title: Interferon beta-1a-induced changes in gene expression in PBMCs derived from CIS patients

status: Public on Jan 13 2009

city: Chapel Hill

first: Silva

last: Markovic-Plese

address: 105 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

summary:
IFNβ, an effective therapy against relapsing-remitting (RR) multiple sclerosis (MS) is naturally secreted during the innate immune response against viral pathogens.  The objective of this study was to characterize the immunomodulatory mechanisms of IFNβ targeting innate immune response and their effects on DC-mediated regulation of T-cell differentiation.  We found that IFNβ−1a in-vitro treatment of human monocyte-derived dendritic cells (DCs) induced the expression of TLR7 and the members of its downstream signaling pathway, including myeloid differentiation factor 88 (MyD88), IL-1R-associated kinase (IRAK)4, and TNF receptor-associated factor (TRAF)6, while it inhibited the expression of IL-1R.  Using siRNA TLR7 gene silencing, we confirmed that IFNβ-1a-induced changes in MyD88, IRAK4 and IL-1R expression were dependent on TLR7.  TLR7 expression was also necessary for the IFNβ-1a-induced inhibition of IL-1β and IL-23, and the induction of IL-27 secretion by DCs.  Supernatant (SN) transfer experiments confirmed that IFNβ-1a-induced changes in DCs’ cytokine secretion inhibit Th17 cell differentiation as evidenced by the inhibition of retinoic acid-related orphan nuclear hormone receptor C (RORC) and IL-17A gene expression and IL-17A secretion.  Our study has identified a novel therapeutic mechanism of IFNβ−1a, that selectively targets the autoimmune response in MS.

Keywords: The effect of IFN beta-1a on the gene expression in patients with clinically isolated syndrome suggestive of MS

overall_design: Gene expression changes induced by IFNβ−1a were tested using Affymetrix Human Genome U133 (HG-U133) arrays (Affymetrix) that contain 45,000 probe sets representing 39,000 transcripts derived from approximately 33,000 human genes.  107 PBMCs per condition derived from 15 CIS patients were stimulated with plate-immobilized αCD3 (1 μg/ml) and αCD28 (5 μg/ml) mAb (BD Biosciences) in the absence or presence of IFNβ-1a (1000 U/ml) (EMD Serono Inc) for 24 h in serum-free medium (Gibco).  Cells were harvested and the total RNA was isolated using a Rneasy kit (Quiagen).  Arrays were hybridized for 16 hours at 45oC in the GeneChip® Hybridization Oven 640 (Affymetrix).  The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip® Fluidics Station 400 (Affymetrix).  The arrays were scanned with a Hewlett Packard GeneArray Scanner.  Affymetrix GeneChip® Microarray Suite 5.0 software was used for washing, scanning and basic analysis.

first: Xin

last: Zhang

first: Jianping

last: Jin

first: Yunan

last: Tang


title: Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development

status: Public on Jan 28 2009

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

country: USA

institute: Pennsylvania State University

summary: The role of six toxin-antitoxin (TA) systems on biofilm development was investigated (MazEF, RelBEF, ChpB, YefM-YoeB, DinJ-YafQ, and TomB-Hha). Although these TA systems were reported previously to not impact bacterial fitness, we found that biofilm formation is decreased by toxins and increased by anti-toxins, in part, through YjgK. Hence, one role of TA systems is to regulate biofilm formation.

overall_design:
Strains: E. coli K-12 BW25113 wild-type and E. coli BW25113 yjgK deleted mutant
Medium: LB
Cells: biofilm cells on glass wool
Time: 8 h
Temperature: 37oC

first: Wood

middle: K

last: Thomas

first: Younghoon

last: Kim

first: Xiaoxue

last: Wang

first: Xue-Song


title: Gene expression in b1-integrin wild-type and knockout mouse heart

status: Public on Jan 15 2009

city: San Francisco

first: Masaki

last: Ieda

state: CA

address: 1650 Owens street,

institute: Gladstone Institute

summary: Growth and expansion of ventricular chambers is essential during cardiogenesis and is achieved by proliferation of cardiac progenitors that are not fully differentiated. Disruption of this process can lead to prenatal lethality. In contrast, adult cardiomyocytes achieve growth through hypertrophy rather than hyperplasia. Although epicardial-derived signals may contribute to the proliferative process in myocytes, the factors and cell types responsible for development of the ventricular myocardial thickness are unclear. Moreover, the function of embryonic cardiac fibroblasts, derived from epicardium, and their secreted factors are largely unknown. Using a novel co-culture system, we found that embryonic cardiac fibroblasts induced proliferation of cardiomyocytes, in contrast to adult cardiac fibroblasts that promoted myocyte hypertrophy. We identified fibronectin, collagen and heparin-binding EGF-like growth factor as embryonic cardiac fibroblast-specific signals that collaboratively promoted cardiomyocyte proliferation in a paracrine fashion. b1 integrin was required for this proliferative response, and ventricular cardiomyocyte-specific deletion of b1 integrin in mice resulted in reduced myocardial proliferation and impaired ventricular compaction. These findings reveal a previously unrecognized paracrine function of embryonic cardiac fibroblasts in regulating cardiomyocyte proliferation.

overall_design: To investigate the mechanisms responsible for the abnormalities in b1 integrin mutant mice, we performed mRNA expression microarray analyses of E12.5 wild-type and mutant hearts, well before any obvious dysfunction. RNA was isolated from wild-type and mutant hearts, and arrays were performed using Affymetrix mouse Gene 1.0 ST arrays. Analysis was performed on three biological replicates of WT and KO mouse hearts.

first: Ru-fang

last: Yeh

first: Deepak

last: Srivastava


title: Comparison between E. coli K-12 MG1655 and E. coli K-12 LVM100 delta 5 TA mutant on biofilm cell development

summary: The role of six toxin-antitoxin (TA) systems on biofilm development was investigated (MazEF, RelBEF, ChpB, YefM-YoeB, DinJ-YafQ, and TomB-Hha).  Although these TA systems were reported previously to not impact bacterial fitness, we found that biofilm formation is decreased by toxins and increased by anti-toxins, in part, through YjgK.  Hence, one role of TA systems is to regulate biofilm formation.

overall_design:
Strains: E. coli K-12 MG1655 and E. coli K-12 LVM100 delta 5 TA mutant
Medium: LB
Cells: biofilm cells on glass wool
Time: 15 h
Temperature: 37oC

first: Qun

last: Ma

first: Xuesong


title: Gene expression in mouse embyonic cardiomyocytes, fibroblasts and adult cardiac fibroblasts

overall_design: To identify candidate fibroblast-derived factors that promote myocyte proliferation, we isolated RNA from Nkx-YFP+ cardiomyocytes, embryonic cardiac fibroblasts, and adult cardiac fibroblasts and profiled mRNA expressions by microarray analyses. Arrays were performed using Affymetrix mouse Gene 1.0 ST arrays. Analysis was performed on three biological replicates of mouse embyonic cardiomyocytes, fibroblasts and adult cardiac fibroblasts.

first: Ru-Fang


title: Expression data from human normal pre-frontal cortex, liver, and colon tissues and colon tumors

status: Public on Jan 18 2009

city: Baltimore

first: rafael

last: irizarry

state: MD

institute: Johns Hopkins University

summary:
DNA methylation, at CpG islands and promoters, is often inversely correlated with gene expression.
We used expression microarrays to determine the relationship between DNA methylation and gene expression in 5 normal prefrontal cortex samples and 5 normal liver samples from the same individuals as well as between 4 colon tumor and matched normal colon mucosa (from the same individuals).

Keywords: human tissue comparison

overall_design: We isolated RNA from pre-frontal cortex and liver tissue from 5 individuals for which we have genome-wide DNA methylation data and hybridized to Affymetrix gene expression microarrays. Similarly, we isolated RNA from 4 tumor and matched normal colon samples that we have genome-wide DNA methylation data.

first: Rafael

last: Irizarry

first: Christine

last: Ladd-Acost

first: Andrew

last: Feinberg


title: Expression data from pulmonary metastases of clear-cell renal cell carcinoma

city: Dresden

first: Wuttig

last: Daniela

address: Fetscherstr. 74

department: Department of Urology

country: Germany

institute: Dresden, University of Technology

summary:
The understanding of metastatic spread is limited and molecular mechanisms causing particular characteristics of metastasis, like varying dormancy periods of Mets originating from the same primary tumor entity or the differing number of Mets in patients with the same primary tumor, are largely unknown. Knowing the molecular fundamentals of these phenomena would support the prognosis of patients´ outcome and facilitate the decision for an appropriate therapy regime.

We analyzed the transcriptome-wide expression profiles of 20 pulmonary metastases of renal cell carcinoma in order to identify expression patterns associated with two important prognostic factors in RCC: the disease-free interval after nephrectomy (DFI) and the number of Mets per patient.

Keywords: comparison of pulmonary metastases from patients with different clinical characteristics

overall_design:
metastases manifested early or late after nephrectomy (DFI less than or equal to 9 vs. greater than or equal to 60 months)

metastases derived from patients with only few or multiple pulmonary metastases (less than or equal to 8 vs. greater than  or equal to 16)

first: Daniela

last: Wuttig

first: Barbara

last: Baier

first: Susanne

last: Fuessel

first: Matthias

last: Meinhardt

first: Alexander

last: Herr

first: Christian

last: Hoefling

first: Marieta

middle: I

last: Toma

first: Marc-Oliver

last: Grimm

first: Axel

last: Meye

last: Rolle

first: Manfred

middle: P

last: Wirth


title: Galanin preproprotein is associated with elevated plasma triglycerides

city: Seattle

first: Christopher

middle: L

last: Plaisier

state: Washington

address: 401 Terry Avenue North

institute: Institute for Systems Biology

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

Keywords: Subcutaneous adipose tissue.

overall_design: Subcutaneous adipose tissue from 49 unrelated individuals.

first: Mira

last: Kittala

first: Daphna

last: Weissglas-Volkov

first: Janet

middle: S

last: Sinsheimer

first: Adriana

last: Huertas-Vazquez

first: Laura

last: Riba

first: Salvador

last: Ramierz-Jimenez

first: Tjerk

middle: W

last: de Bruin

first: Teresa

last: Tusie-Luna

first: Bradley

middle: E

last: Aouizerat

first: Cliver

middle: R

last: Pullinger

first: Mary

middle: J

last: Malloy

first: John

last: Kane

first: Ivette

last: Cruz-Bautista

first: Miguel

middle: F

last: Herrera

first: Carlos

last: Aguilar-Salinas

first: Johanna

last: Kuusisto

first: Markku

last: Laakso

first: Marja-Riitta

last: Taskinen

first: Carla

last: van der Kallen

first: Paivi

last: Pajukanta


title: Glucocorticoid-regulated microRNAs and mirtrons in acute lymphoblastic leukemia

status: Public on Jan 16 2009

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary:
Glucocorticoids (GC) have a major impact on the biology of normal and malignant cells of the lymphoid lineage. This includes induction of apoptosis which is exploited in the therapy of acute lymphoblastic leukemia (ALL) and related lymphoid malignancies. MicroRNAs (miRNAs) and the related mirtrons are ~22 nucleotide RNA molecules implicated in the control of essential biological functions including proliferation, differentiation and apoptosis. They derive from polymerase-II transcripts but whether GCs regulate miRNA-encoding transcription units is not known. We investigated miRNA/mirtron expression and GC regulation in 8 ALL in vitro models and 13 ALL children undergoing systemic GC monotherapy using a combination of expression profiling techniques, real time RT-PCR and northern blotting to detect mature miRNAs and/or their precursors. We identified a number of GC-regulated miRNAs/mirtrons, including the myeloid-specific miR-223 and the apoptosis and cell cycle arrest-inducing mir15~16 cluster. Thus, the observed complex changes in miRNA/mirtron expression during GC treatment might contribute to the anti-leukemic GC effects in a cell context dependent manner.
Keywords: treatment response

overall_design: Glucocorticoid-sensitive T-ALL cell line CCRF-CEM-C7H2 was treated in 3 independent experiments either with 100nM dexametasone (a glucocorticoid) or 0.1% ethanol as an empty carrier control. Samples were taken at various timepoints (6 and 24 hours), RNA extracted and hybridized onto Affymetrix HGU133-plus2 microarrays. The microarray dataset was subsetted to probesets targetting potential primary microRNA transcripts (pri-miRNAs). Differentially expressed pri-miRNAs were identified for the comparisons of the 6h GC versus 6h EtOH (control) and for the 24h GC versus 24h EtOH (control) samples.

first: Christian

last: Ploner

first: Simone

last: Jesacher

first: Andreas

first: Mayra

last: Eduardoff

first: Muhammad

last: Mansha

last: Wasim

first: Renate

last: Panzer

first: Zlatko

last: Trajanoski

first: Harald

last: Niederegger

first: Reinhard

last: Kofler


title: Contribution of sequence and structure to mRNA-binding of Argonaute/miRNA complexes and degradation of miRNA targets

status: Public on Jan 27 2009

city: New York

first: Markus

last: Landthaler

state: NY

address: 1230 York Avenue

institute: Rockefeller University

summary:
Relative contribution of sequence and structural features to the mRNA-binding of Argonaute/miRNA complexes and the degradation of miRNA targets

How miRNAs recognize their target sites is a puzzle that many experimental and computational studies aimed to solve. Several features such as perfect pairing of the miRNA seed, additional pairing in the 3’ region of the miRNA, relative position in the 3’ UTR and the A/U content of the environment of the putative site have been found to be relevant. Here we have used a large number of previously published data sets to assess the power that various sequence and structure features have in distinguishing between putative sites that do and those that do not appear to be functional. We found that although different data sets can give widely different answers when it comes to ranking the relative importance of these features, the sites inferred from most transcriptomics experiments as well as from comparative genomics appear similar at this level. This suggests that miRNA target sites have been selected in evolution on their ability to trigger mRNA degradation. To understand at what step in the miRNA induced response individual features play a role, we further transfected human HEK293 cells with miRNAs and analyzed the association of Argonaute/miRNA complexes with target mRNAs and the degradation of these messages. We found that structural features are only important for Argonaute binding, while sequence features such as the A/U content of the 3’ UTR are important for mRNA degradation.

Keywords: IP-array analysis

overall_design: Ago2 IPs of mock, miRNA-7, and miR-124 transfected cells were analyzed for 2 biological replicates. IPs of the biological replicates were analyzed with 2 technical replicates.

first: Jean

last: Hausser

first: Dimos

last: Gaidatzis

first: Mihaela

last: Zavolan


title: Gene expression profiling of 51 human breast cancer cell lines

status: Public on Jan 12 2009

city: South San Francisco

first: Mark

last: Lackner

address: 1 DNA Way

institute: Genentech

summary:
Basal gene expression levels were determined by global gene expression profiling of breast cancer cell lines.
Molecular subtype was determined using gene expression and HER2 status assesses by HER2 FISH analysis.

Keywords: Basal gene expression (no stimulation or timecourse)

overall_design: RNA was prepared from cell lines cultured in 10% fetal bovine serum


title: Gene expression profiling of 30 human breast cancers

summary:
We used microarrays to profile 30 human primary breast tumors and determine global gene expression patterns and molecular subtypes

Keywords: Basal gene expression in human tumor samples

overall_design: RNA from SNAP frozen human tumor biopsies was analyzed on Affymetrix mircroarrays

first: Tom

last: Januario


title: Gene expression changes upon expression of activated versions of MEK1 and HRAS in MCF10A cells

summary:
MCF10A cells were then transfected with MEK1(S217S221), HRAS(G12V), and null control vectors
Cells were lysed 24 hours post-transfection with collection of total RNA and protein

Keywords: Oncogene inducation of gene expression changes

overall_design: Overexpression of Oncogenic protein was confirmed via Western blot


title: Regulation of epidermal growth factor receptor signaling in human cancer cells by microRNA-7

status: Public on Jan 23 2009

city: Perth

first: Rebecca

last: Webster

address: Rear, 50 Murray St

country: Australia

institute: Western Australian Institute for Medical Research

summary: The epidermal growth factor receptor (EGFR) is frequently overexpressed in cancer and is an important therapeutic target. Aberrant expression and function of microRNAs has been associated with tumorigenesis. Bioinformatic predictions suggest that the human EGFR mRNA 3’-untranslated region contains three microRNA-7 (miR-7) target sites, which are not conserved across mammals. We found that miR-7 down-regulates EGFR mRNA and protein expression in cancer cell lines (lung, breast, and glioblastoma) via two of the three sites, inducing cell cycle arrest and cell death. Because miR-7 was shown to decrease EGFR mRNA expression, we used microarray analysis to identify additional mRNA targets of miR-7. These included Raf1 and multiple other genes involved in EGFR signaling and tumorigenesis. Furthermore, miR-7 attenuated activation of protein kinase B (Akt) and extracellular signal-regulated kinase 1/2 (ERK1/2), two critical effectors of EGFR signaling, in different cancer cell lines. These data establish an important role for miR-7 in controlling mRNA expression and indicate that miR-7 has the ability to coordinately regulate EGFR signaling in multiple human cancer cell types.

overall_design: Four samples are analysed: two biological replicates of A549 cells treated with miR-7 precursor and two biological replicates of A549 cells treated with miR-NC negative control precursor.

first: Keith

middle: M

last: Giles

first: Karina

last: Price

first: Priscilla

last: Zhang

first: John

last: Mattick

first: Peter

last: Leedman


title: Gastrointestinal differentiation marker Cytokeratin 20 is regulated by homeobox gene CDX1

city: Oxford

first: Carol

last: Chan

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: This study is to identify downstream targets of homeobox gene CDX1. The study assayed the expression of 2 pairs of stably transfected colorectal cancer cell lines: The CDX1 nonexpressing CRC cell line HCT116 was stably transfected with either CDX1 cDNA in the pRC/CMV expression vector (HCT116-CDX1) or with vector control (HCT116-Vec). The CDX1-expressing CRC cell line LS174T was similarly transfected with either a pSilencer vector containing a short sequence of CDX1 siRNA (LS174T-siRNA) , or a pSilencer vector containing a scrambled siRNA sequence as a control (LS174T-Vec).

overall_design: 2 pairs of colorectal cancer cell lines were used for comparison

first: Walter

last: Bodmer

first: Jenny

last: Wilding


title: Expression data from primary colorectal cancers

status: Public on Jan 08 2009

city: Parkville

first: Oliver

last: Sieber

state: Victoria

address: 6th floor, Centre for Medical Research,  Royal Melbourne Hospital,  Royal Parade

department: Melbourne Tumour Biology Branch

institute: Ludwig Institute for Cancer Research

summary:
Samples were taken from colorectal cancers in surgically resected specimens from 74 patients. The expression profiles were determined using Affymetrix Human Genome U133Plus 2.0 arrays. Our MSI/MSS classifer was applied to these samples.

Keywords: Expression profiling by array

overall_design: mRNA from 74 fresh-frozen primary colorectal tumour samples were extracted and hybridized to HG-U133Plus 2.0 expression arrays. The MAS5.0 procedure was used to make calls of expression. Data from each sample were quantile normalized with reference to a training set prior to application of our MSS/MSI classifier.


title: Cigarette Smoking Induces Overexpression of a Fat Depleting Gene AZGP1 in the Human Airway Epithelium

status: Public on Jan 06 2009

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Smokers weigh less and have less body fat than non-smokers, and increased body fat and weight gain are observed following smoking cessation. To assess a possible molecular mechanism underlying the inverse association between smoking and body weight, we hypothesized that smoking may induce the expression of a fat depleting gene in the airway epithelium, the cell population that takes the brunt of the stress of cigarette smoke. As a candidate gene we evaluated the expression of alpha2-zinc-glycoprotein1 (AZGP1), a soluble protein that stimulates lipolysis, induces a reduction in body fat in mice and is associated with the cachexia related to cancer, and is known to be expressed in secretory cells of lung epithelium. To assess if smoking upregulates AZGP1 expression, microarray analysis with TaqMan confirmation was used to evaluate large airway epithelial samples obtained by fiberoptic bronchoscopy from 37 normal smokers and 55 normal nonsmokers. Both microarray and TaqMan analysis demonstrated that AZGP1 mRNA levels were higher in the large airway epithelium of normal smokers compared to normal nonsmokers (p<0.05, all comparisons). Western analysis of airway biopsies of smokers compared with nonsmokers demonstrated upregulation of AZGP1 at the protein level, and immunohistochemical analysis demonstrated upregulation of AZGP1 in secretory as well as neuroendocrine cells of smokers. In the context that AZGP1 is involved in lipolysis and fat loss, its overexpression in the airway epithelium of chronic smokers may represent one mechanism for the weight difference in smokers vs nonsmokers.
Keywords: Comparison of gene expression in large airway epithleium of normal non-smokers and normal smokers

overall_design: Airway epithelial cells obtained by bronchoscopy with brushing from healthy smokers and healthy non-smokers

first: Holly

last: Vanni

first: Angeliki

last: Kazeros

first: Ben-Gary

last: Harvey

first: Barbara

last: Ferris

first: Bishnu

last: De

first: Brendan

last: Carolan

first: Ralf-H

last: Hübner

first: Ronald

middle: G

last: Crystal


title: Carboplatin-induced gene expression changes in vitro are prognostic of survival in epithelial ovarian cancer

status: Public on Jan 05 2009

city: Boston

first: dimitrios

last: Spentzos

state: MA

address: 330 Brookilne Ave CLS 541

department: Department of medicine

institute: Beth ISrael Deaconess Medical center

summary:
We performed a time-course microarray experiment to define the transcriptional response to carboplatin in vitro, and to correlate this with clinical outcome in epithelial ovarian cancer (EOC). RNA was isolated from carboplatin and control-treated 36M2 ovarian cancer cells at several time points, followed by oligonucleotide microarray hybridization.  Carboplatin induced changes in gene expression were assessed at the single gene as well as at the pathway level.  Clinical validation was performed in publicly available microarray datasets using disease free and overall survival endpoints.
Time-course and pathway analyses identified 317 genes and 40 pathways (designated time-course and pathway signatures) deregulated following carboplatin exposure.  Both types of signatures were validated in two separate platinum-treated ovarian and NSCLC cell lines using published microarray data.  Expression of time-course and pathway signature genes distinguished between patients with unfavorable and favorable survival in two independent ovarian cancer datasets. Among the pathways most highly induced by carboplatin in vitro, the NRF2, NF-kB, and cytokine and inflammatory response pathways were also found to be upregulated prior to chemotherapy exposure in poor prognosis tumors.

overall_design: we treated the 36M2 cell line with carboplatin 100μM or vehicle-control for 24hrs and cells were harvested and processed for RNA isolation at 24, 30 and 36hrs after treatment.

first: Panagiotis

middle: A

last: Konstantinopoulos

first: Dimitrios


title: Role of inherent strain differences in prenatally induced differential metabolic syndrome phenotype and gene expression

city: toronto

first: brian

last: knight

address: 25 orde st

country: Canada

institute: samuel lunenfeld research institute

summary:
There is much evidence suggesting that gene-environment interactions underlying the developmental origins of the metabolic syndrome. Previously, we have induced a metabolic syndrome phenotype in mice though prenatal undernutrition; however, the C57BL/6J strain exhibited significantly more metrics of the metabolic syndrome than the A/J strain.
We used microarrays to detail the global programme of gene expression underlying the strain differences in the prenatal induction of the adult development of the metabolic syndrome. We focused on liver function and gene expression because of it's centrol role in many aspects of the metabolic syndrome including glucose and lipid control.

Keywords: disease state analysis between mouse strains

overall_design: Pregnant A/J and C57BL/6J mice were either exposed to prenatal undernutrition during pregnancy or control conditions. The livers from 32 male offspring (8 per group within each of the two strains) were dissected out at 7 months of age and total RNA was extracted and hybridization on Affymetrix microarrays.


title: E. coli K-12 10 uM 5-fluorouracil biofilm vs. E. coli K-12 DMF biofilm

status: Public on Jan 02 2009

city: College Station

first: Can

last: Attila

state: TX

address: 524 Jack E. Brown Bldg.

department: Chemical Eng

institute: Texas A&M University

summary: E. coli K-12 ATCC 25404 in LB medium with 5-fluorouracil 10 uM biofilm cells relative to E. coli K-12 ATCC 25404 in LB DMF biofilm cells.  The same amount of stock 5-fluoroacil stock solution (0.1% of the volume) was added as DMF into the LB DMF.

overall_design:
Strain: E. coli K-12 ATCC 25404 wild-type
Medium: LB
Biofilm growth on glass wool
Time: 24 h
Cell type: biofilm

5-fluorouracil vs. DMF

first: Akihiro

last: Ueda

first: Thomas

last: Wood


title: Colon cancer HT29 cells: siHX transfected vs. control

status: Public on Jan 01 2009

city: Hangzhou

first: Qiaoyi

last: Liang

state: Zhejiang

address: 88 Jiefang Road

department: Zhejiang University

country: China

institute: Cancer Insititute

summary:
HT29 cells were transsfected with siRNA (siHX), which is targeting the human endogeous retrovirus HERV-HX. Cells were harvested 72 h after transfection and knock-down of HERV-HX was evaluated by quantitative RT-PCR.

Keywords: Genetic modification

overall_design: Two-condition experiment, siHX vs. control cells. 1 transfected, 1 control.

first: Shu

last: Zheng


title: Transcriptome analysis of human mature oocytes and embryonic stem cells reveals overexpression of the proteasome pathway

city: Montpellier

first: John

last: De Vos

address: 80 av. Augustin Fliche

department: Institute for Research in Biotherapy

country: France

institute: University Hospital of Montpellier

summary:
The first week of human pre-embryo development is characterized by the induction of totipotency and then pluripotency. The understanding of this delicate process will have far reaching implication for in vitro fertilization and regenerative medicine. Human mature MII oocytes and embryonic stem (ES) cells are both able to achieve the feat of cell reprogramming towards pluripotency, either by somatic cell nuclear transfer or by cell fusion, respectively. Comparison of the transcriptome of these two cell types may highlight genes that are involved in pluripotency initiation. Therefore, based on a microarray compendium of 205 samples, produced in our laboratory or from public databases, we compared the gene expression profile of mature MII oocytes and human ES cells (hESC) to that of somatic tissues. We identified a common oocyte/hESC gene expression profile, which included a strong cell cycle signature, a large chromatin remodelling network (TOP2A, DNMT3B, JARID2, SMARCA5, CBX1, CBX5) and 18 different zinc finger transcription factors, including ZNF84. Strikingly, a large set of genes was found to code for proteins involved in the ubiquitination and proteasome pathway. Upon hESC differentiation into embryoid bodies, the transcription of this pathway declines. In vitro, we observed a selective sensitivity of hESC to the inhibition of the activity of the proteasome, resulting in loss of pluripotency and cell growth at doses without any detectable effects on differentiated cells. Taken together, these results suggest that the proteasome pathway may play a role in initiating and maintaining pluripotency during early development and in hESC.
Keywords: cell type comparison

overall_design:
We included in this study 9 samples obtained in our laboratory. These samples were hybridized on U133 Plus 2.0 GeneChips (Affymetrix). All samples were normalized using the MAS5 (GCOS 1.2) algorithm, using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
Human embryonic stem cells (hESC) samples were compared to somatic tissues, human mature oocytes samples were compared to somatic tissues, then the hESC and the mature oocyte signatures were interesected to define an oocyte/hESC signature.

last: DE VOS

first: Said

last: ASSOU

first: Samir

last: HAMAMAH


title: Gene Expression Profiling of Alveolar Soft-Part Sarcoma (ASPS)

city: Frederick

first: Luke

middle: Hunter

last: Stockwin

address: Ft. Detrick

department: DTP

institute: NCI Frederick

summary: Alveolar soft-part sarcoma (ASPS) is an extremely rare, highly vascular soft tissue sarcoma affecting predominantly adolescents and young adults. In an attempt to gain insight into the pathobiology of this enigmatic tumor, we performed the first genome-wide gene expression profiling study.

overall_design: For seven patients with confirmed primary or metastatic ASPS, RNA samples were isolated immediately following surgery, reverse transcribed to cDNA and each sample hybridized to duplicate high-density human U133 plus 2.0 microarrays. Array data was then analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome. Subsequent gene ontology analysis was used to identify transcripts with therapeutic or diagnostic potential. A subset of the most interesting genes was then validated using quantitative RT-PCR and immunohistochemistry.

middle: H

first: David

middle: T

last: Vistica

first: Susan

last: Kenney

last: Schrump

first: Donna

middle: O

last: Butcher

first: Mark

last: Raffeld

first: Robert

last: Shoemaker


title: Small molecule inhibitors of HIF-2a translation link its 5’-UTR Iron-Responsive Element (IRE) to oxygen sensing

city: Charlestown

first: Othon

last: Iliopoulos

address: Bldg 149, 13th Street

department: Cancer Center

institute: Massachusetts General Hospital

summary: Cells transiently adapt to hypoxia by globally decreasing protein translation. However, specific proteins needed to respond to hypoxia evade this translational repression. The mechanisms of this phenomenon remain unclear. We screened for and identified small molecules that selectively decrease HIF-2a translation in an mTOR independent manner, by enhancing the binding of Iron Regulatory Protein 1 (IRP1) to a recently reported Iron-Responsive Element (IRE) within the 5’-untranslated region (UTR) of the HIF-2a message. Knocking down the expression of IRP1 by shRNA abolished the effect of the compounds. Hypoxia de-represses HIF-2a translation by disrupting the IRP1- HIF-2a IRE interaction. Thus, this chemical genetic analysis describes a molecular mechanism by which translation of the HIF-2a message is maintained during conditions of cellular hypoxia through inhibition of IRP-1 dependent repression. It also provides the chemical tools for studying this phenomenon.

overall_design: 3 replicate samples of 786-O human Clear Cell Renal Carcinoma cells untreated, mock treated with DMSO or treated with either of 4 HIF-2a inhibitor compounds identified by chemical genetic screening.

first: Mike

last: Zimmer

first: Benjamin

last: Ebert

first: Justin

last: Lamb


title: Primary prostate cancer cell specific expression

status: Public on Jan 14 2009

city: Ribeirao Preto

first: Ricardo

last: Vêncio

state: SP

address: Av. Bandeirantes, 3900

department: Computing and Mathematics Department

country: Brazil

institute: Universidade de São Paulo

summary:
Cancer cells were MACS sorted from tumor tissue specimem 05-179. Self replicates of CD26+ cancer cells were generated and the expression profiles were determined using Affymetrix U133 Plus 2.0 arrays. These data represent cancer cell type specific transcriptome.
Keywords: disease state analysis

overall_design: Self replicates of the sorted were done.

first: Alvin

last: Liu


title: Identifying Sites Bound by Epstein Barr Nuclear Antigen 1 (EBNA1) in the Human Genome

city: Madison

first: Bill

last: Sugden

state: WI

address: 1400 University Avenue

department: Oncology

institute: University of Wisconsin-Madison

type: Genome binding/occupancy profiling by genome tiling array

summary:
Epstein-Barr virus (EBV) is a ubiquitous gammaherpes virus that establishes a life-long latency in over 90% of the world's population. Epstein Barr Nuclear Antigen 1, EBNA1, is the only viral protein consistently detected in all viral latency programs, as well as in all forms of EBV-associated malignancies. EBNA1 plays critical roles in the viral life cycle by fostering the replication and maintenance of the extrachromosomal viral genome as well as enhancing transcription from multiple viral promoters.
Using chromatin immunoprecipitation and human promoter microarrays (an analysis termed ChIP-chip) we found that EBNA1 binds site specifically within multiple human promoters. To determine whether EBNA1’s binding to these promoters perturbed gene expression, we measured the levels of cellular mRNAs by microarrays when EBNA1 was inhibited by a dominant negative derivative of EBNA1 (DomNeg1).

Keywords: viral regulation of cellular genes

overall_design:
We analysed mRNA expression from the EBV-positive lymphoblastoid cell line 721 transduced with either a control (empty) retroviral vector or a DomNeg1-encoding retroviral vector.

For ChIP-chip, DNA from immunoprecipitated chromatin using a anti-EBNA1 antibody (IH4) along with total chromatin was hybridized to a Nimblegen human promoter arrays (CHAR0150-HP2).  A single ChIP-chip experiment was performed with DNAs pooled equally from three independent ChIP experiments.

first: Lindsay

last: Dresang

last: Vereide


title: Chemotherapy-induced oral mucositis (CIOM) in patients with acute myeloid leukemia (AML)

city: Charlotte

first: Jean-Luc

middle: C

last: Mougeot

state: NC

address: 1542 Garden Terrace

department: Internal Medicine

institute: Carolinas Medical Center

summary:
Chemotherapy may cause DNA damage within the oral mucosa of cancer patients leading to mucositis, a dose-limiting side effect for effective cancer treatment.
We used whole genome gene expression analysis to identify cellular damage to the mucosal tissue occuring two days post induction chemotherapy and identified gene expression patterns that may or may not be predictive of oral mucositis.
Keywords: Treatment effect

overall_design: Punch buccal biopsies from healthy controls (HC, samples BRENC1, BRENC2, BRENC3, n=3) and  five AML patients pre-chemotherapy (Pre-C, samples BREN11, BREN21, BREN41, BREN51, n=4) and (Post-C, samples BREN22, BREN32, BREN42, BREN52, n=4)(Ntotal=11) gave suitable RNA integrity to perform microarray analysis. Samples Pre-C:BREN31 and post-C:BREN12 were not suitable for microarray analysis. Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA) was used to conduct gene expression profiling.

first: Michael

last: Brennan


title: A study of temporal transcriptional changes induced by a low concentration BPDE in cultured human cells

first: Lu

last: XiangYun

address: 388 Yuhangtang Road

institute: Zhejiang University School of Medicine

summary:
The environmental carcinogen, (±)-anti-benzo[a]pyrene-7,8-diol-9,10-epoxide (BPDE), causes bulky-adduct DNA damages, triggers certain signaling pathways, and elicits gene expression changes. Here, we focused on the temporal gene expression changes induced by a low concentration (0.05 µM) BPDE in human amnion epithelial FL cells. Differential gene expression profiles at 1, 10 and 22 h post BPDE treatment were obtained using Affymetrix HG-U133 Plus 2.0 oligonucleotide microarrays.
A cohort of gene expression changes related to cell cycle progression, cell growth or apoptosis, stress response, and post-transcriptional regulation was validated with quantitative real-time RT-PCR. The alteration of several cell cycle-related genes was correlated and possibly contributed to the cell cycle arrest phenotype. Paradoxical transcriptional regulations regarding cell growth or apoptosis emerged in response to BPDE treatment, which indicated that cell fate was determined by integrated signals. The temporal transcriptional changes would be of help to clarify the molecular mechanism of cellular response to BPDE.
Keywords: time course

overall_design: Human amnion epithelial FL cells were exposed to vehicle control (dimethyl sulfoxide) and a low concentration (0.05 µM) (±)-anti-benzo[a]pyrene-7,8-diol-9,10-epoxide, respectively. The differential gene expression profiles at 1, 10 and 22 h post BPDE treatment were obtained using Affymetrix HG-U133 Plus 2.0 oligonucleotide microarrays. The transcriptomic changes at different time points post BPDE treatment would provide insight into the dynamic processes of cellular response to this genotoxic agent.

first: Xiangyun

last: Lu

first: Jimin

last: Shao

first: Hongjuan

last: Li

first: Yingnian

last: Yu


title: Microarray analysis of neural progenitor cells (hNPC) derived from the developing cortex (CTX) and ventral midbrain (VM)

status: Public on Dec 31 2008

first: Hyun-Jung

last: Kim

address: 1500 Highland ave.

department: Waisman center

institute: UW-Madison

summary: Neural progenitor cells (hNPC) derived from the developing human brain can be expanded in culture and subsequently differentiated into neurons and glia.  They provide an interesting source of tissue for both modeling brain development and future cellular replacement therapies.  It is becoming clear that hNPC are regionally and temporally specified depending on which brain region they were isolated from and its developmental stage.   We show here that hNPC derived from the developing cortex (hNPCCTX) and ventral midbrain (hNPCVM) have similar morphological characteristics and express the progenitor cell marker nestin.  However, hNPCCTX cultures were highly proliferative and produced large numbers of neurons, while hNPCVM divided slowly and produced less neurons but more astrocytes.  Microarray analysis revealed a similar expression pattern for some stemness markers between the two growing cultures, overlaid with a regionally specific profile that identified some important differentially expressed neurogenic transcription factors.  By over expressing one of these, the transcription factor ASCL1, we were able to regain neurogenesis from hNPCVM cultures which produced larger neurons with more neurites than hNPCCTX, but no fully mature dopamine neurons. Thus hNPC are regionally specified and can be induced to undergo neurogenesis following genetic manipulation.   While this restores neuronal production with a region specific phenotype, it does not restore full neurochemical maturation which may require additional factors.

overall_design:
G001 and G002 are neural progenitor cells derived from human (German) embryos 8-10 wk old.
After abortion,the cortex and ventral midbrain have been dissected and grown as neurospheres.
4 samples total: G001CTX, G001VM, G002CTX, G002VM

first: Erin

last: McMillan

first: Clive

middle: N

last: Svendsen


title: Global effects of 2-methoxyestradiol on smooth muscle cell hyperproliferation and vascular remodeling in atherosclerosis

city: Zurich

last: Zaugg

address: Raemistrasse 100

department: Anesthesiology

country: Switzerland

institute: Anesthesiology, University Hospital Zurich

summary:
We used microarrays to detail transcriptional changes in cultured human smooth muscle cells in response to acute and chronic 2-methoxyestradiol treatment
2-ME, an endogenous metabolite. of estradiol, not only exerts cytotoxic effects on cancer cells but it also protects against multiple proliferative disorders, including atherosclerosis and injury-induced intimal thickening

Keywords: treatment vs. control

overall_design: Human aortic smooth muscle cells cultures with/without 2-methoxyestradiol (acute/chronic treatment)

first: Eliana

last: Lucchinetti

first: Raghvendra

last: Dubey

first: Federica

last: Barchiesi-Bozzolo


title: Gene expression profiling of human breast cancers and cancer cell lines

first: Mark

last: Lackner

address: 1 DNA Way

institute: Genentech

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

overall_design: Refer to individual Series


title: MERLION LUNG CANCER STUDY

city: Villejuif

first: Philippe

last: Broët

address: 16 Ave Paul Vaillant Couturier

department: Faculty of Medicine

institute: University Paris-Sud

summary:
Series of stage IB lung adenocarcinomas and large cell carcinomas. The aim of the study was to predict outcome using a Copy Number Driven Gene Expression signature.
Keywords: disease state analysis, stage I lung cancer

overall_design: Homogeneous series of 72 cases of lung primary stage IB adenocarcinomas/large cell carcinomas, analyzed using the Human U133Plus 2.0 oligonucleotide arrays (Affymetrix, Santa Clara, CA).

last: Broet

first: Sophie

last: Camilleri-Broet

first: Marco

last: Alifano

first: Patrick

last: Tan

first: Lance

middle: D

last: Miller


title: Multiple Salivary Biomarkers for Early Detection of Pancreatic Cancer

city: Los Angeles

first: Lei

last: Zhang

address: 10833 Le Conte Ave., CHS 73-029

institute: UCLA Dental Research Institute

summary:
Pancreatic cancer is the fourth leading cause of cancer death. Lack of early detection technology for pancreatic cancer invariably leads to a typical clinical presentation of incurable disease at initial diagnosis. Oral fluid (saliva) meets the demand for non-invasive, accessible, and highly efficient diagnostic medium. The level of salivary analytes, such as mRNA and microflora, vary upon disease onset; thus possess valuable signatures for early detection and screening. In this study, we evaluated the performance and translational utilities of the salivary transcriptomic and microbial biomarkers for non-invasive detection of early pancreatic cancer. Two biomarker discovery technologies were used to profile transcriptome in saliva supernatant and microflora in saliva pellet. The Affymetrix Human Genome U133 Plus 2.0 Array was used to discover altered gene expression in saliva supernatant. The Human Oral Microbe Identification Microarray (HOMIM) was used to investigate microflora shift in saliva pellet. Biomarkers selected from both studies were subjected to an independent clinical validation using a cohort of 30 early pancreatic cancer, 30 chronic pancreatitis and 30 healthy matched-control saliva samples. Two panels of salivary biomarkers, including eleven mRNA biomarkers and two microbial biomarkers were discovered and validated for pancreatic cancer detection. The logistic regression model with the combination of three mRNA biomarkers (ACRV1, DMXL2 and DPM1) yielded a ROC-plot AUC value of 0.974 (95% CI, 0.896 to 0.997; P < 0.0001) with 93.3% sensitivity and 90% specificity in distinguishing pancreatic cancer patients from healthy subjects. The logistic regression model with the combination of two bacterial biomarkers (Neisseria elongata and Streptococcus mitis) yielded a ROC-plot AUC value of 0.895 (95% CI, 0.784 to 0.961; P < 0.0001) with 96.4% sensitivity and 82.1% specificity in distinguishing pancreatic cancer patients from healthy subjects. Importantly, the logistic regression model with the combination of four biomarkers (mRNA biomarkers, ACRV1, DMXL2 and DPM1; bacterial biomarker, S. mitis) could differentiate pancreatic cancer patients from all non-cancer subjects (chronic pancreatitis and healthy control), yielding a ROC-plot AUC value of 0.949 (95% CI, 0.877 to 0.985; P < 0.0001) with 92.9% sensitivity and 85.5% specificity. This study comprehensively compared the salivary transcriptome and microflora between pancreatic cancer and control subjects. We have discovered and validated eleven mRNA biomarkers and two microbial biomarkers for early detection of pancreatic cancer in saliva. The logistic regression model with four salivary biomarkers can detect pancreatic cancer specifically without the complication of chronic pancreatitis. This is the first report demonstrating the value of multiplex salivary biomarkers for the non-invasive detection of a high impact systemic cancer.

Keywords: Salivary biomarker, pancreatic cancer, early detection, salivary transcriptome, salivary microflora

overall_design: This study, which was approved by the UCLA Institutional Review Board, started sample collection in February 2006 and ended in April 2008. It had a discovery and verification phase, followed by an independent validation phase. All patients with clinically diagnosed early or locally advanced pancreatic cancer, chronic pancreatitis and matched healthy control were recruited from the UCLA Medical Center. The controls were matched for gender, age, ethnicity and smoking history. We chose early and locally advanced pancreatic cancers because they were considered early stage diseases. All patients were recently diagnosed with primary disease, and had not received any prior treatment in the form of chemotherapy, radiotherapy, surgery, or alternative remedies. No subjects had a history of prior malignancy, immunodeficiency, autoimmune disorders, hepatitis, or HIV infection. Written informed consent was obtained from all patients who agreed to serve as saliva donors. Unstimulated saliva samples were collected and processed as previously described. The saliva bank of pancreatic disease at the UCLA Dental Research Institute has collected 283 saliva samples since 2006. Of these, 114 samples, from 42 pancreatic cancer patients, 30 chronic pancreatitis patients and 42 healthy control subjects, met the following eligibility criteria: the disease subjects’ samples were obtained immediately after primary diagnosis from patients without evidence of metastasis; the saliva sample was free of blood (Table 1 in accompanying manuscript). Of the 114 samples, 12 pancreatic cancer samples and 12 healthy control samples were chosen for the discovery and verification phase. The transcriptomic approach profiled the saliva supernatant samples from 12 pancreatic cancer patients and 12 healthy control subjects using the Affymetrix Human Genome U133 Plus 2.0 Array platform.

first: James

last: Farrell

first: Kai

last: Gao

first: Hui

last: Zhou

first: David

last: Elashoff

first: Bruce

last: Paster

last: Wong


title: Gene expression profiling of LMO2 associated T cell lymphoblastic leukemia induced by insertional mutagenesis

status: Public on Dec 27 2008

city: Cincinnati

first: Gerlinde

last: Layh-Schmitt

state: OH

address: 3333 Burnet Ave

department: Experimental Hematology

institute: Cincinnati Children's Hospital Research Foundation

summary:
Aberrant co-expression of LMO2 and TAL1 is regularly found in T cell acute lymphoblastic leukemia (T-ALL). Here we describe a xenotransplant model for primary T-ALL cells derived from a patient who developed LMO2/TAL1 associated T-ALL after gene therapy for X-SCID (gamma c deficiency) due to insertional activation and a SIL-TAL1 fusion as an additional independent event. We identified a protein complex containing LMO2, TAL1 and E47 in the patient’s T-ALL cells. This complex functions as a transcription regulation complex in undifferentiated hematopoietic cells. However, its role in T-ALL is not fully understood. By comparative gene expression profiling we identified retinaldehyde dehydrogenase (RALDH2) as one of the genes which was highly up regulated in the primary T-ALL cells; the gene product was N-terminally truncated (RALDH2-T), but enzymatically active. To investigate the interference of LMO2 in RALDH2-T expression as well as the role of RALDH2-T in T-ALL development, LMO1 (analogue of LMO2) was down regulated by RNA interference in the T-ALL cell line Jurkat which led to a decrease of RALDH2-T expression and cell viability, indicating that positive regulation of RALDH2-T through an LMO1 or 2 containing transcription regulation complex might be essential for maintaining the T-ALL phenotype.
Keywords: Primary human T-ALL cells and CD8 cells of normal donors

overall_design: To decipher target genes of an LMO2 associated transcription regulation complex in primary T cell acute lymphoblastic leukemia cells and its contribution to the onset of malignancy.

first: Gelinde

first: Michael

last: Jansen

first: Antonia

last: Rosenstiel

first: Wei

last: Wang

first: Stefanie

last: Koch

first: Carmen

last: Wittlinger

first: Charles

last: Klanke

first: Jeff

last: Bailey

first: Peter

last: McCaffery

first: Christof

last: von Kalle


title: Transcriptional responses of Escherichia coli k12 TPEN

last: Crowder

address: High Street

department: Chemistry and Biochemistry

institute: Miami University

summary:
DNA microarrays were conducted on E. coli K12 cells stressed with 10 μM in N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN). Overall, 260 genes varied in expression, 114 up-regulated and 146 down-regulated by Zn deprivation
Keywords: TPEN stress

overall_design: Array hybridizations were carried out for three RNA samples prepared from three independent cultures (control or TPEN-treated).

first: Thusitha

last: Gunasekera


title: A 5’ Sequence of Human HMGB2 Gene for Transcriptional Targeting of Glioblastoma

city: Singapore

first: Jerome

last: Boulaire

address: 31 Biopolis Way

department: Gene Delivery

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

summary: Achievement of specific tumor cell targeting remains a challenge for glioma gene therapy. We report here the identification and characterization of a 5’ sequence of human HMGB2 gene for transcriptional targeting to glioblastoma. We performed microarray analysis and found HMGB2 as one of the genes that had a low level of expression in normal human astrocytes, but was significantly up-regulated in glioblastoma cells. Real-time PCR quantification revealed increase in HMBG2 expression level in glioblastoma tissues and cells between 11 to 79 fold over that in normal human brain tissue. With progressive truncation of a 5’-upstream sequence of the HMGB2 gene, we identified a 500-bp fragment that displayed a high transcriptional activity in glioblastoma cells, but a low activity in normal brain cells. Using the sequence to drive the expression of the herpes simplex virus thymidine kinase gene in the context of a baculoviral vector, glioblastoma cells died in the presence of ganciclovir, whereas normal human astrocytes and neurons were not affected. We further confirmed that after intra-tumor injection, the baculoviral vector effectively suppressed the growth of human glioblastoma cells in a mouse xenograft model. Our results suggest that the 5’-upstream sequence of the HMGB2 gene can be used as an efficient, tumor-selective promoter in targeted vectors for glioblastoma gene therapy.

overall_design: U251 cells (n=3) genes level expression were compared to that of normal astrocytes (n=3) to find overexpressed genes in glioblastoma. Highly expressed genes were compared to those found in the litterature. This was selected to clone promoters of highly expressed genes in glioblastomas

first: Poonam

last: Balani

first: Ying

last: Zhao

first: Jieming

last: Zeng

first: Jiakai

last: Lin

first: Shu


title: Gene expression profiling of liver metastases from colorectal cancer

status: Public on Dec 22 2008

city: Bologna

first: Maria

middle: Abbondanza

last: Pantaleo

state: BO

address: via Massarenti 9

department: Institute of Hematology and Medical Oncology "L.A.Seragnoli"

institute: Policlinico S. Orsola-Malpighi, University of Bologna

summary:
At present, medical treatments of synchronous and metachronous liver metastases from colorectal cancer are not differentiated. The aim of the study was to analyze the gene expression profiling of synchronous and metachronous lesions in order to identify molecular signatures as possible basis for choice of systemic therapies. Fresh tissues specimens from metastases of 18 patients undergone liver surgery were collected (10 synchronous and 8 metachronous lesions). Gene expression profiling was studied using Affymetrix platform. Two different profiles were identified. Pathway related to the Epidermal Growth Factor receptor (EGFr) was upregulated in metachronous lesions whereas pathways mainly related to inflammation in synchronous lesions. Real Time-PCR, Western Blotting and ELISA confirmed that the metachronous lesions had the overexpression of EGFr, but the synchronous ones had the overexpression of Cyclo-oxygenase 2 (COX-2). These results suggest that synchronous or metachronous liver metastases from colorectal cancer could be differently treated on the basis of  different molecular pathways.
Keywords: disease state analysis

overall_design: Gene expression analysis of liver metastases from 18 colorectal cancer patients: 8 metachronous and 10 synchronous single metastatic lesions.

first: Annalisa

last: Astolfi

first: Margherita

last: Nannini

first: Paola

last: Paterini

first: Giulia

last: Piazzi

first: Giorgio

last: Ercolani

first: Giovanni

last: Brandi

first: Pession

last: Andrea

first: Antonio

last: Pinna

first: Guido

last: Biasco


title: Claudin-1 is an Invasion and Metastasis Suppressor of Lung Adenocarcinoma

status: Public on Dec 23 2008

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
Background: Claudin-1(CLDN1), one of the key components of tight junction proteins, was found to be down-regulated in human lung adenocarcinomas. This study we investigated the clinical significance of CLDN1 expression in lung adenocarcinoma patients and its role in cancer progression. Method: CLDN1 mRNA expression was measured in tumor specimens from 51 patients with lung adenocarcinoma. CLDN1 protein expression was also examined by immunohistochemistry on specimens from an independent cohort of 67 lung adenocarcinoma patients. CLDN1 and cancer cell migration, invasion, and in vivo metastasis were studied by compared CLDN1 overexpressed, specific shRNA knockdown cells and controls. The Affymetrix oligonucleotide microarray analysis was performed to identify CLDN1 downstream genes. Results: Lung adenocarcinoma patients with low expression of CLDN1 mRNA had shorter overall survival (p = 0.032, log-rank test). This result was further confirmed by immunohistochemistry of CLDN1 protein expression in an independent cohort of lung adenocarcinoma patients (p=0.024). Over-expression of CLDN1 inhibited lung adenocarcinoma cell migration, invasion, and in vivo metastasis. Knockdown of the exogenous CLDN1 expression in CLDN1 transfectants can restore the cancer cell invasive and metastatic ability. By using Affymetrix microarray we have identified panel of genes altered by CLDN1 over-expression. CLDN1 can up-regulate several cancer invasion/metastasis suppressors such as CTGF, THBS1, DLC1, OCLN, ZO-1, and also down-regulate invasion/metastasis enhancers such as SPP1, CUTL1, TGF-α, SLC2A3, PGF, which support that CLDN1 may behave as an invasion and metastasis suppressor. Conclusions: CLDN is a cancer invasion and metastasis suppressor. CLDN1 expression is a useful prognostic predictor and a potential drug treatment target for lung adenocarcinoma patients.
Keywords: genetic modification

overall_design: Epithelial cells adhere tightly to their neighbors. Several specialized junctional complex including tight junctions (TJs), adherens junctions and desmosomes are responsible for the appropriate polarity, integrity and tensile strength of epithelial sheets. Cell-cell adhesion is an important physiological component of epithelial morphology and function, tightly coupled to major cellular processes including cell proliferation and migration. Changes in epithelial cell-cell adhesions have been implicated in carcinogenesis, tumor invasion and metastasis. .Claudins encode proteins with four transmembrane domains, two extracellular loops, and a carboxyl intracellular tail. The C-terminal sequences of claudins all share a PDZ binding motifs which is required for binding to the PDZ domains of proteins including ZO-1, ZO-2, ZO-3, MUPP1 and PATJ. These protein-protein interactions serve as links to the actin cytoskeleton and also as adapters for the recruitment of cytosolic molecules potentially involved in cell signaling to and from TJs. Several studies have shown an altered expression of different claudins in a wide variety of human malignancies, including colonic, ovarian, pancreatic, breast, liver, and prostatic cancer. The cDNAs encoding full-length human CLDN1 were amplified and subcloned into pCI-neo vector which generated full-length CLDN1. Purified plasmid DNA or vector control were transfected into CL1-5 cells and Gentamycin was used to select stable transfectants. The expression of genes affected by CLDN1 was measured by microarray compared to mock controls in biological duplicate.

first: Yu-Chih

last: Chao

first: Pan-Chyr

last: Yang


title: Induced pluripotent stem cells from a spinal muscular atrophy patient

status: Public on Dec 21 2008

first: Victor

last: Ruotti

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

summary:
Spinal muscular atrophy (SMA) is one of the most common inherited forms of neurological disease leading to infant mortality.  Patients exhibit selective loss of lower motor neurons resulting in muscle weakness, paralysis, and often death.  Although patient fibroblasts have been used extensively to study SMA, motor neurons have a unique anatomy and physiology which may underlie their vulnerability to the disease process.  Here we report the generation of induced pluripotent stem (iPS) cells from skin fibroblast samples taken from a child with SMA.  These cells expanded robustly in culture, maintained the disease genotype, and generated motor neurons that showed selective deficits compared to those derived from the child’s unaffected mother.  This is the first study to show human iPS cells can be used to model the specific pathology seen in a genetically inherited disease.  As such, it represents a promising resource to study disease mechanisms, screen novel drug compounds, and develop new therapies.

Keywords: Affimetrix global gene expression for comparison on all 10 samples

overall_design:
A total of 10 samples were hybridized to the human genome U133 Plus 2.0 GeneChip arrays carrying 54,675 probe sets (Affimetrix).

H1L, H7, H9, H13B, and H14A embryonic stem cells are controls for the iPS cells

iPS(SMA) 3.5 and iPS(SMA)3.6 are from the patient. The clone iPS(SMA) 4.2. is from the parent.

first: Allison

last: Ebert

first: Junying

first: Ferrill

last: Rose

first: Virginia

middle: B

last: Mathis

first: Christian

middle: L

last: Lorson

first: James

last: Thomson

first: Clive

last: Svendsen


title: Nocturnal Hemodialysis Improves Erythropoietin Responsiveness

status: Public on Dec 20 2008

city: Toronto

first: Sara

last: Arab

state: ONT

address: 610 University Avenue

department: Cardiology

institute: Toronto General Hospital

summary:
Nocturnal home hemodialysis (NHD) [5 – 6 times a week, 6-8 hours per session] augments uremia clearance and is associated with an increase in hemoglobin level. We have used microarray to have a global image of the changes at the gene expression.
Keywords: Treatment

overall_design: Sixteen stable end-stage renal disease patients (age: 47 ± 2 years; 9M) [mean ± SEM] were studied. Total RNA (TRNA) was isolated from whole blood before and after 3 months of established NHD. Gene expression before and after NHD was acquired through hybridizations on Human HG-U133_PLUS2 GeneChip and genes with differential gene expression were identified.

first: Christopher

last: Chan

first: Peter

middle: P

last: Liu


title: Age and Gender Related Changes in Human Parotid Gland Gene Expression

city: Rochester

first: Alaka

last: Srivastava

address: 601 Elmwood Avenue

department: Oral Biology

institute: University of Rochester Medical Center

summary:
Previous studies suggest that there may be age and gender related differences in salivary gland function.  However, the limited and often conflicting information available from healthy populations makes it difficult to confirm these differences.  The purpose of the present study was to evaluate and compare changes in gene expression associated with age and gender in the human parotid gland.  Differential expression, defined as statistically significant differences with at least 1.5 fold changes, was detected using the Affymetrix® GeneChip® HGU133plus2.0 microarray in 787 gene probe sets; 320 showed higher expression in males, while 467 showed higher expression in females.  Several genes associated with saliva secretion were differentially expressed in male and female parotid gland including vesicle-associated membrane protein 3 VAMP3, synaptosomal-associated protein SNAP23, RAS oncogene family member RAB1A, syntaxin binding protein STXBP1. When the gene expression results from the youngest (19-38 years old) and the oldest (65-69 years old) female subjects were further evaluated, it was found that the expression of 228 genes were altered during aging; 155 genes were down-regulated, whereas 73 genes were up-regulated in the female parotid gland.  Of the genes that were altered during aging, 24 of the 28 genes (86%) classified as being associated with immune responses were down-regulated in the aged parotid gland.  A panel of differentially expressed, age- and gender-related genes was selected for further study by quantitative, real-time RT-PCR. Comparable differences in gene expression were detected by both Affymetrix array and quantitative, real-time RT-PCR methods.  Taken together, our data suggest that salivary gland function may be adversely affected in the aged population due, at least in part, to the down regulation of several categories of genes. Moreover, the gender specific gene expressions identified in the present study correlates with the previously observed sexual dimorphism in salivary gland function.
Keywords: Human Parotid Gland

overall_design: Human parotid glands were obtained from healthy male and female subjects (19-85 years of age). 3 young female parotid glands were compared with 3 older female parotid gland. 8 Female samples were compared with 5 male samples

first: Jinghua

last: Wang

first: Hui

last: Zhou

middle: E

last: Melvin

first: David

last: Wong


title: Transcript Analysis of E. coli ATCC 35218 suggest a Role of cranberry Juice in Inhibiting the growth of E. coli

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

summary:
Several different mechanisms have been proposed to explain the possible role of cranberries, cranberry juice, and cranberry extracts in inhibiting bacterial growth.  In this report, we showed that Escherichia coli showed slower growth rate in response to the presence of cranberry juice in the growth media. By compareing the global transcript profiles, significant modulation of several genes of E. coli grown in LB broth with 10% cranberry juice were identified and provided identification of the potential mechanisms involved in the inhibitory effects of cranberry juice.  The results presented clearly demonstrate that the inhibitory effect on bacterial growth observed in the presence of cranberry juice/extracts is primarily a result of the iron chelation capacity of PACs and direct disruption of metabolic enzymes.  The results are discussed with a focus on the genes associated with iron chelation capability.

Keywords: growth inhibition of cranberry juice

overall_design: For transcriptome profiling, there were 15 Affymetrix GeneChip® E. coli genome 2.0 arrays total.  There were five conditions:  E. coli grown in LB broth, E. coli grown in LB broth with 10% cranberry juice to generation 50, 160, 210, and 230.  Each condition was done in triplicate.  Five conditions done in triplicates resulted in 15 samples that went onto 15 microarrays.

first: Brandy

middle: J

last: Johnson

first: Robert

last: Rubin

first: Anthony

last: Malanoski

first: Frances

middle: S

last: Ligler


title: E.coli GeneChip study of E.coli responses to osmotic and heat stresses

city: Dayton

first: Oleg

last: Paliy

address: 3640 Col. Glenn Hwy

institute: Wright State University

summary:
We probed the mechanism of cross-regulation of osmotic and heat stress responses by characterizing the effects of high osmolarity (0.3M vs. 0.0M NaCl) and temperature (43oC vs. 30oC) on the transcriptome of Escherichia coli K12 using  E. coli Genome 2 Array (Affymetrix, Inc.). Independent array hybridizations were carried out for 3 biological replicates (independent cultures). Total RNA was extracted using a hot phenol-chloroform method.  cDNA synthesis, fragmentation and labeling, and washing and scanning of E. coli GeneChip Arrays were performed according to the instructions of the manufacturer (Affymetrix Technical Manual, Affymetrix, Inc., USA). Labeled cDNA was hybridized to E. coli Genome 2 Array (Affymetrix, Inc.). Independent array hybridizations were carried out for 3 biological replicates (independent cultures) of each condition.   A number of genes in the SoxRS and OxyR oxidative stress regulons were up-regulated by high osmolarity, high temperature, and/or by the combination of both stresses. This result could account for cross-protection of osmotic stress against oxidative stress.  The trehalose biosynthetic genes were induced by both stresses, in accord with the proposed protective role of this disaccharide against thermal and oxidative damage.
Keywords: Affymetrix microarrays

overall_design: E. coli K12 strain NCM3722 cultures were grown with aeration in K medium containing 10 or 20 mM glucose.  To impose osmotic stress, the osmolarity of the medium was increased to 0.64 osm by supplementation with 0.3 M NaCl. Because E. coli is a methionine auxotroph above 42oC the K medium cultures were supplemented with 0.5 mM methionine. Glycine betaine (GB) was added to the high osmolarity media to a final concentration of 1 mM. Cells taken from a single colony on LB agar were inoculated into 1ml liquid LB and grown to saturation at 37oC, then 0.05 ml were inoculated into i) K medium, 0.5 mM methionine, 10 mM glucose; ii) K medium, 0.5 mM methionine, 10 mM glucose, 0.3 M NaCl; and iii) K medium, 0.5 mM methionine, 10 mM glucose, 0.3 M NaCl, 1 mM GB. The cultures were grown to saturation at 30oC and 43oC, and sub-cultured once into the same medium and grown at the same temperatures as before. Exponentially growing cells form these cultures were then inoculated into Erlenmeyer flasks (starting OD600nm 0.05) containing 40 ml of the same medium, and incubated in the same salt and temperature conditions as used previously, except that the glucose concentration was increased to 20 mM. When the cells reached OD600nm of 0.4-0.5 (~3 doublings), 25 ml were added to a 2.5 ml mixture of cold 95% ethanol and 5% phenol to preserve RNA. The cells were cooled briefly on ice, immediately harvested by centrifugation (4oC), and the pellet was frozen on dry ice. The six different growth conditions used were: C1 - 30oC, no NaCl; C2: 30oC, 0.3 M NaCl; C3: 30oC, 0.3 M NaCl, 1 mM GB; C4: 43oC, no NaCl; C5: 43oC, 0.3 M NaCl; C6: 43oC, 0.3 M NaCl, 1 mM GB.

first: Thusitha

last: Gunasekera

first: Csonka

last: Laszlo


title: Characterization of a Colony Assay Used to Investigate Endothelial Progenitor Cells

status: Public on Dec 19 2008

city: Bethesda

first: Richard

last: Cannon

address: 10 Center Drive

institute: NIH

summary:
Subjects underwent endothelial testing and blood sampling at baseline and after 3 months of exercise training.  Microarray and flow cytometry-based characterization of cells from an endothelial progeniator colony assay was consistent with T lymphocytes, but not endothelial cells.

Keywords: expression analysis

overall_design: blood samples from 12 healthy subjects at baseline (A) and after 3 months (B) of exercise.

first: Aditi

last: Desai

first: Alexander

last: Glaser

first: Delong

first: Nalini

last: Raghavachair

first: Arnon

last: Blum

first: Gloria

last: Zalos

first: Margaret

last: Lippincott

first: Philip

last: McCoy

last: Munson

first: Michael

last: Soloman

last: Danner


title: Decreased Expression of Intelectin 1 in The Human Airway Epithelium of Smokers Compared to Nonsmokers

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Lectins are proteins present on cell surfaces or as shed extracellular proteins that function in innate immune defense as phagocytic receptors to recognize specific bacterial cell wall components. Based on the knowledge that cigarette smoking is associated with increased risk of bacterial infection, we hypothesized that cigarette smoking may modulate the expression of lectin genes in the airway epithelium. Affymetrix HG U133 Plus 2.0 microarrays were used to survey expression of lectin genes in large (3rd to 4th order bronchi) airway epithelium from 9 normal nonsmokers and 20 phenotypic normal smokers and small (10th to 12th order bronchi) airway epithelium from 13 normal nonsmokers and 20 phenotypic normal smokers. From the 72 lectin genes that were surveyed, there were no changes (>2-fold change, p<0.05) in gene expression in either large or small airway epithelium among normal smokers compared to nonsmokers except for a striking down regulation in both large and small airway epithelium of normal smokers of intelectin 1, a recently described lectin that participates in the innate immune response by recognizing and binding to galactofuranosyl residues in the cell walls of bacteria (large airway epithelium, p<0.003; small airway epithelium, p<0.002). TaqMan RT-PCR confirmed the observation that intelectin 1 was down-regulated in both large (p<0.05) and small airway epithelium (p<0.02) of normal smokers compared to normal nonsmokers. Immunohistochemistry assessment of biopsies of the large airway epithelium of normal nonsmokers demonstrated intelectin 1 was expressed in secretory cells, with qualitatively decreased expression in biopsies from normal smokers. Western analysis confirmed the decreased expression of intelectin 1 in airway epithelium of normal smokers compared to normal nonsmokers (p<0.02). Finally, compared to normal nonsmokers, intelectin 1 expression was decreased in small airway epithelium of smokers with early COPD (n= 13, p<0.001) and smokers with established COPD (n= 14, p<0.001), in a fashion similar to that of normal smokers. In the context that intelectin 1 is an epithelial molecule that likely plays a role in defense against bacteria, the down regulation of expression of intelectin 1 in response to cigarette smoking may contribute to the increase in susceptibility to infections observed in smokers, including those with COPD.
Keywords: COPD

overall_design: Comparison of gene expression in airway epithelial cells of normal non-smokers, phenotypic normal smokers, smokers with early COPD, and smokers with COPD.

first: Brendan

last: Carolan

first: Ben-Gary

last: Harvey

first: Bishnu

last: De

first: Holly

last: Vanni

first: Ronald

last: Crystal


title: Atherosclerotic markers in human blood - a study in patients with familial hypercholesterolemia

status: Public on Dec 18 2008

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary: Atherosclerosis is characterized by thickening of the arterial wall and is the primary cause of the coronary artery disease and cerebrovascular disease, two of the most common causes of illness and death worldwide. One of the leading risk factors for development of atherosclerosis is familial hypercholesterolemia. Familial hypercholesterolemia is an autosomal dominant disorder, which is caused by mutations mainly located in the low-density lipoprotein receptor (LDLR) gene. It is characterized by elevated levels of low-density lipoprotein cholesterol, the presence of tendon xanthomas, and premature cardiovascular disease. Aim of this study was to find atherosclerotic markers in white blood cells of patients compared to healthy controls. None of these patients exhibited symptoms of atherosclerosis by standard diagnostic methods; however, transcriptome analysis of blood RNA indicated changes in ubiquitin proteolysis and cell adhesion system as expected in initiation steps of atherosclerosis.

overall_design: Five patients diagnosed with Familial hypercholesterolemia and five age, sex, BMI and smoking status matched controls contributed blood from which total RNA from white blood cells was isolated. RNA samples were analyzed using Affymetrix microarrays and two groups were compared for differentially expressed genes.

first: Tadeja

last: Režen

first: Anja

last: Cvikl

first: Natalija

last: Brecelj

first: Damjana

last: Rozman

first: Irena

last: Keber

first: Klementina

last: Fon Tacer


title: Expression data from myeloma cell lines treated with 500 nM pristimerin or DMSO vehicle alone for 4 hours

city: Scottsdale

first: rodger

last: tiedemann

state: AZ

address: 13400 E Sahuaro Dr

department: Division of Hematology Oncology

institute: Mayo Clinic

summary:
As multiple myeloma tumors universally dysregulate cyclin D genes we conducted high-throughput chemical library screens for compounds that induce suppression of cyclin D2. The top-ranked compound was a natural triterpenoid, pristimerin.
We used gene expression microarray studies to identify co-regulated pristimerin-response genes and to deduce the compound’s direct molecular target(s), utilizing pattern-matching algorithms available at the Connectivity Map (Cmap). The early transcriptional response of cells treated with pristimerin closely resembles cellular responses elicited by proteosome inhibitors, with rapid induction of heat shock proteins, activating transcription factor (ATF) 3 and CHOP. Enzymatic assays and immunoblotting confirm that pristimerin rapidly (<90min) and specifically inhibits chymotrypsin-like proteosome activity at low concentrations (<100nM) and causes accumulation of cellular ubiquitinated proteins. Notably, cytotoxic triterpenoids including pristimerin inhibit NF-kB activation via inhibition of IKKa or IKKb while proteosome inhibitors instead suppress NF-kB function by impairing degradation of ubiquitinated-IkB. By inhibiting both IKK and the proteosome pristimerin causes overt suppression of constitutive NF-kB activity in myeloma cells that may mediate its suppression of cyclin D. Multiple myeloma is exquisitely sensitive to proteosome or NF-kB pathway inhibition. Consistent with this, pristimerin is potently and selectively lethal to primary myeloma cells (IC50<100nM), inhibits xenografted plasmacytoma tumors in mice and is synergistically cytotoxic with bortezomib – providing the rationale for pharmaceutical development of triterpenoid dual-function proteosome/NF-kB inhibitors as therapeutics for human multiple myeloma and related malignancies.

Keywords: small molecule drug response, stress response

overall_design: H929 and U266 human myeloma cell lines were treated with pristimerin 500nM (~2x IC50) or DMSO vehicle and harvested at 4h, prior to the appearance of any macroscopic evidence of perturbed viability. RNA was isolated using Trizol, column purified (Qiagen, Valencia, CA) and hybridized to Hg_U133_plus_2 microarrays (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions. Probe-set signal intensities were PLIER16-normalized using Affymetrix Expression Console software and flagged using Affymetrix Microarray Suite 5 (MAS5) Present/Absent/Marginal detection calls. Expression data was analyzed with GeneSpring 7 (Agilent Technologies, Santa Clara CA) software, with drug-treated samples normalized per cell line to DMSO-treated controls. Gene lists were filtered to exclude non-expressed probe-sets with MAS5 ‘Absent’ detection calls across all samples tested (treated and untreated). Probe-sets upregulated or suppressed by pristimerin in each cell line were delineated by volcano plot filter (>1.5 fold change, FDR<0.25) and the Venn intersection of probe-sets modulated by drug in both cell lines was used in deriving a pristimerin signature.

first: Rodger

last: Tiedemann

first: Keith

last: Stewart


title: Transcriptomes in Healthy and Diseased Gingival Tissues

first: Ryan

last: Demmer

department: Epidemiology

institute: Columbia University

summary:
We examined gene expression signatures in healthy and diseased gingival tissues in 90 patients. Analysis of the gingival tissue transcriptome in states of periodontal health and disease may reveal novel insights of the pathobiology of periodontitis.
Keywords: gingival tissue disease state analysis

overall_design: Ninety non-smokers, 63 with chronic and 27 with aggressive periodontitis, each contributing with >=2 “diseased” interproximal papillae (with bleeding on probing, probing pocket depth >=4mm, and clinical attachment loss >=3mm) and a “healthy” papilla, if available (no BoP, PPD<=4mm and CAL<=2mm). RNA was extracted, amplified, reverse transcribed, labeled, and hybridized with AffymetrixU133Plus2.0 arrays. Transcriptome analysis was conducted on a total of 247 samples (from 183 diseased and 64 healthy sites).

first: Panos

last: Papapanou

first: Paul

last: Pavlidis


title: Laser capture microdissection of endothelial and neuronal cells from human dorsolateral prefrontal cortex

city: Cambridge

first: Laura

middle: Wiseman

last: Harris

address: Tennis Court Road

department: Insitute of Chemical Engineering and Biotechnology

institute: University of Cambridge

summary:
We used laser capture microdissection to isolate both microvascular endothelial cells and neurons from post mortem brain tissue from patients with schizophrenia and bipolar disorder and healthy controls. RNA was isolated from these cell populations, amplified, and analysed using Affymetrix HG133plus2.0 GeneChips. In the first instance, we used the dataset to compare the neuronal and endothelial data, in order to demonstrate that the predicted differences between cell types could be detected using this methodology.

Keywords: cell type comparison, laser capture microdissection

overall_design: The dataset consists of endothelial cell samples from 18 individuals and neuronal samples from an overlapping population of 18 individuals.

middle: W

first: Matthew

last: Wayland

first: Margaret

middle: M

last: Ryan

first: Martin

last: Lan

first: Thomas

last: Giger

first: Helen

last: Lockstone

first: Lan

last: Wang

first: Michael

last: Mimmack

first: Mark

last: Kotter

first: Irene

last: Wuethrich

first: Sabine

last: Bahn


title: Expression data from primary gastric tumors (MSI and MSS) and adjacent normal samples

city: Pomezia(Rome)

first: Emanuele

last: de Rinaldis

address: Via Pontina

institute: IRBM (MERCK)

summary:
Gastric cancers with mismatch repair (MMR) inactivation are characterised by microsatellite instability (MSI). In this study, the transcriptional profile of 38 gastric cancers with and without MSI was analysed.
Unsupervised analysis showed that the immune and apoptotic gene networks efficiently discriminated these two cancer types. Hierarchical clustering analysis revealed numerous gene expression changes associated with the MSI phenotype. Amongst these, the p53-responsive genes maspin and 14-3-3 sigma were significantly more expressed in tumours with than without MSI. A tight immunosurveillance coupled with a functional p53 gene response is consistent with the better prognosis of MSI cancers. Frequent silencing of MLH1 and downregulation of MMR target genes, such as MRE11 and MBD4, characterised MSI tumours. The downregulation of SMUG1 was also a typical feature of these tumours. The DNA repair gene expression profile of gastric cancer with MSI is of relevance for therapy response.

overall_design: Genes differentially expressed between MSI and MSS tumours were identified as follows: (i) gene probe sets were pre-selected for being flagged as ‘PRESENT’ in at least 10 tumour samples (21,324 probe sets); (ii) the probe set signal values on the pre-selected probe sets were used to run a t-test between the two types of tumour samples; (iii) the false discovery rate (FDR) method was applied to the t-test calculated p-values to correct for multiple testing and (iv) a false discovery rate <0.05 and a t-test p-value < 0.01 were chosen as threshold criteria to identify the genes differentially expressed in tumours with and without MSI


title: Down-regulation of the Notch Differentiation Pathway in the Airway Epithelium of Normal Smokers and Smokers with COPD

status: Public on Dec 16 2008

first: Yael

last: Strulovici-Barel

summary:
Down-regulation of the Notch Differentiation Pathway in the Human Airway Epithelium in Normal Smokers and Smokers with Chronic Obstructive Lung Disease

In cigarette smokers, the toxic components of smoke place the epithelium under the constant stress of a variety of mechanisms of injury, with consequent modulation of airway epithelial regeneration and disordered differentiation. Based on the underlying hypothesis that these airway epithelial changes must involve quantitative changes in genes involved with the regulation of differentiation, we assessed the expression of the Notch pathway, a signaling pathway known to play a fundamental role in the embryonic lung as a gatekeeper for differentiation, in the small airway epithelium of non-smokers, normal smokers, and smokers with COPD. Microarray analysis demonstrated that 45 of the 55 Notch pathway-related genes are expressed in the human adult small airway epithelium and TaqMan quantitative PCR confirmed the expression of key genes in the pathway. TaqMan quantitative PCR analysis of the normal small airway epithelium demonstrated that Delta-like ligand 1 is the most highly expressed Notch ligand, Notch2 and 3 the most highly expressed receptor genes, and Hes1 the predominant downstream effector gene. TaqMan PCR was used to compare gene expression in nonsmokers vs healthy smokers vs smokers with COPD. The data show that some key genes in the ligands, receptors and downstream effectors in the Notch pathway are differentially expressed in smokers, with significant downregulation of a greater number of Notch-related genes in smokers with COPD compared to healthy smokers. These observations are consistent with the hypothesis that the Notch pathway, known to play an important role in lung morphogenesis, also likely plays a role in the adult human airway epithelium, with at least some of the Notch pathway gene expression dysregulated in association with smoking and its related disorder, COPD.
Keywords: non-smokers, airway epithelial cells

overall_design: Gene expression in airway epithelial cells of normal non-smokers.

first: Ann

last: Tilley

first: Ben-Gary

last: Harvey

first: Adriana

last: Heguy

first: Neil

middle: R

last: Hackett

first: Ronald

middle: G

last: Crystal


title: HDACI treatment of hepG2 cells

status: Public on Dec 17 2008

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
This study compares HEPG2 cells treated with either ethanol(control) or TSA (0.5uM) for 24 hrs. Gene Expression was profiled on HU-133 plus 2.0 arrays
Keywords: Treaded vs untreated

overall_design: 3 controls vs 3 TSA treated

first: Kuentzel

last: Marcy

first: McCormick

last: Paulette


title: OH-PBDE-induced gene expression profiling in H295R adrenocortical carcinoma cells

status: Public on Dec 25 2008

city: Leicester

first: George

middle: DD

last: Jones

address: Biocentre, University Road

department: Cancer Studies & Molecular Medicine

institute: University of Leicester

summary: Polybrominated diphenyl ethers (PBDEs) are commonly used as flame retardants in a variety of commercial and household products. They have been detected in the environment and accumulate in mammalian tissues and fluids. PBDE toxicity is thought to be associated with endocrine disruption, developmental neurotoxicity and changes in fetal development. Although humans are exposed to PBDEs, our knowledge of the effects of PBDE metabolites on human cells with respect to health risk is insufficient. Two hydroxylated PBDEs (OH-PBDEs), 2-OH-BDE47 and 2-OH-BDE85, were investigated for their effects on cell viability/proliferation, DNA damage, cell cycle distribution and gene expression profiling in H295R adrenocortical carcinoma cells. We show that the two agents are cytotoxic in a dose-dependent manner only at micromolar concentrations, with 2-OH-BDE85 being more toxic than 2-OH-BDE47. However, no DNA damage was observed for either chemical, suggesting that the biological effects of OH-PBDEs occur primarily via non-genotoxic routes. Furthermore, no evidence of aryl hydrocarbon receptor (AHR)-mediated, dioxin-like toxicity was observed. Instead, we report that a micromolar concentration of OH-PBDEs induces transcriptional changes associated with endoplasmic reticulum stress and the unfolded protein response. We discuss whether OH-PBDE bioaccumulation could result in impairment of the adrenocortical secretory function.

overall_design: Gene expression changes in response to hydroxylated polybrominated diphenyl ethers (OH-PBDEs) were analysed by Microarray technology in H295R adrenocortical carcinoma cells. Cells were treated with 10 µM of 2-OH-BDE47 or 2-OH-BDE85 (or growth medium alone) for 24 hours before the OH-PBDE-induced gene expression changes were investigated. Control, 2-OH-BDE47- and 2-OH-BDE85-treated samples were collected from three independent experiments each.

first: Renfang

last: Song

first: Tiago

last: Duarte

first: Gabriela

last: Almeida

first: Peter

last: Farmer

first: Wenbing

last: Zhang

first: Guoying

last: Sheng

first: Jiamo

last: Fu


title: Expression profiling across the pediatric systemic inflammatory response syndrome, sepsis, and septic shock spectrum

status: Public on Dec 12 2008

first: Hector

last: Wong

address: 3333 Burnet Ave

department: Division of Critical Care Medicine

institute: CIncinnati Children's Hospital Medical Center

summary:
Normal children, children with SIRS, children with sepsis, and children with septic shock.

Objectives: To advance our biological understanding of pediatric septic shock, we measured the genome-level expression profiles of critically ill children representing the systemic inflammatory response syndrome (SIRS), sepsis, and septic shock spectrum.
Keywords: Normal vs diseased

overall_design: Prospective observational study involving microarray-based bioinformatics.

first: Natalie

last: Cvijanovich

first: Geoffrey

last: Allen

first: Richard

last: Lin

first: Nick

last: Anas

first: Keith

last: Meyer

first: Robert

last: Freishtat

first: Marie

last: Monaco

first: Kelli

last: Odoms

first: Bhuvaneswari

last: Sakthivel

first: Thomas

last: Shanley


title: Analysis of gene expression response of CLL cells to co-culture with Nurse like cells

status: Public on Dec 11 2008

city: Wuerzburg

first: Andreas

last: Rosenwald

address: Josef-Schneider-Strasse 2

department: Institute of Pathology

institute: University of Wuerzburg

summary: In the marrow and lymphatic tissues, chronic lymphocytic leukemia (CLL) cells interact with accessory cells that constitute the leukemia microenvironment. In lymphatic tissues, CLL cells are interspersed with CD68+ nurselike cells (NLC) and T cells. However, the mechanism regulating co-localization of CLL cells and these accessory cells are largely unknown. To dissect the molecular cross-talk between CLL and NLC, we profiled the gene expression of CD19-purified CLL cells before and after co-culture with NLC. NLC co-culture induced high-level expression of B cell maturation antigen (BCMA) and two chemoattractants (CCL3, CCL4) by CLL cells. Supernatants from CLL-NLC co-cultures revealed high CCL3/CCL4 protein levels. B cell receptor triggering also induced a robust induction of CCL3 and CCL4 expression by CLL cells, which was almost completely abrogated by a specific Syc inhibitor, R406. High CCL3 and CCL4 plasma levels in CLL patients suggest that activation of this pathway plays a role in vivo. These studies reveal a novel mechanism of cross-talk between CLL cells and their microenvironment, namely the secretion of two T cell chemokines by CLL-NLC interaction and in response to BCR stimulation. Through these chemokines, CLL cells can recruit accessory cells, and thereby actively create a microenvironment that favors their growth and survival.

overall_design:
The microarray part of this study included samples of CLL cells from 9 different patients, analyzed directly after purification and after 14 days of co-culture with Nurse like cells .

In detail, RNA was isolated from CD19-purified CLL cells from 9 different patients’ peripheral blood mononuclear cells (PBMC) after Ficoll separation and subsequent purification with CD19 MicroBeads and the MACS® technology according to the manufacturer’s instructions (Miltenyi Biotec, Bergisch Gladbach, Germany). For comparison, the same CLL cell samples were co-cultured for 14 days with NLC ("14d NLC")."). For co-culture with NLC, PBMC from patients with CLL were suspended in complete RPMI medium (RPMI1640 with 10% FCS, penicillin-streptomycin-glutamine, Gibco-BRL, Grand Island, NY) to a concentration of 1 x 107/ml (total 20 ml) and incubated for 14 days in 75 cm2 tissue culture flasks (Techno Plastic Products AG) as described previously3. Nonadherent lymphoid cells then were removed and the NLC layer was washed two times with phosphate-buffered saline (PBS). The complete removal of lymphocytes was verified by phase-contrast microscopy. The nonadherent cells together with the wash-fractions were then used for RNA preparation. In order to purify the CLL B cells prior to RNA isolation, CLL PBMC were passed through a 30 µm nylon mesh to obtain a single-cell suspension. Then CLL B cells were purified with CD19 MicroBeads. Subsequently RNA was extracted.

first: Jan

middle: A

last: Burger

first: Maite

last: Quiroga

first: Elena

last: Hartmann

first: Andrea

last: Bürkle

first: William

last: Wierda

first: Michael

last: Keating


title: Expression, ChIP-chip, and ChIP-Seq data from REH and SEM leukemia cell lines [Expression and ChIP-chip]

status: Public on Dec 15 2008

first: Garrett

last: Frampton

address: 9 Cambridge Center

department: Biology

institute: Whitehead Instute - MIT

summary:
MLL-fusion proteins are potent inducers of cancer in hematopoietic cells, where they are known to cause changes in global gene expression.  How MLL-fusion proteins interact with the genome has not been established, so we have limited understanding of the pathway by which these proteins generate aberrant gene expression programs. Here we describe how the MLL-AF4 protein occupies the genome in human leukemia cells and its striking effects on chromatin states.  We find that the MLL-AF4 fusion protein selectively occupies regions of the genome that contain developmental regulatory genes important for hematopoietic stem cell identity and self-renewal.  These MLL-AF4 bound regions have grossly altered chromatin structure, with histone modifications catalyzed by Trithorax Group (TrxG) proteins and Dot1 extending across unusually large domains.  This indicates that a key feature of MLL-associated leukemogenesis is aberrant targeting of chromatin modifiers to regions of the genome controlling hematopoietic development. Our results define the direct targets of the MLL-fusion protein, reveal the global role of epigenetic misregulation in leukemia, and identify new targets for therapeutic intervention in human cancer.

Keywords: cell type comparison

overall_design:
This dataset includes expression data for two replicates each of SEM and REH leukemia cell lines and ChIP-chip data targeting RNAP2, H3K4me3, H3K79me2, ENL, AF4-C, and MLL-N in SEM and REH leukemia cell lines.
Related ChIP-Seq data are provided in GEO Series GSE38338.


title: Differences between NOR1 and EWS/NOR1

status: Public on Dec 10 2008

city: Tokyo

first: Naganari

last: Ohkura

address: 5-1-1, Tsukiji, Chuo-ku

department: Tumor Endocrinology Project

country: Japan

institute: National Cancer Center Research Institute

summary:
To examine the differences between NOR1 and its fusion gene product EWS/NOR1, we compared the gene expression profiles of NOR1- and EWS/NOR1-overexpressing 293 cells.
Keywords: gene comparison

overall_design: We established 293-tet-On clones stably transfected NOR1- or EWS/NOR1-expressing plasmid. Total RNA was collected from the clones cultured with or without doxycycline.

first: Yuko

last: Nagamura

first: Toshihiko

last: Tsukada


title: mRNA Breast Cancer Cell Line Profiles

status: Public on Dec 01 2008

city: X

first: Alex

middle: T.

last: Adai

state: X

address: X

department: Oncology Diagnostics

institute: Genentech

summary:
mRNA breast cancer cell lines were profiled to study the function of hsa-mir-221 and hsa-mir-222. MCF7 cell lines were profiled after treatment with mir-221/222 mimics, and compared to profiles with transfection controls. Similarly, MDA-MB-231 cell lines were profiled after treatment with mir-221/222 inhibitors, and compared to profiles with transfection controls. Since ESR1 is a predicted target of mir-221/222 we also profiled MCF7 cell lines after disrupting ESR1 with an siRNA. Other breast cancer cell lines are provided because all cell lines were normalized together.
Keywords: breast cancer, cell line, hsa-mir-221, hsa-mir-222, ESR1

overall_design: mRNA breast cancer cell line profiles with some samples in duplicate or triplicate. See summary for more information.


title: Human CD34-derived erythroid progenitors treated with BCL11A siRNAs

status: Public on Dec 05 2008

city: Boston

first: Vijay

middle: G.

last: Sankaran

address: 300 Longwood Avenue

department: Department of Medicine

institute: Children's Hospital Boston

summary:
Differences in the amount of fetal hemoglobin (HbF) that persists into adulthood affect the severity of sickle cell disease and the beta-thalassemia syndromes. Genetic association studies have identified sequence variants in the gene BCL11A that influence HbF levels. Here we examine BCL11A as a potential regulator of HbF expression. The high HbF BCL11A genotype is associated with reduced BCL11A expression. Moreover, abundant expression of full-length forms of BCL11A is developmentally restricted to adult erythroid cells. Down-regulation of BCL11A expression in primary adult erythroid cells leads to robust HbF expression. Consistent with a direct role of BCL11A in globin gene regulation, we find that BCL11A occupies several discrete sites in the beta-globin gene cluster. BCL11A emerges as a therapeutic target for reactivation of HbF in beta-hemoglobin disorders.
BCL11A siRNA label: B, NT siRNA label: N

Keywords: cell type comparsion

overall_design:
Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.  Six samples from the NT control and six samples from the BCL11A siRNA treatment are included.  Cells were harvested on day 7 of erythroid differentiation after introduction of siRNAs on day 0 of the differentiation protocol.
6 BCL11A siRNA datasets, 6 control (NT) datasets