title: Expression data from Tcf1-expressing Thy1+CD25+ T lineage cells

first: Avinash

last: Bhandoola

state: Philadelphia

address: 3620 Hamilton Walk

institute: University of Pennsylvania

summary:
We used microarrays to perform a global gene expression analysis in Tcf1-expressing Thy1+CD25+ T lineage cells that develop on OP9 stroma in the absence of Notch1 signals. We compare this to the starting population, LMPP progenitors, and to control expressing T lineage cells that developed on OP9 stroma expressing Notch ligand DL4. The overall goal of this study was to determine if Tcf1 initiates T lineage specification in lymphoid progenitors. We found that Tcf1 was sufficient to upregulate many T lineage genes as compared to control expressing progenitors on OP9-DL4.
Abstract of manuscript: The thymus imposes the T cell fate on incoming multipotent progenitors, but the molecular mechanisms are poorly understood. We show that transcription factor Tcf1 initiates T-lineage-specific gene expression. Tcf1 is downstream of Notch1 signaling and expressed in early T-cell progenitors. Progenitors deficient for Tcf1 are unable to initiate normal T-lineage specification. Conversely, ectopic expression of Tcf1 in hematopoietic progenitors is sufficient to induce expression of T-lineage specific genes in vitro. Thus, our study identifies Tcf1 as critically involved in the establishment T cell identity.

overall_design: Wiltype LMPPs were isolated by a FACSAria cell sorter and retrovirally transduced with a Tcf1-containing (Tcf1-VEX) or control vector (VEX) retrovirus. Tcf1-expressing cells and control-vector expressing cells were then seeded on OP9 stroma or OP9 stroma expressing Notch ligand DL4, respectively. On day 10, Thy1+CD25+ T lineage cells were sorted from Tcf1-expressing cells on OP9 stroma and compared to sorted LMPPs and Thy1+CD25+ T lineage cells that developed from control-vector expressing cells on OP9-DL4.

first: Weber

last: Brittany

first: Chi

last: Anthony

first: Chavez

last: Alex

first: Yashiro-Ohtani

last: Yumi

first: Bhandoola

last: Avinash


title: Expression data from Tcf1 deficient and Tcf1 wildtype cultured bone marrow lymphoid primed progenitors after four days on Notch ligand expressing stroma  (OP9-DL4).

status: Public on Aug 04 2011

city: Philadelphia

department: Pathology

country: USA

summary:
Tcf1 is necessary for optimal T lineage development. Tcf1 deficient progenitors fail to initiate the T lineage program in vitro and development is severely defective in vivo. We used microarrays to assess the overal global gene expression differences from Tcf1 wildtype and deficient lymphoid biased progenitors cultures on Notch-ligand expressing stroma to determine if Tcf1 deficient progenitors are able to intiate the T lineage specification program.
Abstract of manuscript: The thymus imposes the T cell fate on incoming multipotent progenitors, but the molecular mechanisms are poorly understood. We show that transcription factor Tcf1 initiates T-lineage-specific gene expression. Tcf1 is downstream of Notch1 signaling and expressed in early T-cell progenitors. Progenitors deficient for Tcf1 are unable to initiate normal T-lineage specification. Conversely, ectopic expression of Tcf1 in hematopoietic progenitors is sufficient to induce expression of T-lineage specific genes in vitro.  Thus, our study identifies Tcf1 as critically involved in the establishment T cell identity.

overall_design: Tcf1 wildtype and deficient bone marrow lymphoid primed progenitors (LMPPs, Lineage marker- Sca+kit+Flt3high) were harvested in triplicate and seeded onto OP9-DL4 expressing stroma for 4 days upon which highly pure lineage negative and Thy1+CD25+ T cells were cell sorted for expression analysis. The lineage negative populations represent three seperate mice from each genotype and the Thy1+CD25+T lineage population represents two replicates from the Tcf1 wildtype group. No Thy1+CD25+ T lineage cells develop from Tcf1 deficient progentiors.


title: mRNAs associated with human Pumilio2 protein (PUM2)

status: Public on Aug 01 2011

city: Curitiba

first: PATRICIA

last: SHIGUNOV

state: Paraná

address: Rua Prof. Algacyr Munhoz Mader, 3775

country: Brazil

institute: Instituto Carlos Chagas - FIOCRUZ-PR

summary:
The presence of the PUF (Pumilio/FBF) domain defines a conserved family of RNA-binding proteins involved in repressing gene expression. It has been suggested that a conserved function of PUF proteins is to repress differentiation and sustain the mitotic proliferation of stem cells. In humans, Pumilio2 (PUM2) is expressed in embryonic stem cells and adult germ cells.

To identify mRNAs associated with human PUM2 protein in adipose tissue stem cells (ADSC), we used a modified Ribonucleoprotein-ImmunoPrecipitation Microarray (RIP-Chip). PUM2 ribonucleoprotein (RNP) complexes were performed with 2 µg of anti-Pum2 antibody (goat polyclonal, Santa Cruz Biotechnology, CA, USA) bound to protein G-agarose beads (Sigma, Deisenhofen, Germany). ADSCs were lysed in polysome lysis buffer  (Tris-HCl pH 7.4 15mM, MgCl2 15 mM, NaCl 0,3 M, 1% Triton X-100, 1 mM DTT, 100 U/ml RNase Out, PMSF 1mM and E64 10uM) for one hour at 4°C. Beads were washed, then buffer and cell lysate were added, and the reaction mixtures were tumbled for 2 hours at 4°C. After this incubation, the beads were thoroughly washed again with polysome lysis buffer and then either RNA extracted for microarray and RT-PCR experiments using the RNeasy mini kit (Qiagen). To control for non-specifically enriched RNAs, identical IPs were performed with beads precoated with preimmune goat serum as a negative control. RNA was processed for hybridization with GeneChip 3’ IVT Express (Affymetrix - Santa Clara, USA), according to the manufacturers instruction. Briefly, cDNA was synthesized from immunoprecipitated RNA using reverse transcriptase followed by second strand synthesis to generate double-stranded cDNA. An in vitro transcription reaction was used to generate biotinylated cRNA. After purification and fragmentation, cRNA was hybridized onto GeneChip Affymetrix Human Genome U133 Plus 2.0 arrays. Post hybridization washes were preformed on an Affymetrix GeneChip Fluidics Station 450. Arrays were scanned on an Affymetrix GeneChip Scanner 3000. Scanned arrays were normalized using GCRMA in Partek software (Partek Incorporated. St. Louis, MO). Differentially enriched RNAs were found after performing One-way ANOVA analysis comparing immunoprecipitated samples against control samples. Final lists of genes were obtained by filtering the data from the statistical results according to fold enrichment more than 2 and a p value associated of less than 0.05 for features with signal well above the background.

overall_design: Pum2 IP and control IP samples were analyzed for each of 2 biological replicates.

first: Patrícia

last: Shigunov


title: Human peripheral blood CD4+ T cell subsets

city: Sydney

first: Santi

last: Suryani

state: NSW

address: 384 Victoria Street, Darlinghurst

department: Immunology and Inflammation

country: Australia

institute: Garvan Institute of Medical Research

summary: Cells were isolated from healthy human donors (n=2). Unstimulated cells. Cells were stained with CD4, CD45RA, CCR7 and CXCR7. Using flow cytometry, 4 CD4+ T cell populations were sorted: (1) Naïve (CD45RA+CCR7+CXCR5-), (2) Central memory (CD45RA-CCR7+CXCR5-), (3) Effector memory (CD45RA-CCR7-CXCR5-) and (4) CXCR5+ cells (CD45RA-CCR7-CXCR5+)

overall_design: RNA were extracted from sorted cells and hybridized on Affymetix HU133Plus2 chips. Each population were repeated on different donors such that n=2.

first: Edwin

last: Ho

first: Stuart

middle: G

last: Tangye


title: Expression data from CD71+ cells from the bone marrow of WT, CD70TG, IFNg-/- and CD70TG*IFNg-/- mice.

city: Amsterdam

first: Laura

last: Gutierrez

address: Plesmanlaan 125

department: Blood Cell Research

country: Netherlands

institute: Sanquin Research

summary:
CD70TG mice are a model for sterile chronic immune activation and develop Anemia of Inflammation, which is dependent on the production of Ifng by effector CD4 and CD8 T cells.
We used microarrays to identify Ifng-dependent differentially expressed genes that could account for the erythropoietic defect.

overall_design: CD71+ cells were MACS-enriched from the bone marrow of WT, CD70TG, IFNg-/- and CD70TG*IFNg-/- male mice of 10-12 weeks of age (3 mice per genotype group).

first: Martijn

middle: A

last: Nolte

last: Gutiérrez


title: Exposure of cystic fibrosis bronchial epithelial cells (CFBE 41 o-) to Pseudomonas aeruginosa (PA01) biofilms

city: Hanover

first: Thomas

middle: H

last: Hampton

state: NH

address: North College Street

department: Pharm/Tox

institute: Dartmouth Medical School

summary: In the clinical setting, mutations in the CFTR gene enhance the inflammatory response to P. aeruginosa (PA01) infection, but measurements of the inflammatory response to pathogen stimulation by isolated airway epithelia can yield variable results. In this series, we exposed CFBE41o- cells over-expressing ∆F508/∆F508 CFTR and CFBE41o- cells rescued with wt-CFTR to P. aeruginosa  biofilms. P. aeruginosa elicited a more robust increase in cytokine and chemokine expression (e.g., IL-8, CXCL2,  CXCL3, CXCR4 and TNF-α) in CFBE-wt-CFTR cells compared to CFBE-∆F508-CFTR cells. These results demonstrate that CFBE41o- cells complemented with wt-CFTR mount a more robust inflammatory response to P. aeruginosa than CFBE41o- ∆F508/∆F508-CFTR cells.

overall_design: CFBE41o- cells generously provided by Dr. J.P. Clancy (University of Alabama). The series involved 4 treatment groups: unexposed wild type CFTR cells, unexposed ∆F508/∆F508 CFTR cells,  wild type CFTR cells exposed to PA01, and  ∆F508/∆F508 CFTR cells exposed to PA01. Each treatment group involved 4 replicate polarized monolayers. PAO1 was added to the apical side of exposed monolayers at a multiplicity of infection (MOI) of 30:1 for 1 hour in the absence of antibiotics, and then planktonic PAO1 was removed by replacing the apical medium with MEM supplemented with 0.4% arginine (2). Control monolayers were treated identically except that vehicle only (medium used to grow PAO1, MEM supplemented with 0.4% arginine) was added to the apical side of cells. Five hours after washing planktonic P. aeruginosa from the cell monolayers mRNA was isolated.


title: Expression data from 5 human cell lines exposed to IR (5 Gy)

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary: The cellular response to DNA damage is vital for maintaining genomic stability and preventing undue cell death or cancer formation. The DNA damage response (DDR), most robustly mobilized by double-strand breaks (DSBs), rapidly activates an extensive signaling network that affects numerous cellular systems, leading to cell survival or programmed cell death. A major component of the DDR is the widespread modulation of gene expression. We analyzed transcriptional responses to ionizing radiation (IR) in 5 human cell lines to elucidate the scope of this response and identify its gene targets. According to the mRNA expression profiles most of the responses were cell line-specific. Data analysis identified significant enrichment for p53 target genes and cell cycle-related pathways among groups of up-regulated and down-regulated genes, respectively.

overall_design:
Expression profiles were measured using affymetrix chips in IR- irradiated G361 cells and their time-matched untreated controls. Time points recorded were 0, 3 and 6 hrs. IR dose: 5 Gy

Expression profiles were measured using affymetrix chips in IR- irradiated HepG2 cells and their time-matched untreated controls. Time points recorded were 0, 3 and 6 hrs. IR dose: 5 Gy

Expression profiles were measured using affymetrix chips in IR- irradiated TK6 cells and their time-matched untreated controls. Time points recorded were 0, 3 and 6 hrs. IR dose: 5 Gy

Expression profiles were measured using affymetrix chips in IR- irradiated U2OS cells and their time-matched untreated controls. Time points recorded were 0, 3 and 6 hrs. IR dose: 5 Gy

Expression profiles were measured using affymetrix chips in IR- irradiated BJ cells and their time-matched untreated controls. Time points recorded were 0, 3 and 6 hrs. IR dose: 5 Gy

first: Sharon

last: Rashi-Elkeles

first: Yossi

last: Shiloh


title: Different expressed genes in epithelium and stromal of Benign Prostatic Hyperplasia

status: Public on Aug 10 2011

city: Beijing

first: wujiang

last: Liu

department: Urology

country: China

institute: Peking University

summary:
To identify the genes differently expressed in the epithelium and the stromal of Benign Prostatic Hyperplasia (BPH), we collect the epithelium and the stromal from the patients with benign prostatic hyperplasia by laser micro-dissection.  And then, Affymetrix HG-U133_Plus_2 gene-chip was used to detect and compare the expression level of genes.
To find which genes are most abundantly expressed in epithelium and stromal and what is the role of these genes in the pathogenesis of BPH.

overall_design: 8 prostate tissues were collected from patients undergone transurethral resection of the prostate (TURP) with informed consent. Each tissue was embedded in O.C.T and subsequently used for laser micro-dissection. The total RNA was isolated from each sample and equally mixed for gene-chip assay.

first: Wujiang

first: Jie

last: Jin


title: Kruppel-like factor 5 is Required for Urothelial Maturation

status: Public on Aug 02 2011

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Kruppel-like transcription factor 5 (Klf5) is expressed during late embryogenesis in the forming murine bladder urothelium. Targeted disruption of the Klf5flox alleles by the ShhGfpCre transgene resulted in failure of the bladder urothelium to mature accompanied by hydronephrosis, hydroureter, and vesicoureteric reflux in all E18.5 fetuses.  The bladder urothelium did not stratify nor did it express terminal differentiation markers characteristic of basal, intermediate, and umbrella cells including keratins 20, 14, and 5, and uroplakins.  At E18.5, an ectopic alpha smooth muscle actin positive layer of cells was identified subjacent to the undifferentiated Klf5-deficient urothelium. The effects of Klf5 deficiency were unique to the urothelium since maturation of the epithelium comprising the bladder neck and urethra were unaffected by the lack of KLF5. mRNA microarray analysis of whole E14.5 control and Klf5 deficient bladders identified Ppar-gamma and Grhl3 as putative downstream intermediary transcription factors that regulate urothelial maturation. Transient transfection assays demonstrated that KLF5 regulated expression of the mGrhl3 promoter. These observations show that alterations in maturation of the bladder urothelium alone are sufficient to induce bladder dysfunction leading to prenatal hydronephrosis.

overall_design: Total RNA from E14.5 whole bladders isolated from Klf5D/D and Klf5+/+ShhGfpCre+ embryos (n=3 samples/genotype, each sample a pool of two bladders) was isolated using the Qiagen MicroRNA Kit. The cDNA was then hybridized according to the manufacturer’s protocol to the Affymetrix Mouse Gene 1.0 ST Array

first: Sheila

middle: M

last: Bell

first: Liqian

last: Zhang

first: Angela

last: Mendell

first: James

middle: L

last: Lessard

first: Jeffrey

last: Whitsett


title: The effect of sirtuin 6 overexpression on TNFa stimulation.

status: Public on Jul 31 2011

city: Stevenage

first: Jessica

last: Vamathevan

address: Gunnels Wood Road

department: R&D

country: United Kingdom

institute: GlaxoSmithKline

summary:
SIRT6 has been implicated in a range of biological processes including inflammation, aging and the control of metabolism. Hence inhibitors or activators of SIRT6 have the potential to be therapeutics for a number of indications.
Genome wide expression studies were used to investigate the effect of overexpression of SIRT6 and mutant SIRT6 on a wide range of NFκB dependent gene expression

overall_design: HEK293 cells were transfected with expression vectors encoding wild type SIRT6 or the H133W mutant followed by stimulation with TNFα for one hour.

middle: J

first: Roberto

last: Solari


title: BW25113 with DNA and azlocillin

status: Public on Jul 30 2011

city: State College

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: BW25113 wild type cells grown to OD = 0.8 in LB, add 2 ug/mL nalidixic acid or 10 ug/mL azlocillin for 90 min. Control was without any antibiotic.

overall_design: BW25113 cells untreated or treated with nalidixic acid or azlocillin. One sample each.

first: Xiaoxue

last: Wang

first: Younghoon

last: Kim

first: Qun

last: Ma

first: SeokHoon

last: Hong

first: Karina

last: Pokusaeva

first: Joseph

last: Sturnio

middle: K


title: 1q gain clinical impact in Ewing's Sarcoma: role of DTL

city: Salamanca

first: Carlos

last: Mackintosh

address: Campus Miguel de Unamuno S/N

country: Spain

institute: Centro de Investigación del Cáncer

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Expression data from WT and GABPalpha-deficient Flt3(-) LSK cells

status: Public on Jul 28 2011

city: Nutley

first: Hai-Hui

last: Xue

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack University Medical Center

summary:
GABPalpha is an Ets family transcription factor and involved in regulation of both basic cellular functions such as cell cycle progression and tissue-specific biological processes. We found that GABPalpha is critically required for survival and differentiation of hematopoietic stem cells.
We used microarrays to detect gene expression changes in Flt3(-) LSK cells (which contains both long-term and short-term hematopoietic stem cells) by GABPalpha deficiency.

overall_design: Mx1Cre-GABPa(FL/+) and Mx1Cre-GABPa(FL/-) mice were treated with pIpC to induce inactivation of GABPalpha in bone marrow cells. Four days after last treatment of pIpC, the bone marrow cells were isolated and the Flt3(-)LSK subset was purified by cell sorting. RNA was extracted and hybridized to GeneChip Mouse GENE 1.0 ST arrays (Affymetrix).

first: Shuyang

last: Yu


title: Microarray analysis of skeletal muscle hypertrophy induced by heat-stress in healthy humans

city: Haga-Gun, Tochigi

first: Hidehiko

last: Kondo

address: 2606 Akabane, Ichikai-Machi

department: Biological Science Laboratories

country: Japan

institute: Kao Corporation

summary: This study was aimed at examining the effects of long-term of heat-stress on the gene expression of skeletal muscle hypertrophy. Heat- and stream-generating (HSG) sheets were placed on thigh laterally. The HSG sheets (heat-stress) were applied 8-hrs/day, once a day, 4 days/weeks, for 10 weeks. A muscle biopsy was taken from the vastus lateralis muscle (2 cm depth) of the treated leg before and after the experiment. Oligonucleotide microarray revealed that genes related to ATP-synthesis, protein synthesis and the molecular chaperonic activity were increased by heat stress. These results suggest that heat-stress might be a useful countermeasure for muscular atrophy during aging.

overall_design: Overall design	Five subjects were applied by heat- and stream-generating (HSG) sheets for 10 weeks. Total RNAs obtained from the skeletal muscle before and after the experiment were used for the analysis.

first: Katsumasa

last: Goto

first: Hideshi

last: Oda

first: Takatoshi

last: Murase

first: Tadashi

last: Hase

first: Ichiro

last: Matsumoto


title: miRNAs in ovarian cancer: A systems approach (mRNA data)

status: Public on Jul 29 2011

city: Atlanta

first: Shubin

last: Shahab

state: GA

address: 310 Ferst Drive

department: Biology

institute: Georgia Institute of Technology

summary: MicroRNAs (miRNAs) are short (~22 nucleotides) regulatory RNAs that can modulate gene expression and are aberrantly expressed in many diseases including cancer. We report the results of a systems analysis of miRNA regulation in ovarian cancer. We found that 33 miRNAs are up-regulated and 9 down-regulated in CEPI relative to OSE (p<0.01, ≥2 fold change). Of these, 12 were previously annotated miRNAs (Sanger miRBase) of which 9 are up-regulated and 3 are down-regulated in CEPI relative to OSE. Current models predict that changes in levels of miRNAs will be inversely correlated with changes in the levels of targeted mRNAs due to miRNA regulation. This predicted inverse correlation held for only ~9% of predicted target mRNAs. Computational analyses indicate the unexpected low inverse correlation may be at least partially explained by variation in the number of miRNA binding sites within the 3’ UTRs of targeted mRNAs and by miRNA-mediated changes in levels of transcription factors that can exert overriding trans-regulatory controls on target loci.

overall_design: mRNAs  were collected from three laser captured microdissected ovarian cancer epithelial (CEPI) samples. The mRNA expression pattern was compared with five healthy ovarian surface epithelia samples as controls using the Affymetrix U133 Plus 2.0 3' expression array.

first: Lilya

last: Matyunina

first: Lila

middle: D

last: Walker

first: Nathan

last: Bowen

first: Benedict

middle: B

last: Benigno

first: John

middle: F

last: Mcdonald


title: miRNAs in ovarian cancer: A systems approach (MAS5, plier, GCRMA)

summary: MicroRNAs (miRNAs) are short (~22 nucleotides) regulatory RNAs that can modulate gene expression and are aberrantly expressed in many diseases including cancer. Previous studies have shown that miRNAs inhibit the translation and facilitate the degradation of their targeted mRNAs making them attractive candidates for use in cancer therapy. However, the potential clinical utility of miRNAs in cancer therapy rests heavily upon our ability to understand and accurately predict the consequences of fluctuations in levels of miRNAs within the context of complex tumor cells. To evaluate the predictive power of current models, levels of miRNAs and their targeted messenger RNAs (mRNAs) were measured in laser captured micro-dissected (LCM) ovarian cancer epithelial cells (CEPI) and compared with levels present in ovarian surface epithelial cells (OSE). We found that the predicted inverse correlation between changes in levels of miRNAs and levels of their mRNA targets held for only ~6-11% of predicted target mRNAs. Our results underscore the complexities of miRNA-mediated regulation in vivo and caution against the widespread clinical application of miRNAs and miRNA inhibitors until the basis of these complexities is more fully understood.

overall_design: mRNAs  were collected from 3 miR-7 treated, 2 miR-128 treated , and 3 negative control miRNA treated HEY ovarian cancer cell samples. The mRNA expression pattern was compared between the miR-7 treated cells and the negative control treated cells, and separately between the miR-128 treated cells and the negative control treated cells using the Affymetrix U133 Plus 2.0 3' expression array.


title: Gene expression analysis of human lymphoblastoid cell lines

city: Bologna

first: Daniel

last: Remondini

address: Viale Berti Pichat 6/2

department: Physics and Astronomy - DIFA

country: Italy

institute: Bologna University

summary: Human lymphoblastoid cell lines (EBV-immortalised B cells, LcL) obtained from subjects of different age (young 28-40 years, centenarians >95 years) were analysed for gene expression at basal culture conditions and after 48 hours of serum starvation. Lymphoid B cells from centenarians were more resistant to apoptosis induction and displayed a more developed lysosomal compartment, the most critical component of phagic machinery. In addition, cells from centenarians were capable of engulfing and digesting other cells, i.e. their siblings (even entire cells). This behavior was improved by nutrient deprivation, but strikingly, it was unaffected by the autophagy-modulating drugs rapamycin, an autophagy inducer, and 3-methyladenine, an autophagy inhibitor.

overall_design: 12 samples, divided into 4 groups: young basal, young starved, centenarians basal and centenarians starved.

first: Paola

last: Matarrese

first: Antonella

last: Tinari

first: Barbara

last: Ascione

first: Lucrezia

last: Gambardella

first: Stefano

last: Salvioli

first: Elena

last: Tenedini

first: Enrico

last: Tagliafico

first: Claudio

last: Franceschi

first: Walter

last: Malorni


title: Down-regulation of BLIMP1-alpha by the EBV oncogene, LMP1, disrupts the plasma cell differentiation program and prevents viral replication in B cells

status: Public on Jul 27 2011

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

summary: In this study, we have investigated the effect of BLIMP1α on gene expression, cell differentiation and pathogenesis in normal human GC B cells using a non-viral vector based system

overall_design: Gene expression was compared among BLIMP1α, LMP1-transfected and control vector-transfected GC B cells from two patients. RNA from the FACS-sorted transfected GC B cells was amplified. Fragmented cRNA was hybridized to HG-U133 Plus 2.0 microarrays. Differentially expressed genes were identified using the GCOS pair-wise analysis.

first: Katerina

last: Vrzalikova

first: Martina

last: Vockerodt

first: Sarah

last: Leonard

first: Andrew

last: Bell

first: Alexandra

last: Schrader

first: Kenneth

last: Wright

first: Dieter

last: Kube

first: Martin

last: Rowe

first: Ciaran

last: Woodman

first: Paul

last: Murray


title: Expression data from mouse skin scar after wounding

status: Public on Jul 26 2011

city: Toronto

first: Saeid

last: Amini-Nik

state: ON

address: 101 College St

country: Canada

institute: Hospital For Sick Children

summary: Using a TCF reporter mouse which  contain a LacZ gene downstream of a c-fos minimal promoter and three consensus TCF-binding motifs, we wounded skin and harvested the scar tissue one week post wounding. Healing tissue sorted to group of cells :  β-Gal+ cells (R) expression data with β-Gal- cells (L) , an analysis of gene expression was performed using Partek Genotyping Suite and Ingenuity Systems Software.

overall_design: We used microarrays to  explore the difference in gene expression of B-Gal+ cells compare to Negative cells.Microdissected wound skin tissue was homogenized using a metal tissue smasher which pre-cooled in liquid nitrogen. Total RNA was extracted using Qiagen kit according to manufacturer’s manual. For microarray, RNA was extracted as mentioned and the quality of RNA was assessed with a Bioanalyzer (Agilent Technologies). cDNA was generated and hybridized onto the Affymetrix Mouse Gene 1.0 ST chips.

first: Amini-Nik

last: Saeid

first: Alman

last: Benjamin


title: PhoP regulon in pathogenic Escherichia coli

city: Ann Arbor

first: Christopher

last: Alteri

state: MI

address: 5641 MS II 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

summary:
PhoP is considered a regulator of virulence despite being conserved in both pathogenic and non-pathogenic Enterobacteriaceae.  While Escherichia coli strains represent both non-pathogenic commensal isolates and numerous virulent pathotypes, the PhoP virulence regulator has only been studied in commensal E. coli.  To better understand how conserved transcription factors contribute to virulence, we characterized PhoP in pathogenic E. coli.  Loss of phoP significantly attenuated E. coli during extraintestinal infection.  This was not surprising since we demonstrated that PhoP differentially regulated the transcription of >600 genes.  In addition to survival at acidic pH and resistance to polymyxin B, PhoP was required for repression of motility and oxygen-independent changes in the expression of primary dehydrogenase and terminal reductase respiratory chain components.  All phenotypes have in common a reliance on an energized membrane.
Thus, we hypothesized that PhoP mediated these effects by regulating genes that generate a proton motive force.  Indeed, bacteria lacking PhoP exhibited a hyper-polarized membrane, and dissipation of the transmembrane electrochemical gradient increased the susceptibility of the phoP mutant to acidic pH, while inhibiting respiratory generation of the proton gradient restored resistance to antimicrobial peptides independent of lipopolysaccharide modification.  These findings demonstrate a connection between PhoP, virulence, and the energized state of the membrane.

overall_design: Comparison of gene expression between wild-type CFT073 and a CFT073 phoP deletion mutant during logarithmic phase growth in LB medium.  Three biological replicates were compared from each strain.


title: Expression data from pancreatic islets from Men1flf RIP-Cre mice, Rbp2flf RIP-Cre mice, Men1flf Rbp2flf RIP-Cre mice and matched control.

city: Binney St

last: Cherniack

state: MA

institute: Broad Institute

summary:
The menin tumor suppressor protein (Men1) is deficient in many endocrine tumors and forms an active complex with MLL family histone methyltransferases.  This Men1 complex promotes histone H3 lysine 4 trimethylation at target loci including homeobox genes and cyclin-dependent kinase inhibitor genes. The loss of Men1 may be tumorigenic because it leads to decreased histone H3 lysine 4 trimethylation resulting in expressional changes of specific genes.
Reversing tumorigenesis induced by a Men1 deficiency might be achieved by inhibition of histone H3 lysine 4 demethylase Rbp2 (Kdm5a).  To this end, pancreatic islets from Men1f|f, Rbp2f|f and Men1f|f Rbp2f|f mice were expression profiled to determine what transcriptional changes induced by  a Men1 deficiency are reversed by the loss of Rpb2.

overall_design: Pancreatic islets were isolated from Men1flf RIP-Cre mice, Rbp2flf RIP-Cre mice, Men1flf Rbp2flf RIP-Cre mice and two month old matched control mice.  Total mRNA was extracted from islets and expression profiled on microarrays.

first: Wenchu

last: Lin

first: Matthew

last: Meyerson


title: Human Natural Killer Cell activation by mycobacteria

city: London

first: Damien

last: Portevin

address: The Ridgeway

institute: NIMR-MRC

summary:
Purified NK cells were co-cultured with M. bovis BCG or M. tuberculosis H37Rv (1:1) in the presence of IL-2 (100U/ml) or IL-12 (10pg/ml) for 24h before trizol extraction.
We used microarrays to detail the global gene expression underlying NK cell activation by mycobacteria.

overall_design: NK cell were isolated from the blood of 6 independent donors and activated with different mycobacteria and cytokines in order to study their transcriptional profiles according to mycobacterial virulence.

first: D

last: Young


title: KDM6B-induced gene expression changes in transfected CD10-positive GC B cells

first: Wenbin

last: Wei

summary: In this study, we have investigated the effect of lysine-specific demethylase 6B (KDM6B) on gene expression in normal human germinal center (GC) B cells using a non-viral vector-based system.

overall_design: Gene expression was compared between KDM6B-transfected and control vector-transfected GC B cells from three patients. RNA from the MACS-sorted transfected GC B cells was amplified. 10ug of fragmented cRNA was hybridized to HG-U133 Plus 2.0 microarrays. Differentially expressed genes were identified using Affymetrix GCOS pairwise analysis.

first: Jennifer

last: Anderton

first: Shikha

last: Bose

first: Martina

last: Vockerodt

first: Katerina

last: Vrzalikova

first: Michael

last: Kuo

first: Kristian

last: Helin

first: Jesper

last: Christensen


title: Expression profiles from HEK293 cells by overexpression of TRPM7 channel

status: Public on Jul 23 2011

city: Gwangju

first: Byoung-Cheol

last: Lee

address: 1 Oryong-dong Buk-gu

department: Life science

country: South Korea

institute: Gwangju Institutue Science and Technology

summary:
The functional activity of TRPM7 is essential for cell viability and growth, and its expression is up-regulated in certain pathological conditions. In order to assess the effects of TRPM7 activity on cellular gene expression, inducible HEK293 cell-lines harboring the wild-type mouse TRPM7 and a mutant lacking the kinase domain were established.
By using microarray analysis, we identified genetic profiles altered in transcription significantly and specifically by the expression of the functional TRPM7 channel.

overall_design: Overexpression of TRPM7 channel in HEK cells induce the cell damage and cell death. So we used tetracycline-inducible system for channel expression. However, since the treatment of inducer itself could also affect the transcription profile, we established another cell-line harboring a nonfunctional TRPM7 mutant (TRPM7DKD) as a control in which the entire kinase domain at the C-terminus was deleted. The wild-type and the non-functional TRPM7 channels were induced transiently, and the comparative changes in cellular transcription were investigated

first: Seong-Eui

last: Hong

first: Hyun-Ho

last: Lim

first: Do-Han

last: Kim

first: Chul-Seung

last: Park


title: Expression data from DTL silenced-Ewing Sarcoma's cell lines along with their controls

first: Carlos

last: Mackintosh

summary:
The 1q gain is related to poor survival, and to a profile of cell cycle deregulation in Ewing's Sarcoma (ES). Tumor samples with 1q gain overexpress the gene DTL.
We have silenced DTL in three ES cell lines in order to compare the differential expression pattern produced with the differential expression pattern which characterizes 1q gained-tumors.

overall_design: We silenced DTL in three ES cell lines with two different shRNA constructions by means of lentiviral transduction. pLKO.1-non-targeting control was transduced in the control samples. RNA was extracted and hybridized with Affymetrix expression microarrays.


title: Human T-ALL cell line response to inhibition of Notch signaling

city: Vancouver

first: Andrew

middle: P

last: Weng

state: BC

address: 675 West 10th Ave

institute: BC Cancer Agency

summary: Analysis of five Notch signaling-dependent human T-ALL cell lines (ALLSIL, DND41, HPBALL, KOPTK1, TALL-1) treated with gamma-secretase inhibitor (GSI) to block Notch signaling. Samples include parental cells, cells rescued by retroviral transduction with ICN (a GSI-independent form of activated Notch1), and cells retrovirally transduced with c-Myc (an important downstream target of Notch1). Results allow segregation of bona fide Notch targets from other genes affected by gamma-secretase inhibition as well as from targets downstream of c-Myc.

overall_design: Thirty samples were analyzed. Five human T-ALL cell lines (ALLSIL, DND41, HPBALL, KOPTK1, TALL-1) were treated with gamma-secretase inhibitor (1.0 micromolar compound E) vs. DMSO vehicle control for 12 hours. Each cell line was also retrovirally transduced with ICN or c-Myc, FACS sorted, and then treated with GSI vs. DMSO.


title: Transcriptional profile of Escherichia coli K12  strain JM109 under 200 mM glyphosate shock

status: Public on Jul 22 2011

city: Bei Jing

first: Liang

last: Li

state: Bei Jing

address: Zhongguan Cun Nanda Jie No.12

department: Biotechnology Research Institute

institute: Chinese Academy of Agricultural Sciences

summary: Glyphosate (GLY) is an effective antimetabolite that acts against the shikimate pathway 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase,  However, little is known about the genome-scale transcriptional responses of bacteria after glyphosate shock. To investigate further the mechanisms by which E. coli response to a glyphosate shock, a DNA-based microarray was used for transcriptional analysis of E. coli exposed to 200 mM glyphosate.

overall_design: RNA extracted from cells of E. coli K-12 JM109 cells after 4 h of growth to OD600 achieve 0.4, or cells after 200 mM glyphosate shock for 1 h when their OD600 achieved 0.4.

first: Min

last: Lin

first: Wei

last: Lu

first: Yongliang

last: Yan


title: Expression data of MIAPaCa-2 cells transfected with NDRG1

city: Sydney

first: Zaklina

last: Kovacevic

address: Level 5 Blackburn Building D06, University of Sydney

institute: University of Sydney

summary:
NDRG1 functions as a metastasis suppressor in pancreatic and other cancers. To determine the molecular function of NDRG1 in MIAPaCa-2 pancreatic cancer cells, we performed a whole genome gene array analysis on these cells stably transfected with NDRG1 when compared to empty vector-transfected controls.
The differentially expressed genes indetified in this microarray may represent potential molecular targets of NDRG1 in pancreatic cancer.

overall_design: Two separate RNA extracts of MIAPaCa-2 vector control and NDRG1 transfected cells were collected and hybridised to Affymetrix Human Genome U133 Plus 2.0 chips.

first: Des

middle: R

last: Richardson


title: Transgenic overexpression of Tcfap2c/AP-2gamma results in liver steatosis

city: Bonn

first: Peter

last: Kuckenberg

address: Sigmund Freud Str. 25

department: Institut of Pathology

country: Germany

institute: University Medical School Bonn

summary:
We established a mouse model, in which transcription factor Tcfap2c can be activated in an inducible and reversible manner in somatic tissues, taking advantage of the tetracycline-dependent regulatory system.
Induction of the transgene led to robust expression in all tissues (except brain and testis) and lead to rapid mortality within 3-7 days. In the liver, accumulation of microvesicular lipid droplets and breakdown of major hepatic metabolism pathways resulted in steatosis.

overall_design: Transgenic and control mice were treated with doxycycline (1mg/d i.p.) three times (0, 24 and 48h) and liver samples were collected after 52h. In addition, primary hepatocytes isolated from transgenic and control animals were cultured with doxycycline for 3 days (1µg/ml).

first: Hubert

last: Schorle


title: miRNAs in ovarian cancer: A systems approach

first: Shubin

last: Shahab

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

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
synthetic construct

overall_design: Refer to individual Series


title: Gene expression profiling of oral squamous cell carcinoma (OSCC)

city: Seattle

first: Chu

last: Chen

state: Washington

address: 1100 Fairview Ave. N, PO Box 19024, M/S M5-C800

department: PHS

institute: Fred Hutchinson Cancer Research Center

summary:
OSCC is associated with substantial mortality and morbidity. To identify potential biomarkers for the early detection of invasive OSCC, we compared the gene expressions of OSCC, oral dysplasia, and normal
oral tissue from patients without oral cancer or preneoplastic oral lesions (controls). Results provided models of gene expression to distinguish OSCC from controls.

overall_design: RNA from 167 OSCC, 17 dysplasia and 45 normal oral tissues were extracted and hybridized to Affymetrix U133 2.0 Plus GeneChip arrays. The differentially expressed genes were identified using GenePlus software and the validation was done using RT-PCR, using independent internal and external datasets.

first: Eduardo

last: Mendez

first: John

last: Houck

first: Wenhong

last: Fan

first: Pawadee

last: Lohavanichbutr

first: David

last: Doody

first: Bevan

last: Yueh

first: Neal

last: Futran

first: Melissa

last: Upton

first: Gregory

last: Farwell

first: Stephen

last: Schwartz

first: Lue

last: Zhao


title: Expression data from an ASCL1 siRNA experiment

status: Public on Jul 19 2011

city: Kyoto

first: T

last: Fujiwara

address: 46-29 Yoshida Shimoadachi-cho Sakyo-ku

institute: Kyoto University

summary: To elucidate whether or not a subtype of adenocarcinoma with neuroendocrine nature has poor prognosis, we performed gene expression profiling of an achaete-scute complex homolog 1 (ASCL1) siRNA experiment.

overall_design: siRNA againt ASCL1 was transfected into DMS79 cells.


title: Gene expression data from human CD34+ cord blood cells infected with MIGR1, MIGR1-AML1-ETO or MIGR1-AML1-ETO∆NHR1

city: New York

first: Jeffrey

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary:
Compare the gene expression profile among human CD34+ cord blood cells infected with MIGR1, MIGR1-AML1-ETO or MIGR1-AML1-ETO∆NHR1
AML1-ETO promotes the self-renewal of human hematopoietic stem/progenitor cells (HSPCs). We found deletion of NHR1 domain abrogates AML1-ETO induced expasion of HSPCs.

overall_design: GFP+CD34+ human cord blood cells were sorted by FACS 72 hours after the infection for RNA extraction and hybridyzation for Affymetrix microarrays.

first: Lan

last: Wang

last: Nimer


title: Profiling of Jurkat T cells activated with CD3, CD28 and PMA and multiple kinase inhibitors

status: Public on Jul 16 2011

city: Ede

first: Wynand

last: Alkema

address: Kernhemseweg 2

institute: NIZO Food Research

summary: T lymphocytes are orchestrators of adaptive immunity. Naïve T cells may differentiate into the Th1, Th2, Th17 or iTreg phenotype, depending on environmental co-stimulatory signals. In order to identify the genes and pathways involved in differentiation of Jurkat T cells towards Th1 and Th2 subtypes we performed comprehensive transcriptome analyses of Jurkat T cells stimulated with various stimuli an pathway inhibitors

overall_design: Jurkat T cells were treated with CD3, CD28 and PMA and all pairwise combinations, in the presence of DMSO (control) or kinase inhibitors. RNA was isolated after 8 hrs incubation.

first: Ruben

last: Smeets

first: Paul

last: Vink

first: Frank

last: Wijnands

first: Monika

last: Gorecka

first: Henri

last: Klop

first: Anja

last: Garritsen

first: Susanne

last: Bauerschmidt

first: Mieke

last: Boots


title: Profiling of Jurkat T cells activated with CD3, CD28 and PMA and multiple kinase inhibitors at 1 and 8 hours


title: Expression data from zinc-finger-transcription-factor-induced Fulvestrant-Resistant MCF7 Cell Lines

status: Public on Jul 18 2011

city: Boston

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Multiple gene expression studies have demonstrated that breast cancer biological diversity is associated with distinct transcriptional programs. Transcription factors, because of their unique ability to coordinate the expression of multiple genes, are speculated to play a role in generating phenotypic plasticity associated with cancer progression including acquired drug resistance.  Combinatorial libraries of artificial zinc-finger transcription factors (ZF-TFs) provide a robust means for inducing and understanding various functional components of the cancer phenotype.  Herein, we utilized combinatorial ZF-TF library technology to better understand how breast cancer cells acquire resistance to a fulvestrant, a clinically important anti-endocrine therapeutic agent.  We isolated six ZF-TF library members capable of inducing stable, long-term anti-endocrine drug-resistance in two independent estrogen receptor positive breast cancer cell lines. Comparative gene expression profile analysis of the ZF-TF-transduced breast cancer cell lines revealed a 72-gene cluster that constituted a common signature for the fulvestrant-resistance phenotype.  Pathway enrichment-analysis of gene expression data revealed that the ZF-TF-induced fulvestrant resistance is associated with an estrogen receptor negative-like gene set and four unique myb-regulated gene sets. Furthermore, we identified a set of genes strongly expressed in the ZF-TF-induced fulvestrant-resistant cells that was correlated with a lower probability of distant metastasis-free or death-from-relapse-free survival of breast cancer patients.

overall_design: MCF7-R73 cells, a monoclonal MCF7 subline that is highly sensitive to fulvestrant-induced cytocidal activity, underwent retroviral transduction with the zinc finger transcription factor (ZF-TF) activator library or with a control plasmid encoding only the NF-kB p65 activation domain.  Both populations of cells were enriched for transduced cells by selecting for growth in puromycin and for fulvestrant-resistant cells by selecting with 100 nM fulvestrant. After 6 weeks of continuous treatment with fulvestrant, hundreds of drug-resistant colonies emerged from the population of cells infected with the ZF-TF activator library.  By contrast, as expected, the control MCF7cell line transduced by NF-kB p65-only underwent massive cell death resulting in the complete absence of resistant colonies. DNA encoding the zinc-finger arrays was rescued by PCR from genomic DNA of pooled fulvestrant-resistant cells. The sequences of the ZF-TFs were determined and 46 unique ZF-TF clones identified.  These 46 unique ZF-TFs were re-cloned into the retroviral vector and converted into clonal virus stocks that were used to transduce MCF7-R73 cells.  These 46 retrovirally transduced cell populations were then challenged with fulvestrant.  As compared with the control MCF-238 cells, MCF7-R73 cells transduced with six unique ZF-TFs demonstrated survival and growth in the presence of 100nM fulvestrant.

first: Jeongeun

last: Lee

first: Andrew

middle: S

last: Hirsh

first: Sridhar

last: Ramaswamy

first: J

last: Joung

first: Dennis

middle: C

last: Sgroi


title: Expression data of human pulmonary arterial smooth muscle cells (PASMCs) treated with BMP-4

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

summary: Smad1/5 are transcription factors that engage in BMP-induced transcription. We determined and analyzed Smad1/5 binding sites by ChIP-sequencing. We used expression microarrays to compare the Smad1/5 binding sites identified by ChIP-seq to BMP-induced gene expressions.

overall_design: PASMCs were treated with 50 ng/ml BMP-4 for 0, 2, or 24 hrs. RNA was extracted and hybridized on Affymetrix microarrays.

first: Masato

last: Morikawa

first: Shuichi

last: Tsutsumi

first: Eleftheria

last: Vasilaki

first: Carl-Henrik

last: Heldin

first: Hiroyuki

last: Aburatani

first: Kohei

last: Miyazono


title: Expression data of human umbilical vein endothelial cells (HUVECs) treated with BMP-6 and BMP-9

summary:
Smad1/5 are transcription factors that engage in BMP-induced transcription. We determined and analyzed Smad1/5 binding sites by ChIP-sequencing.
We used expression microarrays to compare the Smad1/5 binding sites identified by ChIP-seq to BMP-induced gene expressions.

overall_design: HUVECs were treated with BMP for RNA extraction and hybridization on Affymetrix microarrays.


title: Follicular B (FoB) cells purified from miR-17-92 transgenic mice

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: We have generated a miR-17-92 transgenic allele (termed miR-17-92 Tg) whose expression can be turned on conditionally by Cre recombinase (Xiao et al, Nature Immunology, 9:405-14, 2008). The mice were crossed to CD19-Cre mice to turn on the transgene expression specifically in B cells.

overall_design:
Follicular B(FoB) cells were purified from CD19-Cre;miR-17~92 Tg/Tg mice (FoBtg1, FoBtg2, FoBtg3) and miR-17~92 Tg/Tg mice (FoBwt1, FoBwt2, FoBwt3) by MACS depletion of cells positive for CD5, CD43, and CD93 (also known as AA4.1).
The purity of follicular B cells was examined by flow cytometry and was greater than 95%  for all samples. Total RNA was extracted using RNeasy kit (QIAGEN).

first: Changchun

last: Xiao

first: Hiroyo

last: Oda


title: Human mural trophectoderm

status: Public on Jul 15 2011

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

country: France

institute: PhyMedExp INSERM U1046

summary: The trophoblast cell lineage is specified as early as the blastocyst stage, leading to the individualization of trophectoderm from pluripotent cells of the inner cell mass. We used a double in vitro transcription mRNA amplification technique and compared trophectoderm with pluripotent stem cells.

first: Said

last: Assou

first: Delphine

last: HAOUZI

first: Jean-Marie

last: RAMIREZ

first: Cécile

last: MONZO

first: Fabienne

last: BEKER

first: Samir

last: HAMAMAH

first: John

last: DE VOS


title: Gene Expression data from human brain tumor or normal brain

status: Public on Jul 12 2011

city: Suwon

first: Myung Ae

last: Lee

state: Gyeonggi-do

address: Woncheon-dong, Yeongtong-gu

institute: ajou univ school of medicine 607

summary: Stem cells from various lineages have well known for its migration tendency toward glioma and become attractive vehicles to deliver therapeutic genes to brain tumors. However, which factors and mechanisms work in these function is not yet known. To identify those factors and mechanisms, we analyzed the brain tumor-specific gene expression profile using microarray analysis

overall_design: To identify genes that are differentially expressed, human brain tumor samples and normal brains were collected from brain tumor patients for RNA extraction and hybridization on Affymetrix microarrays. To obtain samples, we got patients consent to collect and analysis of sample. All of three normal brains (N2, N3, N4) and brain tumor, Gliobalstoma (T2),  Ganglioglioma (T3) and shwannoma(T4), are used for experiment.

first: Myung-ae

first: Jeong-yong

last: Jeon

first: Young-sik

first: Soo-Young

last: Cho

first: Kyunggi


title: Comparison of Differences in Mouse Mammary gland gene expression data at POSTNATAL DAY 70 in Akt1wildtype versus Akt1-deficient mice

city: Providence

first: Mary

middle: L.

last: Hixon

state: RI

address: GE505 70 Ship Street

institute: Brown University

summary:
Akt1, a serine-threonine protein kinase member of the PKB/Akt gene family, plays a critical role in the regulation of several cellular processes including cell proliferation and apoptosis. In this study, we utilized Akt1+/+ and Akt1¬-/- C57/Bl6 female mice to demonstrate that Akt1 is required for normal mammary gland postnatal development and homeostasis. Akt1 deficiency resulted in severely delayed postnatal mammary gland growth as well as a significant decrease in the number of terminal end buds during puberty. Adult Akt1-/- mammary glands exhibited significantly fewer alveolar buds coupled with a significant increase in epithelial cell apoptosis compared to their wild-type counterparts. Microarray analysis revealed that Akt1 deficiency resulted in several altered gene expression changes and biological processes in adult mammary glands, including organismal development, cell death, and tissue morphology. Of particular importance, a significant decrease in expression of Btn1a1, a gene involved in milk lipid secretion, was observed in Akt1-/- mammary glands by both microarray and RT-PCR validation.
Transcriptome analysis of Akt1 wild type and akt1-homozygous mouse mammary glands

overall_design: wild type mammary glands from 3 mice and Akt1-deficient mammary glands from 3 mice were analyzed for differences in gene expression at postnatal day 70

first: Jessica

last: LaRocca

first: Jodie

last: Pietruska


title: Sox17-transgenic hematopoietic stem cell microarray

city: Ann Arbor

first: Shenghui

last: He

state: Michigan

address: 210 Washtenaw Avenue, 5258 LSI

department: Life Science institute

institute: University of Michigan

summary:
The transcription factor SOX17 is expressed by fetal, but not adult hematoipoietic stem cells (HSCs), and is required for the maintenance of fetal and neonatal, but not adult, HSCs. In the current study we show that ectopic expression of Sox17 in adult HSCs and transiently reconstituting multipotent progenitors was sufficient to confer increased self-renewal potential and the expression of fetal HSC genes including fetal HSC surface markers.
To assess the acute effects of ectopic Sox17 expression on global gene expression in adult HSCs, we performed microarray analysis to compare the gene expression profile of adult Sox17-trangenic and control HSCs after short induction of Sox17-transgene expression.

overall_design: Total RNA were isolated from 5 independent, freshly isolated aliquots of 10,000 HSCs isolated from 8-week old Sox17-transgenic ((tetO)7CMVSox17-IRES-NucEGFP;B6.Cg-Gt(ROSA)26Sortm1(rtTA*M2)Jae/J double transgenic) or littermate control mice that were treated with doxycycline for 5 days to induce transgene expression. Purified RNA was reverse transcribed and amplified using the WT-Ovation™ Pico RNA Amplification system (NuGEN Technologies) following the manufacturer’s instructions. Sense strand cDNA was generated using WT-Ovation™ Exon Module (NuGEN), then fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). 2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.

first: Sean

last: Morrison


title: Retroviral Sox17 over-expression adult hematopoietic stem/progenitor cells microarray

summary:
The transcription factor SOX17 is expressed by fetal, but not adult hematoipoietic stem cells (HSCs), and is required for the maintenance of fetal and neonatal, but not adult, HSCs. In the current study we show that ectopic expression of Sox17 in adult HSCs and transiently reconstituting multipotent progenitors was sufficient to confer increased self-renewal potential and the expression of fetal HSC genes including fetal HSC surface markers.
To assess the mechanisms by which ectopic Sox17 expression in adult hematopoietic progenitors increased self-renewal potential and conferred fetal HSC properties, we compared the gene expression profiles of E16.5 fetal liver HSCs, young adult bone marrow HSCs, young adult bone marrow CD48+LSK cells, and Sox17-expressing CD48+LSK cells isolated from mice that had been transplanted with MSCV-Sox17-infected bone marrow cells 12 weeks earlier.

overall_design: Total RNA (~5ng) was isolated from 3 independent, freshly isolated aliquots of 10,000 E16.5 fetal liver HSCs, 10,000 fetal liver CD48+LSK cells, 10,000 adult bone marrow HSCs, 10,000 adult bone marrow CD48+LSK cells, 10,000 Sox17-expressing CD48+LSK cells isolated from primary recipients 12 weeks after transplantation of MSCV-Sox17-infected bone marrow cells. Purified RNA was reverse transcribed and amplified using the WT-Ovation™ Pico RNA Amplification system (NuGEN Technologies) following the manufacturer’s instructions. Sense strand cDNA was generated using WT-Ovation™ Exon Module (NuGEN), then fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). 2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.


title: Transcription factor SOX17 overexpression in hematopoietic stem cells


title: Expression data from mice lacking SIRT3 under dietary stress

status: Public on Jul 11 2011

city: Durham

first: Matthew

last: Hirschey

state: NC

address: 300 N. Duke Street

department: Department of Medicine

institute: Duke University Medical Center

summary:
SIRT3 is a mitochondrial NAD(+)-dependent protein deacetylase, which regulates the enzymatic activity of several mitochondrial proteins.
We used microarrays to identify the differences in gene expression as a result of loss of SIRT3, under standard and high-fat diet conditions

overall_design: Wild-type and SIRT3KO mice were sacrificed at 12weeks of age and RNA was extracted from liver tissue, and hybridized on Affymetrix microarrays, to determine differences in gene expression as a result of diet

first: Eric

last: Verdin


title: Effect of 5a-dihydrotestosterone on breast cancer cell line MDA-MB-453

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center

summary: Analysis of MDA-MB-453 breast cancer cells treated with the androgen 5a-dihydrotestosterone (DHT) for 6h, 16h and 48h to define the genes that are differentially regulated in response to DHT.

overall_design: MDA-MB-453 breast cancer cells were treated with 5a-dihydrotestosterone (DHT) for time course, followed by RNA extraction and hybridization on Affymetrix microarrays, in order to obtain the gene expression profiles at three time points. The vehicle treated samples are used as control.

first: Min

last: Ni

first: Myles

last: Brown


title: Genomic profiling in Down syndrome pediatric acute lymphoblastic leukemia

first: Hon-chiu

middle: Eastwood

last: Leung

address: 1102 Bates Street  Room C1030.09

department: Pediatrics

institute: Baylor College of Medicine

type:
Expression profiling by array
Methylation profiling by array
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary:
Patients with Down syndrome (DS) and acute lymphoblastic leukemia (ALL) have distinct clinical and biological features.  Whereas most DS-ALL cases lack the sentinel cytogenetic lesions that guide risk assignment in childhood ALL, JAK2 mutations and CRLF2 overexpression are highly enriched.  To further characterize the unique biology of DS-ALL, we performed genome-wide profiling of 58 DS-ALL and 35 non-Down syndrome (NDS) ALL cases by DNA copy number, loss of heterozygosity, gene expression, and methylation analyses.  We report novel deletions within the 6p22 histone gene cluster as significantly more frequent in DS-ALL, occurring in 12 DS (24%) and only a single NDS case (3%) (Fisher’s exact p = 0.013).  Homozygous deletions yielded significantly lower histone expression levels, and were associated with higher methylation levels, distinct spatial localization of methylated promoters, and enrichment of highly methylated genes for specific pathways and transcription factor binding motifs.  Gene expression profiling identified CRLF2 overexpression in nearly half DS-ALL cases, and supervised analysis identified an associated 39-gene signature.  However, no expression signature was identified for DS-ALL overall, nor for histone status, suggesting that DS-ALL constitutes several, heterogeneous molecular entities.  Characterization of pathways associated with histone deletions and high CRLF2 expression may identify opportunities for novel targeted interventions.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.

first: Karen

last: Rabin

first: Michael

middle: G

last: Loudin

first: Jinhua

last: Wang

middle: E

first: Sivashankarappa

last: Gurusiddappa

first: Julia

last: Meyer

first: Gregory

last: Condos

first: Debra

first: Anna

last: Tsimelzon

first: Meenakshi

last: Devidas

first: Nyla

last: Heerema

first: Andrew

last: Carroll

first: Sharon

last: Plon

first: Stephen

last: Hunger

first: Giuseppe

last: Basso

first: Andrea

last: Pession

first: Deepa

last: Bhojwani

first: William


title: DACH1 expression in U87 cells

status: Public on Jul 20 2011

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary:
Loss or reduction in function of tumor suppressor genes contributes to tumorigenesis. We identified a novel homozygous deletion of DACH1 in gliomas.
We generated U87TR-Da glioma cell line, where DACH1 expression could be activated by exposure of cells to doxycycline, and examined changing global gene expression by DACH1 expression.

overall_design: Expression of DACH1 in U87TR-Da cells can be induced by exposure of the cells to doxycycline. We analyzed gene expression profiles of DACH1-induced/repressed U87TR-Da cells. And we also compared gene expression profiles of DACH1-induced/repressed U87TR-Da cells under different culture condition, DMEMF(serum-containing) and NBE(serum-free)

first: Hideki

last: Ogiwara

first: Hiroyuki

last: Aburatani


title: Expression Profiling of Mixed Lineage Leukemia Cells Treated with a Potent Small-Molecule DOT1L Inhibitor

city: Cambridge

first: Jesse

middle: Jerome

last: Smith

address: 325 Vassar Street, Suite 2B

department: Biological Sciences

institute: Epizyme

summary: Cell lines bearing MLL translocations (MV4-11 and MOLM-13) were treated with a potent, selective inhibitor of the DOT1L histone methyl transferase.  Treatment of MLL-rearranged cell lines with the DOT1L inhibitor selectively inhibits H3K79 methylation and blocks expression of leukemogenic genes.  Here we provide expression profiling data of cells treated with DOT1L inhibitor or vehicle control.

overall_design: MV4-11 cells were treated with 3 uM EPZ004777 (DOT1L inhibitor) or vehicle control (0.1% DMSO) for 2, 4 and 6 days.  MOLM-13 cells were treated with 3 uM EPZ004777 (DOT1L inhibitor) or vehicle control (0.1% DMSO) for 6 days.  For each unique conditon, 3 biological replicates were generated for expression profiling.

first: Scott

last: Daigle

first: Roy

middle: M

last: Pollock


title: Expression data in cancer cell lines using Affymetrix GeneChip

status: Public on Jul 08 2011

first: Hyun-soo

last: Cho

address: 4-6-1, shirokanedai, minatoku

summary: Microarray analysis to identify down-stream genes after treatment with siKDM3A

overall_design: Purified total RNA  was labeled and hybridized onto Affymetrix GeneChip U133 Plus 2.0 oligonucleotide arrays in cancer cell lines after treatment with siKDM3A

first: Ryuji

last: Hamamoto


title: Gene expression change after LSD1 siRNA treatment in ER-negative breast cancer cells MDA-MB-231

city: Cologne

first: Soyoung

last: Lim

address: Kerpener Str. 62

department: Institute of Pathology

institute: Cologne medical school

summary: Knock-down of LSD1 using siRNA approach induced regulation of several proliferation-associated genes in ER-negative breast cancer cells MDA-MB-231.

overall_design: To identify changes on gene expression caused by treatment with siRNA directed against LSD1 (si) or control siRNA (control) in MDA-MB-231 cells, total RNA was purified from the cells after treatment for 6 days (2 rounds of transfection). Three biological replicates were used.

first: Jutta

last: Kirfel


title: MOG-encoding DNA vaccines ameliorate EAE and display neuroprotective effects in treated mice summary

city: Barcelona

first: Ramil

last: Nurtdinov

address: Dr. Aiguader 88

department: Bioinformatics and Genomics

institute: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology

summary: Vaccination with naked DNA encoding myelin basic protein represents a promising therapeutic strategy in multiple sclerosis (MS). In this study, we assessed the potential of vaccination with a DNA construct coding for the myelin oligodendrocyte glycoprotein (MOG), an important candidate autoantigen in MS, to induce tolerance and protect against experimental autoimmune encephalomyelitis (EAE). Herein, we demonstrated that MOG-DNA vaccination reduced the clinical and histopathological signs of EAE when administered in both prophylactic and therapeutic settings. Further mechanistic experiments revealed that the protective effects of MOG-DNA vaccines were associated with a reduction of antigen-specific Th1 and Th17 cellular immune responses and expansion of regulatory T cells in periphery, and up-regulation in the central nervous system of genes encoding neurotrophic factors and proteins involved in remyelination. These results may set the rationale for the use of MOG-based DNA vaccines to induce tolerance in MS patients.

overall_design: We analyzed brain and spinal cord samples from five treated and five control mice

first: Nocolas

last: Fissolo

first: Carme

last: Costa

first: Marta

last: Bustamante

first: Victor

last: Llombart

first: Maria-Jose

last: Mansilla

first: Carmen

last: Espejo

first: Xavier

last: Montalban

first: Manuel

last: Comabella


title: The HDAC inhibitor LBH589 enhances the anti-myeloma effect of the IGF-1 RTK inhibitor picropodophyllin (PPP)

status: Public on Jul 09 2011

city: Uppsala

first: Prasoon

last: Agarwal

state: Sweden

address: Dag Hammarshkojlds vag 20

department: IGP

country: Sweden

institute: Rudbeck Laboratory, Uppsala University

summary:
Our previous studies have shown that inhibition of the IGF-1R pathway by the IGF-1RTK inhibitor picropodophyllin (PPP) can be achieved and also constitutes a favorable therapeutic window in multiple myeloma (MM). As no complete remission using in vivo models of MM could be obtained, a combinatorial drug screen (HTS) was performed to select the most performant combination with PPP. The HDAC inhibitor LBH589 was shown to act in synergy with PPP on survival of MM cells. The contribution from both drugs and the combination were further monitored for apoptosis, cell cycle distribution, and the impact on downstream gene and protein expression in human and mouse MM models in vitro. In the RPMI 8226 human MM cell line, simultaneous treatment with both compounds for 48h caused a 5-fold increase of apoptotic and late apoptotic/necrotic cells as compared to controls, while treatment with either compound alone only induced a 3-fold increase. After 24h cleavage of apoptotic proteins caspase -9, -8 and -3 could be found in RPMI 8226 cells treated with both drugs individually, but in the combination we observed an additive effect on the cleavage of the active forms of caspase 8 as compared to single drug treatments. The combination of LBH589 and PPP could be monitored as an accumulation of cells in the G2/M phase, and subsequent down-regulation of cell cycle regulated proteins. The effect of both compounds on the expression of cyclin B1, -E and -D2 was additive, as demonstrated by western blot. These data were also confirmed in the mouse 5T33MM cells in vitro. Gene expression analysis and validations of the RPMI 8226 cells reveal that the drug combination has better effects than the single drug alone.  Combined treatment in vivo resulted in a significant prolonged survival of 5T33MM inoculated mice when compared to the control group and to treatment with the drugs alone. In conclusion, the results indicate an improved MM treatment opportunity in using a combination of PPP and LBH589.
We used whole genome Microarray to decipher the changes occuring after treatment of the single and combination of the drugs. And see if the combination has better effects.

overall_design: RPMI 8266 cells were treated with LBH589 (20nM), picropodophyllin (PPP)(0.375uM) , and the combination of these two drugs. RNA was extracted at two different time points 6 and 24 for the microarray.

first: Charlotte

last: Fristedt


title: Breast cancer cell line MDA-MB-453 response to DHT

first: Yiwen

last: Chen

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: fireman vs wt erwinia infection-Impact of the fireman mutation in the Erwinia amylovora response of Arabidopsis

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

summary:
adt09-02_fireman - fireman vs wt erwinia infection - A meta-analysis ot the CATMA transcriptomic data has shown that an orphan gene of Arabidopsis: AT5E39460, recently remaned AT5G 44585, is highly responsive to biotic stresses. An homozygous mutant of this gene, named fireman has been produced and displays less cell death symptoms in comparison to the wild type in response to Erwinia amylovora infection. The purpose of this transcriptomic analysis is to understand which pathways are altered in this mutant versus the wild-type in response to this phytopathogenic bacteria. - 3 inoculated leaves of 5 weeks old plants, per plant, have been harvested 24h after inoculation with H20 or E. amylovora, strain 1430.

Keywords: normal vs disease comparison, normal vs transgenic comparaison

overall_design: 8 dye-swap - CATMA arrays

first: Jean-Pierre

last: Renou

first: Marie-Laure

last: Martin-Magniette


title: Identification of right heart-enriched genes in a murine model of chronic outflow tract obstruction

status: Public on Jul 07 2011

city: Bad Nauheim

first: Pascal

last: Gellert

address: Ludwigstr. 43

department: Cardiac Development and Remodelling

institute: Max Planck Institut for Heart and Lung Research

summary: The right ventricle (RV) differs in several aspects from the left ventricle (LV) including its embryonic origin, physiological role and anatomical design. In contrast to LV hypertrophy, little is known about the molecular circuits, which are activated upon RV hypertrophy (RVH). We established a highly reproducible model of RVH in mice using pulmonary artery clipping (PAC), which avoids detrimental RV pressure overload and thus allows long-term survival of operated mice. Magnetic resonance imaging revealed pathognomonic changes with striking similarities to human congenital heart disease- or pulmonary arterial hypertension- patients. Comparative, microarray based transcriptome analysis of right- and left-ventricular remodeling identified distinct transcriptional responses to pressure-induced hypertrophy of either ventricle, which were mainly characterized by stronger transcriptional responses of the RV compared to the LV myocardium. Hierarchic cluster analysis revealed a RV- and LV-specific pattern of gene activity after induction of hypertrophy, however, we did not find evidence for qualitatively distinct regulatory pathways in RV compared to LV. Data mining of nearly three thousand RV-enriched genes under PAC disclosed novel potential (co)-regulators of long-term RV remodeling and hypertrophy. We reason that specific inhibitory mechanisms in RV restrict excessive myocardial hypertrophy and thereby contribute to its vulnerability to pressure overload.

overall_design: Alternative splicing and gene expression analysis during development of the heart and cardiomyoyte differentiation.

first: Karsten

middle: g

last: Kreymborg

first: Shizuka

last: Uchida

first: André

last: Schneider

first: Thomas

last: Boettger

first: Robert

last: Voswinckel

first: Astrid

last: Wietelmann

first: Marten

last: Szibor

first: Nobert

last: Weissmann

first: Ardeschir

middle: H

last: Ghofrani

first: Ralph

last: Schermuly

first: Dietmar

last: Schranz

first: Werner

last: Seeger

last: Braun


title: Anaplastic lymphoma kinase (ALK) inhibitor response in neuroblastoma is highly correlated with ALK mutation status, ALK mRNA and protein levels.

city: Rotterdam

first: Floor

last: Duijkers

address: Dr. Molewaterplein 50-60 Ee15-02

department: Pediatric Oncology-Hematology

institute: Erasmus MC

summary: High anaplastic lymphoma kinase (ALK) protein levels may be correlated with an unfavorable prognosis in neuroblastoma (NBL) patients, regardless of ALK mutation status. We therefore examined the correlation between levels of ALK, phosphorylated ALK (pALK) and downstream signaling proteins and response to ALK inhibition in a large panel of both ALK mutated (MUT) and wild type (WT) NBL cell lines. Six of the nineteen NBL cell lines had a point mutation and four an amplification of the ALK gene. ALK amplified cell lines showed similar ALK levels and ALK inhibitor sensitivity as WT cell lines and were therefore co-analyzed. The ALK mRNA (p=0.043), ALK 220 kDa (p=0.009) and ALK 140 kDa (p=0.025) protein levels were higher in ALK mutant (n=6) than WT cell lines (n=13). ALK mRNA and protein levels significantly correlated with ERK1 and ERK2 protein levels, and also with PHOX2B mRNA levels, a neural differentiation marker which is mutated in NBL. Response to ALK inhibitor TAE684 was also significantly correlated with ALK levels. ALK mutant cell lines (n=4) demonstrated a higher sensitivity towards ALK inhibitor TAE684 (14.9 fold more sensitive, p=0.004) than eight WT cell lines. These results underline the importance of ALK mutations but also ALK levels for response to ALK inhibitors in NBL cell lines. Furthermore, the strong correlation of PHOX2B and ALK suggests that neural differentiation stage may be correlated with ALK levels in neuroblastoma. These data will enhance understanding of ALK inhibitor response in future patient trials.

overall_design: To study differentially expressed genes in the neuroblastoma cell lines described in the protein analysis study above, 15 cell lines and 2 derivative cell lines were used.


title: Expression data of A375 melanoma cells after DMSO or MLN4924 treatment from 1 hour to 24 hour

first: Hugues

last: Bernard

address: 35 Landsdowne St.

department: Molecular Pathology

institute: Millennium: The Takeda Oncology company

summary: Microarrays were used to determine the change in gene expression of genes involved in the CDT1/NAE pathway

overall_design: A375 cells were grown and then incubated in the presence of either DMSO as control or 650nM MLN4924. Cells were treated for 1, 2, 4, 8, and 24 hours. RNA extraction and hybridization on Affymetrix HG-U133Plus 2.0 arrays were performed.

first: Eric

last: Lightcap

first: Xiaozhen

middle: J

last: Liu


title: Expression data from Down syndrome and non-Down syndrome pediatric acute lymphoblastic leukemia cases

first: Hon-chiu

last: Leung

summary:
Gene expression profiling (GEP) can reveal characteristic signatures associated with distinct biologic subtypes of acute lymphoblastic leukemia (ALL).
We performed GEP on Down syndrome (DS) and comparison non-Down syndrome (NDS) ALL cases to identify biologic differences between these groups.

overall_design: Ficoll-enriched, cryopreserved diagnostic bone marrow samples were obtained from patients with newly diagnosed B-precursor acute lymphoblastic leukemia.

first: Karen

last: Rabin

first: Jinhua

last: Wang

first: William

middle: L

last: Carroll


title: Determinants of sensitivity to DZNep induced apoptosis in multiple myeloma cells

status: Public on Jul 04 2011

city: Singapore

first: Zhigang

last: Xie

address: 14 Medical Drive, CeLS Building #02-07

department: CSI Singapore

country: Singapore

institute: National University of Singapore

summary: The 3-Deazaneplanocin A (DZNep), one of S-adenosylhomocysteine (AdoHcy) hydrolase inhibitors, has shown antitumor activities in a broad range of solid tumors and acute myeloid leukemia. Here, we examined its effects on multiple myeloma (MM) cells and found that, at 500 nM, it potently inhibited growth and induced apoptosis in 2 of 8 MM cell lines. RNA from un-treated and DZNep treated cells was profiled by Affymetrix HG-U133 Plus 2.0 microarray and genes with a significant change in gene expression were determined by significance analysis of microarray (SAM) testing. ALOX5 was the most down-regulated gene (5.8-fold) in sensitive cells and was expressed at low level in resistant cells. The results were corroborated by quantitative RT-PCR. Western-blot analysis indicated ALOX5 was highly expressed only in sensitive cell line H929 and greatly decreased upon DZNep treatment. Ectopic expression of ALOX5 reduced sensitivity to DZNep in H929 cells. Furthermore, down-regulation of ALOX5 by RNA interference could also induce apoptosis in H929. Gene expression analysis on MM patient dataset indicated ALOX5 expression was significantly higher in MM patients compared to normal plasma cells. We also found that Bcl-2 was overexpressed in DZNep insensitive cells, and cotreatment with DZNep and ABT-737, a Bcl-2 family inhibitor, synergistically inhibited growth and induced apoptosis of DZNep insensitive MM cells. Taken together, this study shows one of mechanisms of the DZNep efficacy on MM correlates with its ability to down-regulate the ALOX5 levels. In addition, DZNep insensitivity might be associated with overexpression of Bcl-2, and the combination of ABT-737 and DZNep could synergistically induced apoptosis. These results suggest that DZNep may be exploited therapeutically for a subset of MM.

overall_design: Cells were treated with 0.5 μmol/L DZNep for 48 h. Total RNA was extracted by using the Qiagen RNeasy Mini kit (Germany). Gene expression was performed using the GeneChip® Human Genome U133A Array (Affymetrix) following the manufacturer’s instructions. Data analysis was performed using GeneSpring software from Agilent Technologies.

first: Chonglei

last: Bi

first: Gaofeng

last: Huang

first: Wee

last: Chng


title: Expression data from human Wharton's jelly stem cells

status: Public on Jul 06 2011

city: GRANADA

first: MIGUEL

last: ALAMINOS

address: AV. INVESTIGACION 11, FAC. MEDICINA PTS

department: HISTOLOGY

institute: UNIVERSITY OF GRANADA

summary:
Human umbilical cord Wharton’s jelly stem cells (WHJSC) are gaining attention as a possible clinical source of mesenchymal stem cells for use in cell therapy and tissue engineering due to their high accessibility, expansion potential and plasticity. However, the cell viability changes that are associated to sequential cell passage of these cells are not known. In this analysis, we have identified the gene expression changes that are associated to cell passage in WHJSC.
We used microarrays to detail the global programme of gene expression underlying cell passage on WHJSC.

overall_design: Total RNA was isolated from three different samples corresponding to cell cultures of three different individuals at each cell passage (P1 to P10) of WHJSC.

first: Ingrid

last: Garzón

first: Barbara

last: Pérez-Köhler

first: Victor

last: Carriel

first: Deyanira

last: Serrato

first: Renato

last: Nieto-Aguilar

first: Amparo

last: Montalvo

first: Natalio

last: García-Honduvilla

first: Julia

last: Buján

first: Antonio

last: Campos

first: Miguel

last: Alaminos


title: Expression profiling of human T-LL cell line CUTLL1

city: Boston

first: James

last: Zou

address: 185 Cambridge St.

institute: Harvard University

summary:
Notch is normally activated by cleavage and nuclear translocation of its intracellular domain (ICN1), which turns on downstream target genes. Human T cell acute lymphoblastic leukemia (T-ALL), an aggressive immature T cell malignancy, is associated with Notch 1 gain-of-function mutations in more than 50% of the cases. Efforts to date to identify direct Notch1 targets have been confounded by the lack of a method to turn Notch1 on in a controlled fashion in T-ALL cells that are poised to respond to Notch signals. Of note, because Notch signaling activates transcriptional repressors that feedback to dampen the expression of many target genes (a process referred to as incoherent logic), it is likely that many direct targets are missed in Notch off analyses, which are further complicated by an inability to identify direct targets in a clear-cut fashion. We have overcome this limitation by developing a GSI washout method that results in the rapid translocation of activated Notch1 to the nucleus. We intend to use this method to study the assembly and loading of transcriptional complexes onto downstream targets, the kinetics of target activation. To date, our efforts have been devoted to comparing the gene expression signature of Notch-on and Notch-off in the human T-ALL cell line CUTLL. In addition to previously identified Notch1 target genes, we have also identified a series of novel genes upregulated by GSI washout in the presence of cycloheximide, suggesting that they are likely to be direct targets.
Additional controls included transduction of cells with dominant negative MAML1, a specific antagonist of canonical Notch1 signaling, prior to Notch1 reactivation, and a mock GSI  washout to control for cycloheximide effects.

overall_design: CUTLL1 cells are cultured in triplicates with different treatments. Total RNA was prepared and hybridized to Affymetrix human U133 plus 2.0 microarrays

first: Hongfang

last: Wang

middle: Y

first: Jon

last: Aster


title: Transcriptomes of monocyte-derived DCs stimulated with various compounds

city: Nijmegen

first: Bastiaan

last: Jansen

address: PO Box 9101

department: Tumor Immunology

institute: Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Center Nijmegen

summary:
Little is known about the early transcriptional events in innate immune signaling in immature and tolerogenic monocyte-derived dendritic cells (DCs), the professional antigen-presenting cells of our immune system. TLR ligands usually induce a proinflammatory transcriptional response, whereas IL10 and/or dexamethasone induce a more tolerogenic phenotype.
We used Affymetrix microarrays to obtain detailed information underlying pro- and anti-inflammatory transcriptional responsesand transcriptional networks in DCs

overall_design: A pilot experiment was performed in which monocyte-derived DCs were either treated with TLR4 ligand LPS, or IL10 and dexamethason. Furthermore, IL10/dexamethason treated cells were also stimulated with LPS for an additional 6 hr. All samples were then subjected to global gene expression analysis using Affymetrix technology.

first: Dagmar

last: Eleveld-Trancikova

first: Maaike

last: van Hout-Kuijer

first: Gosse

last: Adema

first: Iziah

last: Sama

first: Huynen

last: Martijn


title: Transcriptomes of human bladder cells and cells in bladder cancer

city: Seattle

first: Alvin

last: Liu

state: WA

address: 815 Mercer Street Box 358056

department: Urology

institute: University of Washington

summary: Characterization of the gene expression profiles of specific cell populations of the human urinary bladder provides an important set of research tools for the study of cellular differentiation and the cancer process. The transcriptome is a definitive identifier of each individual cell types. Surgically resected tissue was digested by collagenase and the different cell types were sorted by antibodies to cluster designation (CD) cell surface antigens. The sorted cells were analyzed by DNA microarrays. The transcriptome datasets were analyzed for differentially expressed genes and plotted on a principal components analysis space for cell lineage relationship. The following bladder cell types were analyzed: CD9+ urothelial, CD104+ basal, CD13+ stromal of lamina propria, CD9+ urothelial carcinoma cancer, and CD13+ urothelial carcinoma-associated stromal. Gene expression differences between the cell types of tumor and their respective non-cancer counterpart provide biomarker candidates. Basal cells of the bladder and prostate, although sharing CD cell surface markers, are quite different in overall gene expression. Furthermore, these cells lack transcript features of stem cell signature of embryonic stem or embryonal carcinoma cells. Cell type-specific transcriptomes are more informative than bulk tissue transcriptomes. The relatedness of different cell types can be determined by transcriptome dataset comparison.

overall_design: Bladder cell types were sorted from tissue specimens, and analyzed by DNA microarrays. The various transcriptomes were compared by principal components analysis for cell lineage relationship.


title: Gene expression profiling of prostate epithelial cells in response to tissue contextual changes

status: Public on Jul 03 2011

city: Tainan city

first: Jimmy

middle: Jiun-Ming

last: Su

address: 1F,No 367,Sheng-Li Rd. North District

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes,Taiwan

summary: To conduct comparative transcriptomic analyses on normal or malignant prostate epithelial cells in response to tissue contextual changes, we cultured immortalized prostate epithelial cells or prostate cancer cells as cell monolayers or three-dimensional organoids and profiled their transcriptomes in respective culture contexts.

overall_design: RWPE-1 (immortalized prostate epithelial cells) and LNCaP cells (prostate cancer cells) were seeded on reconstituted basement membrane (rBM)-coated culture plastics or cultured within three-dimensional (3D) rBM gels. Total RNA samples were collected from cell monolayers or 3D cell clusters (formed at day 2) or acini or spheroids (formed at day 6) in the rBM culture, followed by global gene expression profiling.

first: Kelvin

middle: K

last: Tsai


title: Inhibition of nonsense-mediated RNA decay by the tumor microenvironment promotes tumorigenesis

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

summary: Nonsense-mediated RNA decay (NMD) is regulated by a variety of cellular stresses.  We expose U2OS cells to several stresses and assess RNA expression in the absence of transcription (i.e. stability). These studies identify transcripts that are stabilized by the physiological inhibition of NMD.

overall_design: U2OS cells rendered hypoxia for three hours, treated with tunicamycin for three hours, treated with emetine for three hours, or depleted of Upf1/Rent1 were treated with DRB, and RNA was collected at 0, 1.5, 3 and 4.5 hrs.

first: Ding

last: Zavadil

first: Leenus

last: Martin

first: Fabio

last: Parisi

first: Eugene

last: Friedman

first: David

last: Levy

first: Heather

last: Harding

last: Ron

first: Lawrence

last: Gardner


title: Changes in follistatin levels by BRCA1 may serve as a regulator of ovarian carcinogenesis

status: Public on Jul 02 2011

city: Washington

first: Xin

middle: James

last: Li

state: DC

address: 4000 Reservoir Rd Suite 180

country: USA

institute: Georgetown University

summary: Follistatin is a folliculogenesis regulating protein that has been found in relatively high concentration in the female ovarian tissues. Follistatin acts as an antagonist to the function of Activin, which is often found elevated in ovarian carcinogenesis and thus presents a possibility for therapeutic intervention in controlling ovarian cancer. Most of the ovarian cancer occurs in its ovarian surface epithelium (OSE) cells. Although breast cancer susceptibility gene 1 (BRCA1) is a known tumor suppressor for breast cancer but its role in ovarian cancer is beginning to unfold. We have shown that in ovarian carcinoma cells (SKOV3), stable overexpression of BRCA1 stimulates Follistatin secretion and simultaneously downregulates Activin expression. Moreover, knock down of BRCA1 in immortalized OSE (IOSE) cells from human ovarian tissue demonstrates downregulation of Follistatin secretion with simultaneous up regulation of Activin expression. IOSE cells generated from an ovarian cancer patient with BRCA1 mutation failed to secrete Follistatin in the medium. Our results indicate a novel function for BRCA1 in the form of regulation of the expression of Follistatin in the ovarian cells.

overall_design: 3 treatments vs 3 controls

first: Anju

last: Preet

first: Tejaswita

last: Karve

first: Rosie

last: Sneed

first: Clara

last: Salamanca

first: Jingwen

last: Xu

first: Deepak

last: Kumar

first: Eliot

last: Rosen

first: Tapas

last: Saha


title: Stimulation of BL2 cell line with lipopolysaccharide (LPS) for 6h

status: Public on Jul 01 2011

city: Regensburg

first: Matthias

last: Maneck

address: Franz-Josef-Strauß-Allee 11

department: Department of Pathology

institute: University of Regensburg

summary: Identification of genes up or down regulated in LPS stimulated samples in comparison to control samples.

overall_design: 3 LPS stimulated samples vs. 3 controls were analyzed

first: Alexandra

last: Schrader

first: Dieter

last: Kube

first: Rainer

last: Spang


title: Expression data for MCF-7 treated with PolII inhibitors, Triptolide or alpha-amanitin

city: Taipei

first: Ming-Ta

last: Hsu

address: No.155, Sec.2, Linong Street

institute: National Yang Ming University

summary: Transcription of mRNA in mammalian is mainly performed by RNA polymerase II (PolII). POLRMT is responsible for the production of cytoplasmic and nuclear form of mitochondrial RNA polymerase. The former (mtRNAP) participates in transcription of RNA in the mitochondria while the latter (spRNAP-IV) is responsible for some mRNA transcription in the nucleus. The nature and amount of genes transcribed by spRNAP-IV still remains unclear. Thus, we scanned for possible candidate genes by using Affymetrix.

overall_design: MCF7 cells were cultured in RPMI medium supplemented with 10% fetal bovine serum. To determine the inhibition of PolII transcription, cells were cultured in the presence of 10 μg/ml of alpha-amanitin or 0.3μM of triptolide (Sigma) for 48 or 24 h, respectively.

first: Yu-Ling

last: Lee


title: Expression data for HUVSMC treated with Triptolide

overall_design: HUVSMC cell line was treated with or without 0.3 uM of Triptolide (an inhibitor of PolII) for 24 hours to determine which genes are insensitive to triptolide treatment.


title: Expression data for knockdown of POLRMT or RNA PolII in MCF-7 cell line

overall_design: MCF-7 cell line was subjected to siRNA knockdown of either non-targeting, POLRMT, or PolII for 72 hours


title: Bmpr2 mutation in murine PMVEC

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

summary:
Pulmonary arterial hypertension (PAH) is thought to be driven by dysfunction of pulmonary vascular microendothelial cells (PMVEC). Most hereditary PAH is associated with BMPR2 mutations.
However, the physiologic and molecular consequences of expression of BMPR2 mutations in PMVEC are unknown.

overall_design: PMVEC were isolated from triple transgenic mice carrying the immortomouse gene, a transactivator, and either control, Bmpr2delx4+ or Bmpr2R899X mutation

first: Tom

last: Blackwell


title: Transcription of muscle actin genes by a nuclear form of mitochondrial RNA polymerase

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

overall_design: Refer to individual Series


title: ChIP-seq defined genome-wide map of TGFbeta/SMAD4 targets: implications with clinical outcome of ovarian cancer patients

city: Columbus

first: Brian

middle: Alexander

last: Kennedy

state: Ohio

address: 278 Chittenden AVE

institute: The Ohio State University

summary: Deregulation of the transforming growth factor-β (TGFβ) signaling pathway in epithelial ovarian cancer has been reported, but the precise mechanism underlying disrupted TGFβ signaling in the disease remains unclear. We performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) to investigate genome-wide screening of TGFβ-induced SMAD4 binding in epithelial ovarian cancer. Following TGFβ stimulation of the A2780 epithelial ovarian cancer cell line, we identified 2,362 SMAD4 binding loci and 318 differentially expressed SMAD4 target genes. Comprehensive examination of SMAD4-bound loci, revealed four distinct binding patterns: 1) Basal; 2) Shift; 3) Stimulated Only; 4) Unstimulated Only. SMAD4-bound loci were primarily classified as either Stimulated only (74%) or Shift (25%), indicating that TGFβ-stimulation alters SMAD4 binding patterns in epithelial ovarian cancer cells compared to normal epithelial cells. Furthermore, based on gene regulatory network analysis, we determined that the TGFβ-induced SMAD4-dependent regulatory network was strikingly different in ovarian cancer compared to normal cells. Importantly, the TGFβ/SMAD4 target genes identified in the A2780 epithelial ovarian cancer cell line were predictive of patient survival, based on in silico mining of publically available patient data bases. In conclusion, our data highlight the utility of next generation sequencing technology to identify genome-wide SMAD4 target genes in epithelial ovarian cancer. The results link aberrant TGFβ/SMAD signaling to ovarian tumorigenesis. Furthermore, the identified SMAD4 binding loci, combined with gene expression profiling and in silico data mining of patient cohorts, may provide a powerful approach to determine potential gene signatures with biological and future translational research in ovarian and other cancers.

overall_design:
ChIP-Seq: 1 control lane.  4 unstimulated lanes 4 stimulated lanes

Gene expression: 3 technical replicates each of SMAD4 stimulated and SMAD4 unstimulated cells

middle: A

first: Daniel

last: Deatherage

first: Fei

last: Gu

first: Binhua

last: Tang

first: Michael

middle: W

last: Chan

first: Kenneth

middle: P

last: Nephew

first: Tim

last: Huang

first: Victor

middle: X

last: Jin


title: PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

summary: Histone methylation occurs on both lysine and arginine residues and its dynamic regulation plays a critical role in chromatin biology. Here we identify the UHRF1 PHD domain (PHDUHRF1), an important regulator of DNA CpG methylation, as an unanticipated histone H3 unmodified arginine 2 (H3R2)-recognition modality. This conclusion is based on binding studies and co-crystal structures of the PHDUHRF1 bound to histone H3 peptides, where the guanidinium group of unmodified R2 forms an extensive intermolecular hydrogen bond network, with methylation of H3R2, but not H3K4 or H3K9, disrupting complex formation. We have identified direct target genes of UHRF1 from microarray and ChIP studies. Importantly, we show that UHRF1’s ability to repress its direct target gene expression is dependent on PHDUHRF1 binding to unmodified H3R2, thereby demonstrating the functional importance of this recognition event and supporting the potential for crosstalk between histone arginine methylation and UHRF1 function.

overall_design: UHRF1 protein was depleted in HCT116 cells by shRNA treatment. Total RNA was purified and used to determine the global gene transcription profiles by microarray assays. The UHRF1-regulated genes were identified by comparing the  gene expression profiles of control and UHRF1-depleted HCT116 cells.

first: Zhentian

last: Wang

first: Honghui

last: Ma

first: Yang

last: Shi


title: Reversal of Atopic Dermatitis with Narrow-Band UVB Phototherapy and Biomarkers for Therapeutic Response

city: New York

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: Background: Atopic dermatitis (AD) is a common inflammatory skin disease exhibiting a predominantly Th2/“T22” immune activation and a defective epidermal barrier. Narrow-band UVB (NB-UVB) is considered an efficient treatment for moderate to severe AD. In psoriasis, NB-UVB has been found to suppress the Th1/Th17 immune polarization with subsequent reversal of epidermal hyperplasia. The immunomodulatory effects of this treatment are largely unknown in AD. Our study evaluates the effects of NB-UVB on immune and barrier abnormalities in AD, aiming to establish reversibility of disease and biomarkers of therapeutic response.  Methods: 12 moderate-to-severe chronic AD patients received NB-UVB phototherapy 3 times weekly for up to 12 weeks. Lesional and non-lesional skin biopsies were obtained before and after treatment and evaluated by gene-expression and immunohistochemistry studies.  Results: All patients had at least a 50% reduction in SCORing of AD (SCORAD) index with NB-UVB phototherapy. The Th2, T22, and Th1 immune pathways were suppressed and measures of epidermal hyperplasia and differentiation also normalized after phototherapy. The reversal of disease activity was associated with elimination of inflammatory leukocytes, Th2/“T22”-associated cytokines and chemokines, and normalized expression of barrier proteins.  Conclusions: Our study shows reversal of both the epidermal defects and underlying immune activation in AD.  By determining the correlation of variables with therapeutic response, we have defined a set of biomarkers of disease response that associate resolved Th2 and T22 inflammation with reversal of barrier pathology. This data supports the “inside-out” hypothesis of AD, suggesting that it is a disease primarily driven by an immune stimulus.

overall_design:
genomic profiling of treatment effect of NB-UVB in AD in both lesional and non-lesional AD skin from 10 patients.
Treatment effect , disease state analysis

last: Suárez-Fariñas

first: Emma

last: Guttman-Yasky


title: Inflammation leads to loss of smooth muscle cells but fails to induce invasiveness in a prostate tumor model

city: Vienna

first: Andreas

last: Birbach

address: Schwarzspanierstrasse 17

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Medical University of Vienna

summary: Inflammation has a causal role in many cancers. In prostate cancers, epidemiological data suggest a link between prostatitis and subsequent cancer development, but a proof for this concept in a tumor model has been lacking. A constitutively active version of the IkappaB kinase 2 (IKK2), the molecule activated by a plethora of inflammatory stimuli, was expressed specifically in the prostate epithelium. Signaling of the IKK2/NF-kappaB axis was insufficient for transformation of prostate tissue. However, while PTEN+/- epithelia exhibited intraepithelial neoplasias only recognizable by nuclear alterations, additional IKK2 activation led to an increase in tumor size and formation of cribriform structures and to a fiber increase in the fibroblastic stroma. This phenotype was coupled with inflammation in the prostate gland characterized by infiltration of granulocytes and macrophages. Molecular characterization of the tissues showed a specific loss of smooth muscle markers as well as expression of chemokines attracting immune cells. Isolation of epithelial and stromal cells showed differential chemokine expression by these cells. Correlation studies showed the inflammatory phenotype coupled to loss of smooth muscle in infiltrated glands, but maintenance of the phenotype in glands where inflammation had decreased. Despite the loss of the smooth muscle barrier, tumors were not invasive in a stable genetic background. Data mining revealed that smooth muscle markers are downregulated in human prostate cancers and literature data show that loss of these markers in primary tumors is associated with subsequent metastasis. Our data show that loss of smooth muscle and invasiveness of the tumor are not coupled. Thus, inflammation during early steps of tumorigenesis can lead to increased tumor size and a potential change in the subsequent metastatic potential, but the tumor requires an additional transformation to become a carcinoma.

overall_design: Microarray analysis was used to determine expression differences in lateral prostates from mice with PTEN+/- IKK2ca/ca epithelium (n=3) compared to lateral prostates from mice with PTEN+/- epithelium (n=3).