title: p53 amplifies Toll-like receptor 5 response in MCF-7 cells

status: Public on Aug 26 2015

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

summary:
Using gene expression profiling we characterize the global effect of p53 on the TLR5-mediated transcription in MCF7 cells. We found that combined activation of p53 and TLR5 pathways synergistically increases expression of over 200 genes, mostly associated with immunity and inflammation. The synergy was observed in several human cancer cells and primary lymphocytes.
Oncotarget. 2015 Jul 10;6(19):16963-80, PMID 26220208

overall_design: 10 experimental conditions, each in triplicate, several samples were hybridized twice at two separate ocasions as indicated in 'description' field.  29 samples total and 35 arrays total.

first: Maria

last: Shatz

first: Igor

last: Shats

last: Menendez

first: Michael

last: Resnick


title: Expression data comparing OTX2-overexpressing human neural precursors to human neural precursor cells

status: Public on Aug 25 2015

city: Winnipeg

first: Tamra

last: Werbowetski-Ogilvie

state: Manitoba

address: 611-745 Bannatyne Avenue

department: Biochemistry & Medical Genetics

country: Canada

institute: University of Manitoba

summary:
Medulloblastoma (MB) is the most common malignant primary pediatric brain tumor and is currently divided into 4 subtypes based on different genomic alterations, gene expression profiles and response to treatment: WNT, Sonic Hedgehog (SHH), Group 3 and Group 4. The extensive heterogeneity has made it difficult to assess the relevance of genes to malignant progression. For example, expression of the transcription factor, OTX2, is frequently dysregulated in multiple MB variants; however, it's role may be subtype specific. Here, we utilized human embryonic stem cell-derived neural precursors to determine the role of OTX2 in MB tumor progression using gain and loss of function studies.
We used global gene expression profiling to determine what transcripts and pathways were differentially expressed following overexpression of OTX2 in human embryonic neural precursor cells.

overall_design: OTX2 was stably overexpressed in human embyronic neural precursors (hEN) by lentiviral transduction. OTX2-hENs and control hENs were then grown as neurospheres in defined medium and collected at passage 2. RNA was extracted using the Norgen All-in-One kit.


title: Expression data comparing transformed or neoplastic human neural precursors following OTX2 knockdown to transformed  human neural precursor cells

summary:
Medulloblastoma (MB) is the most common malignant primary pediatric brain tumor and is currently divided into 4 subtypes based on different genomic alterations, gene expression profiles and response to treatment: WNT, Sonic Hedgehog (SHH), Group 3 and Group 4. The extensive heterogeneity has made it difficult to assess the relevance of genes to malignant progression. For example, expression of the transcription factor, OTX2, is frequently dysregulated in multiple MB variants; however, it's role may be subtype specific. Here, we utilized human embryonic stem cell-derived neural precursors to determine the role of OTX2 in MB tumor progression using gain and loss of function studies.
We used global gene expression profiling to determine what transcripts and pathways were differentially expressed following knockdown of OTX2 in transformed or neoplastic human embryonic neural precursor cells.

overall_design: OTX2 was knocked down in transformed human embyronic neural precursors (trans-hEN) using Silencer select siRNAs. trans-hEN OTX2 KD and scrambled control trans-hENs were then grown as neurospheres in defined medium and collected at passage 1. RNA was extracted using the Norgen All-in-One kit.


title: Surface Topography Enhances Differentiation of Mesenchymal Stem Cells Towards Osteogenic and Adipogenic Lineages

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

summary: Surface topography impacts on cell growth and differentiation, but it is not trivial to generate homogeneous surface structures and to define the specific morphological parameters of relevance. In this study, we have compared gene expression profiles of mesenchymal stem cells (MSCs) on nanostructured groove/ridge surfaces. Patterns were generated in polyimide using multi beam laser interference. These structures affected cell size and orientation of human MSCs. Furthermore, the nano-patterns with a periodicity of 650 nm increased differentiation towards osteogenic and adipogenic lineages. However, in absence of differentiation media the surface structures did neither induce differentiation, nor lineage-specific gene expression changes – as assessed by genome wide gene expression profiles with Affymetrix microarray technology. Our results demonstrate that grooves and ridges at a periodicity of 650 nm enhance the propensity of MSCs to differentiate towards adipogenic and/or osteogenic lineages – but they do not directly govern lineage-specific gene expression changes.

overall_design: 9 samples were hybridized to the GeneChip Human Gene 2.0 ST Array (Affymetrix). In comparison to the manuscript the donor IDs refer as follows: donor 1 = AT57; donor 2 = AT58; donor 3 = AT61.

first: Giulio

last: Abagnale

last: Steger

first: Hoa

middle: V

last: Nguyen

first: Nils

last: Hersch

first: Sylvia

last: Joussen

first: Bernd

last: Denecke

first: Rudolf

last: Merkel

last: Hoffmann

first: Uwe

last: Schnakenberg

first: Arnold

last: Gillner


title: Expression array analysis of the hepatocyte growth factor (HGF) invasive program

city: Bethesda

first: Donald

middle: P

last: Bottaro

state: MD

address: Bldg 10 CRC Rm 2-3952, 10 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

summary:
HGF stimulates mitogenesis, motogenesis and morphogenesis in most epithelial target cells. Selective inhibition of HGF signaling blocks spontaneous metastasis, but not primary tumor growth, in the prostate adenocarcinoma derived PC3M cell xenograft model.
To identify the HGF activated genes and pathways that contribute to cell motility and invasion, i.e. the HGF invasive program, expression profiling was performed on PC3M cells that were untreated or were treated with human HGF (hHGF), which drives all 3 primary activities, or with human HGF/NK2 (hNK2) or murine HGF (mHGF), which drive motility and invasion but not proliferation in human cells.
Differences in gene expression profiles among these four groups were used to distiniguish between events associated with invasion (resulting from hNK2 or mHGF treatment) from those associated with the combination of invasion and proliferation (resulting from hHGF treatment).

overall_design: PC3M cells were left untreated or treated with hHGF, hNK2 or mHGF for 8, 16 or 32 hours prior to RNA extraction, cDNA preparation and array hybridization.

first: Fabiola

last: Cecchi

first: Chih-Jian

last: Lih

first: Young

middle: H

last: Lee

first: William

last: Walsh

first: Daniel

middle: C

last: Rabe

first: Paul

middle: M

last: Williams


title: DNA methylation signatures triggered by prenatal maternal stress exposure to a natural disaster: Project Ice Storm

city: Montreal

first: Moshe

last: Szyf

state: Quebec

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

department: Pharmacology

institute: McGill University

type: Methylation profiling by genome tiling array

summary: Background: Prenatal maternal stress (PNMS) predicts a wide variety of behavioral and physical outcomes in the offspring. Although epigenetic processes may be responsible for PNMS effects, human research is hampered by the lack of experimental methods that parallel controlled animal studies. Disasters, however, provide natural experiments that can provide models of prenatal stress. Methods: Five months after the 1998 Quebec ice storm we recruited women who had been pregnant during the disaster and assessed their degrees of objective hardship and subjective distress. Thirteen years later, we investigated DNA methylation profiling in T cells obtained from 36 of the children, and compared selected results with those from saliva samples obtained from the same children at age 8. Results: Prenatal maternal objective hardship was correlated with DNA methylation levels in 1675 CGs affiliated with 957 genes predominantly related to immune function; maternal subjective distress was uncorrelated. DNA methylation changes in SCG5 and LTA, both highly correlated with maternal objective stress, were comparable in T cells, peripheral blood mononuclear cells (PBMCs) and saliva cells. Conclusions: These data provide first evidence in humans supporting the conclusion that PNMS results in a lasting, broad, and functionally organized DNA methylation signature in several tissues in offspring. By using a natural disaster model, we can infer that the epigenetic effects found in Project Ice Storm are due to objective levels of hardship experienced by the pregnant woman rather than to her level of sustained distress.

overall_design: Bisulphite converted DNA from the 34 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Lei

last: Cao-Lei

first: Renaud

last: Massart

first: Matthew

middle: J

last: Suderman

first: Ziv

last: Machnes

first: Guillaume

last: Elgbeili

first: David

last: Laplante

first: Suzanne

last: King


title: Expression profile of ZOS and ZOSM osteosarcoma cell lines

city: Toronto

first: Jinchang

last: Lu

state: Ontario

address: 101 College Street

institute: Princess Margaret Cancer Centre, University of Toronto

summary:
Pulmonary metastasis is the main cause of medical failure and death of osteosarcoma patients. Despite intensive search for new therapeutic strategies, survival has not improved during the last two decades. Therefore, it’s very urgent to understand the underlying mechanisms of tumor progression to identify targets of novel therapies for osteosarcoma.
We used microarrays to identify the metastasis-driving gene during osteosarcoma metastasis

overall_design: Microarrays are performed in ZOS and ZOSM-two syngenic primary human osteosarcoma cell lines with low and high metastatic potential which are established in our lab

first: Jin

last: Wang


title: Dickkopf 3 Promotes the Differentiation of Substantia Nigra Dopaminergic Neurons In Vivo and from Pluripotent Stem Cells In Vitro

status: Public on Aug 22 2015

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
WNT1/beta-catenin signaling plays a crucial role in the generation of mesodiencephalic dopaminergic (mdDA) neurons including the Substantia nigra pars compacta (SNc) subpopulation, whose degeneration is a hallmark of Parkinson’s Disease (PD). However, the precise functions of WNT/beta-catenin signaling in this context remain unknown. Using mutant mice, primary ventral midbrain (VM) cells and pluripotent stem cells (mouse embryonic stem cells and induced pluripotent stem cells), we show that Dickkopf 3 (DKK3), a secreted glycoprotein that modulates WNT/beta-catenin signaling, is specifically required for the correct differentiation of a rostrolateral mdDA precursor subset into SNc DA neurons.
Dkk3 transcription in the murine VM coincides with the onset of mdDA neurogenesis and is required for the maintenance of LMX1A and consequently PITX3 expression in rostrolateral mdDA precursors, without affecting the proliferation or specification of their progenitors. Treatment of primary VM cells or differentiating pluripotent stem cells with recombinant WNT1 and/or DKK3 proteins consistently increases the proportion of mdDA cells with SNc DA neuron identity and promotes their survival in vitro. The SNc DA pro-differentiation and pro-survival properties of DKK3, together with its known anti-tumorigenic effect, therefore make it an ideal candidate for the improvement of regenerative and neuroprotective strategies in the treatment of PD.

overall_design: We performed gene expression microarray analysis on iPSC-derived and FACS-sorted GFP-positive Pitx3GFP/+ mdDA neurons, differentiated in the presence or absence of recombinant human WNT1 and recombinant human DKK3. In addition, we analysed primary and FACS-sorted GFP-positive Pitx3+/GFP mdDA neurons isolated from the E13.5 and E14.5 ventral midbrain of Pitx3+/GFP embryos

first: Yoshiyasu

last: Fukusumi

first: Florian

last: Meier

first: Sebastian

last: Götz

first: Friederike

last: Matheus

first: Benedict

last: Rauser

first: Theresa

last: Faus-Kessler

first: Eleonora

last: Minina

first: Jingzhong

last: Zhang

first: Elizabeth

last: Andersson

first: Johan

last: Ericson

first: Meng

last: Li

first: Ruth

last: Beckervordersandforth

first: Martin

last: Irmler

first: Christof

last: Niehrs

first: Antonio

last: Simeone

first: Wolfgang

last: Wurst

first: Nilima

last: Prakash


title: Transcriptional profiling shows altered expression of wnt pathway- and lipid metabolism-related genes as well as melanogenesis-related genes in melasma.

status: Public on Aug 19 2015

city: Sophia Antipolis

first: CORINNE

last: MENIGOT

address: 2400 route des colles

country: France

institute: GALDERMA R & D

summary: Melasma is a commonly acquired hyperpigmentary disorder of the face, but its pathogenesis is poorly understood and its treatment remains challenging. We conducted a comparative histological study on lesional and perilesional normal skin to clarify the histological nature of melasma. Significantly, higher amounts of melanin and of melanogenesis-associated proteins were observed in the epidermis of lesional skin, and the mRNA level of tyrosinase-related protein 1 was higher in lesional skin, indicating regulation at the mRNA level. However, melanocyte numbers were comparable between lesional and perilesional skin. A transcriptomic study was undertaken to identify genes involved in the pathology of melasma. A total of 279 genes were found to be differentially expressed in lesional and perilesional skin. As was expected, the mRNA levels of a number of known melanogenesis-associated genes, such as tyrosinase, were found to be elevated in lesional skin. Bioinformatics analysis revealed that the most lipid metabolism-associated genes were downregulated in lesional skin, and this finding was supported by an impaired barrier function in melasma. Interestingly, a subset of Wnt signaling modulators, including Wnt inhibitory factor 1, secreted frizzled-related protein 2, and Wnt5a, were also found to be upregulated in lesional skin. Immunohistochemistry confirmed the higher expression of these factors in melasma lesions.

overall_design: Total of 48 chips. 12 patients : 2 biospies per patient: 1 lesional and 1 non lesional: 1 technical replicate per chip

first: J

last: Voegel


title: Gene expression data from CD14++ CD16- classical monocytes from healthy volunteers and patients with pancreatic ductal adenocarcinoma

status: Public on Aug 21 2015

city: London

first: Jenny

last: Cook

address: John Vane Science Centre, Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute

summary:
Transcriptomic profiling of peripheral immune cells can provide a wealth of information.
Classical CD14++ CD16- monocytes were isolated from the peripheral blood of healthy volunteers and patients with pancreatic ductal adenocarcinoma and profiled for differential gene expression using Affymetrix human Genechips 2.1 U133.

overall_design: Differentially expressed genes were identified comparing gene expression profiles between healthy and PDAC.

first: Raphael

last: Zollinger

first: Thorsten

last: Hagemann


title: Gene expression induced by treatment of artemin in HCC.CELls

status: Public on Aug 27 2015

city: Shanghai

first: Jin

last: Hou

address: 800 Xiangyin Road

country: China

institute: Second Military Medical University

summary: HCC cell line SMMC-7721 were treatment with human recombinant artemin for 12 hours. Total RNA was extracted and the induced gene expression was analyzed.

overall_design: Analysis of gene expression induced by artemin treatment

first: Xuetao

last: Cao


title: Gene expression array between wild-type and mutant Hnf1b cells

status: Public on Aug 17 2015

city: Dallas

first: Min Soo

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

department: Department of Clinical Sciences

institute: University of Texas Southwestern

summary:
The complete specrtum of genes that are subject to regulation by Hnf1b in mouse kidney cells is not known.
We used microarray to determine genes that are significenlty deregulated in repsonse to altered HNF1b activity.

overall_design: Cells were cultured for 24 hrs followed by induction of Dominant-negative HNF1b for 48 hours.

first: Karam

last: Aboudehen

first: Peter

last: Igarashi


title: The idiopathic preterm delivery methylation profile in umbilical cord blood

city: Amsterdam

first: Febilla

last: Fernando

address: Meibergdreef 9

department: Reproductive Biology Laboratory

country: Netherlands

institute: Academic Medical Center

summary: Genome wide DNA methylation differences in umbilical cord blood  (UCB) of preterm and term born neonates. The Illumina 450K Human DNA methylation Beadchip was used to obtain the DNA methylation profiles of 12 preterm and 12 term UCB samples  across 450,000 CpGs. 2 samples were removed due to failed quality control, and BMIQ normalization was done with 11 preterm and 11 term samples.

overall_design: The bisulphite converted DNA of 12 preterm and 12 term samples was subjected to whole genome amplification, fragmentation followed by hybridization on Illumina 450K Human methylation bead chip array.

first: Remco

last: Keijser

last: Henneman

first: Anne-Marie

middle: F

last: van der Kevie-Kersemaekers

first: Adri

middle: N

last: Mul

first: Marcel

last: Mannens

first: Joris

middle: A

last: van der Post

first: Gijs

middle: B

last: Afink

first: Carrie

last: Ris-Stalpers


title: Transcriptome analysis of Spinocerebellar Ataxia 17  Aug

city: Atlanta

first: Viren

last: Patel

state: GA

address: 101 Woodruff Circle

department: EICC

institute: Emory University School of Medicine

summary: Transcriptome analysis of extracted total RNA from the the cerebellum and muscle of Spinocerebellar Ataxia 17 knock-in mouse model

overall_design: We analyzed mRNA from 3 wild type mice and 3 SCA17 KI mice (both cerebellum and TA muscle) using the Gene Expression 8 Affymetrix Mouse Gene 1.0ST

first: Shanshan

last: Huang

first: Su

last: Yang

first: Xiao

last: Li


title: Smoking accelerated aging of the small airway epithelium

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: Aging involves multiple biologically complex processes characterized by a decline in cellular homeostasis over time leading to a loss and impairment of physiological integrity and function. Specific cellular hallmarks of aging include abnormal gene expression patterns, shortened telomeres and associated biological dysfunction. Like all organs, the lung demonstrates both physiological and structural changes with age that result in a progressive decrease in lung function in healthy individuals. Cigarette smoking accelerates lung function decline over time, suggesting smoking accelerates aging of the lung. Based on this data, we hypothesized that cigarette smoking accelerates the aging of the small airway epithelium, the cells that take the initial brunt of inhaled toxins from the cigarette smoke and one of the primary sites of pathology associated with cigarette smoking. Using the sensitive molecular parameters of aging-related gene expression and telomere length, the aging process of the small airway epithelium was assessed in age matched healthy nonsmokers and healthy smokers with no physical manifestation of lung disease or abnormalities in lung function. Analysis of a 73 gene aging signature demonstrated that smoking significantly dysregulates 18 aging-related genes in the small airway epithelium. In an independent cohort of male subjects, smoking significantly reduced telomere length in the small airway epithelium of smokers by 14% compared to nonsmokers. These data provide biologic evidence that prior to the clinical manifestation of lung disease; smoking accelerates aging of the small airway epithelium.

overall_design: This study provides biologic evidence that before the clinical manifestation of lung function decline, smoking accelerates aging of the small airway epithelium by dysregulation of age-related gene expression and enhanced telomere erosion.

first: Matthew

middle: S

last: Walters

first: Bishnu

last: De

first: Jacqueline

last: Salit

first: Lauren

last: Buro-Auriemma

first: Tim

last: Wilson

first: Allison

last: Rogalski

first: Lindsay

last: Lief

first: Neil

middle: R

last: Hackett

first: Michelle

last: Staudt

first: Ann

middle: E

last: Tilley

first: Ben-Gary

last: Harvey

first: Robert

last: Kaner

first: Jason

middle: G

last: Mezey

first: Beth

last: Ashbridge

first: Malcolm

last: Moore

first: Ronald

last: Crystal


title: Epigenetic screen of  metastasis-driving genes in osteosarcoma

first: Jinchang

last: Lu

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

overall_design: Refer to individual Series


title: Gene expression profile of human T-ALL cell line JURKAT after TRIB2 knockdown

status: Public on Aug 14 2015

city: Singapore

first: Takaomi

last: Sanda

address: 14 Medical Dr 12-01

country: Singapore

institute: Cancer Science Institute of Singapore, National University of Singapore

summary: To dissect molecular pathways regulated by TRIB2 in T-ALL, we performed microarray gene expression profiling in the TAL1-positive T-ALL cells (Jurkat) after TRIB2 knockdown.

overall_design: A human T-ALL cell line JURKAT cells were transduced with TRIB2 (shTRIB2) or control GFP shRNA (shGFP).  Experiment was done in biological duplicate (dup1 and dup2). A total of 4 RNA samples (2 control and 2 TRIB2 knockdown) were used for microarray gene expression analysis.


title: Expression data from mouse colon dendritic cell subsets

status: Public on Aug 24 2015

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

institute: Singapore Immunology Network

summary: Characterization of colon CD11chigh/MHCII+ myeloid cell subsets

overall_design: Colon lamina propria MHC+CD11chigh cells were sorted on the basis of CD103 and CD11b expression as follows: CD103+CD11b-, CD103+CD11b+, CD103-CD11b+.

first: Christiane

last: Ruedl


title: Annexin A6-mediated tumor suppression requires inhibition of calcium influx and down-regulation of the calcium-activated RasGRF2

status: Public on Aug 15 2015

city: Nashville

first: Amos

last: Sakwe

state: TN

address: 1005 Dr. DB Todd Jr Blvd

department: Biochemistry and Cancer Biology/SOGSR

institute: Meharry Medical Colle

summary: Membrane association of the tumor suppressor, annexin A6 (AnxA6), has been shown to regulate plasma membrane permeability to extracellular Ca2+, inhibit anchorage-independent tumor cell growth and paradoxically, promote tumor cell motility by mechanisms that remains poorly understood. Here, we identified RasGRF2, a Ca2+-activated Ras-specific guanine nucleotide exchange factor, as a major effector of AnxA6-elicited tumor-associated phenotypes in breast cancer cells. We demonstrate that reduced expression or loss of AnxA6 in breast cancer cells is associated with up-regulation of RasGRF2, increased Ras activity and consequently, early onset and rapid growth of xenograft tumors. Meanwhile, up-regulation of AnxA6 in AnxA6-low breast cancer cells is associated with a decrease in Ras activity and growth of xenograft tumors but on the contrary, an increase in Cdc42 activity and EGF-stimulated cell motility. Inhibition of Ca2+ influx into AnxA6-low breast cancer cells via Ni2+-sensitive or non-selective Ca2+ channels dose-dependently suppressed the expression of RasGRF2, induced the expression of AnxA6 and consequently, inhibited tumor cell proliferation. Finally, aberrant expression of RasGRF2 may be triggered by AnxA6-mediated or pharmacological inhibition of non-selective Ca2+ channels and occurs at least in part, by promoter methylation. These data for the first time identify RasGRF2 as a major effector of AnxA6-dependent breast tumor growth and motility and that regulated Ca2+ influx and/or RasGRF2 may be potential therapeutic targets for rapidly growing AnxA6-low breast carcinomas

overall_design: Four replicates of cell lines generated by stable transfection of control and two distinct shRNAs targeting annexin A6 in the mesencymal-like BT-549 breast cancer cell line

first: Jennifer

last: LeBlanc


title: In vitro activation and reversion of human primary hepatic stellate cells

status: Public on Aug 12 2015

city: Brussels

first: Adil

last: El Taghdouini

address: Laarbeeklaan, 103

department: Cell Biology

country: Belgium

institute: Vrije Universiteit Brussel

summary: Liver fibrosis is characterized by the excessive formation and accumulation of matrix proteins as a result of wound healing in the liver. A main event during fibrogenesis is the activation of the liver resident quiescent hepatic stellate cell (qHSC). Recent studies suggest that reversion of the activated HSC (aHSC) phenotype into a quiescent-like phenotype could be a major cellular mechanism underlying fibrosis regression in the liver, thereby offering new therapeutic perspectives for the treatment of liver fibrosis. The goal of the present study is to identify experimental conditions that can revert the activated status of human HSCs and to map the molecular events associated with this phenotype reversion by gene expression profiling

overall_design: Transcriptomic profiling of primary human quiescent HSCs (qHSCs), in vitro activated HSCs (aHSCs) and in vitro reverted HSCs   (rHSCs).  The cell types come from different donors (This is detailed in the original manuscript.).

first: Mustapha

last: Najimi

first: Pau

last: Sancho-Bru

first: Etienne

last: Sokal

first: Leo

last: van Grunsven


title: Cytomegalovirus promotes maintenance and growth of glioblastoma stem cells [Mouse gene expression]

status: Public on Aug 13 2015

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

summary:
We introduced the HCMV IE1 gene into a mouse model of spontaneous glioma driven by p53KD and overexpression of Ras and PDGF and compared the transcriptomes of mouse gliomas +/- IE1. The following plasmids were utilized for glioma induction in equal parts: pT2/C-Luc/PGK-SB100, pT2/Cag-NrasV12, pT2/shP53/GFP4/mPDGF, and pT2/Cag-IE1 or pT2/C-Neo.

Primary human glioma stem cells were maintained in neurosphere growth conditions, treated with IE1 and control siRNA for 48-72h prior to RNA harvesting. Following hybridization to HCMV DNA arrays, data analysis revealed HCMV genes significantly altered by IE1KD, by comparing Samples 1-2 and 3-4 repectively.

overall_design:
Neonatal BALB/c and B6 mice were injected with the above mentioned plasmids at P1. Tumor formation was monitored using bioluminescence. Brain tissue was extracted at 50-60 days post plasmid injection.

Primary human glioma stem cells were maintained in neurosphere growth conditions, treated with IE1 and control siRNA for 48-72h prior to RNA harvesting. RNA was hybridized to HCMV spotted arrays.

first: Liliana

last: Soroceanu


title: Expression data from osteoclasts before and after co-culture with multiple myeloma plasma cells

city: Little Rock

first: Joshua

last: Epstein

department: Myeloma Institute for Research and Therapy

institute: University of Arkansas for Medical Sciances

summary:
To understand how interactions of myeloma cells with osteoclasts and mesenchymal stem cells in the bone marrow affect the clinical course of myeloma, we used microarrays to study changes in gene expression in freshly isolated myeloma plasma cells following co-cultures with osteoclasts (8 experiments) or with mesenchymal stem cells (13 experiments). Interaction with osteoclasts induced changes in the expression of 675 genes, and interaction with mesenchymal stem cells induced changes in the expression of 296 genes. Expression of only 58 genes commonly and similarly changed in both co-culture systems. Among these, we identified genes associated with overall, progression-free, and post-relapse survival, and developed survival prediction models. Gene expression data from 347 patients treated with total therapy 2 protocol, 433 with total therapy 3, and 98 patients who received various treatments (91 of them high-dose therapy with autologous stem cell support) were used for the analysis. Good predictive models were developed only for post-relapse survival, using genes involved in interaction with osteoclasts or with mesenchymal stem cells. The best predictive model used expression of first relapse of 33 probesets whose expression changed in myeloma cells following interaction with osteoclasts, with hazard ratios of 24, 20, and 12 for patients who relapsed following total therapy 2, total therapy 3 and the various other treatments, respectively. Among the probesets used for prediction, only 10, representing 8 genes, were commonly changed after both co-culture systems. These could present favorable target for therapy.

Global gene expression profiling of osteoclasts (OCs) before and after co-culture with primary multiple myeloma plasma cells (MMPCs) was done using Affymetrix microarrays.

overall_design: Eight MMPC and OC co-culture experiments were performed using MMPC isolated from 8 patients and OC prepared from 8 different patients.

first: Shmuel

last: Yaccoby


title: Expression data from multiple myeloma plasma cells and mesenchymal stem cells before and after co-culture

summary:
To understand how interactions of myeloma cells with osteoclasts and mesenchymal stem cells in the bone marrow affect the clinical course of myeloma, we used microarrays to study changes in gene expression in freshly isolated myeloma plasma cells following co-cultures with osteoclasts (8 experiments) or with mesenchymal stem cells (13 experiments). Interaction with osteoclasts induced changes in the expression of 675 genes, and interaction with mesenchymal stem cells induced changes in the expression of 296 genes. Expression of only 58 genes commonly and similarly changed in both co-culture systems. Among these, we identified genes associated with overall, progression-free, and post-relapse survival, and developed survival prediction models. Gene expression data from 347 patients treated with total therapy 2 protocol, 433 with total therapy 3, and 98 patients who received various treatments (91 of them high-dose therapy with autologous stem cell support) were used for the analysis. Good predictive models were developed only for post-relapse survival, using genes involved in interaction with osteoclasts or with mesenchymal stem cells. The best predictive model used expression of first relapse of 33 probesets whose expression changed in myeloma cells following interaction with osteoclasts, with hazard ratios of 24, 20, and 12 for patients who relapsed following total therapy 2, total therapy 3 and the various other treatments, respectively. Among the probesets used for prediction, only 10, representing 8 genes, were commonly changed after both co-culture systems. These could present favorable target for therapy.

Global gene expression profiling of primary multiple myeloma plasma cells (MMPCs) and mesenchymal stem cells (MSCs) before and after co-culture was done using Affymetrix microarrays.

overall_design: Thirteen MMPC and MSC co-culture experiments using MMPCs from 8 patients and MSCs from 5 healthy donors were performed.

first: Igor

last: Entin


title: Expression data from bone marrow-derived dendritic cells cultured in media containing different osmolaric conditions.

city: Heidelberg

first: Thomas

last: Hielscher

address: INF 280

department: Biostatistics

institute: German Cancer Research Center

summary: The functionality of dendritic cells might be influenced by alterations of their biophysic microenvironment, e.g. changes in salt concentration. Microarray analysis aims to evaluate whether dendritic cells cultured in medium containing different salt concentrations  modulate their gene expression profile.

overall_design: Dendritic cells derived from the bone marrow of mice were cultured in cell culture medium in the presence of different salt concentrations -+ LPS. Total RNA was isolated and processed as described in Material and Methods

first: Federica

last: Chessa


title: Gene expression profiling of preneoplastic K8-creERT2/PIK3CAH1047R mammary subsets

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

summary: This study examined the effect of mutant PIK3CAH1047R expression in mammary subsets of preneoplastic mammary glands from K8-creERT2/PIK3CA H1047R mice

overall_design: Mammary cell subpopulations were isolated from K8-creERT2/PIK3CAH1047R and K8-creERT2 control animals 4 weeks after activation of PIK3CA H1047R transgene expression by Tamoxifen injection. Pooled mammary glands of 2-3 estrus-synchronized mice per genotype were sorted in 3 independent sortings and used for microarray analysis (20 samples in total).

first: Shany

last: Koren

first: Stephane

last: Thiry

first: Mohamed

last: Bentires-Alj


title: Gene expression profiling of preneoplastic Lgr5-creERT2/PIK3CAH1047R mammary subsets

summary: This study examined the effect of mutant PIK3CAH1047R expression in mammary subsets of preneoplastic mammary glands from Lgr5-creERT2/PIK3CA H1047R mice

overall_design: Mammary cell subpopulations were isolated from Lgr5-creERT2/PIK3CA H1047R and Lgr5-creERT2 control animals 4 weeks after activation of PIK3CA H1047R transgene expression by Tamoxifen injection. Pooled mammary glands of 2-3 estrus-synchronized mice per genotype were sorted in 3 independent sortings and used for microarray analysis (24 samples in total).


title: Gene expression profiling of Lgr5-creERT2/PIK3CA H1047R and K8-creERT2/PIK3CA H1047R-evoked mammary tumors

summary: This study examined the gene expression profile of mammary tumors derived from Lgr5- and K8-positive cell-of-origins

overall_design: Mammary tumors and reference mammary glands from control mice were collected, cryo-homogenized, total RNA was isolated and analyzed by microarray (total 25 samples).

first: Joana

last: Pinto do Couto


title: MCF10A YAP-OE RNA-seq analysis

city: La Jolla

first: Hyun Woo

last: Park

state: CA

address: 2880 Torrey Pines Scenic Dr

institute: UCSD

type: Expression profiling by high throughput sequencing

summary:
We investigated mRNA expression profile altered by YAP overexpression in mammary gland epithelial cells
Raw data are not available because they were lost by submitter's system breakdown.

overall_design: Compare mRNA level from control versus YAP overexpressing MCF10A cells.

first: Yu

last: Faxing

first: Guan

last: Kun-Liang


title: Intra-gene DNA methylation variability is a clinically independent prognostic marker in women’s cancers

city: Manchester

first: Sacha

last: Howell

address: Oglesby Cancer Research Centre

department: Faculty of Biology, Medicine and Health

institute: The University of Manchester

summary:
Differences in DNA methylation (DNAm) levels are amongst the earliest changes in human carcinogenesis, and are a hallmark of cancer, offering the potential for novel strategies to predict cancer biology and outcome. Hence, DNAm markings might provide a valuable lead for the development of DNA-based cancer biomarkers in tissue and bodily fluids.
The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in a total of 221 samples, including 171 serous, 18 endometrioid, 14 clear cell, 9 mucinous and 9 other histological cancer subtypes.

overall_design: Bisulphite converted DNA from the 221 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

first: Martin

last: Widschwendter


title: Human Cytomegalovirus in Glioblastoma Stemness--Results from Human, Mouse and HCMV DNA arrays

first: Saleena

last: Ghanny

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus
Human betaherpesvirus 5


title: Gene expression analysis of directly converted brown adipocytes (dBAs). [mouse]

city: Kyoto

first: Kenta

last: Yamamoto

address: Kajicho 465

department: Immunology

country: Japan

institute: Kyoto Prefectural University of Medicine

summary:
Comparasion of each cell mRNA expression pattern
Mouse fibroblasts were directly converted into brown adipocytes (dBAs) by transducing some transcription factors. To characterize the dBAs more in detail, RNA extracted from the mouse brown adipose tissue, mouse dBAs, and mouse iPS-derived brown adipocytes (iBAs) were subjected to DNA microarray analysis, and global gene expression profiles of the cells were compared.

overall_design: 3 samples

first: Tsunao

last: Kishida

first: Toshiro

first: Osam

last: Mazda


title: down-regulation of dermcidin by shRNA in breast cancer cell line MDA-MB-361

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: DCD is a gene amplified and overexpressed in a subset of breast tumors acting as a growth and survival factor. Patients with DCD-positive breast cancer have worse prognostic features. To investigate the role of DCD in breast tumorigenesis, we analyzed the consequences of its downregulation in human breast cancer cell lines using three specific shRNA lentivirus vectors. Genes up- and down-regulated by DCD were identified using Affymetrix microarray and analyzed by MetaCore Platform. We found that loss of DCD expression led to reduced cell proliferation, resistance to apoptosis, and suppressed tumorigenesis in immunodeficient mice. Network analysis of gene expression data revealed perturbed ERBB signaling following DCD shRNA expression including changes in the expression of ERBB receptors and their ligands. These findings imply that DCD promotes breast tumorigenesis via modulating the activity of the ERBB signaling pathways. As ERBB signaling is also important for neural survival, HER2+ breast tumors may highjack DCD’s neural survival-promoting functions to promote tumorigenesis.

overall_design: MDA-MB-361 human breast cancer cell line expressing DCD-targeting shRNA in pLKO vector (clones 1, 2 and 3) and pLKO control vector

first: Jasna

last: Markovic

first: Dayson

last: Moreira

first: Daniel

last: Carrasco

first: Jun

last: Yao

first: Dale

last: Porter

first: Ricardo

last: Moura

first: Anamaria

last: Camargo

first: Cibely

last: Fontes-Oliveira

first: Miguel

last: Malpartida

first: Silvia

last: Carambula

first: Edouard

last: Vannier

first: Bryan

last: Strauss

first: Alda

last: Wakamatsu

first: Venancio

last: Alves

first: Angela

last: Logullo

first: Fernado

last: Soares

first: Jose

last: Belizario


title: Reduction of DNA methylation suppresses colon carcinogenesis through induction of tumor cell differentiation

status: Public on Aug 05 2015

city: Tokyo

first: Yasuhiro

last: Yamada

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

department: Department of Molecular Pathology

institute: University of Tokyo

summary: In this study, we analyzed global gene expressions of colon tumors from DNA hypomethylated and the control mice. We found that DNA hypomethylated tumors express significantly higher levels of intestinal differentiation-related genes when compared with the control tumors. These results suggest that DNA methylation may play a role in the maintenance of undifferentiated state of colon tumor cells.

overall_design: Two different Dnmt1 mutant alleles were used in this study; hypomorphic Dnmt1chip allele and conventional KO Dnmt1c allele, which described previously. Previous studies indicated that Dnmt1chip/c mice have reduced DNA methylation contents at pericentromeric satellite repeats, while Dnmt1chip/+ mice have the same levels of genomic methylation as wildtype mice. Experimental mice in an isogenic F1 hybrid background were obtained by breeding Dnmt1c/+; ApcMin/+ mouse in the C57BL/6 background with Dnmt1chip/chip; Apc+/+ mouse in the 129Sv4 background. Six-week-old DNA hypomethylated (Dnmt1chip/c; ApcMin/+) and the control (Dnmt1chip/+; ApcMin/+) mice were fed with 2% (w/v) dextran sodium sulfate (DSS), a potent promoter for colon carcinogenesis. At 20 weeks of age, colon tumors were harvested from both cohorts (n=3 for both DNA hypomethylated tumors and the control tumors) and analyzed for their gene expressions.

first: Katsunori

last: Semi


title: Epigenetic landscape correlates with genetic subtype but does not predict outcome in childhood acute lymphoblastic leukemia

status: Public on Aug 11 2015

city: Newcastle upon Tyne

first: Alem

middle: Selassie

last: Gabriel

address: Queen Victoria Rd

department: Northern Institute for Cancer Research

institute: Newcastle University

summary: We analyzed 52 Diagnostic samples from childhood Acute lymphoblastic leukemia samples

overall_design: We compared methylation profiles with four ALL cytogentic subtypes using (n=26) long term remission vs. (n=26) that went on to relapse

first: A


title: Gene expression profile (GEP) of miR-486-3p overexpressing CD34+ HPCs

status: Public on Aug 07 2015

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary:
The transcription factor c-Myb plays a key role in human primary CD34+ hematopoietic progenitor cells (HPCs) lineage choice, by enhancing erythropoiesis at the expense of megakaryopoiesis. We previously demonstrated that c-Myb affects erythroid versus megakaryocyte lineage decision in part by transactivating KLF1 and LMO2 expression. To further unravel the molecular mechanisms through which c-myb affects lineage fate decision, we profiled the miRNA and mRNA changes in myb-silenced CD34+ HPCs. The integrative analysis of miRNA/mRNA expression changes upon c-myb silencing in human CD34+ HPCs highlighted a set of 19 miRNA with 150 anticorrelated putative target mRNAs. Among the miRNAs downregulated in myb-silenced progenitors with the highest number of predicted target mRNAs, we selected hsa-miR-486-3p based on the in vitro effects of its overexpression on HPCs commitment. Indeed, morphological and flow cytometric analyses after liquid culture showed that hsa-miR-486-3p overexpression in HPCs enhanced erythroid and granulocyte differentiation while restraining megakaryocyte and macrophage differentiation. Moreover, collagen-based clonogenic assay demonstrated a strong impairement megakaryocyte commitment upon hsa-miR-486-3p overexpression in CD34+ cells.
Moreover, in order to identify the mRNA target through which hsa-miR-486-3p affects lineage fate decision, we profiled the mRNA changes in mimic transfected CD34+ HPC by means of Affymetrix GeneAtlas U219 strip array. Gene expression profiling of hsa-miR-486-3p overexpressing CD34+ cells enabled us to identify a set of 8 genes downregulated and computationally predicted, putative hsa-miR-486-3p targets. Among them, we selected c-maf transcript as upregulated upon myb silencing. Worth of note, c-maf silencing in CD34+ progenitor cells was able to reverse the affects of myb silencing on erythroid versus megakaryocyte lineage choice.  Integrative miRNA/mRNA analysis highlighted a set of miRNAs and anticorrelated putative target mRNAs modulated upon myb silencing, therefore potential players in myb-driven HPCs lineage choice. Among them, we demonstrated the hsa-miR-486-3p/c-maf pair as partially contributing to the effects of myb on HPCs commitment. Therefore, our data collectively identified myb-driven hsa-miR-486-3p upregulation and subsequent c-maf downregulation as a new molecular mechanism through which cMyb favours erythropoiesis while restraining megakaryopoiesis.

overall_design: Gene expression profile (GEP) was performed on total RNA derived from three independent experiments at 24h after the last nucleofection.

first: Elisa

last: Bianchi

first: Jenny

last: Bulgarelli

first: Giorgia

last: Sacchi

first: Samantha

last: Ruberti

first: Ruggiero

last: Norfo

first: Sebastiano

last: Rontauroli

first: Valentina

last: Pennucci

first: Roberta

last: Zini

first: Simona

last: Salati

first: Zelia

last: Prudente

first: Sergio

last: Ferrari


title: Gene expression analysis of directly converted brown adipocytes (dBAs).

first: Kenta

last: Yamamoto

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

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: IL-8 Confers Acquired Resistance to EGFR Inhibitors through Regulating Stem Cell-like Properties in Lung Cancer

city: Taipei

first: Jin-Yuan

last: Shih

address: #7, Chung-Shan South Road,

department: Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital

summary:
Previous study has demonstrated that PC9/gef cells are resistant to gefitinib-induced aspoptosis. To investigate the regulators contributed to gefitinib resistance in lung cancer, we analyzed the gene expression profiles between PC9 and PC9/gef cells.
Our results showed that IL-8 contributes to gefitinib resistance and cancer stemness. In contrast, IL-8 knockdown decreased stem-like characteristics and increased gefitinib-induced apoptosis in PC9/gef cells.

overall_design: RNAs extracted from gefitinib-sensitive PC9 cells and gefitinib-resistant PC9/gef cells were hybridized on Affymetrix microarrays. We tried to compare the differential gene expression profiles between PC9 and PC9/gef cells to identify the possible regulators in gefitinib resistance.

first: Yi-Nan

last: Liu

first: Tzu-Hua

last: Chang

first: Meng-Feng

last: Tsai

first: Shang-Gin

last: Wu

first: Hsuan-Yu

last: Chen

first: Sung-Liang

last: Yu

first: James

last: Yang


title: Gene expression profile (GEP) of myb-silenced CD34+ HPCs

first: Rossella

last: Manfredini

summary:
The transcription factor cMyb plays a key role in human primary CD34+ hematopoietic progenitor cells (HPCs) lineage choice, by enhancing erythropoiesis at the expense of megakaryopoiesis. We previously demonstrated that cMyb affects erythroid versus megakaryocyte lineage decision in part by transactivating KLF1 and LMO2 expression. To further unravel the molecular mechanisms through which cmyb affects lineage fate decision, we profiled the miRNA and mRNA changes in myb-silenced CD34+ HPCs. mRNA and miRNA expression for each sample were profiled by Affymetrix GeneAtlas U219 strip array and Exiqon Human miRNome PCR Panel, respectively. miRNA/mRNA data were integrated by Ingenuity Pathway Analysis.
The integrative analysis of miRNA/mRNA expression changes upon c-myb silencing in human CD34+ HPCs highlighted a set of 19 miRNA with 150 anticorrelated putative target mRNAs. Among the miRNAs downregulated in myb-silenced progenitors with the highest number of predicted target mRNAs, we selected hsa-miR-486-3p based on the in vitro effects of its overexpression on HPCs commitment. Indeed, morphological and flow cytometric analyses after liquid culture showed that hsa-miR-486-3p overexpression in HPCs enhanced erythroid and granulocyte differentiation while restraining megakaryocyte and macrophage differentiation. Moreover, collagen-based clonogenic assay demonstrated a strong impairement megakaryocyte commitment upon hsa-miR-486-3p overexpression in CD34+ cells. Gene expression profiling of hsa-miR-486-3p overexpressing CD34+ cells enabled us to identify a set of 8 genes downregulated and computationally predicted, putative hsa-miR-486-3p targets. Among them, we selected c-maf transcript as upregulated upon myb silencing. Worth of note, c-maf silencing in CD34+ progenitor cells was able to reverse the affects of myb silencing on erythroid versus megakaryocyte lineage choice.  Integrative miRNA/mRNA analysis highlighted a set of miRNAs and anticorrelated putative target mRNAs modulated upon myb silencing, therefore potential players in myb-driven HPCs lineage choice. Among them, we demonstrated the hsa-miR-486-3p/c-maf pair as partially contributing to the effects of myb on HPCs commitment. Therefore, our data collectively identified myb-driven hsa-miR-486-3p upregulation and subsequent c-maf downregulation as a new molecular mechanism through which cMyb favours erythropoiesis while restraining megakaryopoiesis.

overall_design: RNA from CD34+ HPCs transfected once/twice/3 times with c-myb-targeting/non targeting control siRNAs was collected for a set of 5 independent experiments.

first: Elisa

last: Bianchi

first: Jenny

last: Bulgarelli

first: Giorgia

last: Sacchi

first: Samantha

last: Ruberti


title: Expression data from cortical thymic epithelial cells ectopically expressing Aire

status: Public on Aug 03 2015

city: Tokushima

first: Mitsuru

last: Matsumoto

address: 3-18-15 Kuramoto

department: Division of Molecular Immunology

institute: Institute for Enzyme Research, Tokushima University

summary:
Aire in medullary thymic epithelial cells plays an essential role in the negative selection through expression of broad arrays of tissue-restricted antigens.
We asked whether Aire could also activate the expression of tissue-restricted antigens in cortical thymic epithelial cells.

overall_design: We established a semi-knockin strain of NOD-background mice expressing Aire under control of the promoter of β5t, a thymoproteasome expressed exclusively in the cortex. We extracted RNA from cortical thymic epithelial cells ectopically expressing Aire and hybridization was performed on Affymetrix. microarrays.

first: Hitoshi

last: Nishijima


title: Gene expression of human hepatocellular carcinoma cells in response to acyclic retinoid

status: Public on Aug 08 2015

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN Center for Integrative Medical Sciences

summary: To better understand the molecular basis of the anticancer effects of acyclic retinoid (ACR), a genome-wide screening was applied to identify novel targets of ACR in human hepatocellular carcinoma (HCC) cells JHH7. Gene expression profiles of JHH7 were measured at 0h, 1h and 4 hours after treatment with1 μM All-trans retinoic acid (AtRA) or 10 μM ACR. Hierarchical clustering with Ward’s method of 44,907 genes demonstrated diverse expression changes in HCC cells treated with ACR for 4h. A total of 973 differentially expressed genes in response to ACR by comparing with AtRA for 4h treatments were identified with a fold change more than 2. Then, network analysis was performed on the altered gene expression profiles using Ingenuity Pathways Analysis (IPA) program. The most highly populated networks were associated with the regulation of cell cycle and DNA replication, as ACR is well known to induce apoptosis and suppress cell proliferation in HCC cells. Moreover, networks related with amino acid metabolism, protein synthesis and lipid metabolism, such as the biological network entitled “Lipid Metabolism, Small Molecular Biochemistry, Vitamin and Mineral Metabolism” were also observed. Of interest, this network contains genes that play critical roles in controlling the development of tissues and organs such as the nuclear orphan receptor nuclear receptor subfamily 2, group F, member 2 (NR2F2), suggesting potential drug targets to prevent/treat HCC.

overall_design: Gene expression profiles of JHH7 were measured at 0h, 1h and 4 hours after treatment with 1μM AtRA or 10 μM ACR.

first: Soichi

last: Kojima


title: Transcriptional analysis of human cranial compartments with different embryonic origins

city: Seattle

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Previous investigations suggest that the different embryonic origins of the calvarial tissues (neural crest or mesoderm) may account for the different molecular mechanisms underlying sutural development. The aim of this study was to evaluate the differences in the gene expression of human cranial tissues and assess the presence of an expression signature reflecting their embryonic origins. Using microarray technology, we investigated global gene expression of cells from the frontal and parietal bones and the metopic and sagittal intrasutural mesenchyme (ISM) of four human fetal calvaria.

overall_design: Tissues samples were obtained from fetal crania of 4 normal human fetuses (two females ages 94 and 103 days and two males ages 97 and 98 days). All dural and extracranial soft tissues were removed from the parietal and frontal bones. 2-3 mm tissue compartments were excised from frontal and parietal bones and metopic and sagittal ISM. To avoid contamination with osteoblasts, ISM tissue was dissected from the central portion of each suture. Similarly, bone was harvested at least 3mm from the margin of the suture to avoid contamination with ISM. Media was changed every 3-4 days. After reaching 75-80% confluence, the cells were trypsinized with TrypLEExpress (Life Technologies, Denmark) and passaged. During the fourth and final passage, 180,000 cells were plated in triplicate in 6-well plates and cultured for 5 days followed by RNA extraction.

first: Negar

last: Homayounfar

first: Sara

last: Park

first: Zahra

last: Afsharinejad

first: Theo

middle: K

last: Bammler

middle: W

first: Federico

last: Farin

first: Brigham

last: Meecham

first: Michael

middle: L

last: Cunningham


title: Epigenetic profiling of well differentiated and dedifferentiated liposarcoma identifies H3K9me3 and Kruppel-like factor 6 (KLF6) as determinants of aggressiveness in sarcoma (expression)

status: Public on Aug 04 2015

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: Little is known about the epigenomics of liposarcoma (LPS).  Here, we profiled the global expression of 9 epigenetic marks in well differentiated (WD) and dedifferentiated (DD) LPS from 151 patients and found increased H3K9me3 among DDLPS tumors.  We performed ChIP-seq and gene expression profiling of patient derived cell lines to discover functionally significant regions of differential H3K9me3 enrichment between WDLPS and DDLPS associated with concomitant gene expression changes.

overall_design: We performed genome-wide transcriptional profiling of dedifferentiated liposarcoma (DDLPS) and well differentiated liposarcoma (WDLPS) cell lines using the Affymetrix U133A GeneChip array

first: Emily

middle: Z

last: Keung

first: Lynda

last: Chin


title: Epigenome-wide and Transcriptome-wide Analyses Reveal Gestational Diabetes is Associated with Alterations in the Human Leukocyte Antigen Complex

city: Los Angeles

first: Alexandra

last: Binder

state: California

address: 650 Charles Young Drive, South

department: Department of Epidemiology

institute: University of California Los Angeles

type:
Expression profiling by array
Methylation profiling by array


title: PIK3CA(H1047R)-evoked breast tumorigenesis

first: Tim

last: Roloff


title: HP1β has distinct subnuclear localizations, chromatin binding features and functions in embryonic stem cells and differentiating cells [expression]

status: Public on Aug 02 2015

city: Jerusalem

first: Eran

last: Meshorer

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary: We used microarrays to identify the gene expression changes in Cbx1-/- (HP1beta) knockout embryonic stem cells (ESCs) and Cbx5-/- (HP1alpha) knockout ESCs compared to WT ESCs and in embryoid bodies (EBs) differentiated from those three ESC types.

overall_design: ESCs were grown and the pluripotent SSEA1-positive cells from all ESC types using MACS were sorted and harvested or sorted and differentiated into EBs. Total RNA from all samples was extracted.

first: Anna

last: Mattout


title: The niche for extramedullar hematopoiesis in the spleen

status: Public on Aug 01 2015

city: Dallas

first: Bo

last: Zhou

address: 5323 Harry Hines Blvd.

department: Children's Research Institute

institute: University of Texas Southwestern Medical Center

summary: Adult hematopoietic stem cells (HSCs) reside primarily in bone marrow. However, hematopoietic stresses such as myelofibrosis, anemia, pregnancy, infection or myeloablation can mobilize HSCs to the spleen and induce extramedullary hematopoiesis (EMH). While the bone marrow HSC niche has been studied intensively, the EMH niche has received little attention. Here, we systematically assessed the physiological sources of the key niche factors, SCF and CXCL12, in the mouse spleen after EMH induction by cyclophosphamide plus granulocyte colony-stimulating factor, blood loss, or pregnancy. In each case, Scf was expressed by endothelial cells and Tcf21+ stromal cells, primarily around sinusoids in red pulp, while Cxcl12 was expressed by a subset of Tcf21+ stromal cells. EMH induction markedly expanded the Scf-expressing endothelial cells and stromal cells by inducing proliferation. Most splenic HSCs were adjacent to Tcf21+ stromal cells in red pulp. Conditional deletion of Scf from spleen endothelial cells or Scf or Cxcl12 from Tcf21+ stromal cells severely reduced spleen EMH and reduced blood cell counts without affecting bone marrow hematopoiesis. Endothelial cells and Tcf21+ stromal cells thus create the splenic EMH niche, which is necessary for the physiological response to diverse hematopoietic stresses.

overall_design: Unfractionated spleen cells (2 replicates) and FACS-sorted VE-cadherein negative Scf-GFP positive cells (3 replicates)

first: Christopher

last: Inra


title: Polyamines induce the glutamate decarboxylase acid response system by increasing the level of the σ38 subunit (RpoS) of Escherichia coli RNA polymerase via gadE regulon

status: Public on Aug 06 2015

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: To study the physiological roles of polyamines, we have carried out a global microarray analysis on the effect of adding polyamines to an Escherichia coli mutant that lacks polyamines because of deletions in the genes in the polyamine biosynthetic pathway. Previously, we have reported that the earliest response to the polyamine addition is the increased expression of the genes for the glutamate dependent acid resistance system (GDAR). We also presented preliminary evidence for the involvement of rpoS and gadE regulators. In the current study further confirmation of the regulatory roles of rpoS and gadE is shown by a comparison of genome-wide expression profiling data from a series of microarrays comparing the genes induced by polyamine addition to polyamine-free rpoS+/gadE+ cells with genes induced by polyamine addition to polyamine-free ∆rpoS and ∆gadE cells. The results indicate that most of the genes in the E. coli GDAR system that are induced by polyamines require rpoS and gadE. Our data also show that, gadE is the main regulator of GDAR and other acid-fitness-island genes. Both polyamines and rpoS are necessary for the expression of gadE genes from the three promoters of gadE (P1, P2 and P3). The most important effect of polyamine addition is the very rapid post-transcriptional increase in the level of RpoS sigma factor. Our current hypothesis is that polyamines increase the level of RpoS protein, and that this increased RpoS level is responsible for the stimulation of gadE expression, which in turn induces the GDAR system in E. coli.

overall_design: Three replications for E. coli strains HT874, HT873, HT875, HT873 treated with or no polyamines(PA)

first: Manas

last: Chattopadhyay

first: Weiping

first: Chithra

last: Keembiyehetty

first: Herbert

last: Tabor


title: Analysis of the molecular dialogue between gray mold (Botrytis cinerea) and grapevine (Vitis vinifera) reveals a clear shift in defense mechanisms during berry ripening

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

institute: University of Verona

summary: Mature grapevine berries at the harvesting stage (MB) are very susceptible to the gray mold fungus Botrytis cinerea while veraison berries (VB) are not. We conducted simultaneous microscopic and transcriptomic analyses of the pathogen and the host to investigate the infectious process developed by B. cinerea on MB versus VB, and the plant defense mechanisms deployed to stop the fungus development. On the pathogen side, our genome-wide transcriptomic data revealed that B. cinerea genes up-regulated during infection of MB are enriched in functional categories related to necrotrophy such as degradation of plant cell wall, proteolysis, membrane transport, reactive oxygen species generation and detoxification. Quantitative-PCR on a set of representative genes related to virulence and microscopic observations further demonstrated that the infection is also initiated on VB but stops at the penetration stage. On the plant side, genome-wide transcriptomic analysis and metabolic data revealed a defense pathways switch during berry ripening. In response to B. cinerea infection, VB activated a burst of reactive oxygen species (ROS), the salicylate (SA)-dependent defense pathway, the synthesis of the resveratrol phytoalexin and cell-wall strengthening. In opposite, infected MB activated the jasmonate (JA)-dependent pathway which does not stop the fungal necrotrophic process.

overall_design: Grapevine berries at veraison (VB) and harvesting stages (MB) were inoculated with Botrytis cinerea B05-10 and samples were taken at 24h and 48h post-inoculation. An additional uninfected control sample taken at 0h post-inoculation was included in the experimental design. 3 replicates per sample were performed. The total-RNA samples were labeled and used for hybridization on NimbleGen 12plex Vitis vinifera gene expression array.

first: Jani

last: Kelloniemi

first: Sophie

last: Trouvelot

first: Marie-Claire

last: Héloir

first: Adeline

last: Simon

first: Bérengère

last: Dalmais

first: Patrick

last: Frettinger

first: Agnès

last: Cimerman

first: Marc

last: Fermaud

first: Jean

last: Roudet

first: Sylvain

last: Baulande

first: Christophe

last: Bruel

first: Mathias

last: Choquer

first: Linhdavanha

last: Couvelard

first: Mathilde

last: Duthieuw

first: Victor

last: Flors

first: Pascal

last: Le Pêcheur

first: Elise

last: Loisel

first: Guillaume

last: Morgant

first: Nathalie

last: Poussereau

first: Jean-Marc

last: Pradier

first: Christine

last: Rascle

first: Lucie

last: Trdá

first: Benoit

last: Poinssot

first: Muriel

last: Viaud


title: Epigenome analysis of the effects of JQ1 on DNA methylation

city: Chicago

first: Erika

last: Moen

state: IL

department: Medicine

institute: University of Chicago

summary: Genome wide DNA methylation profiling of four female lymphoblastoid cell lines treated with DMSO control for 250 nM JQ1. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,000 CpGs.

overall_design: Bisulphite converted DNA from the 8 samples, which were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.


title: Genome-wide DNA methylation analysis of seminoma-like TCam-2 cells during transition into an embryonal carcinoma-like state

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Universitätsstr. 1

department: Urology

institute: University Hospital Düsseldorf

summary: Illumina 450k DNA methylation microarray analysis of seminoma-like TCam-2 cells xenografted in nude mice. 2120EP embryonal carcinoma cells served as control. TCam-2 cells acquire pluripotency and become epigenetically reprogrammed to an embryonal carcinoma-like state during in vivo growth. This analysis is part of the article 'BMP inhibition in seminomas initiates acquisition of pluripotency via NODAL signaling resulting in reprogramming to an embryonal carcinoma' by Nettersheim et al., 2015. PLoS Genetics

overall_design: Genomic DNA was isolated from tumors of TCam-2 and 2102EP cells xenografted for 1, 2, 4 and 6 weeks as well as 4 and 8 weeks, respectively. In vivo samples of TCam-2 cells were analyzed in biological duplicates. In vitro cultivated TCam-2 / 2102EP cells as well as 2102EP xenografted for 4 and 8 weeks were analyzed once.

first: Hubert

last: Schorle


title: Gene expression in undifferentiated or cyclic adenosine monophosphate-exposed BeWo trophoblast cells

city: London

first: Stephen

last: Renaud

address: 1151 Richmond St, MSB428

institute: University of Western Ontario

summary: BeWo trophoblast cells differentiate in response to expsure to cyclic adenosine monophosphate (cAMP) analogs. Differentiation includes syncytialization (fusion) and hormonogenesis. The goal of this study was to globally determine transcripts differentially expressed in BeWo trophoblast cells following a 24-h exposure to 250 uM 8-bromo-cAMP.

overall_design: 3 replicates undifferentiated BeWo trophoblast cells; and 3 replicates BeWo trophoblast cells treated with 250 uM 8-Br-cAMP for 24 h.

first: Michael

last: Soares


title: Hematopoietic cell differentiation is required for initiation of acute myeloid leukemia [Microarray expression]

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: Leukemia initiating cells (LICs) of acute myeloid leukemia (AML) may arise from self-renewing hematopoietic stem cells (HSCs) and from committed progenitors. However, it remains unclear how leukemia-associated oncogenes instruct LIC formation from cells of different origins and if differentiation along the normal hematopoietic hierarchy is involved. Here, using murine models with the driver mutations MLL-AF9 or MOZ-TIF2, we found that regardless of the transformed cell types, myelomonocytic differentiation to the granulocyte macrophage progenitor (GMP) stage is critical for LIC generation.  Blocking myeloid differentiation through disrupting the lineage-restricted transcription factor C/EBPa eliminates GMPs, blocks normal granulopoiesis, and prevents AML development. In contrast, restoring myeloid differentiation through inflammatory cytokines “rescues” AML transformation. Our findings identify myeloid differentiation as a critical step in LIC formation and AML development, thus guiding new therapeutic approaches.

overall_design: Primary KSL, CMP, and GMP cells from wildtype controls and C/Ebpa knockouts were used for RNA extraction and hybridization on Affymetrix microarrays. We also compared the microarray samples of leukemic granulocyte macrophage progenitor compartments (L-GMPs)   from  MLL-AF9 transformed control or cytokine rescued  C/EBPa KO leukemic mouse bone marrow and their secondary recipients with those non-Leukemia KSLs and CMPs from  MLL-AF9 transduecd KO recipients with no leukemia development.

first: Min

last: Ye

first: Hong

last: Zhang

first: Henry

last: Yang

first: Philipp

last: Staber

first: Elena

last: Levantini

first: Robert

last: Welner

first: Christinan

last: Bach

first: Junyan

first: Scott

last: Armstrong

last: Tenen


title: Gene expression profile of SKOV3 cells cultured with a novel 3D cell culture method

status: Public on Jul 31 2015

city: Shiraoka

first: Ayako

last: Otani

state: Saitama

address: 1470 Shiraoka

department: Medical Materials group

institute: Nissan Chemical Industries

summary:
Preclinical cancer drug discovery efforts have employed two-dimensional (2D)-cell-based assay models, which fail to forecast in vivo efficacy and contribute to a lower success rates of clinical approval.  Three-dimensional (3D) cell culture models are recently expected to bridge the gap between 2D and in vivo models. We have developed a novel 3D culture method that improves the growth of spheroid-forming cancer cells under anchorage-independent condition by leveraging a feature of FP001, a bacteria-derived polysaccharide.
Gene microarrays were used to observe the global gene expression in SKOV3 cells cultured with adhesion condition (2D, control) or with low adhesion condition (FP001) and identified distinct classes of up or down-regulated genes.

overall_design: SKOV3 cells were cultured for 11 days in normal attachment plates with normal medium (as control) or low-attachment plates with FP001 containing medium. Each sample was collected three times.

last: Aihara


title: Gene expression profile of A549 cells cultured with FP001

summary:
Preclinical cancer drug discovery efforts have employed two-dimensional (2D)-cell-based assay models, which fail to forecast in vivo efficacy and contribute to a lower success rates of clinical approval.  Three-dimensional (3D) cell culture models are recently expected to bridge the gap between 2D and in vivo models. We have developed novel 3D culture method that improves the growth of spheroid-forming cancer cells under anchorage-independent condition by leveraging a feature of FP001.
Gene microarrays were used to observe the global gene expression in A549 cells cultured in multi-well plate with or without FP001 and identified distinct classes of up or down-regulated genes.

overall_design: A549 cells were cultured for 5 days in normal attachment plate with normal medium (as control) or normal attachment plate with FP001 containing medium. Each sample was collected three times.


title: Retinoic acid directs the development and transcriptional programming of intestinal dendritic cells

city: Palo Alto

first: Eugene

middle: C.

last: Butcher

address: 3801 Miranda Avenue

department: Pathology

institute: Stanford School of Medicine

type:
Expression profiling by array
Third-party reanalysis

summary: This file contains gene microarray data from bone marrow pre-ul DC, in vitro derived CD103+CD11b+ and CD103+CD11b- cDC with or without retinoic acid.

overall_design:
We analyze transcript expression data from bone marrow pre-uDC, Splenic and SI cDC1 and cDC2 (GSE15907 - 18 samples), in vitro derived CD103+CD11b+ and CD103+CD11b- cDC from C57Bl/6 mice.

The complete dataset is linked below as a supplementary file.

first: Ruizhu

last: Zeng


title: Expression data from untreated vs. BMP4-treated cultured wild-type and MuSK null muscle cells (myoblasts and myotubes)

city: Basel

first: Atilgan

last: Yilmaz

address: Mattenstrasse 26

department: D-BSSE

institute: ETH Zürich

summary: Bone morphogenic proteins (BMPs) function in virtually all tissues with cell-type specific outcomes. Since there are a relatively small number of BMP receptors this exquisite signaling specificity requires additional molecules to regulate the output of this pathway.  We demonstrated that the receptor tyrosine kinase MuSK that is selectively expressed in muscle and plays a critical role in synapse formation and maintenance binds to BMP4 and related BMPs. Since BMPs regulate the transcription of a set of genes, we performed microarrays for wild-type and MuSK null muscle cells to test if MuSK regulates BMP responses in muscle cells.

overall_design: We shought to determine if MuSK regulates BMP responses in muscle cells and if the cell context made any difference in MuSK regulation of BMP pathway. To test this, expression profiles of untreated vs. BMP4-treated undifferentiated myoblast and differentiated myotube cultures were generated for both wild-type and MuSK-null genotypes. All conditions were done in triplicates. In total 24 arrays were analyzed.

first: Christoph

last: Schorl

first: Justin

last: Fallon


title: Gene Expression Profile of high grade glioma in Nestin-creERT2 and NG2-creERTM driven tumor suppressors knockout mouse model

status: Public on Jul 30 2015

first: Daochun

last: Sun

department: Cancer Biology and Genetics

summary: Mouse model with P53f/f;Nf1f/+;Ptenf/+ configuration driven by Nestin-creERT2 and NG2-creERTM induced at 1 month postnatal forms high grade glioma in the brain. Tumors were harvested and total RNA were extracted for gene expression profile.

overall_design: Three tumors were harvested from the Nestin-creERT2 mouse model and 5 tumors were harvested from the NG2-creERTM mouse model with desired genotype when mice show neurological symptomes. Three control brain tissue for each model were harvested at corresponding anatomical position in the control mice. Total RNA were extracted from the tumor tissue and control tissue

first: Wang

last: Zilai

first: Sun

last: Daochun

first: Parada

last: Luis


title: Identification of a new subclass of ALK negative ALCL expressing aberrant levels of ERBB4 transcripts

status: Public on Oct 22 2015

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary: Anaplastic Large Cell Lymphoma (ALCL) is a clinical and biological heterogeneous disease including ALK positive and ALK negative systemic forms. To discover biomarkers and/or genes involved in ALK negative ALCL pathogenesis, we applied the Cancer Outlier Profile Analysis (COPA) algorithm to a gene expression profiling data set including 249 cases of T-NHLs and normal T-cells. Ectopic co-expression of ERBB4 and COL29A1 genes was detected in 24% of ALK negative ALCL patients. RNA sequencing and 5'RNA Ligase Mediated Rapid Amplification of cDNA Ends (RLM-RACE) identified two novel ERBB4 truncated transcripts, displaying intronic Transcription Starting Sites. ERBB4 expression was confirmed at protein level by western blotting and immunohistochemistry. Moreover, by luciferase assays we defined that the expression of ERBB4 aberrant transcripts is promoted by endogenous intronic Long Terminal Repeats (LTRs). In conclusion, we identified a new subclass of ALK negative ALCL characterized by aberrant expression of ERBB4 truncated transcripts carrying intronic 5'UTRs.

overall_design: To discover genes putatively involved in the pathogenesis of ALK negative ALCL patients, we applied the Cancer Outlier Profile Analysis (COPA) algorithm10 to a large gene expression profiling (GEP) data set including 249 cases of T-NHLs and normal T-cells, obtained as previously described (PMID: 22740451 http://www.ncbi.nlm.nih.gov/pubmed/22740451).

first: Irene

last: Scarfò

first: Elisa

last: Pellegrino

first: Ivo

last: Kwee

first: Elisabetta

last: Mereu

last: Bergaggio

first: Francesco

last: Abate

first: Manuel

last: Caputo

first: Domenico

last: Novero

first: Andrea

last: Rinaldi

first: Enrico

last: Tiacci

first: Sara

last: Serra

first: Silvia

last: Deaglio

first: Antonino

last: Neri

first: Brunanagelo

last: Falini

first: Raul

last: Rabadan

last: Bertoni

first: Giorgio

last: Inghirami

first: Roberto

last: Piva


title: Comparison of Huh6 and Huh7 cells under IFNgamma treatment

city: Heidelberg

first: Volker

last: Lohmann

address: Im Neuenheimer Feld 345

department: Molecular Virology

institute: University of Heidelberg

summary: All major types of interferon (IFN) efficiently inhibit hepatitis C virus (HCV) replication in vitro and in vivo. Remarkably, HCV replication is not sensitive to IFNγ in the hepatoma cell line Huh6, despite an intact signaling pathway. We performed transcriptome analyses between Huh6 and Huh-7 to identify effector genes of the IFNγ response and thereby identified the DExD/H box helicase DDX60L as a restriction factor of HCV replication. DDX60L and its homolog DDX60 were both induced upon viral infection and IFN treatment in primary human hepatocytes. However, exclusively DDX60L knockdown increased HCV replication in Huh-7 cells, and rescued HCV replication from type II IFN as well as type I and III IFN treatment, suggesting that DDX60L is an important effector protein of the innate immune response against HCV. DDX60L had no impact on replication of hepatitis A virus (HAV), but severely impaired production of lentiviral vectors, arguing for a potential antiretroviral activity. Detection of endogenous DDX60L protein turned out to be difficult due to instability. DDX60L knockdown did not alter interferon stimulated gene (ISG) induction after IFN treatment, suggesting that it is a direct effector of the innate immune response. It most likely inhibits viral RNA replication, since we found no impact of DDX60L on translation or stability of HCV subgenomic replicons, nor additional impact on entry and assembly of infectious virus. Similar to its homolog DDX60, DDX60L had a moderate impact on retinoic acid-inducible gene I (RIG-I)-dependent activation of innate immunity arguing for additional functions in the sensing of viral RNA.

overall_design: Gene Expression was compared between two cell lines, Huh6 and Huh7, under interferon-gamma or interferon-alpha treatment. We intended to identify genes that are more strongly upregulated in Huh-7 than in Huh6 in response to interferon treatment.

first: Marc

middle: P

last: Windisch

first: Michael

last: Frese

first: Ralf

last: Bartenschlager

first: Martin

last: Trippler

first: Marco

last: Binder

first: Katharina

last: Esser-Nobis

first: Anna

last: Reustle


title: Epigenome-wide and Transcriptome-wide Analyses Reveal Gestational Diabetes is Associated with Alterations in the Human Leukocyte Antigen Complex [methylation]

first: Alexandra

summary: Gestational diabetes mellitus (GDM) affects approximately 18% of pregnancies in the United States and increases the risk of adverse health outcomes in the offspring. These adult disease propensities may be set by anatomical and molecular alterations in the placenta associated with GDM. To assess the mechanistic aspects of fetal programming, we measured genome-wide methylation (Infinium HumanMethylation450 Beadchips) and expression (Affymetrix Transcriptome Microarrays) in placental tissue of 41 GDM cases and 41 matched pregnancies without maternal complications from the Harvard Epigenetic Birth Cohort. Specific transcriptional and epigenetic perturbations associated with GDM status included alterations in the major histocompatibility complex (MHC) region, which were validated in an independent cohort, the Rhode Island Child Health Study. Gene ontology enrichment among gene regulation influenced by GDM revealed an over-representation of immune response pathways among differential expression, reflecting these coordinated changes in the MHC region. Our study represents the largest investigation of transcriptomic and methylomic differences associated with GDM, providing comprehensive insight into the molecular basis of GDM induced fetal (re)programming.

overall_design: Bisulphite converted DNA extracted from the placentas (maternal-side) of 41 clinically-confirmed cases of GDM and 41 pregnancies without maternal complications were hybridised to the Illumina Infinium HumanMethylation450 Beadchips

middle: M


title: Tissue-specific patterns of gene expression in the epithelium and stroma of normal colon in healthy individuals in an aspirin intervention trial

first: John

middle: D

last: Potter

address: 1100 Fairview Ave N

department: Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

summary:
The objectives of this study were to measure effects of an aspirin intervention on gene expression in normal colonic epithelial and stromal tissue in healthy humans and to determine whether response differed by UGT1A6*2 genotype. We also sought to characterize gene expression differences within colonic tissue microenvironments by identifying genes that were differentially expressed between epithelial and stromal tissue.
No statistically significant differences in gene expression were observed in response to aspirin or UGT1A6 genotype, but tissue PGE2 levels were lower with aspirin compared to placebo (p <0.001). Transcripts differentially expressed between epithelium and stroma (N = 4916, P <0.01, false discovery rate <0.001), included a high proportion of genes involved in cell signaling, cellular movement, and cancer. Genes preferentially expressed in epithelium were involved in drug and xenobiotic metabolism, fatty acid and lipid metabolism, apoptosis signaling, and ion transport. Genes preferentially expressed in stroma included those involved in inflammation, cellular adhesion, and extracellular matrix production. Wnt-Tcf4 pathway genes were expressed in both epithelium and stroma but differed by subcellular location.
Our results suggest that, in healthy individuals, subtle effects of aspirin on gene expression in normal colon tissue are likely overwhelmed by inter-individual variability in microarray analyses. Differential expression of critical genes between colonic epithelium and stroma suggest that these tissue types need to be considered separately.

overall_design:
In a randomized, cross-over, placebo-controlled trial of 44 healthy men and women, homozygous for UGT1A6*1 or UGT1A6*2, we explored differences between global epithelial and stromal expression, using Affymetrix U133 + 2.0 microarrays and tested effects of 60-day aspirin supplementation (325 mg/d) on epithelial and stromal gene expression and colon prostaglandin E2 (PGE2) levels
Participants were randomly assigned, blocked on sex and genotype, to the order in which they received  treatment A or treatment B. (Note: The type of treatment i.e., pill type active or placebo is masked. Please contact the study authors directly if you would like access to this information).  The washout period between intervention periods was three months. A sigmoidoscopy was performed at least 60 days after day 1 of each intervention period. Therefore, two biopsies were obtained from each participant and then processed, where by, epithelial and stromal fractions were separated and analyzed using Affymetrix U133+2.0 microarrays. This resulted in obtaining total RNA from 88 epithelial and and 88 matched stromal samples. A total of 176 gene arrays were measured.
Participants were labeled consecutively. There are 4 samples from each person designated A1-A4 (participant 1); A5-A6 (participant 2); B1-B4 (participant 3) etc. to W1-W4 (participant 44). Within each person, odd numbers (1 & 3) are epithelial tissue and even numbers (2 & 4) are stromal tissue. The epithelial and stroma from each intervention period are paired together (e.g., A1 & A2 are from the first treatment Participant 1 received; A3 & A4 are from the second treatment Participant 1 received).

first: Sushma

last: Thomas

first: Karen

last: Makar

first: Lin

last: Li

first: Yingye

last: Zheng

first: Peiying

last: Yang

first: Lisa

last: Levy

first: Rebecca

middle: Y

last: Rudolph

first: Paul

last: Lampe

first: Min

last: Yan

first: Sanford

last: Markowitz

first: Jeannette

last: Bigler

first: Johanna


title: Gene expression profile of A549 cells cultured with novel 3D cell culture method

first: Ayako

last: Otani

summary:
Preclinical cancer drug discovery efforts have employed two-dimensional (2D)-cell-based assay models, which fail to forecast in vivo efficacy and contribute to a lower success rates of clinical approval.  Three-dimensional (3D) cell culture models are recently expected to bridge the gap between 2D and in vivo models. We have developed novel 3D culture method that improves the growth of spheroid-forming cancer cells under anchorage-independent condition by leveraging a feature of FP001.
Gene microarrays were used to observe the global gene expression in A549 cells cultured with normal adhesion plate (2D, control) or with low adhesion plate (+FP001) and identified distinct classes of up or down-regulated genes.

overall_design: A549 cells were cultured for 5 days in three different conditions as follows. (1) Normal attachment plates with normal medium (as control), (2) low-attachment plates with normal medium, (3) low-attachment plates with FP001 containing medium. Each sample was collected three times.

last: Aihara


title: Different expression patterns in leukemia cells caused by decreased expression of TNF-α

status: Public on Jul 29 2015

city: Wuhan

first: Shiqiu

last: Zhou

address: Liberation Road

institute: Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary:
To design an effective antibody therapy to improve clinical outcomes in leukemia, the identification of novel cell surface antigens is needed. Herein, we demonstrate a role for transmembrane tumor necrosis factor-αin leukemia. To characterize tmTNF-α expression in acute leukemia, normal hematopoietic cells, and non-hematopoietic tissues, we used a monoclonal antibody, termed C1, which specifically recognizes the tmTNF-α domain. We found that tmTNF-α was preferentially expressed by acute leukemia and leukemia stem cells. More abundant expression correlated with poor risk stratification, extramedullary infiltration, and adverse clinical parameters. Moreover, knockdown of tmTNF-α+ expression rendered leukemia cells more sensitive to chemotherapy in vitro and delay regeneration of leukemia in NOD–SCID mice. Targeting tmTNF-α by C1 resulted in leukemia cell killing via antibody-dependent cell-mediated and complement -dependent cytotoxicity in vitro, and inhibited leukemia cell growth in vivo while simultaneously sparing normal hematopoietic cells. Notably, C1 administration impaired the regeneration of leukemia in secondary serial transplantationin to NOD-SCID mice.
To further understand the different expression patterns in leukemia cells and potential mechanisms underlying the effects caused by decreased expression of tmTNF-α, total RNA was extracted with TRIzol from SKM-1 stably transfected with control or tmTNF-α shRNA, tmTNF-α+ or - cells sorted from a primary AML sample, and human CD45+ leukemia cells from micetreated with C1 or IgG1 after first transplantation of 7052, and were then subjected to the microarray analysis.

overall_design: We extracted total RNA from SKM-1 stably transfected with control or tmTNF-α shRNA, tmTNF-α+ or - cells sorted from a primary AML sample, and human CD45+ leukemia cells from mice treated with C1 or IgG1 after first transplantation of 7052 (leukemia cell line initially derived from patients with primary acute leukemia who remained stably transplantable in NOD–SCID mice). These were then subjected to the GeneChip probe arrays (Affymetrix GeneChip® Human Genome U133 Plus 2.0). Using SKM-1 stably transfected with control (NC), tmTNF-α+ cells sorted from the primary AML sample and CD45+ leukemia cells from mice treated with IgG1 as reference samples respectively, we compared the different expression patterns in leukemia cells caused by decreased expression of TNF-α (SKM-1 89-1/NC-1, 89-2/NC-2; 70-C1-2/70-IgG-1, 70-C1-3/70-IgG-2; AMLTNFα- 1/+ 1; AMLTNFα- 2/+ 2). Two replicates were included for each pair of samples.

first: Xiaoxi

first: Jianfeng

first: Zhuoya


title: Expression Analysis of Human Adipose-Derived Stem Cells During In Vitro Differentiation to an Adipocyte Lineage

city: Pittsburgh

first: Sandeep

last: Kathju

state: PA

address: 200 Lothrop Str

department: Plastic Surgery

institute: University of Pittsburgh

summary: Adipose tissue-derived stromal stem cells (ASCs) represent a promising regenerative resource for soft tissue reconstruction. To understand the changes in cell function during the transition of ASCs into fully mature fat cells, we compared the transcriptome profiles of cultured undifferentiated human primary ASCs under conditions leading to acquisition of a mature adipocyte phenotype by microarray analysis.

overall_design: Microarray analysis was performed on total RNA extracted from separate ACS isolates of six human adult females before and after 7 days (7d: early stage) and 21 days (21d: late stage) of adipocyte differentiation in vitro.

first: Kacey

last: Marra

first: J

last: Rubin

first: Latha

last: Satish

first: Phillip

last: Gallo


title: Ginkgolic acids and Ginko biloba extract inhibit Escherichia coli O157:H7 biofilm formation

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

summary: Contamination with enterohemorrhagic Escherichia coli O157:H7 (EHEC) is a worldwide problem but there is no effective therapy available for EHEC infection. Biofilm formation is closely related with EHEC infection and is one of the mechanisms of antimicrobial resistance. Antibiofilm screening of 560 plant secondary metabolites against EHEC shows that ginkgolic acids C15:1 and C17:1 at 5 μg/ml and Ginko biloba extract at 100 μg/ml significantly inhibited EHEC biofilm formation on the surface of polystyrene, nylon membrane, and glass. Importantly, the working concentration of ginkgolic acids and G. biloba extract did not affect bacterial growth and has been known to be non-toxic to human. Transcriptional analyses showed that ginkgolic acid C15:1 repressed curli genes and prophage genes in EHEC, which were corroborated by reduced fimbriae production and biofilm reduction in EHEC. Interestingly, ginkgolic acids and G. biloba extract did not inhibit the biofilm formation of commensal E. coli K-12 strain. The current study suggests that plant secondary metabolites are important resource of biofilm inhibitors, as well as other bioactive compounds.

overall_design: E. coli GeneChip Genome 2.0 Array (Affymetrix, P/N 900551, Santa Clara, USA) was used to study the differential gene expression of the E. coli O157:H7 cells after the treatment with ginkgolic acid C15:1 (0.005 mg/ml). Cells were inoculated into 25 ml LB medium in 250 mL shake flasks with a starting OD600 of 0.05, and cultured at 37oC for 8 h without shaking in the presence or absence of ginkgolic acid C15:1 (5 μg/ml). To prevent RNA degradation, RNase inhibitor (RNAlater, Ambion, TX, USA) was added, and the EHEC cells were collected by centrifugation at 10,000 rpm for 1 min. The cell pellets obtained were immediately frozen with dry ice and stored at -80°C.  Total RNA was isolated using a Qiagen RNeasy mini Kit (Valencia, CA, USA).

first: Jin-Hyung

first: Yong-Guy

last: Kim

first: Shi

last: Ryu

first: Moo

middle: H

last: Cho


title: Gene Expression Profiling in Omental Adipose Tissue of Morbidly Obese Diabetic African Americans

first: Ayo

last: Doumatey

state: MD

address: 12 South Drive

department: NHGRI

institute: NIH

summary: Adipose tissues play an important role in the pathophysiology of obesity-related disease including type 2 diabetes. To describe gene expression patterns and functional pathways in obesity-related type 2 diabetes, we performed global transcript profiling of omental adipose tissue in morbidly obese individuals with or without diabetes.

overall_design: Fourteen (14) morbidly obese diabetics (cases) and 6 morbidly obese non-diabetics (reference) were included in this study.

first: Huichun

last: Xu

first: Hanxia

last: Huang

first: Niraj

last: Trivedi

first: Lin

last: Lei

first: Abdel

last: Elkahloun

first: Adebowale

last: Adeyemo

first: Charles

last: Rotimi


title: DNA methylation data from 11 normal and 9 chronic periodontitis patients from site USC

city: Toronto

first: Daniel

last: De Carvalho

state: ON

address: 101 College St

institute: Princess Margaret Cancer Centre

summary: Microarray methylation (Infinium®HumanMethylation 450 BeadChip from Illumina) was performed on 11 normal and 9 chronic periodontitis (CP) patients

overall_design: Bisulphite converted DNA from the 20 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Aline

last: Planello

first: Rajat

last: Singhania


title: Fibrocytes differ from macrophages but can be infected with HIV-1

status: Public on Jul 28 2015

city: Honjo, Chuo-ku, Kumamoto City

first: Shinya

last: Suzu

state: kumamoto

department: center for aids research

institute: kumamoto university

summary: Fibrocytes (fibroblastic leukocytes) are recently identified as unique hematopoietic cells with features of both macrophages and fibroblasts. Fibrocytes are known to contribute to the remodeling or fibrosis of various injured tissues. However, their role in viral infection is not fully understood. Here we show that differentiated fibrocytes are phenotypically distinguishable from macrophages but can be infected with HIV-1. Importantly, fibrocytes exhibited persistently infected cell-like phenotypes, the degree of which was more apparent than macrophages. The infected fibrocytes produced replication-competent HIV-1, but expressed HIV-1 mRNA at low levels and strongly resisted HIV-1-induced cell death, which enabled them to support an extremely long-term HIV-1 production at low but steady levels. More importantly, our results suggested that fibrocytes were susceptible to HIV-1 regardless of their differentiation state, in contrast to the fact that monocytes become susceptible to HIV-1 after the differentiation into macrophages. Our findings indicate that fibrocytes are the previously unreported HIV-1 host cells, and suggest the importance of considering fibrocytes as one of long-lived persistently infected cells for curing HIV-1.

overall_design: To find the surface maker for fibrocyte and to analyze why fibrocyte show low HIV-1 replication we done the microarray analysis between fibrocyte(EA1065_65), macrophage(EA1065_02), fibrocyte infected with HIV-1 at Day12(EA1168_08) and macrophage infected with HIV-1 at Day3(EA1168_02).


title: Interplay between promoter methylation and chromosomal loss in gene silencing at 3p11-p14 in cervical cancer

status: Public on Sep 14 2015

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

summary:
We performed integrative methylation, gene dosage and expression profiling to explore the interplay between promoter methylation and loss in gene silencing at 3p11-p14 in cervical cancer.
Totally 26 hypermethylated genes were identified by comparing the methylation level of individual CpG sites with corresponding data of normal cervical tissue. Candidate methylation regulated genes in tumors were proposed from the correlation between methylation and gene expression. Integrated analysis of methylation, gene dosage and expression revealed three significant regulation patterns encompassing 8 hypermethylated genes; a methylation driven pattern, a gene dosage driven pattern, and a combined methylation and gene dosage driven pattern.  For the LRIG1 gene, patients with both hypermethylation and loss had a worse outcome compared to those harboring only hypermethylation or none of the events. C3orf14 emerged as a novel methylation regulated suppressor gene, for which knockdown was found to promote invasive growth in human papilloma virus (HPV)-transformed keratinocytes.

overall_design: Methylation levels from Illumina 450K methylation arrays were correlated with Illumina gene expression data in cohort 1 and validated in cohort 2.

first: Malin

last: Lando

first: Christina

middle: S

last: Fjeldbo

first: Saskia

last: Wilting

middle: F

last: Forsberg

first: Gunnar

middle: B

last: Kristensen

first: Renske

last: Steenbergen


title: LncRNA and mRNA expression data  involved in benzene hematotoxicity

status: Public on Jul 27 2015

city: beijing

first: ai

middle: aa

last: gao

address: NO10, Xi tou tiao, Youanmen,Fengtai District

institute: School of Public Health, Capital Medical University

summary:
Benzene is a ubiquitous environmental pollutant and an established human hematotoxicant and leukemogen. New insights into the pathogenesis of benzene hematotoxicity are urgently needed. Long non-coding RNA（lncRNA）can regulate gene expression and widely participate in the various physiological and pathological processes.
Microarray analysis was used to identify the differentially expressed lncRNA and mRNA that were likely to be critical for benzene hematotoxicity. An integrated analysis of lncRNA and mRNA expression profiles was performed to identify key hub genes, pathways and biological processes.

overall_design: Peripheral blood samples were randomly obtained from four patients of chronic benzene poisoning, three benzene-exposed workers and three health controls without benzene exposure. The occupational history, age, gender, lifestyle such as smoking, drinking, recent drug use situation and medical history in each group were matched. Total RNA was extracted and an integrated analysis of lncRNA and mRNA expression profiles was performed by GeneChip Human Gene 2.0 ST Array (Affymetrix).

first: Ai

last: Gao

last: Tian


title: The Senescent Methylome and its relationship with cancer, ageing, and germline genetic variation in humans (methylation experiment 1)

status: Public on Jul 26 2015

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

summary: Cellular senescence is a stable arrest of proliferation and is considered a key component of processes associated with carcinogenesis and other ageing-related phenotypes. However, till now, biological markers that define senescence on a genome-wide scale have been limited. Here, we report a DNA methylomic analysis of actively dividing and deeply senescent normal human epithelial cells, identifying 3,852 senescence-associated differentially methylated positions (senDMPs). We find that this human senDMP signature is positively and significantly correlated with both cancer and ageing-associated methylomic dynamics. We also identify germline genetic variants, including those associated with the p16INK4A locus, that are associated with the presence of in vivo senDMP signatures. Importantly, we also demonstrate that the senDMP signature can be effectively reversed in a newly-developed protocol of transient cellular rejuvenation. The senDMP signature has significant potential for understanding some of the key (epi)genetic etiological factors that lead to cancer and age-related diseases in humans.

overall_design: Bisulphite converted DNA from the HMECs at early passage (EP), deep senescence (DS), deep senescence + p16 siRNA (DS+p16siRNA) at two different time points and FACS for cell cycle at EP were hybridised to the Illumina Infinium 450k Human Methylation Beadchip