title: Functional analyses of miR-210 involvement in the aggressive phenotype of high grade breast tumors

city: brussels

first: Françoise

last: Rothé

address: boulevard de waterloo 127

country: Belgium

institute: Jules Bordet Institute

summary: As miR-210 expression is correlated to poor prognosis both in estrogen-positive and in estrogen-negative breast cancer (BC) patients, we aimed to investigate the biological processes regulated by miR-210 and which may elucidate its function in the aggressive phenotype of high grade breast cancer. We performed in silico functional analyses of the genes deregulated upon miR-210 overexpression in MCF7 BC cell line and upon miR-210 repression in MDA-MB-231 BC cell line using lentiviral transduction. Gene expression profiling analysis of these cells revealed the deregulation of genes involved in several biological pathways including cell adhesion, extracellular structure organization, epithelial cell proliferation, cell division, cell cycle and immune response.

overall_design: MCF-7 cells overexpressing miR-210 (or control) and MDA-MB-231 cells in which miR-210 (or control) is repressed were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Carole

last: Chaboteaux

first: Samira

last: Majjaj

first: Naima

last: Kheddoumi

first: Martine

last: Piccart

first: Christos

last: Sotiriou


title: A Novel Pro-Survival Function of Cyclin-D1 Underlies Its Oncogenic Role and Potential as a Therapeutic Target in Human and Murine Mantle Cell Lymphoma

status: Public on Jul 01 2011

city: Pamplona

first: Vicente

middle: Jose

last: Fresquet

state: Navarra

address: Av Pio XII 55

department: Division of Oncology

country: Spain

institute: Center for Applied Medical Research (Cima)

summary: The chromosomal translocation t(11;14)(q13;q32) leading to cyclin-D1 over-expression plays an essential role in the development of mantle cell lymphoma (MCL), an aggressive tumor that   remains incurable with current therapies. Cyclin-D1 has been postulated as an effective therapeutic target, but its evaluation has been hampered by our incomplete understanding of its oncogenic functions and by the lack of valid MCL murine models. To address these issues, we generated a cyclin-D1-driven mouse model whereby cyclin-D1 expression can be externally regulated. These mice developed lymphomas capable of recapitulating most features of human MCL. We found that cyclin-D1 inactivation was not sufficient to induce lymphoma regression in vivo. However, using a combination of in vitro and in vivo assays, we identified a novel pro-survival cyclin-D1 function in MCL cells. Specifically, we demonstrate that cyclin-D1 sequestrates the pro-apoptotic protein BAX, thereby favoring BCL2 anti-apoptotic function. Accordingly, cyclin-D1 inhibition sensitized the lymphoma cells to apoptosis through BAX release. Thus, genetic or pharmacologic targeting of cyclin-D1 combined with a pro-apoptotic BH3 mimetic synergistically killed murine lymphomas and human MCL cells. Our study identifies a novel role of cyclin-D1 in deregulating apoptosis and highlights the potential benefit of simultaneously targeting cyclin-D1 and survival pathways in patients with MCL.

overall_design: Dose response involving 20 samples. Two replicates for each cell line, 4 cell lines sensitive to ABT-737 and 6 cell lines resistant to ABT-737. Mantel cell lymphoma cell lines sensitive to ABT-737 vs. Mantel cell lymphoma cell lines resistant to ABT-737

first: Elena

last: Beltran

first: Javier

last: Martinez-Useros

first: Jose

middle: A

last: Ritcher-Larrea

first: Ainara

last: Sagardoy

first: Izaskun

last: Sesma

first: Luciana

middle: L

last: Almada

first: Santiago

last: Montes-Moreno

first: Reiner

last: Siebert

first: Stefan

last: Gesk

first: Maria

middle: J

last: Calasanz

first: Raquel

last: Malumbres

first: Felipe

last: Prosper

first: Miguel

last: Piris

first: Martin

middle: E

last: Fernandez-Zapico

last: Martinez-Climent


title: Differential gene expression in SN12C.19 renal cells with insertion of the chromosomal 3p arm

city: Houston

first: Nanyue

last: Chen

state: TX

address: 1515 Holcombe Blvd

country: USA

institute: UT MD Anderson Cancer Center

summary:
SN12C.19 is a renal carcinoma cell line with loss of heterozygosity in the 3p chromosomal region near the centromere.  It is believed that a tumor suppressor gene is located in this region.  In studies with athymic nude mice, tumor formation followed injection of SN12C.19 cells.  Tumor formation did not follow by injection of the hybrid cell line SN19(3i)YY, which includes a very small fragment insertion of the 3p chromosomal arm.  The goal of this array experiment was to identify genes differentially expressed in SN12C.19 by the introduction of a normal copy of the chromosomal 3p arm.
SN12C.19 and SN19(3i)YY cells were hybridized to Affymetrix U133 Plus 2.0 Chips.  Array quality was inspected with output from dChip software.  Gene expression was quantified with PDNN software.  There were 57 probesets showing differential expression on the 3p arm, corresponding to 46 genes.

overall_design: A suppression subtractive hybridization (SSH) library was previously constructed using as starting materials microcell hybrid clones which mapped the NRC-1 locus and containing defined fragments of chromosome 3p12 which were either suppressed or unsuppressed for tumorigencity following injection of microcell hybrid clones into athymic nude mice

first: Ann

middle: M

last: Killary


title: Ascl1, Nurr1 and Lmx1 convert mouse and human fibroblasts into functional dopaminergic neurons without passing through an intermediate precursor state

status: Public on Jul 04 2011

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

summary: Lineage-specific transcription factors, which drive cellular identity during embryogenesis, have been shown to convert cell fate when express ectopically in heterologous cells. Herein, we screened the key molecular factors governing the dopaminergic neuronal specification during brain development for their ability to generate similar neurons directly from mouse and human fibroblasts. Remarkably, we found a minimal set of three factors Mash1, Nurr1 and Lmx1a/b able to elicit such cellular reprogramming. Molecular and transcriptome studies showed reprogrammed DA neurons to faithfully recapitulate gene expression of their brain homolog cells while lacking expression of other catecholaminergic neuronal types. Induced neurons showed spontaneous electrical activity organized in regular spikes consistent with the pacemaker activity featured by brain DA neurons. The three factors were able to elicit DA neuronal conversion in human fibroblasts from prenatal or adult fibroblasts of healthy donors and a Parkinson’s disease patient. Generation of DA induced neurons from somatic cells might have significant implications in studies of neural development, disease in vitro modeling and cell replacement therapies.

overall_design: We infected mouse embryonic fibroblasts (MEFs) isolated from TH-GFP knock-in mice embryos at E14.5, with lentiviruses expressing the three dopaminergic transcription factors  Ascl1, Lmx1a and Nurr1. TH-GFP MEFs infected (Ind) by a pool of the three previously mentioned dopaminergic lentiviruses were shifted in a neuronal medium for 12 days and  sorted for GFP-positive cells. Thus we extracted mRNA from Ind-GFP-positive cells and compared them to not infetced (NI) cells by means of RNA-microarray analysis.

first: Massimiliano

last: Caiazzo

first: Dejan

last: Lazarevic

first: Stefano

last: Gustincich

first: Vania

last: Broccoli


title: Expression data from peripheral blood mononuclear cells in multiple sclerosis patients and controls

city: Cambridge

first: Anu

last: Kemppinen

address: Addenbrooke's Hospital, Hills Road

country: United Kingdom

institute: University of Cambridge

summary:
Multiple sclerosis (MS) is a neurodegenerative disease with a presumed autoimmune component. Expression profiling in immune cells can therefore be used in order to identify genes and pathways involved in MS pathogenesis.
We conducted a genome-wide expression study in peripheral blood mononuclear cells (PBMC) from 12 MS patients and 15 controls in order to identify differentially expressed genes and pathways in MS.

overall_design: PBMCs were isolated from whole blood and total RNA was extracted.

first: Janna

last: Saarela


title: Differentiation of NUT midline carcinoma by epigenomic reprogramming

city: boston

first: Chris

last: French

state: MA

address: 75 francis st.

department: Pathology

institute: BWH

summary: Knockdown of the oncogene, BRD4-NUT, in a rare cancer, termed NUTmidline carcinoma (NMC), results in morphologic features consistent with squamous differentiation.  Treatment with the HDAC-inhibitor, TSA, appears to cause the same phenotype.  Here, we use gene expression profiling to compare the changes in gene expression following BRD4-NUT knockdown and TSA treatment.

overall_design: RNA was extracted from two BRD4-NUT-expressing NMC cell lines, PER-403 and TC-797, 24h following siRNA knockdown versus control in duplicate. RNA was extracted from two BRD4-NUT-expressing NMC cell lines, PER-403 and TC-797,  24h following treatment with TSA versus etoh control in triplicate

first: Brian

last: Schwartz

first: Matthias

middle: D

last: Hofer

first: Madeleine

last: Lemieux

first: Daniel

last: Bauer

first: Michael

last: Cameron

first: Nathan

middle: H

last: West

first: Elin

middle: S

last: Agoston

first: Nicolas

last: Reynoird

first: Saadi

last: Khochbin

first: Tan

last: Ince

first: Amanda

last: Christie

first: Katherine

last: Janeway

first: Sara

middle: O

last: Vargas

first: Antonio

middle: R

last: Perez-Atayde

first: Jon

middle: C

last: Aster

first: Stephen

last: Sallan

first: Andrew

last: Kung

first: James

last: Bradner

first: Christopher


title: Blood genomic expression profile for Behçet’s disease.

city: Lisbon

first: Sofia

last: Oliveira

state: Portugal

address: Av. Prof Egas Moniz

department: Edificio Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

summary:
Behçet’s disease (BD) is a multisystemic immuno-inflammatory disorder characterized by a generalized vasculitis, particularly at the orogenital mucosa and eye. It is a complex disease with unclear pathogenesis.
To better understand BD´s etiology, we performed genomic expression profiling of patients and controls.

overall_design: Gene expression profiling was performed in peripheral blood mononuclear cells (PBMCs) of 15 patients and 14 sex- and age-matched controls using Affymetrix microarrays. The ages of the patients and controls do not match on a one-to-one basis, but they match very well on average. The average age at examination of cases and controls is 37y.

first: Tiago

last: Krug

first: Joana

last: Xavier

first: Benedita

middle: V

last: Fonseca

first: Gorete

last: Jesus

first: Filipe

last: Barcelos

last: Vedes

first: Manuel

last: Salgado

first: José

last: Patto

first: Jorge

last: Crespo


title: Novel HLA ligands and Tcell epitopes for immunotherapy of lung cancer

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

country: Germany

institute: University Tuebingen

summary: Analysis of gene expression data to evaluate candidate targets for immunotherapy.

overall_design: Analysis of gene expression data to evaluate candidate targets for immunotherapy, We analyse 7 lung cancer samples and 3 reference samples (2x kidney, 1x lung).

first: Anneke

last: Neumann

first: Stefan

last: Stevanović

first: Bonin

last: Michael


title: Expression data from interleukin-stimulated HUVEC

city: Berlin

first: Gürkan

last: Bal

address: Augustenburger Platz 1

department: Institute for Transfusion Medicine

institute: Charité - Universitätsmedizin Berlin

summary:
In the hematopoietic microenvironment, endothelial cells (ECs) play an important role in the regulation of hematopoietic cell proliferation and trafficking. We previously demonstrated that EC stimulated with tumor necrosis factor alpha (TNF-α) induce the generation of dendritic cells from CD34(+) stem cells, whereas in contrast, interleukins were capable of inducing the proliferation of hematopoietic and myeloid progenitors.
In order to identify potentially new soluble factors which greatly impact the self-renewal, proliferation and differentiation of CD34+ hematopoietic stem cells (HSC), we examined the expression profiles of IL-1ß, IL-3 and IL-6 stimulated human umbilical vein endothelial cells (HUVEC).

overall_design: we processed seven different umbilical cords and isolated 129 samples for total RNA, and pooled them into 18 groups corresponding to each stimulant, control and time point.

first: Thomas

last: Häuple

first: Matthias

last: Futschik

first: Anja

last: Moldenhauer


title: Global gene-expression profiles analysis of iPSCs

status: Public on Jun 30 2011

city: Beijing

first: Yixuan

last: Wang

address: No. 7, Science Park Road, Zhongguancun Life Science Park

country: China

institute: National Institute of Biological Sciences, Beijing, China

summary: Global gene-expression profiles analysis of hESCs, patient-specific iPSCs, gene-corrected iPSCs, and patient fibroblast cells.

overall_design: Affymetrix GeneChip® Human Genome U133 plus 2.0 Array (Affymetrix, Inc.) was used for microarray hybridizations to examine the global gene expression of hES cells, piPS7 cells, ciPS5 cells and patient fibroblast cells. Briefly, total RNA was isolated using Trizol reagent (Invitrogen). cDNA was synthesized and amplified with WT cDNA Synthesis and Amplification Kit (Affymetrix, Inc.), labeled with biotin using WT Terminal Labeling Kit (Affymetrix, Inc.), hybridized to Affymetrix GeneChip® Human Genome U133 plus 2.0 Array and analyzed by GeneChip® Scanner 3000 7G3000 (Affymetrix, Inc.). All samples were prepared in three biological repeats. Data were analyzed using GCOS 1.4 software provided by Affymetrix.

first: Chen-Guang

last: Zheng

first: Yonghua

last: Jiang

first: Jiqin

last: Zhang

first: Jiayu

last: Chen

first: Chao

last: Yao


title: Expression in Huh7 cells 72 hours after treatment with scramble, SPTLC123, or DEGS siRNA

city: Groton

first: Wanida

last: Ruangsiriluk

state: CT

address: Eastern Point Road

department: CVMED

institute: Pfizer Inc.

summary: Dysregulation of ceramide synthesis has been associated with metabolic disorders such as atherosclerosis and diabetes mellitus. Using a human hepatoma cell line (Huh7), we investigated the changes in lipid homeostasis and gene expression when the synthesis of ceramide is perturbed by knocking down serine transferases subunits 1, 2 and 3 (SPTLC123) or dihydroceramide desaturase (DEGS1). While the inhibition of serine palmitoyl transferase (SPTLC) affects ceramide production differently at the subspecies level depending upon which SPTLC subunit is silenced; depleting DEGS1 is sufficient to produce a similar outcome as knocking down all SPTLC subunits. Both the distribution of multiple lipid classes, especially at the subspecies level, and the global transcriptional profile is altered differently when either SPTLC123 or DEGS1 were silenced. The overall transcriptional changes indicate a negative regulation in biosynthetic processes and a down-regulation of genes involved in general endomembrane trafficking for both DEGS1 and SPTLC123 siRNA treated cells, but also the up-regulation of genes involved with cell migration function in DEGS1 siRNA cells. Pathway analysis indicate changes in amino acid, sugar and nucleotide metabolisms as well as vesicle trafficking between organelles occurred more robustly in DEGS1 silenced cells. Although either SPTLC123 or DEGS1 siRNA treatment positively regulated numerous genes involved with endocytosis and endosomal recycling, depleting SPTLC123 caused transcriptional changes in genes primarily involved with lipid metabolism. The alterations reflect how SPTLC or DEGS1 silenced cells respond differently to disruption in lipid flux, but also maintain cellular lipid pools through increasing endocytotic processes and down-regulating metabolic biosynthesis without developing endoplasmic reticulum stress. Also, these results are the first to demonstrate that reducing ceramide synthesis by decreasing the function of either SPTLC or DEGS1 affects cellular function differently at the level of lipid synthesis and gene expression.

overall_design: Differential gene expression was assessed by Affymetrix microarray experiments for 9 Huh7 cell samples across 3 siRNA treatment groups (scramble siRNA conrol had 3 samples, SPTLC123 siRNA had 3 samples, DEGS1 siRNA had 3 samples)

first: Shaun

last: Grosskurth

first: Omar

last: Francone

first: Max

last: Kuhn

first: Shelley

middle: G

last: des Etages

first: Daniel

last: Ziemek


title: Expression of HOXB genes is significantly different in acute myeloid leukemia with a partial tandem duplication of MLL vs. a MLL translocation: a cross-laboratory study

city: Taipei

first: Hsi-Che

last: Liu

address: No. 92, Sec. 2, Chung-San North Rd.

country: Taiwan

institute: Mackay Memorial Hospital

summary: In acute myeloid leukemia (AML), the mixed lineage leukemia (MLL) gene may be rearranged to generate a partial tandem duplication (PTD), or fused to partner genes through a chromosomal translocation (tMLL). In this study, we first explored the differentially expressed genes between MLL-PTD and tMLL using gene expression profiling of our cohort (15 MLL-PTD and 10 tMLL) and one published data set. The top 250 probes were chosen from each set, resulting in 29 common probes (21 unique genes) to both sets. The selected genes include four HOXB genes, HOXB2, B3, B5, and B6. The expression values of these HOXB genes significantly differ between MLL-PTD and tMLL cases. Clustering and classification analyses were thoroughly conducted to support our gene selection results. Second, as MLL-PTD, FLT3-ITD, and NPM1 mutations are identified in AML with normal karyotypes, we briefly studied their impact on the HOXB genes. Another contribution of this study is to demonstrate that using public data from other studies enriches samples for analysis and yields more conclusive results.

overall_design: 25 bone marrow samples of acute myeloid leukemia patients were hybridized to Affymetrix HG-U133 plus 2 GeneChips.

first: H-C

first: L-Y

last: Shih

first: M-J

first: C-C

first: T-C

last: Yeh

first: T-H

last: Lin

first: C-Y

first: C-J

first: D-C

last: Liang


title: Expression data from mouse heart with and without GATA4 S105A mutation; with and without adrenergic stress

city: Cincinnati

first: Bruce

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

summary:
Serine 105 phosphorylation of GATA4 is necessary for stress-induced cardiac hypertrophy in vivo.
We used microarrays to detail global gene expression program alterations that arise in response to the ablation of the Gata4 S105 phosphorylation site in basal and adrenergic-stressed heart ventricles.

overall_design: Wildtype and genetically engineered mice were subjected to control or pseudoephedrine treatment and heart ventricle RNAs were extracted and hybridized on Affymetrix microarrays. Comparisons consisted of identifying treatment- and genotype-affected gene expression patterns.

first: Jop

last: van Berlo

first: William

middle: T

last: Pu

first: John

last: Elrod

first: Jeffery

last: Molkentin


title: Smoking-induced Disarray of the Apical Junctional Complex Gene Expression Architecture in the Human Airway Epithelium

status: Public on Jun 27 2011

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: The apical junctional complex (AJC), composed of tight junctions and adherens junctions, is essential for maintaining epithelial barrier function. Since cigarette smoking and chronic obstructive pulmonary disease (COPD), the major smoking-induced disease, are both associated with increased lung epithelial permeability, we hypothesized that smoking alters the transcriptional program regulating AJC integrity in the small airway epithelium (SAE), the primary site of pathological changes in COPD. Transcriptome analysis revealed a global down-regulation of physiological AJC gene expression in the SAE of healthy smokers (n=53) compared to healthy nonsmokers (n=59), an observation associated with changes in molecular pathways regulating epithelial differentiation such as PTEN signaling and accompanied by induction of cancer-related AJC genes. Genome-wide co-expression analysis identified a smoking-sensitive AJC transcriptional network. The overall expression of AJC-associated genes was further decreased in COPD smokers (n=23). Exposure of human airway epithelial cells to cigarette smoke extract in vitro resulted in down-regulation of several AJC-related genes, accompanied by decreased transepithelial resistance. Thus, cigarette smoking alters the AJC gene expression architecture in the human airway epithelium, providing a molecular basis for the dysregulation of airway epithelial barrier function during the development of smoking-induced lung disease.

overall_design: The apical junctional complex (AJC), composed of tight junctions and adherens junctions, is essential for maintaining epithelial barrier function. Since cigarette smoking and chronic obstructive pulmonary disease (COPD), the major smoking-induced disease, are both associated with increased lung epithelial permeability, we hypothesized that smoking alters the transcriptional program regulating AJC integrity in the small airway epithelium (SAE), the primary site of pathological changes in COPD. In this study, microarray analysis of the SAE obtained from 53 healthy nonsmokers, 59 healthy smokers, and 23 smokers with COPD was performed to determine physiological AJC gene expression architecture in the SAE and its modification by cigarette smoking and during the development of COPD.

first: Renat

last: Shaykhiev

first: Fouad

last: Otaki

first: Prince

last: Bonsu

first: David

last: Dang

first: Matthew

last: Teater

first: Jacqueline

last: Salit

first: Ben-Gary

last: Harvey

first: Ronald

last: Crystal


title: Transcriptome analysis of normal erythroid progenitors and erythroleukemia cells

status: Public on Jun 23 2011

city: Bronx

first: Sandeep

middle: Nagaraj

last: Wontakal

address: 1300 Morris Park Ave Chanin 402

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: We compared the transcriptomes of ES cell derived erythroid progentor cells (ES-EP) and murine erythroleukemia (MEL) cells stably transfected with Gata-1 fused to ER.

overall_design: RNA was isolated from duplicate proliferating cultures of MEL and ES-EP using Affymetrix GeneChip Mouse Gene 1.0 ST.

middle: N

first: Arthur

middle: I

last: Skoultchi


title: Dendritic cell response to hypoxia and poly I:C

status: Public on Jun 29 2011

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

summary:
Investigation whether hypoxic stabilization of HIF-1alpha quantitatively or qualitatively modifies the gene expression pattern induced by poly I:C, a TLR ligand that does not induce normoxic HIF-1alpha stabilization on its own (non-HIF-1alpha-stabilizing TLR ligand).

Keywords: Comparison of single and combined treatment

overall_design: Bone marrow derived Dendritic Cells from mice were stimulated under normoxic or hypoxic conditions for 16h with media or poly I:C. Total cellular RNA was harvested, labeled and hybridised to Affymetrix Mouse Gene ST 1.0 GeneChips. Cel files were normalized with RMA.

first: Jonathan

last: Jantsch


title: Lack of Toll-like Receptor Signaling Improves Host Defense in Severe Septic Peritonitis in Severe Septic Peritonitis

status: Public on Jun 28 2011

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

institute: Technische Universität München

summary: TLRs are considered important for innate immune responses that combat bacterial infections. Here, the role of TLRs in severe septic peritonitis using the colon ascendens stent peritonitis (CASP) model was examined. We demonstrate that mice deficient for MyD88 and TRIF had markedly reduced bacterial numbers both in peritoneal cavity and peripheral blood, indicating that bacterial clearance in this model is inhibited by TLR signals. Moreover, survival of Myd88-/-;TrifLps2/Lps2 mice was significantly improved. The lack of TLR signals prevented the excessive induction of inflammatory cytokines and of IL 10. Notably, the expression of IFN-gamma, which has an essential protective role in septic peritonitis, and of IFN-regulated genes including several p47 and p65 GTPases as well as IP 10 was independent of TLR signaling. These results provide evidence that, in severe septic peritonitis, TLR deficiency balances the innate immune response in a favorable manner by attenuating deleterious responses such as excessive cytokine release, while leaving intact protective IFN-gamma production.

overall_design: In this dataset, expression data of genes induced by septic peritonitis in spleens from TLR-deficient and wildtype mice are included. 3 groups (septic TLR-deficient mice, septic wildtype mice, and untreated wildtype mice) with 4 replicates each.

first: Bernhard

last: Holzmann


title: Genome-wide Mapping of Imprinted Genes by DNA Methylation Profiling of Human Placentas from Triploidies

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

country: Canada

institute: University of British Columbia

summary: Genome-wide DNA methylation profiling of placentas from diandric and digynic triploidies. DNA methylation profiles across more than 27,000 CpGs were obtained by using the Illumina Infinium 27k Human DNA methylation Beadchip v1.2. Placentas of 10 diandric and 10 digynic triploidies were included.

overall_design: Bisulfite converted DNA from the 20 samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Ryan

middle: K

last: Yuen

middle: P


title: Comparison of gene expression profiles for hormone induction in the presence and absence of AP1 binding.

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

summary: Gene expression array analysis component. Ligand-dependent transcription by the nuclear receptor glucocorticoid receptor (GR) is mediated by interactions with co-regulators. The role of these interactions in determining selective binding of GR to regulatory elements remains unclear.  Recent findings indicate a large fraction of genomic GR binding coincides with chromatin that is accessible prior to hormone treatment, suggesting that receptor binding is dictated by proteins that maintain chromatin in an open state.  Combining nucleolytic cleavage and chromatin immunoprecipitation with high-throughput sequencing, we identify the activator protein 1 (AP1) as a major partner for productive GR-chromatin interactions.  AP1 is critical for GR-regulated transcription and recruitment to co-occupied regulatory elements, illustrating an extensive AP1-GR interaction network. Importantly, the maintenance of baseline chromatin accessibility facilitates GR recruitment and is dependent on AP1 binding.  We propose a model where the basal occupancy of transcription factors act to prime chromatin and direct inducible transcription factors to select regions in the genome.

overall_design: Dexamethasone treatment of cells at zero hour untreated control and 4 hour treatment times, in the absence and presence of acidic-fos (A-fos), an AP1 dominant negative. A-fos expression is under tetracycline control (Tet-Off). This is part of a larger study: Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding. There are 2 replicates per condition per time point.

first: J

first: G

middle: L

last: Hager


title: Transcriptome analysis of E. coli MG1655

status: Public on Jun 14 2011

city: La Jolla

last: Palsson

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary: Expression profiling of wild type and purR deletion strains of E. coli K-12 MG1655 under both M9 minimal media and addition of adenine.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: An eight chip study with two different strains under two separate culture conditions.

first: Byung-Kwan

last: Cho

first: Steve

last: Federowicz

first: Mallory

last: Embree

first: Young-Seoub

last: Park

first: Karsten

last: Zengler


title: Expression data from breast samples of postmenopausal women

status: Public on Jun 17 2011

first: Ilana

last: Belitskaya-Levy

address: 650 First Avenue, 5th Floor

department: Environmental Medicine

institute: New York University School of Medicine

summary: The objective of the study was to comprehensively compare the genomic profiles in the breast of parous and nulliparous postmenopausal women to identify genes that permanently change their expression following pregnancy.

overall_design: The study was designed as a two-phase approach. In the discovery phase, we compared breast genomic profiles of 37 parous with 18 nulliparous postmenopausal women. In the validation phase, confirmation of the genomic patterns observed in the discovery phase was sought in an independent set of 30 parous and 22 nulliparous postmenopausal women.


title: Human endothelial gene expression under estradiol and oxLDL treatments

status: Public on Jun 10 2011

city: Valencia

first: Carlos

last: Hermenegildo

address: Avda. Blasco Ibanez 15

institute: University of Valencia

summary: DNA microarrays were used to investigate global gene expression patterns in cultured human umbilical artery endothelial cells (HUAECs) exposed to 1 nmol/L estradiol and/or 100 µg/ml oxidized low density lipoprotein (oxLDL) for 24 hours compared to control cells.

overall_design: HUAECs from 15 separate cultures were exposed to control (0.1% ethanol), 1nmol/L estradiol, 100 µg/ml oxLDL, or 1nmol/L estradiol + 100 µg/ml oxLDL treatments for 24 h. Total cellular RNA was extracted. Equal amounts of RNA extracted from 3 control cells or 3 estradiol-treated cells obtained from three different cultures were pooled, achieving five biological replicates of the control, five replicates that were treated with estradiol, five replicates that were treated with oxLDL and five replicates that were treated with estradiol+oxLDL . Therefore, a total number of 20 microarrays were developed.

first: Andres

last: Laguna-Fernandez


title: Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids

status: Public on Jun 13 2011

city: Los Angeles

first: Juyong

middle: Brian

last: Kim

address: 675 Charles Young Dr.

department: Department of Medicine

institute: UCLA School of Medicine

summary: Oxidized phospholipids are thought to promote atherogenesis by stimulating endothelial cells (ECs) to produce inflammatory cytokines, such as IL-8. In studies with mouse models, we previously demonstrated that genetic variation in inflammatory responses of endothelial cells to oxidized lipids contributes importantly to atherosclerosis susceptibility. We now show that similar variations occur in cultured aortic ECs derived from multiple heart transplant donors. These variations were stably maintained between passages and, thus, reflect either genetic or epigenetic regulatory differences. Expression array analysis of aortic EC cultures derived from 12 individuals revealed that >1,000 genes were regulated by oxidized phospholipids. We have used the observed variations in the sampled population to construct a gene coexpression network comprised of 15 modules of highly connected genes. We show that several identified modules are significantly enriched in genes for known pathways and confirm a module enriched for unfolded protein response (UPR) genes using siRNA and the UPR inducer tunicamycin. On the basis of the constructed network, we predicted that a gene of unknown function (MGC4504) present in the UPR module is a target for UPR transcriptional activator ATF4. Our data also indicate that IL-8 is present in the UPR module and is regulated, in part, by the UPR. We validate these by using siRNA. In conclusion, we show that interindividual variability can be used to group genes into pathways and predict gene-gene regulatory relationships, thus identifying targets potentially involved in susceptibility to common diseases such as atherosclerosis.

overall_design: Twelve individual HAEC lines were treated in duplicate (in 35-mm dishes) for 4 h in media containing PAPC (40 μg/ml) or oxidized PAPC (OxPAPC) at 20 ug/ml or 40 μg/ml. Cytoplasmic RNA was isolated by using an RNAeasy kit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity. Double-stranded cDNAs were synthesized from total RNA by using the cDNA Synthesis System (Invitrogen, Carlsbad, CA). Biotin-labeled cRNA was generated and used to probe Affymetrix (Santa Clara, CA) Human Genome U133 Plus 2.0 arrays according to the manufacturer’s recommendations (Affymetrix). The Microarray Suite 5.0 software (Affymetrix) was used to analyze image data and make the absolute call for each measurement. The array data were normalized with the median invariant method (31).

first: Bin

last: Zhang

first: Peter

last: Gargalovic


title: Establishment of human trophoblast progenitor cell lines from the chorion

status: Public on Jun 22 2011

city: SAN FRANCISCO

first: Susan

last: Fisher

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

summary: Placental trophoblasts are key determinants of in utero development. Mouse trophoblast stem cells (mTSCs), which were first derived over a decade ago, are a powerful cell culture model for studying their self-renewal or differentiation. Our attempts to isolate an equivalent population from the trophectoderm of human blastocysts generated colonies that quickly differentiated in vitro. This finding suggested that the human placenta has another progenitor niche. Here we show that the chorion is one such site. Initially, we immunolocalized pluripotency factors and trophoblast fate determinants in the early-gestation placenta, amnion and chorion. Immunoreactive cells were numerous in the chorion. We isolated these cells and plated them in medium containing FGF and an inhibitor of activin/nodal signaling, which is required for human embryonic SC self-renewal. Colonies of polarized cells with a limited lifespan emerged. Trypsin dissociation yielded continuously self-replicating monolayers. Colonies and monolayers formed the two major human trophoblast lineages—multinucleate syncytiotrophoblasts and invasive cytotrophoblasts (CTBs). Transcriptional profiling experiments revealed the factors associated with the self-renewal or differentiation of human chorionic trophoblast progenitor cells (TBPCs). They included imprinted genes, NR2F1/2, HMGA2 and adhesion molecules that were required for TBPC differentiation. Together, the results of these experiments suggested that the chorion is one source of epithelial CTB progenitors. These findings explain why CTBs of fully formed chorionic villi have a modest mitotic index and identify the chorionic mesoderm as a niche for TBPCs that support placental growth.

overall_design: TBPC colonies (3 biological replicates), TPBC monolayers (2 biological replicates), CTB (3 biological replicates), hESC (3 biological replicates)


title: Deregulated apoptosis signaling in core binding factor leukemia differentiates clinically relevant, molecular marker independent subgroups

status: Public on Jun 11 2011

first: Lars

last: Bullinger

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary: Core binding factor (CBF) leukemias, characterized by translocations t(8;21) or inv(16)/t(16;16) targeting the core binding factor, constitute acute myeloid leukemia (AML) subgroups with favorable prognosis. However, about 40% of patients relapse, and the current classification system does not fully reflect this clinical heterogeneity. Previously, gene expression profiling (GEP) revealed two distinct CBF leukemia subgroups displaying significant outcome differences and identified apoptotic signaling, MAPKinase signaling and chemotherapy-resistance mechanisms among the most significant differentially regulated pathways. We now tested different inhibitors of the respective pathways in a cell line model (six cell lines reflecting the CBF subgroup specific gene expression alterations), and found apoptotic signaling to be differentiating between the CBF subgroup models. In accordance, primary samples from newly diagnosed CBF AML patients (n=23) also showed differential sensitivity to in vitro treatment with a Smac mimetic such as BV6, an antagonist of inhibitor of apoptosis (IAP) proteins , and ABT-737, a BCL2 inhibitor. Furthermore, GEP revealed the BV6 resistant cases to resemble the previously identified unfavorable CBF subgroup. Thus, our current findings show deregulated IAP expression and apoptotic signaling to differentiate clinically relevant CBF subgroups, which were independent of known molecular markers, thereby providing a starting point for novel therapeutic approaches.

overall_design: All samples were obtained from untreated patients at the time of diagnosis. Cells used for microarray analysis were collected from the purified fraction of mononuclear cells after Ficoll density centrifugation. Routine diagnostic algorithms, including the characterization of molecular markers are performed.

first: Sonja

last: Lück

first: Annika

last: Russ

first: Ursula

last: Botzenhardt

last: Paschka

first: Richard

middle: F

last: Schlenk

first: Hartmut

last: Döhner

first: Simone

last: Fulda

first: Konstanze


title: GATA2 in human vascular endothelial cells

city: Tokyo

first: Yasuharu

last: Kanki

address: 4-6-1 Komaba, Meguro-ku

country: Japan

institute: The University of Tokyo

summary: GATA2 is well recognized as a key transcription factor and regulator of cell type specificity and differentiation. Here, we carried out comparative chromatin immunoprecipitation with comprehensive sequencing (ChIP-seq) to determine genome-wide occupancy of GATA2 in endothelial cells and erythroids, and compared the occupancy to the respective gene expression profile in each cell type. Although GATA2 was commonly expressed in both cell types, different GATA2 bindings and distinct cell specific gene expressions were observed. By using the ChIP-seq with epigenetic histone modifications and chromatin conformation capture assays; we elucidated the mechanistic regulation of endothelial-specific GATA2 mediated endomucin gene expression, that was regulated by the endothelial-specific chromatin loop with a GATA2 associated distal enhancer and core promoter. Knockdown of endomucin markedly attenuated endothelial cell growth, migration and tube formation. Moreover, abrogation of GATA2 in endothelium demonstrated not only a reduction of endothelial specific markers, but also induction of mesenchymal transition promoting gene expression. Our findings provide new insights into the correlation of endothelial expressed GATA2 binding, epigenetic modification, and the determination of endothelial cell specificity.

overall_design:
Total 4 samples were derived from duplicate or triplicate arrays in HMVEC or K562 cells.
Then, HMVEC were transfected with si-RNA against GATA2 in biological duplicate.
Overall, 6 samples were uploaded.

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Tatsuhiko

last: Kodama

first: Takashi

last: Minami


title: Expression data from ileum of inducible intestine-specific GATA6 knockout mice

status: Public on Jun 07 2011

city: Austin

first: James

last: Fleet

address: 1400 Barbara Jordan Blvd

department: Nutritional Sciences

institute: University of Texas at Austin

summary:
GATA6 is a transcription factor involved in the differentiation of intestinal epithelial cells into differentiated absorptive epithelial cells.
GATA6 is expressed in all segments of the small intestine.  We examined the impact of deleting GATA6 from intestinal epithelial cells of the adult ileum

overall_design: 6-8 week old Villin-CreERT2 mice or Villin-CreERT2 mice crossed to GATA6 flox/flox mice were treated with a single injection of tamoxifen. (100 mg/ml) for 5 consecutive days.  28 days later the ileum was dissected and RNA prepared from the whole ileal segment using the RNAeasy method with DNAse treatment.  Three individual mice were examined in each of the control and GATA6 KO groups.

first: Eva

last: Beuling

first: Nana

last: Baffour-Awauh

first: Kelly

last: Stapleton

first: Taeko

last: Noah

first: Noah

last: Shroyer

first: Stephen

last: Duncan

middle: D

last: Krasinski


title: Effects of genome architecture and epigenetic factors on susceptibility of promoter CpG islands to aberrant DNA methylation induction.

status: Public on Jun 06 2011

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

institute: Hoshi University

type: Methylation profiling by genome tiling array

summary: Aberrant DNA methylation is induced at specific promoter CpG islands (CGIs) in contrast with mutations. The specificity is influenced by genome architecture and epigenetic factors, but their relationship is still unknown. In this study, we isolated promoter CGIs susceptible and resistant to aberrant methylation induction during prostate and breast carcinogenesis. The effect of genome architecture was more evident for promoter CGIs susceptible in both of the two tissues than for promoter CGIs susceptible only in one tissue. Multivariate analysis of promoter CGIs with tissue-nonspecific susceptibility showed that genome architecture, namely a remote location from SINE (OR=5.98; 95% CI=2.33-15.34) and from LINE (OR=2.08; 95% CI=1.03-4.21), was associated with increased susceptibility, independent of epigenetic factors such as the presence of RNA polymerase II (OR=0.09; 95% CI=0.02-0.48) and H3K27me3 (OR=3.28; 95% CI=1.17-9.21). These results showed that methylation susceptibility of promoter CGIs is determined both by genome architecture and epigenetic factors, independently.

overall_design: DNA obtained from each cells was immunoprecipitated by anti 5-methylcytidine antibody.  IP DNA and input DNA were labeled with Cy5 and Cy3, respectively, and then analyzed by using human CpG island microarray provided by Agilent Technologies.


title: Gene-chip studies of adipogenesis-regulated microRNAs in mouse primary adipocytes and human obesity

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

institute: University of Stirling

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

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Refer to individual Series


title: Comparative gene expression in the human conjunctiva and cornea

status: Public on Jun 09 2011

first: Martin

last: Nakatsu

address: 200 Stein Plaza

institute: Jules Stein Eye Institute

summary: The identification of a marker that is expressed in the conjunctival epithelium but not in the corneal epithelium has been a growing need. A more specific marker of limbal and conjunctival epithelia would be necessary to detect non-corneal epithelial cells on the corneal surface. To search for conjunctival specific marker(s), we first performed preferential gene profiling in the conjunctiva in direct comparison to that in the cornea using microarray technique.

overall_design: The study consisted of gene expression profiles comparing the cornea and conjunctiva.

first: Sophie

middle: X

last: Deng


title: The Human Airway Epithelial Basal Cell Transcriptome

first: Yael

last: Strulovici-Barel

institute: Weill Cornell Medical College

summary:
Background. The human airway epithelium consists of 4 major cell types: ciliated, secretory, columnar and basal cells. During natural turnover and in response to injury, the airway basal cells function as stem / progenitor cells for the other airway cell types. The objective of this study is to better understand basal cell biology by defining the subset of expressed genes that characterize the signature of human airway epithelial basal cells.
Methodology / Principal Findings. Microarrays were used to assess the transcriptome of basal cells purified from the airway epithelium of healthy nonsmokers obtained by bronchial brushings in comparison to the transcriptome of the complete differentiated airway epithelium. This analysis identified the “human airway basal cell signature” as 1,161 unique genes with >5-fold higher expression level in basal cells compared to the differentiated epithelium. The basal cell signature was suppressed when the basal cells differentiated into a ciliated airway epithelium in vitro. The human airway basal cell signature displayed extensive overlap with genes expressed in basal cells from other human tissues and murine airway basal cells. Consistent with self-modulation as well as signaling to other airway cell types, the airway basal cell signature was characterized by genes encoding extracellular matrix components, and growth factors and growth factor receptors, including genes related to EGFR and VEGFR signaling. However, while human airway basal cells share similarity with basal-like cells of other organs, the human airway basal cell signature has features not previously associated with this cell type, including a unique pattern of genes encoding extracellular matrix components, integrins, G protein-coupled receptors, neuroactive ligands and receptors, and ion channels.
Conclusion / Significance. The human airway epithelial basal cells signature identified in the present study provides novel insights into the ontogeny, molecular phenotype and biology of the stem / progenitor cells of the human airway epithelium.

overall_design: This study was designed to distinguish the transcriptome of the airway epithelium basal cell from that of differentiated airway epithelium.  A basal cell signature was derived and analyzed for functional significance.  The signature was also evaluated as basal cells differentiated into ciliated epithelium in vitro.

first: Neil

last: Hackett

first: Renat

last: Shaykhiev

first: Matthew

middle: S

last: Walters

first: Rui

last: Wang

first: Rachel

last: Zwick

first: Ronald

last: Crystal


title: FN1 expression is a marker of radioresistance in head and neck squamous cell carcinoma

first: Roland

last: Grafström

address: Nobelsväg 13

department: Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

summary: The goal of this project was to analyze differential expression in head and neck cancer cells with various intrinsic radiosensitivity. The gene expression profiles of the cell lines were determined using the Human Genome U133 plus 2.0 Arrays (Affymetrix, Santa Clara, CA).

overall_design: The UTSCC cells were cultured in DMEM (Gibco) supplemented with 2mM glutamine, 1% non-essential amino acids, 100 IU/ml penicillin-G, 50ug/ml streptomycin, and 5% fetal bovine serum (all from Gibco, Paisley, UK). Total RNA was prepared from 3 x 10^6 cells using the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany). The study included a total of 10 samples with 2 seperate experiments from 5 cell lines respectivley.

first: Fredrik

last: Jerhammar

first: Rebecca

last: Ceder

first: Stina

last: Garvin

first: Reidar

last: Grénman

first: Karin

last: Roberg


title: Expression data of the human hepatoblastoma cell line HepG2 treated with TGF-beta

status: Public on Jun 08 2011

first: Daizo

last: Koinuma

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

department: Pathology

institute: University of Tokyo

summary: Smad2/3 are transcription factors that engage in TGF-beta-induced transcription. We determined and analyzed HepG2 and Hep3B-specific Smad2/3 binding sites by ChIP-chip. We used expression microarrays to compare the Smad2/3 and HNF4alpha binding sites identified by ChIP-chip or ChIP-seq, respectively, to TGF-beta-induced gene expressions.

overall_design: HepG2 cells were transfected with control or HNF4A siRNAs and treated with 3 ng/ml TGF-beta for 0, 1.5 and 24 h (6 samples in total, no replicates). Total RNA was extracted and expression microarray analysis was performed as described in the protocols.

first: Anna

last: Mizutani

first: Shuichi

last: Tsutsumi

first: Masato

last: Morikawa

first: Hiroshi

last: Suzuki

first: Kohei

last: Miyazono

first: Hiroyuki

last: Aburatani


title: Expression Data from 226 patients of the REMAGUS02 trial

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary:
Identification of predictive markers of response to treatment is a major objective in breast cancer. A major problem in clinical sampling is the variability of RNA templates, requiring accurate management of tumour material and subsequent analyses for future translation in clinical practice. Our aim was to establish the feasibility and reliability of high throughput RNA analysis in a prospective trial.
Our data showed that strict quality criteria for RNA integrity assessment and well calibrated and standardized RT-qPCR allows multicentre analysis of genes transcripts with high accuracy in the clinical context. More stringent criteria are needed for transcriptome analysis for clinical applications.

overall_design: The transcriptome of 226 patients of the REMAGUS02 trial were analyzed using Affymetrix U133plus2 Arrays.

first: Patricia

last: de Cremoux

first: Fabien

last: Valet

first: David

last: Gentien

first: Jacqueline

last: Lehmann-che

first: Véronique

last: Scott

first: Carine

last: Tran-Perennou

first: Catherine

last: Barbaroux

first: Sophie

last: Vacher

first: Brigitte

last: Sigal-Zafrani

first: Marie-Christine

last: Mathieu

first: Philippe

last: Bertheau

first: Jean-Marc

last: Guinebretière

first: Bernard

last: Asselain

first: Michel

last: Marty

first: Frédérique

last: Spyratos


title: Naturally transmitted segmented filamentous bacteria segregate with diabetes protection in NOD mice

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Vertebrates typically harbor a rich gastrointestinal microbiota, which has co-evolved with the host over millennia and is essential for several of its physiological functions, in particular maturation of the immune system. Recent studies have highlighted the importance of a single bacterial species, segmented filamentous bacteria (SFB), in inducing a robust T helper (Th)17 population in the small intestinal lamina propria (SI-LP) of the mouse gut. Consequently, SFB can promote IL-17-dependent immune and autoimmune responses, gut-associated as well as systemic, including inflammatory arthritis and experimental autoimmune encephalomyelitis. Here, we exploit the incomplete penetrance of SFB colonization of NOD mice in our animal facility to explore its impact on the incidence and course of type-1 diabetes in this prototypical, spontaneous model. There was a strong co-segregation of SFB-positivity and diabetes protection in females, but not in males, which remained relatively disease-free regardless of the SFB status. In contrast, insulitis did not depend on SFB colonization. SFB-positive, but not SFB-negative, females had a substantial population of Th17 cells in the SI-LP, which was the only significant, repeatable difference in the examined T cell compartments of the gut, pancreas or systemic lymphoid tissues. Th17 signature transcripts dominated the very limited SFB-induced molecular changes detected in SI-LP CD4+ T cells. Thus, a single bacterium, and the gut immune system alterations associated with it, can either promote or protect from autoimmunity in predisposed mouse models, likely reflecting their variable dependence on different Th subsets.

overall_design: All gene expression profiles were obtained from highly purified T cell populations sorted by flow cytometry. Cells were sorted from individual mice with at least four replicates generated for all groups. RNA from 1-5 x 104 cells was amplified, labeled, and hybridized to Affymetrix Mo GENE 1.0ST microarrays. Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.

first: Martin

last: Kriegel

first: Esen

last: Sefik

first: Jonathan

last: Hill

first: Hsin-Jung

last: Wu

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: MICROARRAY-BASED GENE EXPRESSION ANALYSIS OF HUMAN OSTEOBLASTS IN RESPONSE TO ROUGHNESS AND FLUORIDE TREATMENT OF TITANIUM IMPLANTS

city: Palma de Mallorca

first: Marta

last: Monjo

state: Illes Balears

address: Edifici del IUNICS, 1er pis, Laboratori de Biologia Molecular.Universitat de les Illes Balears. Cra. Valldemossa km 7.5

department: IUNICS (Health Sciences Research Institute)

institute: UIB (University of the Balearic Islands)

summary: Tissue response following implantation determines the success of the healing process. This response is not only dependent on the chemical properties of the implant surface but also by the surface topography or its roughness. Although in vitro and in vivo studies show improved results with rough- and fluoride-modified implants, the mechanisms behind these findings are still unknown. Here, we have used a two step procedure to identify novel genes related to the early cell response of primary human osteoblasts to roughness and fluoride-modified titanium implants. 217 genes were identified by microarray analysis as response genes to roughness and 198 genes as response genes to fluoride. 11 of these identified genes have been related to bone and mineralization and were further investigated by real-time RT-PCR. After one day of culture, TLR3, ANKH, DCN, OC and RUNX2 were classified as responsive genes to roughness; DLX2 and TUFT1 as responsive genes to fluoride treatment. COLL-I, PTHLH, HES1, FST, ENPP1 and THRA as responsive genes to both, roughness and fluoride treatment.  In conclusion, our strategy was useful for identifying novel genes that might be involved in the early response of osteoblasts to roughness and fluoride treatment of titanium implants.   Tissue response following implantation determines the success of the healing process. This response is not only dependent on the chemical properties of the implant surface but also by the surface topography or its roughness. Although in vitro and in vivo studies show improved results with rough- and fluoride-modified implants, the mechanisms behind these findings are still unknown. Here, we have used a two step procedure to identify novel genes related to the early cell response of primary human osteoblasts to roughness and fluoride-modified titanium implants. 217 genes were identified by microarray analysis as response genes to roughness and 198 genes as response genes to fluoride. 11 of these identified genes have been related to bone and mineralization and were further investigated by real-time RT-PCR. After one day of culture, TLR3, ANKH, DCN, OC and RUNX2 were classified as responsive genes to roughness; DLX2 and TUFT1 as responsive genes to fluoride treatment. COLL-I, PTHLH, HES1, FST, ENPP1 and THRA as responsive genes to both, roughness and fluoride treatment.  In conclusion, our strategy was useful for identifying novel genes that might be involved in the early response of osteoblasts to roughness and fluoride treatment of titanium implants.

overall_design: Human osteoblasts were cultured for 24 hours on titanium disks modified either with polished surfaces (P), grit-blasted surfaces (GB), or grit-blasted High Fluor treated surfaces (GB-HF). After 24 hours of culture RNA was isolated. 3 arrays were hybridized, one with the isolated RNA from cells cultured on titanium polished surfaces (P), one with the isolated RNA from cells cultured on titanium grit-blasted surfaces (GB) and one with the isolated RNA from cells cultured on titanium grit-blasted HF treated surfaces (GB-HF).

first: Joana

middle: M

last: Ramis

first: Sébastien

last: Taxt-Lamolle

first: Staale

last: Lyngstadaas

first: Janne

middle: E

last: Reseland

first: Jan

last: Ellingsen


title: Identification of Notch targets in human endothelial cells

first: Alex

middle: CY

last: Chang

state: British Columbia

institute: British Columbia Genome Science Center

summary: Human umbilical vein endothelial cells (HUVECs) were transduced with either MIY-N1IC (Notch1 intracellular domain) or MIY vector control. The cells were sorted for YFP, and RNA was extracted using Trizol (Invitrogen) and analyzed by the Affymetrix Human Genome U133 Plus 2.0 Array. Results were analyzed using the GCRMA algorithm to identify genes with a minimum of 2-fold induction or reduction. This global gene expression study was used to identify Notch targets in the endothelium.

overall_design: Expression profiling of primary HUVECs transduced with N1IC. HUVEC primary cells were isolated, transduced with N1IC or vector (MIY) control in three biological replicates, and evaluated on Affymetrix Human Genome U133 Plus 2.0 arrays.

first: Kyle

last: Niessen

first: Yangxin

last: Fu

middle: C

first: Aly

last: Karsan


title: Gene expression profiling of MCF10A (miR-221/222 vs control)

city: South San Francisco

first: Peng

last: Yue

address: 1 DNA Way

institute: Genentech Inc

summary:
Analysis of gene expression of MCF10A to identify the targets of miR-221 and miR-222
Keywords: MCF10, miR-221, miR-222

overall_design: RNA profiles of human MCF10A cell line

first: David

last: Dornan


title: Analysis of Human Tendinopathy Gene Expression

city: Cambridge

first: Scott

last: Jelinsky

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

summary: Chronic tendon injuries, also known as tendinopathy, are common among professional and recreational athletes.  These injuries result in a significant amount of morbidity and health care expenditure and yet little is known about the molecular mechanism leading to tendinopathy.  We have used histological evaluation and molecular profiling to determine the gene expression changes in 23 human patients undergoing surgical procedures for the treatment of chronic tendinopathy.  Diseased tendons have altered extracellular matrix, fiber disorientation, increased cellular content and vasculature and the absence of inflammatory cells.  Global gene expression profiling identified 1783 transcripts with significant different expression patterns in the diseased tendons.  Global pathway analysis further suggests altered expression of extracellular matrix proteins and the lack of an appreciable inflammatory response.  We have identified pathways and genes regulated in tendinopathy samples that will help contribute to the understanding of the disease towards the development of novel therapeutics.

overall_design: A prospective study was initiated to collect tissue from patients undergoing surgery as standard of care for tendinopathy.  Biopsies (~3mm^3) of diseased tendons as well as a section of grossly normal appearing tendon were collected from 23 patients.  Written informed consent was obtained from all patients prior to any study related procedure.


title: Expression data from pure/mixed blood and breast to test feasability of deconvolution of clinical samples

first: Ting

last: Gong

address: 45 Sidney street

institute: Novartis Institutes for Biomedical research

summary:
Samples collected from human subjects in clinical trials possess a level of complexity, arising from multiple cell types, that can obfuscate the analysis of data derived from them. Blood, for example, contains many different cell types that are derived from a distinct lineage and carry out a different immunological purpose. Failure to identify, quantify, and incorporate sources of heterogeneity into an analysis can have widespread and detrimental effects on subsequent statistical studies.

We used microarrays to detail a statistical approach to model expression from a mixed cell population as the weighted average of expression from different cell types. Consequently, we can accurately and efficiently estimate the abundance of various cell populations. Favoring computation over manual purification has its advantages, such as measuring responses of multiple cell types simultaneously, keeping samples intact, and identifying biologically relevant differentially expressed genes.

overall_design: We mixed breast and blood biospecimens derived from female adults at the cRNA homogenate level in different proportions. Data was RMA normalized.

first: N

last: Hartmann

first: S

last: Bongiovanni

first: J

last: Szustakowski

first: T

first: M

last: Letzkus

first: F

last: Staedtler


title: AIRE-deficient CD8+CD28low regulatory T lymphocytes fail to control experimental colitis

city: Adelaide

first: Mark

middle: B

last: Van der Hoek

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

summary: Mutations in the gene encoding the transcription factor AutoImmune REgulator (AIRE) are responsible for the ‘Autoimmune PolyEndocrinopathy Candidiasis Ecodermal Dystrophy’ syndrome. AIRE directs expression of tissue restricted antigens in the thymic medulla and in lymph node stromal cells and thereby substantially contributes to induction of immunological tolerance to self-antigens. Data from experimental mouse models showed that AIRE-deficiency leads to impaired deletion of autospecific T cell precursors. However, a potential role for AIRE in the function of regulatory T cell populations, which are known to play a central role in prevention of immunopathology, has remained elusive. Regulatory T cells of CD8+CD28low phenotype efficiently control immune responses in experimental autoimmune and colitis models in mice. We here show that CD8+CD28low Treg from AIRE-deficient mice are transcriptionally and phenotypically normal, exert efficient suppression of in vitro immune responses, but completely fail to prevent experimental colitis in vivo. Our data therefore demonstrate that AIRE plays an important role in the in vivo function of a naturally occurring regulatory T cell population.

overall_design: Total RNA was extracted from CD8+CD28low regulatory T lymphocytes isolated from wildtype and Aire-deficient C57BL/6 mice for comparison of gene expression profiles.

first: Céline

last: Pomié

first: Rita

last: Vicente

first: Yirajen

last: Vuddamalay

first: Brita

last: Lundgren

last: van der Hoek

first: Geneviève

last: Enault

first: Jérémy

last: Kagan

first: Nicolas

last: Fazilleau

first: Hamish

last: Scott

first: Paola

last: Romagnoli

first: Joost

last: van Meerwijk


title: Cell-type-specific target selection by combinatorial binding of Smad2/3 and hepatocyte nuclear factor 4-alpha in HepG2 cells

first: Daizo

last: Koinuma

type: Genome binding/occupancy profiling by genome tiling array

type: Genome binding/occupancy profiling by high throughput sequencing


title: The landscape of promoter DNA hypomethylation in liver cancer (expression data)

status: Public on Jun 04 2011

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

summary: Extensive loss of DNA methylation is a hallmark of cancer. The role of hypomethylation in altering gene expression in cancer cells has been poorly understood. Hepatic cellular carcinoma (HCC) is one of the most common human cancers. We use HCC as a model to investigate hypomethylation in cancer by a combination of methylated DNA immunoprecipitation and hybridization with comprehensive promoter arrays. We identify approximately 2,800 promoters that are hypomethylated in tumor samples. The hypomethylated promoters appear in clusters across the genome suggesting a high-level organization behind the epigenomic changes in cancer. The genes whose promoters are demethylated are mainly involved in cell growth, cell adhesion and communication, signal transduction, mobility and invasion; functions that are essential for cancer progression and metastasis. Previous studies suggested that MBD2 was involved in demethylation of uPA and MMP2 genes in human breast and prostate cancer cell lines. We extend these results here showing that whereas MBD2 depletion in normal liver cells has little or no effect, its depletion in the human hepatocellular carcinoma cell line HepG2 and the adenocarcinoma cell line SkHep1 results in suppression of cell growth, anchorage-independent growth and invasiveness, as well as an increase in promoter methylation and silencing of several of the genes that are hypomethylated in tumors. Our studies establish for the first time the rules governing hypomethylation of promoters in liver cancer and define the potential functional role of hypomethylation in cancer.

overall_design: Cancerous and normal adjacent tissue samples were obtained from 11 patients with HCC from the Chinese National Human Genome Center at Shanghai, China (Dr. Ze-Guang Han). For three patients, the cancer samples were dissected using the laser capture microdissection technique. Gene expression profiles for these patients were generated using Affymetrix expression microarrays.

first: Bishnu

last: Bhattacharyya

first: Matthew

last: Suderman

first: Jian

last: Huang

first: Ze-Guang

last: Han

first: Michael

last: Hallett


title: The landscape of promoter DNA hypomethylation in liver cancer


title: CLN3 patients with differing progression of the disease

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

summary:
Mutations in the CLN3 gene lead to juvenile neuronal ceroid lipofuscinosis, a pediatric neurodegenerative disorder characterized by visual loss, epilepsy and psychomotor deterioration. Although most CLN3 patients carry the same 1 kb deletion in the CLN3 gene, their disease phenotype can be variable. The aims of this study were (1) to identify genes that are dysregulated in CLN3 disease regardless of the clinical course that could be useful as biomarkers, and (2) to find modifier genes that affect the progression rate of the disease.
Genome-wide expression profiling was performed in 8 CLN3 patients, homozygous for the 1 kb deletion, with different disease progression and compared to seven age and gender matched controls.

overall_design: Lymphocytes from eight patients diagnosed with CLN3 disease,all homozygous for the 1 kb deletion in the CLN3 gene and classified as having rapid (n = 2), average (n=4), and slow disease progression (n = 2), were used. These eight patients did not receive anticonvulsive medication. In addition, lymphocytes of seven age and gender matched controls were included in the study. Lymphocytes were prepared from fresh patient blood samples by Ficoll-gradient centrifugation (Biocoll®, Biochrom AG, Berlin, Germany) according to the manufacturer’s protocol and used for RNA isolation (RNeasy® Micro Kit, Qiagen, Hilden, Germany).

first: Anne-Hélène

last: Lebrun

first: Angela

last: Schulz


title: Sema4A, a novel serum marker of multiple sclerosis, implicates Th17 pathology and efficacy of interferon-β.

status: Public on Jun 01 2011

city: Kobe

first: Akiko

last: Matsui

address: 6-7-5, Minatojima-Minamimachi, Chuo-ku

department: Department of Molecular & Cellular Biology

institute: Nippon Boehringer Ingelheim, Co. Ltd

summary:
Background: Multiple sclerosis (MS) is a demyelinating autoimmune disease of the central nervous system and the leading cause of lasting neurological disabilities in young adults. Increasing evidence suggests that early treatment prevents the development of disability. However, there have been no reliable serum markers to assist the early diagnosis. In addition, interferon (IFN)-β, which is the major treatment for MS, is not always effective. Therefore, the development of simple serological test to help the early diagnosis and predict responsiveness to IFN-β is of clinical importance. On the other hand, a transmembrane-type semaphorin, Sema4A, has been implicated in experimental autoimmune encephalomyelitis (EAE) by regulating helper T (Th) cell differentiation. Thus, we aimed to identify the implications of Sema4A in diagnosis and pathogenesis of MS. Methods: We assayed serum Sema4A in 59 patients with relapsing-remitting MS (RRMS), 22 patients with clinically isolated syndrome (CIS) and 126 patients with other neurological diseases (OND) by developing a sandwich ELISA. To identify a source of soluble Sema4A and characteristics of MS patients with high levels of Sema4A, we analyzed peripheral blood mononuclear cells (PBMCs) from MS patients and healthy controls by flow cytometry (FACS) and gene chip analysis. The effect of Sema4A was examined in vitro and in vivo using an EAE model. Findings: Sema4A was significantly increased in sera of patients with MS and CIS compared to controls. Sema4A expression was increased on the surface of DCs in MS patients and shed from these cells in a metalloproteinase-dependent manner, affecting the Th17skewing. In addition, patients with high Sema4A levels exhibited more severe disabilities, and IFN-β treatment was not beneficial to those patients. Interpretation: Measuring Sema4A is a practical laboratory test to help diagnose MS and to predict responsiveness to IFN-β therapy.

Microarray analysis showed that metalloproteinases such as ADAM 10 and MMPs 1, 3, 9, 12 and 25, which are reported to be involved in the pathogenesis of MS, were increased in PBMCs from MS patients with high Sema4A levels compared to those with low Sema4A and healthy controls. However, ADAM 17 and MMP 2 and 7 did not correlate with Sema4A levels. Taken together, these findings strongly suggest that Sema4A, abundantly expressed on monocytes and DCs in MS patients, is enzymatically cleaved and shed in a portion of the patients, which contributes to the high soluble Sema4A detected by the ELISA.

overall_design: Multiple sclerosis patients were classified according to Serum Sema4A levels. RNA from peripheral blood from 4 healthy controls, 3 MS patients with high serum Sema4A levels and 3 MS patients with low serum Sema4A levels was extracted and hybridized on Affymetrix microarrays. We sought to see whether there is corrlated genes with serum Sema4A levels or not, especially for genes for varions proteases.

first: Yuji

last: Nakatsuji

first: Tatsusada

last: Okuno

first: Masayuki

last: Moriya

first: Tomoyuki

last: Sugimoto

first: Makoto

last: Kinoshita

first: Hyota

last: Takamatsu

first: Satoshi

last: Nojima

first: Tetsuya

last: Kimura

first: Sujin

last: Kang

first: Yukinobu

last: Nakagawa

first: Toshihiko

last: Toyofuku

first: Kazushiro

last: Takata

first: Misa

last: Nakano

first: Masato

last: Kubo

first: Sinobu

last: Suzuki

last: Matsui-Hasumi

first: Ayako

last: Uto-Konomi

first: Saburo

last: Sakoda

first: Atsushi

last: Kumanogoh


title: Gene expression data from chronic lymphocytic leukemia samples

city: NEW YORK

first: Piali

last: Mukherjee

state: New York

department: Medicine

institute: Weill Cornell Medicine

summary:
MicroRNA-155 is frequently over-expressed in CLL and is associated with worse clinical prognosis.  To understand the role of miR-155 in CLL pathogenesis, we used microarrays to identify genes that are expressed at significantly lower levels in CLLs that harbor
higher levels of miR-155 expression in an attempt to determine the relevant gene targets of miR-155 in CLL.

overall_design: MiR-155 levels of 38 CLL samples were determined and ranked.  6 CLLs with the highest and 6 CLLs with the lowest miR-155 within the IgVH unmutated group, and 5 CLLs with the highest and 5 CLLs with the lowest miR-155 within the IgVH mutated group were selected for Affymetrix array analyses.

first: Jan

last: Davidson-Mocada

first: Taotao

last: Zhang

first: Wayne

last: Tam


title: Gene expression analysis of relapse and no-relapse Wilms tumor

city: Campinas

first: Mariana

last: Maschietto

state: São Paulo

address: Rua Márcia Mendes, 619

department: Research Center

country: Brazil

institute: Boldrini Children's Hospital

summary: Wilms tumor (WT), the commonest renal tumor of the childhood, is originated from pluripotent metanephric blastemal cells resulting in tumors with triphasic histology, composed by blastemal, epithelial, and stromal cells. Histological subtype and tumor stage have long been recognized as important prognostic factors and used for the current therapeutic approach with blastema considered as the component with the highest clinical impact. Current clinical and molecular research is directed toward identifying prognostic factors for both purposes, definition of the minimal or intense required therapy for successful treatment of children with low or high risk of relapse, respectively. In this study, to identify molecular prognostic markers predictive of tumor relapse, samples from 26 advanced (Stage III or IV) blastemal WT, whose patients presented (13 samples) or did not present (13 samples) relapse, were interrogated by 4,608 human genes immobilized in a customized cDNA platform. This analysis revealed a set of 69 differentially expressed genes, where the nine top genes were evaluated by qRT-PCR in the initial WT samples. TSPAN3, NCOA6, CDO1, MPP2 and MCM2 were technically confirmed showing down-regulation in relapse WT. TSPAN3 and NCOA6 were validated in an independent sample group. Gene trios containing these two genes combined with one of the remaining three reported a reasonable capability of discriminating relapse and no-relapse WT. Negative protein expression of MCM2 and NCOA6 was observed in around 62% and 72% of 34 independent stage III and IV WT patients, respectively without association with relapse. However, a significant association between MCM2 negative staining and chemotherapy as first treatment was observed suggesting that MCM2 protein expression is implicated anyhow with chemotherapy treatment in WT.

overall_design: Twenty-six blastemal-enriched advanced stage (III or IV) WT samples from sporadic and favorable histology WT were received from Children Oncology Group (COG) and used were used for microarray experiments, from which 13 samples were from patients without relapse in 5 years of follow up. Tumors were taken from primary nephrectomy at the time of initial diagnosis. Blastemal histological component was isolated following protocol described in Maschietto et al. (2008). Only samples with >80% of blastemal cells were used. Total RNA was isolated using TRIzol (Sigma) according to manufacturer´s instructions. RNA quantity and integrity was assessed by spectrophotometry (Nanodrop) and microfluidics-based electrophoresis (Agilent 2100 Bioanalyzer, Agilent), respectively, selecting only RNA samples with OD around 2.0 and RIN>5.0. A two-round RNA amplification procedure (Gomes et al. 2003) was carried out for all samples. Labeled cDNA was generated in a reverse transcriptase reaction using 4 ug of amplified RNA (aRNA), random hexamer primer (Invitrogen Life Technologies, Carlsbad, CA), Alexa-3 or 5-labeled dCTP (Amersham, Biosciences) and IMPROM (PROMEGA) using oligo-dT7(24), following manufacture recommendations. Five µg of test and reference cDNA reverse color Alexa-labeled aRNA targets were competitively hybridized against the cDNA probes in a customized cDNA platform with 4,608 ORESTES representing human genes. Dye-swap was performed for each sample as control for dye bias and used as replicate. Pre-hybridization and hybridization were performed as described (Maschietto et al. 2008). A pool of RNAs obtained from 15 distinct human cell lines as was used as reference. Signal intensities capture and analysis were performed as described in Maschietto et al (2008).


title: Patterns of gene expression and evolution in the human developing cerebral cortex

city: Brussels

first: Vincent

last: Detours

address: 808 Route de Lennik

department: School of Medicine

institute: Free University of Brussels

summary:
The cerebral cortex underwent a rapid expansion and complexification during recent primate evolution, but the underlying developmental mechanisms remain essentially unknown.
In order to uncover genetic networks underlying the development of the human cerebral cortex, we profiled the transcriptome of human fetal cortical domains containing language areas of Broca and Wernicke, as well as associative areas. We thus identified hundreds of genes displaying differential expression between the two areas or between distinct temporal stages. A subset of these genes was further validated by qRTPCR and in situ hybridization, revealing novel patterns of area and layer-specific expression throughout the developing cortex at midgestation, a critical period of cortical patterning.
Computational genomic analyses revealed that the proportion of genes located close to evolutionarily accelerated regions was far more abundant among the genes differentially expressed between the two cortical areas examined, but not among those differentially expressed between different stages of development. In silico screening enabled to identify accelerated regions displaying increased turnover of change in transcription factor binding sites, which were enriched among those closer to genes differentially expressed between cortical areas.
Overall our work points to the identification of cortical genes that display a unique combination of patterns of evolution and expression, which may constitute an important part of the genetic framework underlying human-specific neural traits and diseases.

overall_design: We determined gene expression patterns in cortical domains that contain areas thought to have undergone significant divergence during primate evolution, including language areas of Broca and Wernicke, as well as association areas of the frontal and parieto-temporal cortex in the right and left sides of human fetal brains at 17 and 19 gestional weeks.

first: Nelle

last: Lambert

first: Marie-Alexandra

last: Lambot

first: Pierre

last: Vanderhaeghen


title: A phenotype-based model for rational selection of novel targeted therapies in treating aggressive breast cancer

first: Adam

last: Gustafson

state: MA

address: 44 Cummington St

institute: Boston University

summary: Treating unselected cancer patients with new drugs dilutes proof of efficacy when only a fraction of patients respond to therapy. We conducted a meta-analysis on eight primary breast cancer microarray datasets representing diverse breast cancer phenotypes. We present a high-throughput protocol which incorporates drug sensitivity signatures to guide preclinical testing for effective therapeutic agents. Specifically, we focus on drug classes currently undergoing early phase clinical testing. Our genomic and experimental results suggest that the majority of basal-like breast cancers should respond to inhibitors of the phosphatidylinositol-3-kinase pathway, and that a relatively low toxicity histone deacetylase inhibitor, valproic acid, may target aggressive breast cancers. For a subset of drugs, prediction of sensitivity associates with tumor recurrence, suggesting clinical relevance. Preclinical studies using both cell lines and patient tumors grown in 3-dimensional in vitro and orthotopic in vivo preclinical models provide an efficient and highly relevant assessment of drug sensitivity in tumor phenotypes, and validate our genomic analyses. Together, our results show that high-throughput transcriptional profiling can significantly impact drug selection for breast cancer patients. Pre-identification of patient response may not only improve therapeutic response rates, it can also assist in quickly identifying the optimal inclusion criteria for clinical trials. Our model facilitates personalized drug therapy for cancer patients and may be generalized for study of drug efficacy in other diseases.

overall_design: Breast cancer pleural effusion samples from triple negative patients. Compared samples that are computationally predicted to be sensitive to valproic acid and those that are not predicted to be sensitive.

first: Jeffrey

middle: T

last: Chang

first: Bryan

last: Welm

first: Stefanie

last: Jeffrey

first: Andrea

middle: H

last: Bild


title: Autotaxin and its product lysophosphatidic acid suppress brown adipose differentiation and promote diet-induced obesity in mice

city: Lexington

first: Susan

last: Smyth

address: 741 S. Limestone Street

institute: University of Kentucky

summary: Brown adipose tissue (BAT) is a thermogenic organ that dissipates stored energy as heat to maintain body temperature in infants and small mammals.  This process may also provide protection from development of diet-induced obesity.  We found that the bioactive lipid mediator lysophosphatidic acid (LPA) markedly decreases differentiation of cultured primary brown adipocyte precursors, while potent selective inhibitors of the LPA-generating enzyme autotaxin (ATX) promote differentiation.  Transgenic mice overexpressing ATX exhibited reduced expression of BAT-related genes in peripheral white adipose tissue and accumulated significantly more fat than wild-type controls when fed a high fat diet.  Our results indicate that ATX and its product LPA are physiologically relevant negative regulators of brown fat adipogenesis and suggest that a decrease in peripheral brown adipose tissue results in increased susceptibility to diet-induced obesity in mice.

overall_design: Primary BAT cell cultures were established as previously reported with some minor modifications (Cannon B., 2001; Néchad M., 1983). Four- to 6-week-old mice were euthanized under aseptic conditions and interscapular BAT (IBAT) dissected, finely minced in digestion buffer containing 123 mM NaCl, 5mM HCl, 1.3 mM CaCl2, 5mM glucose, 1.5% (w/v) crude bovine serum albumin fraction V, 100 mM HEPES, 0.2% collagenase type II (Sigma-Aldrich Corp., St. Louis, MO), pH 7.4, and digested in 10 ml of the same buffer for 30 min at 37°C. The supernatant obtained was then filtered using a 250 µm nylon mesh and kept in ice for 15 minutes to allow fat droplets and mature cells to float. The resulting infranatant was filtered through a 30 µm nylon mesh to enrich the fraction with precursor cells and centrifuged at 700g for 10 min. The pellet obtained was washed once in warm DMEM and resuspended in DMEM medium containing 10% newborn calf serum, 10 mM HEPES, 4mM glutamine, 25 µg/ml sodium ascorbate (Sigma-Aldrich Corp., St. Louis, MO)., 100U/ml penicillin and 100mg/ml streptomycin. Cells were seeded onto 35mm dish plates. Insulin treatment was started on day 1 at 50 nM and the concentration increased to 100 nM at day 5 and 200 nM at day 7. Differentiated/confluent cells were collected for biochemical analysis (~day 9). To identify genes regulated by ATX and LPA signaling, 9 DIV primary BAT cultures were treated with the vehicle (DMSO), specific ATX inhibitor HA155 (2.5µM), or LPA (1-Oleoly-LPA, 5µM) (Avanti Polar Lipids, AL, USA) during differentiation. Treatment of the BAT cultures did not affect confluence or markers of proliferation. RNA was extracted from three cultures per condition using TRIzol reagent (Invitrogen, Carlsbad, CA) as described previously (Blalock EM., 2003).

first: Lorenzo

last: Federico

first: Hongmei

last: Ren

first: Paul

last: Mueller

first: Jelena

last: Popovic

first: Wu

last: Tao

first: Eric

last: Blalock

first: Wouter

last: Moolenaar

first: Huib

last: Ovaa

first: Harald

last: Albers

first: Gordon

last: Mills

first: Andrew

middle: J

last: Morris


title: Microarray analysis of the astrocyte transcriptome in the ageing brain: relationship to Alzheimer's pathology and ApoE genotype

city: Sheffield

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

summary:
Astrocyte dysfunction impacts their normal function, including neuronal support, thereby contributing to neurodegenerative pathologies including Alzheimer's disease (AD). Therefore to understand the role of astrocytes in the pathogenesis of age-related disorders we analysed the gene expression profile of astrocytes with respect to Alzheimer-type pathology.
The aim of the present study was to combine immuno-LCM and microarray analysis to characterise the astrocyte transcriptome at different Braak stages, and with respect to ApoE genotype, in post-mortem human temporal cortex sampled dervied from the Medical Research Council Cognitive Function and Ageing Study (MRC-CFAS).

overall_design:
GFAP-positive astrocytes were isolated from age, sex and brain pH-matched cases derived from the MRC-CFAS cohort, using immuno laser capture microdissection. The extracted RNA was amplified and applied to HGU133 Plus 2.0 Affymetrix gene arrays. Genes were considered differentially expressed if they showed a minimum 1.5 fold change at p<0.02 in all 6 individual cases in each stage of pathology [18 cases in total: 6 cases Braak stages I-II (3 cases carried at least one ApoE epsilon4 allele and 3 were ApoEe4 negative); 6 cases Braak stages III-IV (3 ApoEe4 positive and 3 ApoEe4 negative; 6 cases Braak stages V-VI (3 ApoEe4 positive and 3 ApoEe4 negative)].
keywords: human GFAP-positive astrocytes

first: Julie

last: Simpson

middle: G

last: Ince

first: Pamela

last: Shaw

middle: R

first: Rohini

last: Raman

first: Claire

last: Garwood

first: Catherine

last: Gelsthorpe

first: Lynne

last: Baxter

first: Gillian

last: Forster

first: Fiona

last: Matthews

first: Carol

last: Brayne

first: Stephen

last: Wharton


title: Regulation of gene expression in ALK inhibitor CH5424802-treated NCI-H2228 xenograft tumors

status: Public on Jun 03 2011

city: Kamakura

first: Hiroshi

last: Sakamoto

address: Kajiwara 200

institute: Chugai Pharmaceutical co. ltd.

summary: To clarify the downstream signal pathway of EML4-ALK in NSCLC, we performed Affymetrix GeneChip analysis using ALK inhibitor CH5424802-treated NCI-H2228 xenograft tumors, and comprehensively characterized the gene expression regulated by inhibition of activated ALK.

overall_design: Mice bearing NCI-H2228 cells were orally administered at dose of 0 (vehicle), 4 or 20 mg/kg of CH5424802, and the tumors were collected and lysed at 6 hours post-dose. Total RNA were extracted from xenograft tumors.

first: Toshiyuki

last: Tsukaguchi


title: Molecular Mechanisms of Bortezomib Resistant Adenocarcinoma cells

city: Phoenix

first: Jonathan

last: Keats

state: Arizona

address: 445 N. Fifth Street

department: Integrated Cancer Genomics

institute: Translational Genomics Research Institute (TGen)

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: Galectin-3 regulates the expression of various genes in human gastric cancer cells

status: Public on May 31 2011

city: Goyang-si

first: Kyung-Hee

last: Chun

state: Gyeonggi-do

address: 323 ilsan-ro

department: Division of Translational & Clinical Research I

country: South Korea

institute: National Cancer Center

summary: Although galectin-3 is known to modulate the cell proliferation, RNA processing, tumorigenesis, metastasis and apoptosis and also, which is highly expressed in human cancers, the function of galectin-3 is still controversy in gastric cancer. Here, we demonstrated the function of galectin-3 on gastric cancers by silencing with synthetic double-stranded small interfering RNA (siRNA). After silencing of galectin-3, cell numbers decreased and cell shapes changed in round. To determine the mechanism, microarray analysis was used to detect the changes in gene expression by galectin-3 silencing.

overall_design: we silenced galectin-3 in AGS as a gastric cancer cells with synthetic double-stranded small interfering RNA (siRNA), and performed the microarray analysis to detect the changes in gene expression by galectin-3 silencing.

first: Sang-Geun

last: Jang

first: Teak-Chin

last: Cheong

first: Seok-Jun

last: Kim


title: Gene-chip studies of adipogenesis-regulated microRNAs in mouse primary adipocytes and human obesity (Affymetrix)

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

institute: University of Stirling

summary: Adipose tissue abundance relies partly on the factors that regulate adipogenesis, i.e. proliferation and differentiation of adipocytes. While the transcriptional program that initiates adipogenesis is well-known, the importance of microRNAs in adipogenesis is less well studied. We thus set out to investigate whether miRNAs would be actively modulated during adipogenesis and obesity. Several models exist to study adipogenesis in vitro, of which the cell line 3T3-L1 is probably the most well known, albeit not the most physiologically appropriate. We used a microarray strategy to provide a global profile of miRNAs in brown and white primary murine adipocytes (prior to and following differentiation) and evaluated the similarity of the responses to non-primary cell models, through literature data-mining. We found 65 miRNAs regulated during in vitro adipogenesis in primary adipocytes. When we compared our primary adipocyte profiles with those of cell lines reported in the literature, we found a high degree of difference in adipogenesis-regulated miRNAs. We evaluated the expression of 10 of our adipogenesis-regulated miRNAs using real-time qPCR and then selected 5 miRNAs that showed robust expression levels and profiled these by qPCR in subcutaneous adipose tissue of 20 humans with a range of body mass indices (BMI, range=21-48). Of the miRNAs tested, mir-21 was both highly expressed in human adipose tissue and positively correlated with BMI (R2=0.49, p<0.001). In conclusion, we provide the preliminary analysis of miRNAs important for primary cell in vitro adipogenesis and find that the inflammation-associated miRNA, mir-21, is up-regulated in subcutaneous adipose tissue in human obesity.

overall_design: A global transcriptomic survey of subcutaneous adipose tissue from human subjects characterised as having normal glucose tolerance, glucose intolerance or frank type 2 diabetes.

first: James

middle: A

last: Timmons


title: Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.

city: Segrate, Milano

first: Clelia

last: Peano

address: Via Fratelli Cervi 93

department: Institute of Biomedical Technologies

institute: National Research Council

summary: Promoter recognition by bacterial RNA polymerase is mediated by σ subunits, which assemble transiently to RNA polymerase core enzyme (E) during transcription initiation. σ subunits drive transcription of specific sets of genes by allowing RNA polymerase to interact with different promoter sequences. However, σ70, the housekeeping σ subunit, and σS, an alternative σ subunit mainly active during slow growth and in response to cellular stresses, appear to recognize almost identical promoter sequences, raising the question of how promoter selectivity is achieved in the bacterial cell. To identify sequence determinants for selective promoter recognition, we performed a run-off/microarray experiment (ROMA): in vitro transcription experiments were carried out with RNA polymerase saturated either with σ70 (Eσ70) or with σS (EσS) using the whole Escherichia coli genome as DNA template, and transcript levels were determined by microarray analysis. We found that several genes associated with bacterial growth (e.g., ribosomal operons) were transcribed more efficiently by Eσ70. In contrast, EσS transcribed preferentially genes involved in stress responses, secondary metabolism, as well as regulatory RNAs and intergenic regions with yet unknown function. Genes preferentially recognized in vitro by EσS showed reduced expression in EσS -deficient mutant strain of E. coli. Sequence comparison of Eσ70- versus EσS –dependent promoters confirms that the presence of a -35 sequence and the relative location of UP elements affect promoter interaction with either form of RNA polymerase, and suggests that a G/C bias in the -2/+1 nucleotides would favour efficient promoter recognition by Eσ70.

overall_design: We have performed in vitro transcription experiments with either Eσ70 or EσS, using the whole E. coli genome as template, to identify promoter regions selectively recognized by two forms of RNA polymerase by using E.coli genome 2.0 GeneChips.

first: Anna

last: Maciąg

first: Alessandro

last: Pietrelli

first: Thomas

last: Egli

first: Gianluca

last: De Bellis

first: Paolo

last: Landini


title: Molecular Mechanisms of Bortezomib Resistant Adenocarcinoma cells [GEP data]

summary:
Copy number and Gene expression profiling of HT-29 wild-type and bortezomib resistant cell lines
Identification of mechanisms of bortezomib resistance

overall_design: Gene expression differences between HT-29 cell line variants

first: Christopher

last: Kirk


title: Human CD34+-derived erythoblast (polychromatophilic and orthochromatic) response to co-culture with Plasmodium falciparum 3D7

city: South Bend

first: Kasturi

last: Haldar

email: khaldar@nd.edu, ptamez@nd.edu

state: IN

address: 107 Galvin Life Sciences

department: Biology

institute: University of Notre Dame

summary: Global, genomic responses of erythrocytes to infectious agents have been difficult to measure, because these cells are e-nucleated. We have previously demonstrated that in vitro matured, nucleated erythroblast cells at the orthochromatic stage can be efficiently infected by the human malaria parasite Plasmodium falciparum. We now show that infection of orthochromatic cells induces change in 609 host genes. 592 of these transcripts are up-regulated and associated with metabolic and chaperone pathways unique to P. falciparum infection, as well as a wide range of signaling pathways that are also induced in related apicomplexan infections of mouse hepatocytes or human fibroblast cells. Our data additionally show that polychromatophilic cells, which precede the orthochromatic stage and are not infected when co-cultured with P. falciparum, up-regulate a small set of 35 genes, 9 of which are associated with pathways of hematopoiesis and/or erythroid cell development. These data unexpectedly predict that blood stage P. falciparum may induce host responses common to infections of other pathogens. Further P. falciparum may modulate gene expression in bystander erythroblasts and thus influence pathways of erythrocyte development.

overall_design: Human primary erythroid cells were differentiated from CD34+ hematopoietic stem cells isolated from growth factor-mobilized peripheral blood (ALL Cells, Inc.). Cells from five donors were cultured until polychromatophilic and orthochromatophilic stages of differentiation and served as uninfected control samples. Of the five donors, three were used to initiate Plasmodium falciparum (3D7) infection at a multiplicity of infection = 5. Infected cells were harvested 24 hours post-infection, and RNA was isolated with Trizol (Invitrogen) and purified with RNeasy columns (QIAGEN) according to manufacturer recommendations. Microarray labeling and hybridizations were done according to Affymetrix protocols using HG U133 plus 2.0 chips. For GenePattern analysis, all samples (5 control and 3 infected samples) were analyzed; for Dchip analysis, only three samples were analyzed (the same 3 donors served as control and infected samples).

first: Pamela

last: Tamez

first: Hui

last: Liu

first: Amittha

last: Wickrema


title: Human bone marrow-derived mononuclear cells (BMMC): rheumatoid arthritis vs. osteoarthritis

city: Ibaraki

first: Norihiro

last: Nishimoto

state: Osaka

address: 7-7-20, Saito-Asagi

institute: Wakayama Medical University

summary: Gene expression profiling of BMMC from patients with rheumatoid arthritis (RA) vs. osteoarthritis (OA).

overall_design: Bone marrow was obtained from patients with RA (n=9) or OA (n=10). The bone marrow samples from the 10 OA patients are used as controls.

first: Hooi-Ming

last: Lee

first: Hidehiko

last: Sugino

first: Chieko

last: Aoki

first: Yasunori

last: Shimaoka

first: Ryuji

last: Suzuki

first: Takahiro

last: Ochi


title: Expression data from highly purified MMTV-Neu Tumor Initiating Cells (TICs) and the non-TIC CD24- fraction

status: Public on May 28 2011

city: Toronto

first: Jeff

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

institute: University Health Network

summary:
The cancer stem cell model maintains that tumors are organized in a hierarchy driven by tumor initiating cells (TICs), and that patient survival inversely correlates with TIC gene expression. Here we generated a prognostic signature for HER2+ breast cancer from TICs purified from MMTV-Her2/Neu mammary tumors. TICs from this model, identified as Lin-:CD24+:JAG1- at a frequency of 2-5% by serial and single cell transplantation assays, showed elevated expression of proliferation genes and low expression of differentiation genes (compared to non-TIC fraction CD24- of the same tumor).
We used microarrays to detect differentially expressed genes in the TIC fraction compared to the non-TIC fraction of the same tumor

overall_design: Cells from each primary tumor were separated by FACS into TIC and non-TIC fractions and total RNA was extracted and hybridized on Affymetrix microarrays.

first: Tao

last: Deng

first: Sean

last: Egan

first: Eldad

last: Zacksenhaus