affymetrix GeneChipTM Human Genome U133 Plus 2.0 array (~47,000 transcripts, Affymetrix, Santa Clara, CA), and Agilent Whole Human Genome Oligo Microarray (~41,000 transcripts, Agilent Technologies, Tokyo, Japan), were compared using the same RNA sample extracted from a human neuroblastoma tissue sample.

first: Keiko

first: Megu

last: Ohtaki

last: Otani

first: Kenichi

last: Satoh

first: Takeshi

last: Shimamoto

first: Dokki

last: Mohamad

first: Masataka

last: Andoh

first: Tonda

last: Tetsuji

first: Masakazu

last: Kohda

first: Yasushi

last: Okazaki

first: Masahiko

last: Nishiyama


title: IP Staufen1

status: Public on Jan 18 2008

city: Montréal

first: Luc

last: DesGroseillers

state: Québec

address: 2900 Edouard Montpetit

department: Biochimie

institute: Université de Montréal

summary:
In human cells, Staufen1 is double-stranded RNA-binding protein involved in several cellular functions including mRNA localization, translation and decay. We used a genome wide approach to identify and compare the mRNA targets of mammalian Staufen1. The mRNA content of Staufen1 mRNPs was identified by probing DNA microarrays with probes derived from mRNAs isolated from immunopurified Staufen-containing complexes following transfection of HEK293T cells with a Stau1-HA expressor. Our results indicate that 7% of the cellular RNAs expressed in HEK293T cells are found in Stau1-containing mRNPs. There is a predominance of mRNAs involved in cell metabolism, transport, transcription, regulation of cell processes and catalytic activity.
Keywords: Immunoprecipitation, Staufen, microarray

overall_design: HEK293 cells were transiantly transfected with plasmids coding for Staufen1-HA. Cell extracts were immunoprecipitated using anti-HA antibodies and co-immunoprecipitated mRNAs were purified and used to hybridize microarrays. As control, cell extract from mock transfected cells were used.

last: Furic

first: Marjolaire

last: Maher-Laporte


title: TFAP2C regulates multiple pathways of estrogen signaling

status: Public on Dec 17 2007

city: Iowa City

first: Ronald

last: Weigel

state: IA

address: 200 Hawkins Drive, Room 1509 JCP

department: Surgery

institute: University of Iowa

summary:
We were interested in determining what genes might be controlled by TFAP2C and/or TFAP2A, either directly or indirectly through regulation of ER-alpha and potentially other signaling pathways. We performed an microarray analysis in MCF7 cells with elimination of either TFAP2C or TFAP2A. The patterns of gene expression with alteration of TFAP2 activity were compared to changes in expression induced by estrogen exposure. Knock-down of TFAP2C in the presence of estrogen altered the pattern of several known ERalpha-regulated genes and a number of genes outside the estrogen-regulated pathways.
Keywords: Various siRNA treatments

overall_design:
6 samples were analyzed.
1. MCF7 cells treated with TFAP2C siRNA, without the presence of estrogen.
2.MCF7 cells treated with TFAP2C siRNA, with the presence of estrogen.
3.MCF7 cells treated with TFAP2A siRNA, without the presence of estrogen.
4.MCF7 cells treated with TFAP2A siRNA, with the presence of estrogen.
5.MCF7 cells with no siRNA treatment, without the presence of estrogen.
6.MCF7 cells with no siRNA treatment, with the presence of estrogen.

first: George

middle: W

last: Woodfield

first: Yizhen

last: Chen


title: Strength of T cell stimulation

status: Public on Dec 18 2007

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

institute: IOR

summary:
The strength of T cell stimulation determines IL-7 responsiveness, recall potential and lineage commitment of primed human CD4+IL-7Rhi T cells

We analyzed how the strength of antigenic stimulation - as determined by dendritic cell (DC) number, DC maturation state and antigen concentration - controls in human CD4+ T cells IL-7R? expression and responsiveness to IL-7, IL-15 and antigen. We found that T cells primed by different strengths of stimulation expressed IL-7R? in different proportions and preferentially on cells that maintained expression of the central memory marker CCR7. However, while CCR7+IL-7Rhi cells generated at high strength of stimulation proliferated vigorously in response to IL-7 or IL-15, CCR7+IL-7Rhi cells generated at low strength of stimulation responded poorly. High cytokine responsiveness was associated with reduced PTEN expression and enhanced s6-kinase activation, consistent with efficient receptor coupling to downstream signalling pathways. Interestingly, while intermediate-stimulated CCR7+IL-7Rhi cells were non-polarized, self-renewed with IL-7 and expanded with antigen, high-stimulated cells generated Th1 effector cells with cytokines but showed impaired IL-2 production and survival with antigen. Gene expression analysis suggested that high-stimulated cells represented pre-Th1 cells with low recall potential and high metabolic state. Taken together these results demonstrate that IL-7 receptor expression and coupling are instructed in T cells by the strength of stimulation and suggest that memory subsets may derive from CCR7+IL-7Rhi precursors that received different strengths of stimulation.
Keywords: comparison

overall_design: two samples treated with weaker dendritic stimulus, two samples treated with stonger dendritic stimulus.

first: Laura

last: Lozza

last: Rivino

first: Greta

last: Guarda

first: David

last: Jarrossay

first: Andrea

last: Rinaldi

first: Federica

last: Sallusto

first: Antonio

last: Lanzavecchia

first: Jens

last: Geginat


title: Staufen1 regulates a variety of mammalian transcripts

status: Public on Dec 26 2007

summary:
It is currently unknown how extensively the double-stranded RNA binding protein Staufen (Stau)1 is utilized by mammalian cells to regulate gene expression.  To date, Stau1 binding to the 3’ untranslated region (3’UTR) of ARF1 mRNA has been shown to target ARF1 mRNA for Stau1-mediated mRNA decay (SMD).  ARF1 SMD depends on translation and recruitment of the nonsense-mediated mRNA decay factor Upf1 to the ARF1 3’UTR by Stau1.  Here, we use microarray analyses to examine changes in the abundance of cellular mRNAs that occur when Stau1 is depleted.  Results indicate that 1.1% and 1.0% of the 11,569 HeLa-cell transcripts that were analyzed are, respectively, upregulated and downregulated at least two-fold in three independently performed experiments.  Additionally, we localize the Stau1 binding site to the 3’UTR of four mRNAs that we define as natural SMD targets.  Together, these and substantiating results suggest that Stau1 influences the expression of a wide variety of physiologic transcripts and metabolic pathways.
Keywords: Staufen1-mediated mRNA decay; Stau1 downregulation by siRNA.

overall_design: We report the results of three independently performed microarray analyses that examined changes in the abundance of transcripts from HeLa-cell genes upon Stau1 depletion. HeLa cells were transiently transfected with either a nonspecific Control small interfering (si)RNA or Stau1 siRNA.  Stau1 siRNA reduced the level of cellular Stau1 to as little as 4% of normal, where normal is defined as the level in the presence of Control siRNA (data not shown).  RNA from three independently performed transfections was separately hybridized to microarrays.

first: Yoon-Ki

last: Kim

first: Marc

last: Parisien

first: François

last: Major

first: Lynne

last: Maquat


title: gene expression profiles in T-lymphocytes and Monocytes of participants of the Tour de France 2005

first: Sandy

last: Mosig

summary:
Exercise has an measureable impact on gene expression profiles of white blood cells. While subpopulations of white blood cells undergo specific changes in answer to physical load we focused on pan T-lymphocytes and Monocytes. These cells are in direct contact to organs influenced by exercise and additionally should be affected by alterations of nutrient and gas composition in blood, which occur as a consequence of exercise. We screened the gene expression profiles of top athletes at the beginning and the end of the Tour de France 2005 and at at the annual rest period in order to find functional processes that are differentially expressed in answer to the longtime and high load training and competition. Therefor we filtered out genes with significant changes in gene expression more than 1.5fold between two of the three conditions and build overlap lists of this list and GO (gene ontology) lists and KEGG (kyoto encyclopedia of genes and genomes) lists. We observed a strong decline in immune functions and an equal decline in metabolic processes.
Keywords: response of gene expression to long-time and high load exercise

overall_design: 12 professional  cyclists from two german top teams gave written agreement to participate to this study. We collected 12ml of whole blood at each time point and isolated T-lymphocytes out of 4ml and monocytes out of 8ml whole blood.  The experimental groups are divided into rest (6 replicates in Tcells/ 7 replicates in Monocytes), start (10 replicates in each cell type) and final (8 replicates in Tcells/ 9 replicates in Monocytes). This means that we collected samples at the beginning and the end of the Tour de France and during the annual rest period of the athletes.

first: Petra

last: Büttner

first: Stefan

last: Vogt

first: Lothar

last: Heinrich

first: Andreas

last: Schmid

first: Yorck

last: Schubert

first: Hans-Hermann

last: Dickhuth

first: Arnd

last: Brandenburg

first: Ernst

last: Jakob

first: Manfred

last: Baumstark

first: Harald

last: Funke


title: Specific plasma membrane protein phenotype of culture-amplified and native human bone marrow mesenchymal stem cells

status: Public on Dec 15 2007

city: Berlin

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

institute: Charité

summary:
We have studied the plasma membrane protein phenotype of human culture-amplified and native Bone Marrow Mesenchymal Stem Cells (BM MSCs). We have found, using microarrays and flow cytometry, that cultured cells express specifically 113 transcripts and 17 proteins that were not detected in hematopoietic cells. These antigens define a lineage-homogenous cell population of mesenchymal cells, clearly distinct from the hematopoietic lineages, and distinguishable from other cultured skeletal mesenchymal cells (periosteal cells and synovial fibroblasts). Among the specific membrane proteins present on cultured MSCs, 9 allowed the isolation from BM mononuclear cells of a minute population of native MSCs. The enrichment in Colony-Forming Units-Fibroblasts was low for CD49b, CD90 and CD105, but high for CD73, CD130, CD146, CD200 and integrin alphaV/beta5. Additionally, the expression of CD73, CD146 and CD200 was down-regulated in differentiated cells. The new marker CD200, because of its specificity and immunomodulatory properties, deserves further in depth studies.
Keywords: cell type comparison

overall_design: Expression profiles of bone marrow MSC were compared with different lineages of purified hematopoietic cells from bone marrow to identify characteristic markers for human BM-MSC

first: Bruno

last: Delorme

first: Jochen

last: Ringe

first: Nathalie

last: Gallay

first: Yves

last: LeVern

first: Dominique

last: Kerboeuf

first: Christian

last: Jorgensen

first: Philippe

last: Rosset

first: Luc

last: Sensebé

first: Pierre

last: Layrolle

last: Charbord


title: Summarizing probe levels of Affymetrix arrays taking into account day-to-day variability

status: Public on Dec 12 2007

city: Nerviano

first: Roberta

last: Bosotti

state: MI

address: viale Pasteur,10

department: Biotechnology

country: Italy

institute: Nerviano Medical Sciences srl

summary:
Day-to-day variability in microarray experiments is a recognized source of variation that can impede the analysis of large microarray studies where samples are processed on different days. In this study, we have applied an algorithm, called D2Dsum, which is based on a log-linear fixed effect model to cope with this kind of issues on a data set of 45 microarrays.
Keywords: time course

overall_design:
A2780 human ovarian cancer cell lines have been treated (TRT) with two different chemical compounds (A and B) or left untreated (CTRL). RNA was collected form 1 to 6 hour every hour. For each time point a technical duplicate or triplicate has been performed. Samples were subjected to complete randomisation experimental design and the effect of hybridisation day has been evaluated.
processed on 4 different days

first: Paolo

last: Magni

first: Angela

last: Simeoni

first: Sandra

last: Healy

first: Antonella

last: Isacchi


title: Gene Expression Changes in Response to Baculoviral Vector Transduction of Neuronal Cells In Vitro

status: Public on Dec 13 2007

city: Singapore

first: Jerome

last: Boulaire

address: 31 Biopolis Way

department: Gene Delivery

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

summary:
Recombinant baculoviral vectors efficiently transduce several types of cells in the brain. To characterize host responses to viral challenge, thus verifying the suitability of using the virus for the development of gene therapy strategies in the central nervous system, we used cDNA microarray technology to examine in vitro and in vivo global cellular gene expression profiles after viral transduction. We demonstrated that the transduction induced host antiviral responses as a major reaction in all three types of samples profiled, including the rat brain, cultured human astrocytes and human neuronal cells. The related genes were mainly those associated with innate immunity. Several genes of the major histocompatibility complex molecules, an important component of the host adaptive immunity to exogenous pathogens, were up-regulated in the rat brain and human astrocytes, but not in neuronal cells. We also observed that genes related to cell death and apoptosis were up-regulated and genes related cell cycle regulation were down-regulated in neuronal cells, but not obviously affected in astrocytes. These findings should be useful in understating the molecular basis for neural cell response to baculoviral transduction and guiding rational applications of baculoviral vectors in the central nervous systems
Keywords: Baculovirus, brain, astrocytes, neurons, transduction, Infection, gene expression analysis, DNA microarray

overall_design:
CMV-Luc baculovirus with a luciferase reporter gene under the control of hCMV promoter and CMV-GFP baculovirus with a gene encoding for a green fluorescence protein were constructed as described previously (Wang et al., 2006). Both vectors were used to confirm baculoviral transduction. Our pilot test, as well as previous studies (Stilwell and Samulski, 2003; Zhao et al., 2005), demonstrated no detectable difference between viral vectors with and without a reporter gene in affecting global gene expression profiles. Thus, CMV-Luc baculovirus was used throughout microarray experiments.

Recombinant baculovirus vectors were produced and propagated in Spodoptera frugiperda (Sf9) insect cells according to the manual of the Bac-to-Bac baculovirus expression system (Invitrogen). Sf9 insect cells pre-adapted to Sf-900 II serum-free medium were purchased from Invitrogen (Carlsband, CA) and grown in spinner flasks at 27.5oC. Budded viruses in the insect cell culture medium were collected and filtered through a 0.45-μm pore size filter (Minipore, Bedford, MA, USA) to remove any contamination, and concentrated by ultracentrifugation at 28,000g for 60 min. Viral pellets were re-suspended in appropriate volumes of 0.1 M phosphate-buffered saline (PBS) and their infectious titers (plaque-forming units, pfu) were determined by plaque assay on Sf9 cells.
For in vitro study, normal human astrocytes (Lonza, Basel, Switzerland) were cultured in Astrocyte Basal Medium (ABM) supplemented with the AGM SingleQuots. Cells were maintained according to manufacturer’s instructions. Human neuronal cells, transdifferentiated from human Cord Blood Stem Cell culture, were obtained from Celprogen (San Pedro, CA). The cells were cultured on flasks coated with neuronal expansion matrix in human neuronal expansion complete media and maintained according to the manufacturer’s instructions. Cells were transduced with baculoviruses in Optimem (Invitrogen) at an MOI of 50 and incubated at 37°C for 1 h. After the incubation, the medium containing the viruses was replaced by fresh growth medium, and the cells were collected 48 hours later for analysis.

middle: L

first: Shu

last: Wang


title: Human mesenchymal stem cells

status: Public on Dec 06 2007

city: Modena

first: Enrico

last: Tagliafico

state: MO

address: Via Campi 287

department: Center for Genome Research

institute: University of Modena and Reggio Emilia

summary:
The identity of cells that establish the hematopoietic microenvironment (HME) in human bone marrow (BM), and of skeletal ("mesenchymal") stem cells (SSCs) found in BM stroma, have long remained elusive. We show that MCAM/CD146-expressing, subendothelial cells in human BM stroma are both the self-renewing SSCs and the cells that transfer the HME at heterotopic sites upon transplantation.
Establishment and self-renewal of SSCs in developing BM in vivo occurs via specific, dynamic interactions with developing sinusoids. Non-differentiated SSCs residing on the sinusoidal wall, but not differentiated osteoblasts, express Angiopoietin-1 (a pivotal molecule of the HSC "niche" involved in vascular remodeling).
Our data reveal the functional relationships between establishment of the HME in vivo, establishment of SSCs in BM sinusoids, and angiogenesis.
Keywords: comparative genomics, genetic modification

overall_design: The series is composed by 7 samples hybridized to Affymetrix GeneChips. 4 of these samples (A18, A22, A23 e A27) are different clones of mesenchymal stem cells, while the other 3 represent different treatments of one of these clones with specific growth factors.

first: Benedetto

last: Sacchetti

first: Alessia

last: Funari

first: Stefano

last: Michienzi

first: Silvia

last: Di Cesare

first: Stefania

last: Piersanti

first: Isabella

last: Saggio

last: Ferrari

first: Pamela

last: Gehron Robey

first: Mara

last: Riminucci

last: Bianco


title: Identification of genes modulated by acid and bile in a Barrett's oesophagus cell line

status: Public on Dec 05 2007

city: Leeds University, Leeds

first: Clare

last: Donnellan

state: West Yorkshire

address: LIGHT Laboratories

department: Molecular Epidemiology

country: United Kingdom

institute: Leeds University

summary:
The major aetiological risk factor for Barrett's oesophagus and oesophageal adenocarcinoma is gastroesophageal reflux.  This study's aim was to identify genes involved in the celular response to reflux in vitro.  The Barrett’s oesophagus cell line, CP-A hTERT, was exposed to media with acid, deoxycholic acid or a primary bile salt mixture.  RNA expression was compared with controls on Affymetrix U133 Plus 2.0 arrays.  In CP-A hTERT, the greatest number of changes in gene expression was observed after treatment with deoxycholic acid, pH 4.5; 152 genes were up-regulated at 2 hours (91 at 6 hours) and 10 down-regulated at 2 hours (34 at 6 hours).  12 genes were identified and were subsequently assessed in patients with non-erosive reflux disease, oesophagitis, Barrett's oesophagus and oesophageal adenocarcinoma
Background and Aims: The major etiological risk factor for Barrett’s esophagus and esophageal adenocarcinoma is gastro-esophageal reflux.  This study’s aim was to identify genes involved in the cellular response to components of reflux both in vitro and in patients with reflux-related disease.
Methods: The Barrett’s cell line, CP-A hTERT, was exposed to media with acid, deoxycholic acid or a primary bile salt mixture.  RNA expression was compared with controls on Affymetrix U133 Plus 2.0 arrays.  12 genes of interest were analysed by Real Time PCR both in cell line and biopsies from 110 patients with non-erosive reflux disease, esophagitis, Barrett’s esophagus and esophageal adenocarcinoma.
Results: In CP-A hTERT, the greatest number of changes in gene expression was observed after treatment with deoxycholic acid, pH 4.5.  Of 12 genes analysed in biopsies, 10 were significantly different between the 4 groups with the largest change for anterior gradient homolog 2, which may modulate p53 function.  This had highest expression in biopsies from Barrett’s esophagus (median gene fold change for Barrett’s esophagus versus non-erosive reflux disease, 411.2 (95% CI 290.5-682.7; p<0.01); esophageal adenocarcinoma versus non-erosive reflux disease 68.1 (20.5-161.4; p<0.01)).  In addition 4 genes associated with development/differentiation were upregulated in Barrett’s biopsies compared to those from non-erosive reflux disease (SEL1L, MFNG, CRIP1 and EFNA1).
Conclusions: Novel genes have been identified, whose expression is altered after acid and bile exposure in vitro and in biopsies from patients with reflux related diseases.  These genes may have utility as biomarkers of response to reflux and should be assessed in prospective studies.
Keywords: Acid (pH 4.5) and bile (mixture of primary bile salts or the secondary bile salt deoxycholic acid, both at pH 4.5) challenge to a Barrett's oesophagus cell line.  RNA extraction at 2 and 6 hours. Comparison of treatment RNA to control (non-treatment) RNA,

overall_design: The Barrett's oesophagus cell line CP-A hTERT was treated with a 15 minute exposure of acid (pH 4.5), a mixture of primary bile acids (pH 4.5) or deoxycholic acid (pH 4.5).  RNA extraction occurred in treatment and non-treated cells at 2 hours and 6 hours.  The treatments were performed in duplicate on 2 different days.  RNA was compared in each treatment to each control at the relevant time points, in a 2 x 2 manner by using Affymetrex U133 Plus 2.0 arrays.  Results of 12 genes were confirmed by Real Time PCR and were subsequently assessed in patients with non-erosive reflux disease, oesophagitis, Barrett's oesophagus and oesophageal adenocarcinoma.

first: Laura

last: Hardie


status: Public on Jan 30 2008

city: Los Angeles

first: William

last: Lowry

address: 621 Charles Young Drive

department: MCDB

institute: UCLA

summary:
Expression profile of dermal fibroblasts reprogrammed to a pluripotent state
Keywords: cell-type comparison

overall_design: Compared fibroblasts to reprogrammed fibroblasts to human ES cells


title: Response to estradiol-ERalpha, estradiol-Erbeta, and ERE Binding defective mutants

status: Public on Dec 04 2007

city: Rochester

first: Stephen

last: Welle

address: 601 Elmwood Avenue

institute: University of Rochester

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

overall_design: Refer to individual Series


title: Cysteine deprivation in liver cell line

city: Ithaca

first: Wei

address: T2-003 Vet Res Tower

institute: Cornell University

summary:
First experiment: Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free).  Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys)
Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid).  Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys).
Keywords: amino acid deprivation

overall_design:
First experiment: Three plates of cells were cultured under each condition.  Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free).  Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys).
Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid).  Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys).

first: Jeong-In

last: Lee

first: John

last: Dominy

first: Lawrence

last: Hirschberger

first: Martha

last: Stipanuk


title: Conjugated linoleic acid (CLA) and Caco-2 cells

city: Cork

first: Eileen

middle: Frances

last: Murphy

address: Biosciences Institute

department: Department of Food & Nutritional Sciences

country: Ireland

institute: University College Cork

summary:
The effect of CLA on gene expression in Caco-2 cells
Keywords: Human

overall_design: Caco-2 cells were treated with  linoleic acid (LA; the parent and control fatty acid) trans-10, cis-12 CLA or cis-9, trans-11 CLA for 12 d.

middle: F

first: Kevin

middle: D

last: Cashman

first: Guido

last: Hooiveld

first: Raffaele

middle: A

last: Calogero

first: Michael

last: Muller


title: Regulation of gene expression in MDAMB231 breast cancer cells by Parvin-beta in 2D vs 3D culture conditions

status: Public on Dec 14 2007

city: East Melbourne

first: Cameron

middle: N

last: Johnstone

state: Vic

address: 2 St. Andrew's Place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

summary:
Parvin-beta is a focal adhesion protein downregulated in human breast cancer cells.  Loss of Parvin-beta contributes to increased integrin-linked kinase activity, cell-matrix adhesion, and invasion through the extracellular matrix in vitro.  The effect of ectopic Parvin-beta expression on the transcriptional profile of MDA-MB-231 breast cancer cells, which normally do not express Parvin-beta was evaluated.  Particular emphasis was placed upon propagating MDA-MB-231 breast cancer cells in three-dimensional culture matrices. Gene expression profiles of vector control and Parvin-beta transfected MDA-MB-231 cells cultured on (A) monomeric type I collagen coated plastic, (B) embedded in a type I collagen gel, and (C) embedded in basement membrane (growth factor reduced Matrigel), were compared.  Interestingly, Parvin-beta re-expression in MDA-MB-231 cells increased the mRNA expression, serine 82 phosphorylation (mediated by CDK9), and activity of the nuclear hormone receptor, peroxisome proliferator-activated receptor gamma (PPARgamma) and a concomitant increase in lipogenic gene expression as a downstream effector of PPARgamma.  Importantly, Parvin-beta suppressed breast cancer growth in vivo with associated decreased proliferation. These data suggest that Parvin-beta might influence breast cancer progression..
Keywords: Gene expression profiling in two dimensional vs three dimensional cell culture

overall_design: The MDA-MB-0231 transfectants were cultured for 7 days in each growth condition and total RNA isolated using Trizol reagent (Invitrogen). Genes either upregulated or downregulated in Parvin-beta transfectants versus vector control cells were compared among the 3 different growth conditions. Venn diagrams were generated using GeneSpring software and used to produce gene lists that were unique to a particular growth condition, or shared between two or all three growth conditions. The focus was primarily on gene expression alterations observed in the 3D collagen type I and 3D Matrigel conditions.

first: Perry

middle: S

last: Mongroo

first: Gregory

last: Hannigan

first: Anil

last: Rustgi


title: Gene Expression Changes in Response to Baculoviral Vector Transduction of Normal Human Astrocytes In Vitro

first: Jerome

last: Boulaire

first: Shu

last: Wang


title: Response to estradiol-ERbeta and estradiol-ERbeta ERE binding defective mutant

first: Stephen

summary:
In addition to the estrogen responsive element (ERE)-dependent gene expression, E2-ERbeta regulates transcription through functional interactions with transfactors bound to their cognate regulatory elements on DNA, hence the ERE-independent signaling pathway.  However, the relative importance of the ERE-independent pathway in E2-ERbeta signaling is unclear.  Our studies in infected ER-negative cell models with an ERbeta mutant (ERbetaDBD) that functions exclusively at the ERE-independent pathway demonstrated that genomic responses assessed by microarrays from the ERE-independent pathway to E2-ERbeta are not sufficient to alter cellular growth, death or motility.  These findings suggest that the ERE-dependent pathway is the canonical E2-ERbeta signaling in model cell lines.
Keywords: MDA-MB-231 cells

overall_design: Cells were infected with the recombinant adenovirus bearing no cDNA (CMV) or a cDNA for ERbeta, or cDNA for ERbeta mutant defective in binding to ERE (ERbDBD). for 48 hours.  Infected cells were then treated with 1 nM Estradiol 17beta for 6h. All experiments were repeated six independent times conducted at at six different days

first: Mesut

last: Muyan

first: Xiaodong

last: Li

first: Stephanie

last: Nott

first: Yanfang

last: Huang

first: Russell

last: Hilf

first: Robert

last: Bambara

first: Xing

last: Qiu

first: Andrei

last: Yakovlev


title: Expression analyses of glioblastoma derived neurosphere cultures

city: Hamburg

first: Hauke

middle: Simon

last: Guenther

address: Martinistraße 52

department: Neurochirurgie

institute: UKE

summary:
Recent studies demonstrated that tumor cells with stem cell-like properties can be cultured from human glioblastomas by using conditions that select for the expansion of neural stem cells. We established glioblastoma stem-like (GS-) cell cultures from 9 different glioblastomas, 8 of which generated stably expandable cell lines. Analyzing GS-cell cultures, we discovered two clearly discernable phenotypes.
Microarray analysis showed that the 4 GSf cell lines shared expression profiles dominated by genes involved in nervous system development and neuropeptide signaling, while the 5 GSr lines shared expression signatures enriched for extracellular matrix-proteins.
Keywords: Cell line comparison

overall_design: Affymetrix HG-U133 Plus 2.0 chips were employed for expression profiling from 9 different glioblastoma derived neurosphere cultures in two biological replicates.

last: Günther

first: Nils-Ole

last: Schmidt

first: Heidi

last: Phillips

first: Dirk

last: Kemming

first: Samir

last: Kharbanda

last: Soriano

first: Zora

last: Modrusan

first: Hildegard

last: Meissner

first: Manfred

last: Westphal

first: Katrin

last: Lamszus


title: Response to estradiol-ERalpha

first: Stephen

last: Welle

summary:
In addition to the estrogen responsive element (ERE)-dependent gene expression, E2-ERalpha regulates transcription through functional interactions with transfactors bound to their cognate regulatory elements on DNA, hence the ERE-independent signaling pathway.  However, the relative importance of the ERE-independent pathway in E2-ERalpha signaling is unclear.  Our studies in infected ER-negative cell models with an ERalpha demonstrated that genomic responses assessed by microarrays from the  alter cellular growth, death or motility.
Keywords: MDA-MB-231 cells

overall_design: Cells were infected with the recombinant adenovirus bearing no cDNA (CMV) or cDNA  for ERalpha for 48h.  Infected cells were then treated with 1 nM Estradiol 17beta for 6h. All experiments were repeated six independent times conducted at at six different days

first: Mesut

last: Muyan

last: Nott

first: Yanfanf


title: Response to estradiol-ERalpha ERE Binding defective mutant

summary:
In addition to the estrogen responsive element (ERE)-dependent gene expression, E2-ERalpha regulates transcription through functional interactions with transfactors bound to their cognate regulatory elements on DNA, hence the ERE-independent signaling pathway.  However, the relative importance of the ERE-independent pathway in E2-ERalpha signaling is unclear.  Our studies in infected ER-negative cell models with an ERalpha mutant (ERalpha 203/204/211E) that functions exclusively at the ERE-independent pathway demonstrated that genomic responses assessed by microarrays from the ERE-independent pathway to E2-ERalpha are not sufficient to alter cellular growth, death or motility.  These findings suggest that the ERE-dependent pathway is the canonical E2-ERalpha signaling in model cell lines.
Keywords: MDA-MB-231 cells

overall_design: Cells were infected with the recombinant adenovirus bearing no cDNA (CMV) or cDNA  for ERalpha 203/204/211E (3411E) for 48h.  Infected cells were then treated with 1 nM Estradiol 17beta for 6h. All experiments were repeated six independent times conducted at at six different days

first: Stephanie

last: Huang


title: Trisomy 21 fibroblasts (pevsn-affy-human-512801)

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Down syndrome (DS) is caused by an extra copy of chromosome 21. We are characterizing protein changes in human skin fibroblasts. We propose to study corresponding changes at the DNA level (by SNP analysis) and the RNA level (using Affymetrix chips). These studies will detail transcriptional and translational regulation in trisomy.
The Specific Aim is to obtain data on RNA transcript levels using Affymetrix expression arrays in a group of trisomy 21 and euploid fibroblast cell lines. In parallel, we will acquire SNP data to determine both genotype (call) and copy number changes for trisomic samples. The results will allow us to identify the patterns of change in a trisomic chromosome (relative to control).
[1] We hypothesize that in genomic DNA samples derived from trisomy 21 (TS21) fibroblasts there will be an increased copy number on chr21 with additional microdeletions and microdeletions.
[2] We hypothesize that the RNA transcripts derived from chr21 will be elevated relative to euploid controls.
[3] We hypothesize that altered RNA transcript levels will be significantly correlated with altered protein levels from these same fibroblast cell lines.
The experimental design is as follows. All samples are from deidentified individuals and were obtained from the Brain and Tissue Bank for Developmental Disorders at the University of Maryland, with Johns Hopkins IRB approval.[1] There are five trisomy 21 samples and five euploid samples (total n=10). Fibroblasts were grown in culture to comparable confluency and passage number. Cells were harvested. Total RNA was isolated with a Qiagen kit. The quantity and purity of the RNA was confirmed by spectrophotometry and by electrophoresing an aliquot on a 1% agarose gel. Approximately 10 micrograms of total RNA will be sent to TGen on dry ice for analysis on Affymetrix U133 PlusTwo arrays. Data analysis will be with Affymetrix and Partek software.
Keywords: other

first: Jonathan

last: Pevsner


title: Normal human colorectal mucosa, cecum, ascending, transverse,  sigmoid and rectum

status: Public on Dec 01 2007

city: North Ryde

first: Lawrence

last: LaPointe

state: NSW

address: 11 Julius Ave

institute: Clinical Genomics

summary:
Normal human colorectal mucosa was sampled at points along the colon.
Keywords: normal human tissue

first: Robert

last: Dunne

first: Daniel

last: Worthley

first: Peter

last: Molloy

first: David

last: Wattchow

first: Graeme

middle: P

last: Young


title: Reprogramming of human somatic cells to pluripotency with defined factors

status: Public on Dec 10 2007

city: Boston

first: In-Hyun

last: Park

state: MA

address: 300 Longwood

department: Hem/Onc

institute: Children's Hospital Boston

summary:
Pluripotency, the capacity of embryo-derived stem cells to generate all tissues in the organism, can be induced in somatic cells by nuclear transfer into oocyte, fusion with embryonic stem cells, and for male germ cells by cell culture alone. Recently, murine fibroblasts have been reprogrammed directly to pluripotency by ectopic expression of four transcription factors (Oct4, Sox2, Klf4, and Myc) to yield induced Pluripotent Stem (iPS) cells. Using the same four factors, we have derived iPS cells from human embryonic stem cell-derived fibroblasts, primary human fetal cells, and diverse cells of neonatal and adult human origin. The human iPS cells manifest the colony morphology, gene expression patterns, and epigenetic characteristics of human Embryonic Stem (hES) cells, and form well-differentiated teratomas in immune-deficient mice. These data demonstrate that defined factors can reprogram human cells to pluripotency, and establish a method whereby patient-specific cells might be established in culture.

Biological replicates:
GSM248201 and GSM248202; GSM248205 and GSM248206; GSM248207 and GSM248208; GSM248209 and GSM248210; GSM248211 and GSM248212; GSM248213 and GSM248214.

Sample descriptions:
H1-OGN: ES cells expressing GFP-NEO marker under OCT4 promoter
dH1f: differentiated H1-OGN fibroblasts
dHcf16: differentiated H1-OGN cloned fibroblasts
MRC5: fetal lung fibroblasts
BJ1: neonatal fibroblasts
Keywords: cellular reprogramming

overall_design: RNA samples from hES cells, differentiated hES cells, human fibroblasts, iPS cells from differentiated hES cells, and iPS cells from human fibroblasts. Gene expression of those cells were analyzed.

first: I

first: George

middle: Q

last: Daley


title: Gene Expression is associated with Progesterone Receptor Status in Meningioma

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary:
Examine gene expression for meningioma cases by hormone receptor status and indicate a stronger association with progesterone than with estrogen receptors
Keywords: comparative gene expression

overall_design: The data are surgical specimens from 31 meningioma patients undergoing neuro-surgical resection at Brigham and Women’s Hospital from 3/15/2004-5/10/2005. Progesterone (PR) and estrogen (ER) hormone receptors were measured via immunohistochemistry and compared with gene expression profiling results.

first: Elizabeth

middle: B

last: Claus


title: Prediction of Recurrence-Free Survival in Postoperative NSCLC Patients—a Useful Prospective Clinical Practice

status: Public on Nov 20 2007

city: seoul

first: Jhinkook

last: Kim

country: South Korea

institute: samsung medical center

summary:
Background:
One of the main fields of lung cancer research is identifying patients who are at high risk of post-resection recurrence. Individual recurrence risk evaluation by accurate but simple and reproducible method is needed for the clinical practice.

Results:
The log-rank test and further selection by our criteria of assayability generated 87 genes from microarray data with significant level 5%. Of these, by PTQ-PCR, the expression of most significant 18 genes was obtained. Using these gene expression information and clinical parameters, by stepwise variable selection method, the recurrence prediction model, which composed of 6 genes (CALB1, MMP7, SLC1A7, GSTA1, CCL19, IFI44) and pStage and cell differentiation, were developed. Validation into the two independent cohorts showed good results of the proposed model (p=0.0314, 0.0305, respectively). The predicted median recurrence-free survival times for each patient were reflected real ones well.

Conclusions:
Our method of individualized recurrence risk prediction is accurate, technically simple and reproducible to be used in clinical practice. Therefore, it would be useful in customizing the lung cancer management strategies.
Keywords: Recurrence Free Survival Analysis

overall_design:
Methods:
At first, we selected the statistically significant genes from the analysis of time-to-recurrence and censoring information from 138 whole-genome wide microarray data. Then, we further reduced the number of genes which could be reliably reproducible by RTQ-PCR. With these assayable genes and clinical parameters, construction of recurrence prediction model by Cox proportional hazard regression was done. After validation into two independent cohorts (n=59 and n=56), the model was transformed into recurrence prediction for the each patient.

first: Dae-Soon

last: Son

first: Sung-Hyun

first: Jisuk

last: Jo

first: Heesue

first: Young

middle: H

last: Choi

first: Youngja

last: Jung

first: Miyeon

first: Yoo-Sung

last: Lim

first: Jinseon

last: Lee

first: Eung-Sirk

first: Jhingook


title: Clinical, radiographic, and biomarker characterization of multiple myeloma patients with osteonecrosis of the jaw.

status: Public on Nov 29 2007

city: boston

first: sonia

last: vallet

address: 44 binney street

department: medical oncology

institute: dana-farber cancer institute

summary:
BACKGROUND:
Osteonecrosis of the jaw (ONJ) has been reported in patients with a history of aminobisphosphonate use.
METHODS:
In order to define ONJ and gain insights into its pathophysiology, clinical, radiographic, biochemical, and microarray profiling studies were conducted in 11 patients with multiple myeloma (MM) and ONJ.
RESULTS:
Eleven patients between the ages of 57 and 81 yrs were treated with either pamidronate (n=3), zoledronate (n=4), or both agents sequentially (n=4) for a mean of 38.7 months. Radiographic studies demonstrated radiolucency and sclerosis on plain films. Functional imaging with positron emission tomography (PET) demonstrated a visual increase in glucose metabolism and mineralization at sites of ONJ, using fluorodeoxyglucose (FDG) and sodium fluoride (NaF), respectively. Quantitative regional analysis confirmed an increased standardized uptake value (SUVmax) in areas of ONJ. The target to background ratio of SUVmax was significantly greater for NaF-PET than FDG-PET scans, suggesting that NaF-PET may provide superior image quality for identifying ONJ. Transcriptional profiling of peripheral blood mononuclear cells (PBMCs) using the Affymetrix U133Plus 2.0 gene chip in all 11 MM patients compared with 10 age matched MM controls and 5 healthy volunteers demonstrated that genes involved in osteoblast and osteoclast signaling cascades were significantly downregulated in patients with ONJ, as were proteins confirmed by ELISA.
CONCLUSIONS:
ONJ is seen in patients with a history of aminobisphosphonate use. Functional imaging with NaF PET confirms the diagnosis of ONJ. Gene and protein studies are consistent with altered bone remodeling, evidenced by suppression of both bone resorption and formation.
Keywords: Therapy complication analysis

overall_design: Transcriptional profiling of peripheral blood mononuclear cells (PBMCs) was performed using the Affymetrix U133Plus 2.0 Gene Chip (Affymetrix, Santa Clara, CA, USA) in 11 patients with osteonecrosis of the jaw and multiple myeloma and compared with the profiles of the 10 myeloma patients on bisphosphonate therapy without osteonecrosis of the jaw and 5 healthy volunteers.

first: Noopur

last: Raje

first: Sonia

last: Vallet

first: Shweta

last: Chhetri


title: Comparative transcriptomic profiling of unstimulated and inflamed HUVEC exposed to apple procyanidin oligomers

status: Public on Nov 21 2007

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

institute: CEBAS-CSIC

summary:
We used microarrays to investigate changes in gene expression of human vascular endothelial cells (HUVEC) exposed to an apple extract enriched in procyanidins of low-medium molecular weight (dp3.9) to determine possible protective effects induced by these plant derived compounds on the endothelial cells.
Keywords: Comparative gene expression, Control vs Treated cells (response to exposure with xenobiotics plant polyphenols)

overall_design: We used unstimulated and TNF-α-inflamed confluent monolayers of HUVEC exposed to low doses of oligomeric procyanidins extracted from apple, to determine whether these apple polyphenols exerted any protective effects on human endothelial cells.

middle: G

last: Conesa

first: Jesús

last: Cantalejo

first: Paul

last: Kroon


title: Transcriptome Profile of the Vascular Endothelial Cell Response to Candida albicans

city: Memphis

first: Katherine

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

summary:
We perform microarray analysis of HUVECs upon stimulation with virulent wildtype C. albicans strain SC5314 or its efg1/efg1 cph1/cph1 hyphal-deficient derivative strain CAN34 to compare the gene expression profiles elicited from HUVECs in response to these strains.  In addition, these responses are compared to that of TNF-alpha induced responses to determine which responses are Candida-specific.
Keywords: comparison of host response to different Candida albicans morphologies

overall_design: HUVECs are co-cultured for 3 or 8 hours in M199 medium alone or with CAN34, SC5314, or TNF-alpha.  Total RNA is isolated, cRNA is synthesized and labeled, and labeled cRNA is hybridized onto Affymetrix chips.  Each Candida and TNF sample is compared to its corresponding medium alone sample to determine fold changes in expression at each time point.

first: Hyunsook

last: Park

first: Q

middle: T

last: Phan

first: Lijing

last: Xu

first: Ramin

last: Homayouni

first: Teresa

last: Liu

first: P

last: Rogers

first: Scott

last: Filler


title: Effects of exercise on gene expression in human neutrophils

status: Public on Nov 19 2007

city: Irvine

first: Shlomit

last: Radom-Aizik

state: CA

address: 101 Academy

department: Pediatrics

institute: University of California, Irvine

summary:
Relatively brief bouts of exercise alter gene expression in peripheral blood mononuclear cells (PBMCs), but whether or not exercise changes gene expression in circulating neutrophils (whose numbers, like PBMCs, increase) is not known.  We hypothesized that exercise would activate neutrophil genes involved in apoptosis, inflammation, and cell growth and repair, since these functions in leukocytes are known to be influenced by exercise.   Blood was sampled before and immediately after 30-min of constant, heavy (about 80% peak O2 uptake) cycle-ergometer exercise in 12 healthy men (19-29 yr old) of average fitness.  Neutrophils were isolated using density gradients; RNA was hybridized to Affymetrix U133+2 Genechip arrays.  Using FDR<0.05 with 95% confidence a total of 526 genes were differentially expressed between before and after exercise.   316 genes had higher expression after exercise. The Jak/STAT pathway, known to inhibit apoptosis, was significantly activated (EASE score, p<0.005), but 14 genes were altered in a way likely to accelerate apoptosis as well.  Similarly, both proinflammatory (e.g., IL32, TNFSF8 and CCR5) and anti-inflammatory (e.g., ANXA1) were affected.  Growth and repair genes like AREG and FGF2 receptor genes (involved in angiogenesis) were also activated.  Finally, a number of neutrophil genes known to be involved in pathological conditions like asthma and arthritis were altered by exercise, suggesting novel links between physical activity and disease or its prevention.  In summary, brief heavy exercise leads to a previously unknown substantial and significant alteration in neutrophil gene expression.
Keywords: stress response

overall_design: Twelve healthy men (19-29 yr old) participated in this study. A baseline blood sample was taken before the onset of exercise and immediately after 30-min exercise bout. Neutrophils were isolated using OptiPrep Density Gradient Medium (SIGMA). Total RNA was extracted using TRIzol. cRNA was hybridized onto Affymetrix U133+2 arrays (total of 24 chips).

first: Szu-Yun

last: Leu

first: Frank

last: Zaldivar

first: Dan

middle: M

last: Cooper


title: Expression data from intracranial arteries and intracranial aneurysms

city: Detroit

first: Gerard

last: Tromp

address: 3309 Scott Hall, 540 East Canfield Ave

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

summary:
Gene expression information is useful in prioritizing candidate genes in linkage intervals. The data can also identify pathways involved in the pathophysiology of disease.
We used microarrays to identify which genes are expressed in either intracranial arteries (control) or in intracranial aneurysms (case), and can therefore contribute to the disease phenotypes.
We used microarrays to identify the pathway membership of expressed genes and the overrepresentation of pathways with expressed genes in the known linkage intervals for intracranial aneurysms.
Keywords: Characterization of expression in both diseased and non-diseased intracranial arteries.

overall_design: Intracranial vessels and intracranial aneurysms were obtained from cadavers and preserved in RNAlater. RNA was isolated in pools for aneurysms and some arteries, due to limited amounts of tissue and RNA, whereas intracranial artery RNA for 5 samples was obtained from single individuals.

first: Helena

last: Kuivaniemi

first: Shantel

last: Weinsheimer

first: Guy

last: Lenk


title: Primary nasal epithelium exposed to house dust mite extract shows activated expression in allergics

status: Public on Nov 10 2007

city: Amsterdam

first: Aram

middle: Ben

last: Vroling

address: meibergdreef 9

department: ENT

country: Netherlands

institute: AMC

summary:
Response to allergen was studied in epithelial cells derived from allergic pantients and from healthy controls. Cells were cultured after isolation from a nasal biopsy. Cells were exposed to Housed dust mite or vessel (saline)
Microarray data was analysed using bioinformatics and biostaistics. We conclude  that a marked difference in basal expression and in response to hous dust mite exists
Keywords: cellular response to allergen

overall_design: We used 5 monotypic house dust mite allergic patients and 5 non-allergic healthy controls, the cells obtained from the biopsies were cultured in two wells, for two different conditions.

first: Martijs

middle: J

last: Jonker

first: Silvia

last: Luiten

first: Timo

last: Breit

first: Wytske

last: Fokkens

first: Cornelis

last: van Drunen


title: Expression data from cumulus cells that surround oocytes resulting in early or late cleaving embryos

city: maastricht

first: Aafke

last: van Montfoort

department: Obstetrics & Gynaecology

institute: Academic hospital Maastricht

summary:
Besides the established selection criteria based on embryo morphology and blastomere number, new parameters for embryo viability are needed to improve the clinical outcome of in vitro fertilization (IVF) and more particular of elective single embryo transfer (eSET). The aim of the study was to analyse genome-wide whether the embryo viability was reflected by the expression of genes in the oocyte surrounding cumulus cells. Early cleavage (EC) was chosen as a parameter for embryo viability.
Keywords: class comparison

overall_design: Consenting patients visiting the IVF clinic underwent an IVF or ICSI treatment. Immediately following ultrasound-guided cumulus-oocyte-complex (COC) retrieval, a proportion of the cumulus cells surrounding the oocyte were removed. Gene expression in cumulus cells from eight oocytes resulting in an early cleavage embryo (EC-CC; n=8) and from eight oocytes resulting in a non-EC embryo (NEC-CC; n=8) derived from six patients were analysed using microarrays (n=16). To exclude a differential gene expression due to differences in patient characteristics, samples were paired. From four patients both an EC-CC and a NEC-CC sample were used. From two additional patients two EC-CC as well as two NEC-CC samples were used.

first: Joep

last: Geraedts

first: John

last: Dumoulin

first: Alphons

last: Stassen

first: Johannes

last: Evers

first: Torik

last: Ayoubi


title: Transcriptome changes in hMSCs during expansion

status: Public on Nov 07 2007

city: Temple

first: Joni

last: Ylostalo

state: TX

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

summary:
Human mesenchymal stem cells or multipotent stromal cells (MSCs) are of interest for clinical therapy, in part because of their capacity for proliferation and differentiation.  However, results from clinical trials and in vitro models have been variable, possibly due to MSC heterogeneity and a lack of standardization between MSC in vitro expansion protocols.  Here we defined changes in MSCs during expansion in vitro.  In low density cultures, MSCs expand through distinct lag, exponential growth and stationary phases.  We assayed cultures of passage 2 human MSCs from three donors at low density (50 cells/cm2) at about 5% confluence on Day 2 and after the cultures had expanded to about 70% confluence on Day 7.  On Day 2 genes involved in cell division were up-regulated.  On Day 7 genes for cell development were up-regulated.  The variations between three donors were less than the variation within the expansion of MSCs from a single donor.  The microarray data for selected genes were confirmed by real-time PCR, ELISA and FACScan.  About 50% of cells at Day 2 were in S-phase compared to 10% at Day 7.  The results demonstrated major differences in early and late stage cultures of MSCs that should be considered in using the cells in experiments and clinical applications.
Keywords: Time course

first: Benjamin

middle: L

last: Larson

first: Darwin

last: Prockop


title: Identification of human metapneumovirus-induced gene networks in airway epithelial cells by microarray analysis

city: Galveston

first: Antonella

last: Casola

email: ancasola@utmb.edu, xibao@utmb.edu

address: Children's Hospital. Rm#2.364, 301 University Blvd

institute: University of Texas Medical Branch(UTMB)

summary:
This experiment is designed to study the effects to HMPV on A549 over time
Keywords: time course

overall_design: Confluent monolayers of A549 cells were infected with hMPV at MOI of 1 in serum-free media and harvested at 6, 12, 24, 48, or 72 hours post-infection to extract total RNA using RNAqueous®-Midi Kit (Ambion, Austin, TX), according to manufacturer’s instruction;3 Affymetrix HG-U133 plus 2.0 were used for hybridization.

first: X

last: Bao

first: M

last: Sinha


title: Reanalysis of GSE8884 Samples with Leukocyte Samples from GSE3284.

status: Public on Nov 01 2007

city: Winston-Salem

first: Jennifer

last: Hipp

state: NC

address: Medical Center Blvd

institute: Wake Forest School of Medicine

summary:
To understand the differentiation process of embryonic stem cells into hemangioblasts, gene expression profiles of ES, EB and Blast cells (BL) were analyzed.
Keywords: time course

overall_design: Total RNA was isolated from purified BC cells, day3.5-EBs and undifferentiated ESCs (from two hESC lines, H1 and H9) using the Qiagen RNAeasy kit  We sought to obtain homogeneous populations of cells at each developmental stage in order to increase the purity of each sample.

first: Shi

last: Lu


title: Validation of Genome-wide Expression patterns in Pediatric Septic Shock

city: Cincinnati

first: Hector

middle: R

last: Wong

state: OH

address: 3333 Burnet Ave

department: Division of Critical Care Medicine

institute: CIncinnati Children's Hospital Medical Center

summary:
Rationale:  We previously generated genome-wide expression data in children with septic shock, based on whole blood-derive RNA, having the potential to lead the field into novel areas of investigation.
Objective:  Herein we seek to validate our data through a bioinformatic approach centered on a validation patient cohort.
Methods:  Microarray- and bioinformatics-centered analyses involving our previous data as a training data set (n = 42) and a new, validation cohort (n = 30) as the test data set.
Measurements and Main Results:  Class prediction modeling using the training data set and the previously reported genome-wide expression signature of pediatric septic shock correctly identified 93 to 100% of septic shock patients in the test data set, depending on the class prediction algorithm and the gene selection method. Subjecting the test data set to an identical filtering strategy as that used for the training data set, demonstrated 72% concordance between the two gene lists. Subjecting the test data set to a purely statistical filtering strategy, with highly stringent correction for multiple comparisons, demonstrated less than 50% concordance with the previous gene filtering strategy. However, functional analysis of this statistics-based gene list demonstrated similar functional annotations and signaling pathways as that seen in the learning data set. In particular, we validated that pediatric septic shock is characterized by large scale repression of genes related to zinc homeostasis and lymphocyte function.
Conclusions:  These data demonstrate that the previously reported genome-wide expression signature of pediatric septic shock is applicable to a validation cohort of patients.
Keywords: Inflammation; sepsis; innate immunity; T cells; MHC antigen; zinc

overall_design:
Table 1:  Clinical and demographic data for all subjects in test data set.

				Controls		Septic Shock
No. of individual subjects		15			30
Mean age (years) ± S.D.		3.1 ± 3.5		3.2 ± 2.9
Mean PRISM Score ± S.D.		n/a		18.9 ± 12.3
Gender (Male/Female)		8/7		16/14
Race (no.)			A.A./Black (6)	A.A./Black (2)
				Asian (4)		White (26)				White (5)		Unreported (2)

first: NAtalie

last: Cvijanovich

first: Thomas

last: Stanley

first: Richard

last: Lin

first: Geoffrey

last: Allen

first: Neal

last: Thoams

first: Paul

last: Checcia

first: Nick

last: Anas

first: Robert

last: Freishtat

first: Marie

last: Monaco

first: Kelli

last: Odoms

first: Bhuvaneswari

last: Sakthivel


title: Gene profiling of keloid fibroblasts shows altered expression in multiple fibrosis-associated pathways

status: Public on Nov 26 2007

city: Nashville

first: Shirley

middle: Brody

last: Russell

address: 519 Light Hall

department: Medicine

institute: Vanderbilt University

summary:
Keloids are benign tumors of the dermis that form during a protracted wound healing process.  Susceptibility to keloid formation occurs predominantly in people of African and Asian descent.  The key alteration(s) responsible for keloid formation has not been identified and there is no satisfactory treatment for this disorder. The altered regulatory mechanism is limited to dermal wound healing, although several diseases characterized by an exaggerated response to injury are prevalent in individuals of African ancestry.  We have observed a complex pattern of phenotypic differences in keloid fibroblasts grown in standard culture medium or induced by hydrocortisone.   In this study Affymetrix-based microarray was performed on RNA obtained from fibroblasts cultured from normal scars and keloids grown in the absence and presence of hydrocortisone.  We observed differential regulation of approximately 500 genes of the 38,000 represented on the Affymetrix chip.  Of particular interest was increased expression of several IGF-binding and IGF-binding related proteins and decreased expression of a subset of Wnt pathway inhibitors and multiple IL-1-inducible genes.  Increased expression of CTGF and IGFBP-3 was observed in keloid fibroblasts only in the presence of hydrocortisone. These findings support a role for multiple fibrosis-related pathways in the pathogenesis of keloids
Keywords: cell-type comparison, drug treatment comparison

overall_design: Cell cultures were initiated from human biopsy material from normal dermal scars and keloids of adult males and females. Experimental cultures were derived from the first passage of cells thawed from liquid nitrogen. Cultures of fibroblasts from samples were grown with or without 1.5 micromolar hydrocortisone. RNA from each cell strain was isolated from three independent cell cultures and pooled, then run on an Affymetrix Human Genome U133 Plus 2.0 GeneChip.

first: Joan

last: Smith

first: Braden

last: Boone

first: Susan

last: Opalenik

first: Scott

last: Williams


title: Reanalysis of GSE8884 Samples with Endothelial Samples from GSE3998.

first: Jennifer

last: Hipp

first: Shi

last: Lu


title: Reanalysis of GSE8884 Samples with Stromal Samples from GSE3998.


title: Expression data from human embryonic stem cells, early stage embryoid bodies, and hES-derived blast cells.


title: Comparison of ES, EB, and Blast cells to breast epithelial, leuckocytes, endothelial and stromal cells

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

overall_design: Refer to individual Series


title: Skeletal Muscle Transcript Profiles in Trained or Sedentary Young and Old Subjects

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

summary:
Aging  is associated with mitochondrial dysfunction and insulin resistance. We conducted a study to determine the role of long-term vigorous endurance exercise on age-related changes in insulin sensitivity and various indices of mitochondrial functions.
Keywords: The effect of excises in young and old human subjects by transcription profiling

overall_design: Skeletal muscle transcript profiling was done using  Vastus Lateralis muscle biopsy samples from 10 young sedentary (YS), 10 older sedentary (OS), 10 young trained (YT) and 10 older trained (OT) men and women.  Note that YT2, YS1, and OT1 didn't pass the Quality Control Step of dChip (high array/single outliers). Sedentary subjects exercised less than 30 min/day, twice per week.  Trained subjects performed ≥ 1 hour cycling or running 6 days/week over the past 4 years.

middle: W

first: K

last: Nair

first: Ian

last: Lanza

first: Daniel

middle: K

last: Short

first: Kevin

first: Maureen

last: Bigelow

first: Michael

last: Joyner


title: Activation of inflammation and nfkb signaling in infants born to arsenic exposed mothers

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary:
We are investigating the transcriptional response of newborns in response to prenatal arsenic exposure
We used microarrays to detail the global programme of gene expression response due to prenatal arsenic exposure
Keywords: dose (arsenic)

overall_design: cord blood was collected at birth from infants whose mothers were exposed or unexposed to arsenic

middle: C

first: Panida

last: Navasumrit

first: Chandni

last: Valiathan

first: J

last: Svensson

first: Bradley

last: Hogan

first: Manlin

last: Luo

first: Sanchita

last: Bhattacharya

first: Krittinee

last: Kandjanapa

first: Sumitra

last: Soontararuks

first: Sumontha

last: Nookabkaew

first: C

last: Mahidol

first: Mathuros

last: Ruchirawat

first: Leona

middle: D

last: Samson


title: Genes regulated by the processed form of AIbZIP/CREB3L4 in LNCaP prostate cancer cells

status: Public on Oct 31 2007

city: Quebec

first: Ezequiel

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

summary:
Androgen-induced bZIP (AIbZIP) is a basic leucine zipper (bZIP)
transcription factor that is encoded by the CREB3L4 (cAMP responsive element
binding protein 3-like 4) gene. In humans, AIbZIP mRNA is most abundant in
the prostate but it is also present, albeit at much lower levels, in the
pancreas and other tissues. The full-length AIbZIP protein localizes to the
endoplasmic reticulum and the available data suggest that AIbZIP is
processed to its transcriptionally active form by regulated intramembrane
proteolysis (RIP). To define the transcriptional programme that is initiated
by AIbZIP, we generated LNCaP prostate cancer cell lines that conditionally
express the processed form of AIbZIP. The recombinant protein consists of
the first 290 amino acids of AIbZIP fused to a C-terminal HA epitope.
Conditional expression was achieved using the RheoSwitch expression system.
Clone number 7-11 was exposed to the inducing agent (RSL1) for 6 and 24 hr
and Affymetrix microarrays were used to identify AIbZIP-regulated
transcripts. Candidate genes were identified by comparing the probe set
intensities of RSL1-treated cells and control cells (cells exposed to
vehicle). Forty-eight genes were then validated by Northern blot analysis.
Keywords: time course

overall_design:
Clone 7-11 cells (passage 42) were plated in 24 10-cm culture dishes.
Sixteen dishes were cultured in medium containing RSL1 (500 nM) and eight
dishes were cultured in medium containing an equivalent amount of the RSL1
vehicle (DMSO). Eight RSL1-treated dishes were harvested 6 hr after addition
of RSL1 and another eight dishes were harvested 24 hr after addition of
RSL1. At each time point, the dishes were pooled two by two to yield a total
of 12 individual samples i.e. 4 controls, 4 exposed to RSL1 for 6 hr, and 4
exposed to RSL1 for 24 hr. One sample of each group was processed to nuclear
extracts to assess the levels of recombinant AIbZIP by immunoblotting. The
three other samples of each group were processed separately to cRNA probes
which were then hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays
(Batch nos. 4003850 and 4003847).

first: Claude

last: Labrie


title: Laser capture microdissected vervet monkey lateral geniculate nucleus hybridized to the Rhesus Macaque Genome Array.

status: Public on Nov 12 2007

city: Montreal

first: Pascal

last: Lachance

state: QC

address: 1205 Ave. Dr. Penfield

department: Psychology

institute: McGill University

summary:
This report is based on an ongoing study to examine gene expression differences in monkey lateral geniculate nucleus (LGN). For this study, samples from an Old World species, vervet monkey (Cercopithecus aethiops), were cross-hybridized to the Rhesus Macaque Genome Array (Affymetrix). Microarray analysis was performed using laser capture microdissected populations of individual neuronal cell bodies isolated from the LGN compared to heterogeneous samples from whole lamina. We show here that cross-species hybridization of microdissected brain tissue samples from vervet monkeys to the Rhesus array produced reliable and biologically relevant data sets. We present the first list of genes enriched in the large neuronal cell bodies of the LGN. We found that these cell bodies are concentrated with genes involved in metabolic processes and protein synthesis, whereas signaling molecules including chemokines and integrins were expressed at higher levels within heterogeneous samples. Our data set provides support for a contribution of Wnt signaling in adult monkey LGN.
Keywords: gene expression profile

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Samples originated from magnocellular and parvocellular layers of the Lateral Geniculate Nucleus of vervet monkeys (Cercopithecus aethiops). We obtained neuronal cell body samples and heterogeneous layer samples from each layer, with N = 3 individual adult male animal replicates for each sample group (N = 12 total samples). Samples were hybridized to the Rhesus Macaque Genome Array. Two of the samples were also hybridized to the human HGU-133plus2 array for comparison.

first: Avi

last: Chaudhuri


title: Plasmodium Circumsporozoite Protein Promotes the Development of the Liver Stages of the Parasite

status: Public on Oct 30 2007

city: San Diego

first: John

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
The liver stages of malaria sporozoites develop in the hepatocyte cytoplasm inside a parasitophorous vacuole (PV). The circumsporozoite (CS) protein, the major surface protein of sporozoites, traverses the PV membrane and enters the cytoplasm and nucleus of hepatocytes. CS export into the cytoplasm requires the presence of pexel/VTS motifs. The transport of CS into the host nucleus is then mediated by importin (Imp) alpha3/beta1 that binds to the nuclear localization signal of CS localized in the conserved region II-plus. The NLSs of CS and of NFkB p50 share the same Imp. The entry of NFkB p50 into the nucleus is strongly inhibited in cell lines expressing CS, and in infected hepatocytes.  Micro-array data from CS expressing cell line shows that 40 NFkB targets were significantly down regulated. Among them inflammation related MIP3a and PTGS transcripts were 65 and 22 fold down regulated, thus explaining the notable absence of inflammatory cells surrounding exo-erythrocytic forms (EEFs). The presence of CS in the cytoplasm of hepatocytes enhances EEF growth both in vitro and in vivo. Therefore Plasmodium blood stages and EEFs use the same strategy to secrete proteins into the cytoplasm of host cells and remodel it to the parasite’s advantage.
Keywords: treatment and construct

overall_design: cells were isolated after inducing CSP and stimulating with TNF

first: Agam

middle: P

last: Singh

first: Carlos

middle: A

last: Buscaglia

first: Qian

last: Wang

first: Agata

last: Levay

first: Daniel

last: Nussenzweig

first: Elizabeth

last: Winzeler

first: Hodaka

last: Fujii

first: Beatriz

last: Fontoura

first: Victor


title: Features of TAP independently presented MHC ligands revealed by quantitative mass spectrometry.

status: Public on Oct 27 2007

city: Tuebingen

first: Andreas

middle: Oliver

last: Weinzierl

address: Auf der Morgenstelle 15

department: Department of Immunology

institute: University of Tuebingen

summary:
The TAP transporter is responsible for transferring cytosolic peptides into the ER where they can be loaded onto MHC molecules. Deletion of TAP results in a drastic reduction of MHC surface expression and alters the presented peptide pattern. Using the TAP deficient cell line LCL721.174 and its TAP expressing progenitor cell line LCL721.45, we have identified and quantified more than 160 HLA ligands, 50 out of which were presented TAP independently. Peptides which were predominantly presented on the TAP deficient LCL721.174 cell line had a decreased MHC binding affinity according to their SYFPEITHI and BIMAS score. About half of the identified TAP independently presented peptides were not derived from signal sequences and may partly be generated by the proteasome. Furthermore, we have excluded that different HLA presentation ratios were due to varying expression of the respective protein or due to changes in the antigen loading complex. Features of TAP-independently presented peptides as well as proteasomal contribution to their generation provides an insight into basic immunological mechanisms.
Keywords: differential mass spectrometry, TAP independent, antigen presentation

overall_design: Two B-LCL cell lines (TAP1/2 +/+ and TAP1/2 -/-) were compared in their gene and protein expression as well as in their HLA peptide repertoire

middle: O

first: Despina

last: Rudolf

first: Nina

last: Hillen

first: Stefan

last: Tenzer

first: Hansjörg

last: Schild

first: Hans-Georg

last: Rammensee

last: Stevanovic


title: Definition of an ulcerative colitis preinflammatory state

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary:
The samples are a part of a study aiming at diagnosing ulcerative colitis from genome-wide gene expression analysis of the colonic mucosa. Colonic mucosal samples were collected as endoscopic pinch biopsies from ulcerative colitis patients and from control subjects. Samples with and without macroscopic signs of inflammation were collected from the patients.
Keywords: Disease state analysis

overall_design: The series contain eight UC samples with macroscopic signs of inflammation, 13 UC smaples without macroscopic signs of inflammation, five control subjects.

first: Ole

middle: H

last: Nielsen

first: Clausio

last: Csillag

first: Jacob

last: Seidelin


title: Expression data from peripheral blood from healthy and predisposed individuals

city: Helsinki

first: Antti

last: Kokko

address: POBOX 63 (Haartmaninkatu 8)

department: Dept of Medical Genetics

country: Finland

institute: University of Helsinki

summary:
Characterization of the underlying genetic defects in patients with a rare and peculiar phenotype is challenging. Here we have utilized whole genome expression profiling, and identified a homozygous germline mutation in the DDB2 gene in a patient with several facial tumors. The feasibility of using blood derived RNA, diminishing costs of the technology, and the limited number of samples needed provide this approach a powerful new tool that may substantially aid in such gene identification efforts.
Keywords: disease vs control

overall_design: RNA from patient’s and his parents’ blood samples, as well as from twelve individuals available from other projects, were subjected to Human GeneChip U133 Plus 2.0 whole genome expression arrays (Affymetrix).

first: Pia

last: Vahteristo

first: Olli

last: Saksela

first: Kristiina

last: Aittomäki

first: Lauri

last: Aaltonen


title: Gene Expression Profiling in Peripheral Blood in Untreated New Onset Systemic Juvenile Idiopathic Arthritis

city: cincinnati

first: ndate

last: fall

address: 3333 burnet av

department: rheumatology

institute: Cincinnati children's hospital medical center

summary:
Systemic Juvenile Idiopathic Arthritis (sJIA) has been strongly associated with macrophage activation syndrome (MAS).  To better understand the pathogenesid of sJIA and to facilitate the search for MAS biomarkers, we examine gene expression profiles in untreated new onset sJIA.
17 new onset sJIA patients were included in the study.  5 of the 17 patients showed evidence of subclinical MAS and 2 eventually developed overt MAS.
Keywords: disease versus control

overall_design: Peripheral blood mononuclear cells (PBMCs) were separated using a Ficoll gradient from the 17 new onset sJIA patients and 30 normal control.  RNA was extracted from the PBMCS and subsequently hybridized to Affymetrix microarrays

first: Ndate

last: Fall

first: Michael

last: Barnes

first: Sherry

last: Thornton

first: Lorie

last: Luyrink

first: Kristi

last: Jennings

first: Judyann

last: Olson

first: Norman

last: Ilowit

first: Thomas

last: Griffin

first: David

last: Sherry

first: Susan

last: Thompson

last: Glass

first: Robert

last: Colbert

first: Alexei

last: Grom


title: Reanalysis of GSE8884 Samples with Breast Epithelial Samples from GSE3744.

first: Jennifer

last: Hipp

first: Shi

last: Lu


title: Reduced expression of mitochondrial oxidative metabolism genes in skeletal muscle of women with PCOS

status: Public on Oct 20 2007

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

institute: Roskilde Hospital

summary:
Recently, abnormalities in mitochondrial oxidative phosphorylation (OXPHOS) have been implicated in the pathogenesis of skeletal muscle insulin resistance in type 2 diabetes. In the present study, we hypothesized that decreased expression of OXPHOS genes could be of similar importance for insulin resistance in the polycystic ovary syndrome (PCOS).
Using the HG-U133 Plus 2.0 expression array from Affymetrix, we analyzed gene expression in skeletal muscle from obese women with PCOS (n=16) and age- and body mass index-matched control women (n=13) metabolically characterized by euglycemic-hyperinsulinemic clamp and indirect calorimetry. To identify pathways of importance for the pathogenesis of insulin resistance in PCOS, we performed biological pathway analysis using Gene Set Enrichment Analysis (GSEA 1.0) and Gene Microarray Pathway Profiler (GenMAPP 2.0). The expression of 9 genes, selected according to biological relevance, was evaluated by quantitative real time PCR (q-RT-PCR).
Women with PCOS were characterized by fasting hyperinsulinemia and impaired insulin-stimulated glucose disposal - caused by reduced glucose oxidation and storage - as well as impaired suppression of lipid oxidation (all P<0.01). GSEA and GenMAPP both revealed the same set of genes involved in OXPHOS, which was also the most downregulated biological pathway (P<0.01). These results were confirmed by q-RT-PCR of six genes from the OXPHOS gene set as well as three transcription factors known to regulate the transcription of these genes.
Our results, for the first time, provide evidence for an association between insulin resistance and impaired mitochondrial oxidative metabolism in skeletal muscle in women with PCOS. This may contribute to the increased risk of type 2 diabetes observed in these women
Keywords: PCOS, DNA microarray, global pathway analysis, mitochondrial oxidative metabolism, qantitative real time PCR, insulin resistance, skeletal muscle

overall_design: 16 insulin resistant PCOS patients of fertile age were matched to 13 healthy control subjects.

first: Dorte

last: Glintborg

first: Steen

last: Knudsen

last: Jensen

first: Qihua

last: Tan

first: Torben

last: Kruse

first: Klaus

last: Brusgaard

first: Henning

last: Beck-Nielsen

first: Kurt

last: Højlund


title: Genomic profiling in CLL and subtypes of del13q14

status: Public on Oct 06 2007

city: Ann Arbor

first: Sami

middle: N

last: Malek

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

summary:
Chronic lymphocytic leukemia (CLL) is a biologically heterogeneous illness with a  variable clinical course. Loss of chromosomal material on chromosome 13 at  cytoband 13q14 is the most frequent genetic abnormality in CLL, but the  molecular aberrations underlying del13q14 in CLL remain incompletely  characterized.  We analyzed 171 CLL cases for LOH and sub-chromosomal copy loss on  chromosome 13 in DNA from FACS-sorted CD19+ cells and paired buccal cells  using the Affymetrix XbaI 50K SNP-array platform.  The resulting high-resolution genomic maps, together with array-based  measurements of expression levels of RNA in CLL cases with and without  del13q14 and Q-PCR-based expression analysis of selected genes support the  following conclusions: i) del13q14 is heterogeneous and composed of multiple  subtypes with deletion of Rb or the miR15a/16 loci serving as anatomic  landmarks, respectively ii) del13q14 type Ia deletions are relatively uniform in  length and extend from breakpoints close to the miR15a/16 cluster to a newly  identified telomeric breakpoint cluster at ~50.2-50.5 Mb physical position iii)  LATS2 RNA levels are ~2.6-2.8-fold lower in cases with del13q14 type I that do  not delete Rb as opposed to all other CLL cases and iv) ~15% of CLL cases  display marked reductions in miR15a/16 expression often but not invariably  associated with bi-allelic miR15a/16 loss.  This data should aid future investigations into biological differences  imparted on CLL by different del13q14 subtypes including investigations into  LATS2 as one of the genes found deregulated as part of del13q14.
Keywords: Chronic lymphocytic leukemia, CLL, gene expression comparison, del13q14, del13q

overall_design: The goal of this analysis is to detect probesets that are differentially expressed between CLL patients with wild type chromosome 13 and 13q-deleted samples.  There are a total of 20 arrays.

first: Peter

last: Ouillette