title: Expression analysis of Sinorhizobium meliloti 1021rpoH1 rpoH2 mutant during heat shock

city: Sendai

first: Hisayuki

last: Mitsui

address: 2-1-1, Katahira, Aoba-ku

department: Graduate School of Life Sciences

institute: Tohoku University

summary:
Investigation of whole genome gene expression level changes in a Sinorhizobium meliloti 1021 rpoH1 rpoH2 double mutant, compared to the wild-type strain.  The mutations engineered into this strain render it deficient in symbiotic nitrogen fixation.
The mutants analyzed in this study are further described in Mitsui, H, T. Sato, Y. Sato, and K. Minamisawa. 2004. Sinorhizobium meliloti RpoH1 is required for effective nitrogen-fixing symbiosis with alfalfa. Mol Gen Genomics 271:416-425.

overall_design: A twenty chip study using total RNA recovered from four separate cultures of a wild-type strain grown at 25°C, four separate cultures of a wild-type strain with heat shock at 37°C for 10 min after a shift from 25°C, four separate cultures of a wild-type strain with heat shock at 37°C for 40 min after a shift from 25°C, four separate cultures of a rpoH1 rpoH2 double mutant strain with heat shock at 37°C for 10 min after a shift from 25°C, and four separate cultures of a rpoH rpoH2 double mutant strain with heat shock at 37°C for 40 min after a shift from 25°C.  Each chip measures the expression level of 6,197 genes from Sinorhizobium meliloti 1021 with four 60-mer perfect-match probes per gene, with two-fold technical redundancy.


title: SILENCING OF PNPLA6, THE NEUROPATHY TARGET ESTERASE (NTE) CODIFYING GENE, ALTERS HUMAN NEURODIFFERENTIATION IN VITRO

status: Public on Oct 06 2014

city: Varese (VA)

first: Marco

last: Fabbri

address: via dunant 5

country: Italy

institute: Università dell'Insubria

summary: Neuropathy Target Esterase (NTE) is a protein involved in the development of a polyneuropathy caused by exposure to certain organophosphorus compounds. In vivo and in vitro studies have also associated NTE with embryonic development since NTE null mice embryos are non-viable, and silencing the NTE-codifying gene (Pnpla6) in mouse embryonic stem cells strongly alters the differentiation of vascular and nervous systems. In this paper, human embryonal carcinoma stem cells (hNT2) are used as in vitro neurodifferentiation model to determine whether PNPLA6 gene silencing is able to alter the differentiation into a neuronal phenotype. In controls, the PNPLA6 mRNA levels increased in parallel with other neuroectodermal markers during the neurodifferentiation. PNPLA6 gene silencing with specific interference RNA led to a 97% maximum decrease in gene expression by day 3 after transfection, with a maximum of 50% reduction in NTE enzymatic activity by day 4. Microarray analyses of the PNPLA6-silenced cells showed alterations in several developmental processes, mainly neurogenesis and epithelium tube morphogenesis. PNPLA6 silencing also led to a reduction in electrical activity and an altered neuronal phenotype. This work is the first proof supporting the hypothesis that NTE protein plays a critical role in human early neurodevelopment using a human cell differentiation model.

overall_design: PNPA6 gene silencing in undifferentiatied hNT2 cells was performed, together with a Control (non-gene silencing cells) and a Negative Control (non-specific RNA silencer). Three biological replicates.

first: David

last: Pamies

first: Miguel

middle: A

last: Sogorb

first: Laura

last: Gribaldo

first: Angelo

last: Collotta

first: Bibiana

last: Scelfo

first: Eugenio

last: Vilanova

first: Georgina

last: Harris

first: Anna

last: Bal-Price


title: Gene expression signatures for bladder cancer tissues and normal adjacent tissues

status: Public on Sep 22 2014

city: Guangzhou

first: Wang

last: He

state: Guangdong

address: 107th, Yanjiangxi Road

department: Urology

country: China

institute: Sun Yat-sen Memorial Hospital

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

summary: To identify aberrantly expressed long intergenic noncoding RNAs (lincRNAs) in bladder cancer tissues compared with normal adjacent tissues, we have employed microarray expression profiling as a discovery platform to identify lincRNAs that may play important roles in bladder cancer origin and progression. Samples of fresh frozen cancer tissues, together with normal adjacent tissues (3 cm away from the tumor), were obtained during surgical resection, and total RNA was extracted for microarray analysis.

overall_design: Two pairs of fresh frozen bladder cancer tissues and corresponding normal adjacent tissues were used in the microarray analysis.

first: Tianxin

last: Lin


title: Gene expression profiles for Pancreatic ductal adenocarcinoma cell lines and their corresponding normal and fresh frozen tissues.

status: Public on Aug 27 2014

city: Oslo

first: Vandana

last: Sandhu

state: oslo

address: Ullernchausseen 70

department: Department of Genetics

country: Norway

institute: Radiumhospitalet, Oslo

summary: To demonstrate that the generated cell lines represent the parental tumours we compared the mRNA expression patterns obtained from the generated cell lines, the original tumours, as well as non-tumorigenic pancreatic tissue from the same patients

overall_design: Total RNA was isolated from the cell lines PpaX1, PpaX6 and PpaX8 as well as their corresponding original tumours and adjacent normal tissue from patient Ppa6 and Ppa8 and analysed by microarray analysis using the 60K agilent platform. The expression profiles were background corrected and quantile normalized. Filtering of controls, unannotated genes and low expressed probes was done. 10,947 genes were used to demonstarte the relationship between the cell lines and parental tumors.

first: Elin

last: Kure


title: Gene expression analysis of human bone marrow cells (hMSC-TERT) transfected with mIR-320c or miR-negative control at 72hrs post-transfection

status: Public on Sep 09 2014

city: Riyadh

first: Nehad

middle: M

last: Alajez

address: 1st floor College of Medicne

department: Anatomy

country: Saudi Arabia

institute: King Saud University College of Medicine

summary: We have employed whole genome microarray  to identify changes in gene expression in human bone marrow MSCs (hMSC-TERT) transfected with miR-320c or miR-negative control at 72hrs post-transfection

overall_design: Human MSC line (hMSC-TERT) were transfected with miR-320c (30 nM) or miR-negative control (30 nM), subsequently, RNA was extracted using Norgen total RNA isolation kit at 72hrs post-transfection. Extracted RNA was labeled and then hybridized to the one-color Agilent Human GE 8x60K Microarray chip.


title: UNC50 prompts G1/S transition and proliferation in HCC through regulation of epidermal growth factor receptor trafficking

status: Public on Nov 17 2014

city: Shanghai

first: Long

last: Yu

address: No.2005, Songhu Road

institute: Fudan University

summary: Background: UNC50 has long been recognized as a Golgi apparatus protein in yeast, and is involved in nicotinic receptor trafficking in Caenorhabditis elegans, but little is known about UNC50 gene function in human biology despite it being conserved from yeast to high eukaryotes.  Objectives: We investigated the relation between UNC50 and human hepatocellular carcinoma (HCC) and the potential mechanisms underlying HCC development.  Methods: UNC50 mRNA expression patterns in 12 HCC and adjacent non-cancerous tissues determined using northern blotting were confirmed by real-time PCR in another 44 paired tissues. Microarray experiments were used to screen for global effects of UNC50 knockdown in the Hep3B cell line, and were confirmed by real-time PCR, western blotting, flow cytometry, and tetrazolium assay in both UNC50 overexpression and knockdown Hep3B cells.  Results: UNC50 expression levels were upregulated in HCC tissues in comparison with the adjacent non-cancerous tissues. UNC50 knockdown reduced mRNA levels of the downstream targets of the epidermal growth factor receptor (EGFR) pathway: cyclin D1 (CCND1), EGF, matrix metalloproteinase-7 (MMP7), aldose reductase-like 1 (AKR1B10), cell surface–associated mucin 1 (MUC1), and gastrin (GAST). Moreover, UNC50 influenced EGF, inducing cell cycle entry by affecting cell surface EGFR amounts.  Conclusions: UNC50 is a potential oncogene that promotes HCC progression by affecting the EGFR pathway.

overall_design: To gain insight into the role UNC50 plays in HCC progression, we used microarray analyses to identify indirect evidence of UNC50 gene function via the knockdown strategy in Hep3B cells. Hep3B cells transfected with the shRNA expression plasmids shR-467, shR-554, shR-749, and shR-MOCK were purified with 1ug/ml puromycin, and the total RNA from each cell was extracted and analyzed with oligo microarrays.

first: Lihuan

last: Cao

first: Zhou

last: Fang

first: Linuo

last: Zhou


title: Global gene expression analysis reveals importance of thermal effect in cellular response to millimeter wave exposure

status: Public on Aug 12 2014

city: Fougeres

first: Denis

last: Habauzit

address: 10 B rue Claude Bourgelat

department: TC unit

country: France

institute: ANSES

summary:
To evaluate the effect of millimeter waves (MMW) exposure on the gene expression, we have employed whole genome microarray expression profiling.
Neonatal primary Keratinocyte cells pooled from 3 healthy donors were exposed ex vivo, 3 hours at 20 mW/cm². At this condition, corresponding to the maximum power density authorized for public use, MMW exposure induces a significant increase of the temperature and 665 genes were found differentially expressed. To determine the role of hyperthermia in this response, several controls were performed. When the temperature artificially maintained constant, no specific gene modifications were observed after exposure. However, a heat shock control did not mimic exactly the MMW effect: 34-gene signatures were identified between 20 mW/cm2 MMW exposure and its relative heat shock control.
Differential expression of seven genes (ADAMTS6, NOG, IL7R, FADD, JUNB, SNAI2 and HIST1H1A) from this signature were confirmed by duplication of the whole experiment and real-time PCR analysis.

overall_design: Gene expression in human keratinocytes was measured after a 60 GHz-exposure at 20 mW/cm2, for 3 h (Expo). It was compared to cells cultured in unexposed condition (Sham). As millimeter wave (MMW) exposure increase temperature in the cell medium, two controls were performed: 1) MMW exposure (3 h, 60 GHz, 20 mW/cm²) with the heat increase compensated to maintain constant the physiological temperature (CompT_Expo); 2) Heat shock control (HSC) to mimicking the heat effect of MMW exposure.

first: Catherine

last: Le Quement

first: Maxim

last: Zhadobov

last: Martin

first: Marc

last: Aubry

first: Ronan

last: Sauleau

first: Yves

last: Le Dréan


title: Genomic Run On (GRO): determination of the nascent transcriptional rate and mRNA amount during alkaline stress response

status: Public on Dec 01 2014

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

summary: We study the transcriptional response of wt S. cerevisiae cells to alkaline pH by using a genome-wide method (Genomic run-on) that allows for the determination of transcription rates (TR) and mRNA amounts (RA) for each gene. The stabilities of the mRNAs can be calculated from the TR and RA data.

overall_design: S. cerevisiae cells grown in YPD pH 5.5 to exponential phase and transfered for the indicated times to pH 8, at each time aliquots were subjected to Genomic Run On.  Conventional mRNA levels were obtained from cDNA labelling on the same array. Home-made microarrays containing 6035 ORF were used.  Three replicates of the experiment were done.

first: José

middle: E

last: Pérez-Ortín

last: García-Martínez

first: David

last: Canadell

first: Joaquín

last: Ariño


title: Gene expression analysis of 35S::JMJ30-HA overexpression transgenic lines grown at 22°C under long day conditions

status: Public on Aug 31 2014

city: Singapore

first: Toshiro

last: Ito

address: 1 Research Link, National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

summary:
Analysis of overexpression of JMJ30 in Arabidopsis thaliana (Col). JMJ30 encode the histone demethylases that contain the catalytic JmjC domain.
The trimethylation of Histone H3 lysine 27 (H3K27me3) plays a key role in gene repression and developmental regulation. It is actively and dynamically deposited and removed in plants. However, while the H3K27 methyltransferases had been extensively studied, findings on the H3K27 demethylase were few. Here, we show that JMJ30 encodes a H3K27me3 demethylase, and genes up-regulated in 35S::JMJ30-HA transgenic lines are enriched for H3K27me3 targets.

overall_design: Columbia wild-type (Col WT) and 35S::JMJ30-HA transgenic plants were grown at 22°C under long day conditions, and seedling samples were collected at 13 day-after-germination (DAG). Two independent sets of WT and 35S::JMJ30-HA seedling mRNA samples were used for this array.

first: Eng-Seng

last: Gan


title: Comparative gene expression profile of human limbal stromal cells, bone marrow mesenchymal cells, adipose cells and foreskin fibroblasts

status: Public on Jul 01 2014

city: Kuala Lumpur

first: Moon

middle: Nian

last: Lim

address: Jalan Pahang

department: Haematology Unit

country: Malaysia

institute: Institute for Medical Research

summary: Limbal stromal cells were reported to resemble mesenchymal stem cells (MSCs) with multipotential differentiation cability. However, little is known about their gene expression profiles compared to MSC derived from various sources. In this study, the gene expression profile of limbal stromal cells was compared to bone marrow, adipose stromal cells and foreskin fibroblasts. In addition, we also explored the gene expression changes of ex vivo expanded limbal stromal cells when cultured in two different systems. Expanded limbal stromal cells were divided into two groups; each cultured separately on a matrigel-coated plate in DMEM/F12 medium supplemented with bFGF and LIF and the other on a normal plate in DMEM medium supplemented with 10% fetal bovine serum (FBS). Cryopreserved bone marrow mesenchymal cells, adipose stromal cells and foreskin fibroblasts were cultured-expanded until confluent. Total RNA was extracted from all the samples and subjected to microarray experiments with an Agilent platform by using Human GE 8x60k microarrays. Data analysis was carried out with GeneSpring software. A total of 871 genes were upregulated when the limbal stromal cells were cultured in the matrigel system, whereas 58 genes were consistently differentially expressed in limbal stromal cells compared to other lineages. Besides the long intergenic non-coding RNA and unknown genes, these genes represent gene ontology for cellular components, molecular function and biological process. Samples derived from the same source were closely clustered by Hierachical clustering analysis. The limbal stromal cells have a distinct molecular signature compared to MSCs from other lineages. The culture system affected the gene expression profile of limbal stromal cells tremendously.

overall_design: Derived limbal stromal cells were cultured using two different methods, one with matrigel and the other with FBS. Their gene expression profiles were compared. The gene expression profile of limbal stromal cells that were cultured with FBS also was compared to the gene expression profiles of bone marrow mesenchymal stem cells, adipose stromal cells and foreskin fibroblasts.

middle: N

first: N

middle: H

last: Hamidah


title: A dominant-negative isoform of IKAROS expands primitive normal human hematopoietic cells

status: Public on Sep 14 2014

city: Vancouver

first: Philip

last: Beer

address: 675 West 31st Avenue

department: Terry Fox Laboratory

country: Canada

institute: BC Cancer Agency

summary: Human cord blood CD34+ cells transduced with control of IK6 lentivirus were transplanted into NSG mice. Control and IK6 transduced CD34+38- progeny were acquired 10 weeks later by FACS

overall_design: Comparison of control and IK6+ human CD34+38- progenitor cells

first: P

first: D

middle: J

last: Knapp

first: C

last: Eaves


title: Gene expression analysis of overexpression and loss-of-function at JUMONJI30

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

overall_design: Refer to individual Series


title: The effect of bisphenol A on human preadipocyte differentiation.

status: Public on Apr 15 2014

city: Ottawa

first: Ella

last: Atlas

state: Ontario

address: 50 Colombine Driveway

institute: Health Canada

summary:
Background: Exposure to the endocrine-disrupting chemical bisphenol A (BPA) is correlated with obesity and promotes adipogenesis of human preadipocytes into mature adipocytes. However, the mechanism of action of BPA-induced human adipogenesis in vitro remains to be fully characterized.
Methods: In this study, potential mechanisms of BPA-induced adipogenesis in primary human preadipocytes were evaluated using gene expression microarray analysis. Preadipocytes from donors with normal body mass indexes were differentiated in the presence of 50 µM BPA or 1 µM dexamethasone (DEX) for 48 hours.
Results: Microarray analysis revealed 235 up-regulated and 138 down-regulated genes following BPA treatment, including sterol regulatory element binding factor 1 (SREBF1), a key transcription factor known to regulate many components of lipid metabolism and adipogenesis. For DEX treated preadipocytes, 1136 genes were up-regulated, including the adipogenic marker lipoprotein lipase, while 1031 genes were down-regulated. Ingenuity Pathway Analysis was used to identify functional annotations of the gene expression changes associated with response to BPA and DEX treatments. BPA exposure was associated with expression changes in the genes involved in the accumulation of triacylglycerol while DEX was linked to metabolism of triacylglycerol and cleavage of fatty acids. The analysis also revealed enrichment of genes in pathways known to be associated with BPA exposure including thyroid-receptor/retinoic X receptor (TR/RXR) activation, mammalian target of rapamycin (mTOR) signaling and cholesterol biosynthesis, whereas DEX treatment was linked to cholesterol biosynthesis and ethanol degradation. Interestingly, alterations in the mTOR pathway in response to BPA did not occur in DEX-treated preadipocytes.
Conclusions: Our data suggest that potential mechanisms of action of BPA-induced adipogenesis involve SREBF1, the TR/RXR and the mTOR pathways.

overall_design: The study used 40 samples in total which included 5 replicates (cells from 5 unique donors) of 8 different treatments. The 8 treatments were as follows: 1) untreated (negative) control for 48 hours, 2) 25 uM BPA treated for 48 hours, 3) 50 uM BPA treated for 48 hours, 4) untreated (negative) control + insulin for 48 hours, 5) 25 uM BPA + insulin treated for 48 hours, 6) 50 uM BPA +  insulin treated for 48 hours, 7) 1uM Dexamethasone + insulin treated for 48 hours, 8) 1uM Dexamethasone + insulin treated for 96 hours.

first: Jonathan

middle: G

last: Boucher

first: Mainul

last: Husain

first: Andrea

last: Rowan-Carroll

first: Andrew

last: Williams

first: Carole

middle: L

last: Yauk


title: Clinically non-involved skin of patients with psoriasis, lichen planus, and healthy individuals

status: Public on May 31 2014

city: Munich

first: Kilian

last: Eyerich

address: Biedersteiner Strasse 29

department: Department of Dermatology and Allergy

country: Germany

institute: Technische Universität München

summary: To investigate differences in the kinetics of allergic contact dermatitis reactions in psoriasis patients, molecular changes in clinically non-involved skin of psoriasis patients was investigated

overall_design: whole genome expression arrays of clinically non-involved skin of psoriasis (n=8), lichen planus (n=3), and healthy individuals (n=7) were performed

first: Maria

last: Quaranta

first: Bettina

first: Stefanie


title: Intra-individual genome expression analysis reveals a specific molecular signature of psoriasis and eczema

status: Public on May 01 2014

summary: Comparing molecular signatures of psoriasis and eczema in patients co-affected by both diseases provides a comprehensive understanding of disease pathogenesis as well as a diagnostic tool to differentiate these widespread inflammatory skin diseases.

overall_design:
In patients affected by both psoriasis and non-atopic or atopic eczema simultaneously (n=24), whole genome expression arrays of psoriasis, eczema, and non-involved skin were performed
Arrays MQ_35 and MQ_41 did not pass quality control and thus were not normalized and were excluded from this Series.


title: Large-scale East-Asian eQTL mapping reveals novel candidate genes for LD mapping and the genomic landscape of transcriptional effects of sequence variants

status: Public on Jun 23 2014

city: Kyoto

first: Maiko

last: Narahara

address: 53 Shogoin Kawaharacho, Sakyo-Ku

country: Japan

institute: Kyoto University

summary: Profiles of sequence variants that influence gene transcription are very important for understanding mechanisms that affect phenotypic variation and disease susceptibility. Using genotypes at 1.4 million SNPs and a comprehensive transcriptional profile of 15,454 coding genes and 6,113 lincRNA genes obtained from peripheral blood cells of 298 Japanese individuals, we mapped expression quantitative trait loci (eQTLs). We identified 3,804 cis-eQTLs (within 500 kb from target genes) and 165 trans-eQTLs (>500 kb away or on different chromosomes). Cis-eQTLs were often located in transcribed or adjacent regions of genes; among these regions, 5’ untranslated regions and 5’ flanking regions had the largest effects. Epigenetic evidence for regulatory potential accumulated in public databases explained the magnitude of the effects of our eQTLs. Cis-eQTLs were often located near the respective target genes, if not within genes. Large effect sizes were observed with eQTLs near target genes, and effect sizes were obviously attenuated as the eQTL distance from the gene increased. Using a very stringent significance threshold, we identified 165 large-effect trans-eQTLs. We used our eQTL map to assess 8,069 disease-associated SNPs identified in 1,436 genome-wide association studies (GWAS). We identified genes that might be truly causative, but GWAS might have failed to identify for 148 out of the GWAS-identified SNPs; for example, TUFM (P=3.3E-48) was identified for inflammatory bowel disease (early onset); ZFP90 (P=4.4E-34) for ulcerative colitis; and IDUA (P=2.2E-11) for Parkinson's disease. We identified four genes (P<2.0E-14) that might be related to three diseases and two hematological traits; each expression is regulated by trans-eQTLs on a different chromosome than the gene.

overall_design: The study subjects were 301 apparently healthy individuals residing in Nagahama City, Japan. Whole blood was collected from each participant when in a non-stimulated state.

first: Fumihiko

last: Matsuda

first: Ryo

last: Yamada

first: Koichiro

last: Higasa

first: Seiji

last: Nakamura

first: Yasuharu

last: Tabara

first: Kawaguchi

last: Takahisa

first: Miho

last: Ishii

first: Kenichi

last: Matsubara


title: Impact of the 3D Microenvironment of Phenotype, Gene Expression, and EGFR Inhibition of Colorectal Cancer Cell Lines

status: Public on May 09 2014

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

summary: Comparison of gene expression of different colon carcinoma cell lines under 2D and 3D culturing conditions

overall_design: Cells were seeded under 2D and 3D culturing condition. After seven days total RNA was isolated and used for cDNA synthesis.

first: Anna

middle: C

last: Luca

first: Sabrina

last: Mersch

first: René

last: Deenen

first: Stephan

last: Schmidth

first: Isabelle

last: Messner

first: Karl-Ludwig

last: Schäfer

last: Baldus

first: Wolfgang

last: Huckenbeck

first: Roland

middle: P

last: Piekorz

first: Wolfram

middle: T

last: Knoefel

first: Andreas

last: Krieg

first: Nikolas

last: Stoecklein


title: Adult AML with complex karyotype

status: Public on Mar 04 2014

city: Hannover

first: Doris

middle: Johanna

last: Steinemann

department: Institute of Human Genetics

institute: Hannover Medical School

type: Genome variation profiling by genome tiling array

summary:
Define minimal deleted regions (12p) in CK_AML
Identification of commonly inactivated genes

overall_design: 20 samples


title: Regional complexity in breast tumors reveals patterns of prognostic value

status: Public on May 21 2014

first: Miriam

middle: Ragle

last: Aure

address: Ullernchauséen 70

department: Dept. of Cancer Genetics

institute: Oslo University Hospital Radiumhospitalet

summary:
Genomic complexity in breast tumors has been associated with aggressive disease and less favorable outcome. Recently, we developed an algorithm to calculate complexity scores per chromosome arm in order to sub-classify breast tumors with respect to progression paths and prognosis. We have further developed this method to calculate probe-focused complexity scores per sample, enabling identification of regions with recurrent complexities and grouping of tumors according to genome-wide complexity patterns. Probe-focused complexity scores were calculated based on data derived from aCGH analyses of 394 invasive ductal breast carcinomas. These continuous complexity scores (CCI) were used to identify regions with recurrent high level complexity, and the regional complexity scores were correlated to clinicopathological variables and survival data.
A total of 25 recurrent regions with high level complexity were identified. Regional complexities on chromosome arms 8p, 11q and 17q were each associated with clinical parameters associated with aggressive disease. Complexity patterns were different between tumors of different gene expression subtypes. Multivariate Cox analysis revealed that regional complexity on 17q21.32-q21.33 was significantly associated with shorter survival, independent of established clinical variables.

overall_design: 394 invasive ductal breast carcinomas were analyzed using whole genome CGH arrays from Agilent. In addition 20 normal breast biopsies were included as controls, a total of 414 samples. All samples were hybridized to the arrays together with a commercial female reference sample from Promega.

first: Jorgen

last: Aaroe

first: Simen

last: Myhre

first: Vilde

middle: D

last: Haakensen

first: Aslaug

last: Helland

first: Xi

last: Zhao

first: Hans

middle: K

last: Vollan

first: Hege

last: Russnes

first: Eldri

middle: U

last: Due

first: Lars

middle: O

last: Baumbusch

first: Fredrik

last: Warnberg

first: Johan

last: Botling

first: Jan

last: Alsner

first: Jens

last: Overgaard

first: Therese

last: Sorlie

first: Ole

last: Lingjaerde

first: Anne-Lise

last: Borresen-Dale


title: Gene expression analysis upon stable SmcHD1 Knock Down

status: Public on Jan 31 2014

city: Burnaby

first: Gratien

middle: G.

last: Prefontaine

state: British Columbia

address: 8888 University Drive

department: Faculty of Health Sciences

institute: Simon Fraser University

summary:
To study the role of SmcHD1 in regulating gene expression, we have stably knocked down SmcHD1 in HEK293 cells and looked at change in gene expression.
shRNA3 and shRNA4 were used to target the expression of the  SmcHD1 gene (Genbank Accession number NM_015295). The protein levels of SmcHD1 were knocked down in excess of 90% normal levels in 293 cells. shRNA NC5 a scrambled control shRNA and did not change SmcHD1 protein levels in 293 cells.

overall_design: Agilent single color 28004 was used on 9 Samples.

first: Shabnam

last: Massah

first: Anne

last: Haegert


title: Frozen tumour samples of 131 gastric cancer patients [array CGH]

status: Public on May 06 2014

first: Hua

last: Dong

address: 199 Liangjing Rd.

institute: astrazeneca

summary: We sought to illustrate molecular subtypes associated with clinical prognosis and to identify genetic aberrations for potential targeted therapeutics through comprehensive whole-genome analysis of 131 Chinese gastric cancer tissue specimens using whole-genome array CGH.

overall_design: We profiled 131 Chinese gastric cancer genomes using Agilent 244K array CGH technology.   70 samples Among them were further profiled by Affymetrix Hu133Plus2 arrays for mRNA expression.

first: Ziliang

last: Qian

first: Guanshan

last: Zhu

first: Jiafu

last: Ji

first: Qunsheng


title: NcRNA profiling after Influenza A/WSN/33 infection I

status: Public on Jan 29 2014

city: Berlin

first: Carla

last: Winterling

address: Charitéplatz 1

institute: Max Planck Institute for Infection Biology

summary: A growing body of evidence suggests gene regulatory functions for the majority of non-protein-coding RNAs (ncRNAs). Besides small RNAs (sRNAs), the diverse class of long ncRNAs (lncRNAs) recently came into focus of research. So far, the relevance of lncRNAs in infection processes remains elusive. Here, we report the differential expression of several classes of lncRNAs during influenza A virus (IAV) infection in human lung epithelial cells.

overall_design:
2 biological replicates of each condition were hybridzed in an independent color-swap;
A549 cells were washed with PBS and then infected with viruses at MOI 1 in infection buffer for for 60 min at room temperature. Cells were incubated for the indicated time periods at 37 °C in DMEM supplemented with 0.2% bovine serum albumin, 4 mM l-glutamine and antibiotics.
Supernatants of A/WSN/33 (H1N1) virus infected A549 cells (MOI 5, 4hpi) were exposed to UV light for 5 min and then used to stimulate A549 cells for 4 h
Supernatants of A/WSN/33 (H1N1) virus infected A549 cells (MOI 5, 8hpi) were exposed to UV light for 5 min and then used to stimulate A549 cells for 8 h

first: Fernando

last: Garcia

first: Manuel

last: Koch

first: Alexander

last: Karlas

first: Max

last: Köppel

first: Thomas

middle: F

last: Meyer


title: Inadequate mito-biogenesis in primary dermal fibroblasts from old humans is associated with impairment of PGC1A-independent stimulation.

status: Public on Apr 08 2014

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Extrinsic skin ageing converges on the dermis, a post-mitotic tissue compartment consisting of extracellular matrix and long-lived fibroblasts prone to damage accumulation and maladaptation. Aged human fibroblasts exhibit mitochondrial and nuclear dysfunctions, which may be a cause or consequence of ageing. We report on a systematic study of human dermal fibroblasts retrieved from female donors aged 20-67years and analysed ex vivo at low population doubling precluding replicative senescence. According to gene set enrichment analysis of genome wide array data, the most prominent age-associated change of the transcriptome was decreased expression of mitochondrial genes. Consistent with that, mitochondrial content and cell proliferation declined with donor age. This was associated with upregulation of AMP-dependent protein kinase (AMPK), increased mRNA levels of PPARγ-coactivator 1α (PGC1A) and decreased levels of NAD(+)-dependent deacetylase sirtuin 1. In the old cells the PGC1A-mediated mito-biogenetic response to direct AMPK-stimulation by AICAR was undiminished, while the PGC1A-independent mito-biogenetic response to starvation was attenuated and accompanied by increased ROS-production. In summary, these observations suggest an age-associated decline in PGC1A-independent mito-biogenesis, which is insufficiently compensated by upregulation of the AMPK/PGC1A-axis leading under baseline conditions to decreased mitochondrial content and reductive overload of residual respiratory capacity.

overall_design: Donors: 15 human female donors included in the study were aged 20, 21, 23, 26, 26, 40, 41, 42, 43, 49, 60, 62, 63, 64 and 67 years, thus covering the age spectrum 20 – 67 years and providing five biological replicates for each of the age groups “young” (20-30 years), “middle” (40-50 years) and “old” (60-70 years). Human dermal fibroblasts were isolated from skin specimen removed in the course of cosmetic surgery from the bottom side of female breast. Isolation and primary culture of the cells followed published procedures (Tigges and others 2013). Cells were not expanded beyond 12 population doublings, while replicative cell cycle arrest was determined to not occur before 40 population doublings.

first: Fritz

last: Boege

first: Beatrice

last: Bornholz

first: Melanie

last: Börries

first: Rene

last: Deenen

first: Ellen

last: Fritsche

first: Christine

last: Götz-Rösch

first: Faiza

middle: M

last: Kalfalah

first: Sebastian

last: Ohse

first: Karl

last: Köhrer

first: Jean

last: Krutmann

first: Stefan

last: Sobek

first: Julia

last: Tigges


title: CD271 on melanoma cell is an IFN-γ-inducible immunosuppressive factor that mediates downregulation of melanoma antigens

status: Public on Apr 01 2014

city: Chuo

first: Takashi

last: Inozume

state: Yamanashi

address: Shimokato 1110

department: Dermatology

institute: University of Yamanashi

summary: In this study, we have identified candidates for IFN-γ-inducible CTLs-suppressive factors in melanoma cells using cDNA microarray analysis

overall_design: Double-stranded cDNAs were synthesized from mRNAs extracted from melanoma cell lines that express melanoma-associated antigen recognized by T cells 1 (MART-1) and HLA-A*0201 (526mel, 1833mel, 2487mel, and 501Amel), with or without pretreatment with recombinant human IFN-γ (rhIFN-γ, 1000 U/mL, 48hours).

first: Shinji

last: Shimada


title: Integrated genomic and prospective clinical studies show the importance of modular pleiotropy for disease susceptibility, diagnosis and treatment (dataset 1)

status: Public on Mar 07 2014

city: Xuzhou

first: Hui

last: Wang

state: Jiangsu

address: 209 Tongshan Rd

institute: Xuzhou Medical University

summary: Medical research focuses on disease-specific genes. By contrast, here we systematically examined the roles of shared genes for disease susceptibility and as therapeutic and diagnostic targets. Meta-analysis of all published disease-related genome-wide association studies (GWAS) showed that T helper (Th) cell differentiation was the most shared pathway. Expression profiling data from highly diverse CD4+ T cell-associated diseases revealed shared disease-associated genes, which were enriched for Th cell differentiation, but also metabolic and proliferative pathways. This pleiotropy suggested that altered functions of shared genes could generally increase disease susceptibility. Indeed, compared to specific genes, the shared genes were enriched for disease-associated SNPs identified by all published disease-related GWAS. To examine if the shared genes induced disease-relevant pathways, we focused on transcription factors (TFs) that induced Th differentiation. Those TFs were enriched among the shared genes, as well as for disease-associated SNPs identified by GWAS, and disease-phenotypes in mice knock-out studies. Original GWAS and profiling data from patients with multiple sclerosis and allergy confirmed enrichment of disease-associated SNPs in the TFs, and that the TFs were differentially expressed at early disease stages, and their targets increased in parallel with disease development. From a clinical perspective, the shared genes were significantly enriched for known diagnostic and therapeutic targets. Prospective clinical studies of multiple sclerosis and allergy showed that shared or specific genes could be used to stratify patients for individualized medicine. Our findings show that shared disease genes generally increase disease susceptibility and are important therapeutic and diagnostic targets.

overall_design: Patients with seasonal allergic rhinitis (SAR) show considerable variations in response to glucocorticoids (GCs) treatment. Peripheral blood mononuclear cells (PBMCs) were collected from 8 high responders (HR) and 8 low responders (LR) to GC treatment. PBMCs were challenged with diluent, grass pollen extract (ALK-Abelló A/S; 100 μg/mL) as well as grass pollen extract plus glucocorticoids (100ug/mL) for one week.  Total CD4+ T cells were enriched for the gene expression microarray analysis, which was performed using SurePrint G3 Human Gene Expression 8X60K microarrays.

first: Mika

last: Gustafsson

first: Måns

last: Edström

first: Fredrik

last: Barrenäs

first: Sören

last: Bruhn

first: Ingrid

last: Kockum

first: Tomas

last: Olsson

first: Colm

last: Nestor

first: Jan

last: Ernerudh

first: Mikael

last: Benson


title: Host cell responses to persistent mycoplasmas--different stages in infection of HeLa cells with Mycoplasma hominis

status: Public on Feb 06 2014

last: Koehrer

summary: M. hominis adherence, colonisation and invasion of HeLa cells were characterised in a time-course study using microarray-based analysis of the HeLa cell transcriptome: 0 h to monitor the baseline of transcription, 4 h to examine host reactions to mycoplasma attachment, 48 h to capture in addition the initiation of invasion, and 2 weeks post infection to examine a chronically infected host cell. At 4 h post infection, cytoadherence of M. hominis to the HeLa cell surface was accompanied by differential regulation of 723 host genes (>2 fold change in expression). Genes associated with immune responses and signal transduction pathways were mainly affected and components involved in cell-cycle regulation, growth and death were highly upregulated. At 48 h post infection, when mycoplasma invasion started, 1588 host genes were differentially expressed and expression of genes for lysosome-specific proteins associated with bacterial lysis was detected. In a chronically infected HeLa cell line (2 weeks), of the 1972 regulated host genes, components of the ECM-receptor interaction pathway and phagosome-related integrins were markedly increased. The immune response was quite different to that at the beginning of infection, with a prominent induction of IL1B gene expression, affecting pathways of MAPK signalling, and genes connected with cytokine-cytokine interactions and apoptosis. These data show for the first time the complex, time-dependent reaction of the host directed at mycoplasmal clearance and the counter measures of this pestering pathogen.

overall_design: To elucidate the host-reactions at the different stages of M. hominis infection, four time points post infection (0h, 4h, 48h, 2 weeks) were chosen for microarray gene expression analyses. Total RNA was prepared from infection assays (MOI 100) in parallel with uninfected HeLa cells and the host cell transcriptomes were determined by comparative microarray analyses.

first: Miriam

last: Hopfe

first: René

last: Deenen

first: Daniel

last: Degrandi

first: Birgit

last: Henrich


title: A module-based translational strategy shows a central role for S100A4 in allergy

status: Public on Feb 05 2014

city: Linköping

address: Ryddalsgatan 8a

country: Sweden

institute: Linköping University

summary: The involvement of thousands of genes complicates the identification of clinically relevant candidate genes in common diseases. We hypothesized that genes co-regulated with a key gene in allergy, IL13, would form a module that could help to discover novel candidate genes. We identified a Th2 cell module by siRNA mediated knock down of 25 putative IL13-regulating transcription factors (TFs) followed by expression profiling.

overall_design: Human CD4+ T cells (hBP CD4+ T cells, 2W-200, Lonza, Vallensbak Strand, Denkmark) were nucleofected either with nucleofection buffer, 1 µM human on target plus SMART pool siRNA against ELK1, GATA3, NFATC3, MAF, NFKB1, JUN, STAT3 (Dharmacon, Lafayette, CO) or non-targeting siRNA using the AMAXA nucleofection program U-014. Six hours after then nucleofection cells were washed, activated and polarized towards Th2. The CD4+ cells were activated with plate bound anti-CD3 (500ng / ml for coating of the plate), with soluble anti-CD28 (500ng / ml) and with IL-2 (17ng /ml, all purchased from R&D). Th2 polarization was induced with anti-IL-12 (5µg/ml) and IL-4 (10ng / ml). For RT-PCR and microarray analyisis the cells were harvested 12 hours of polarization and total RNA was extracted.

first: Yu

last: Fang

first: Yelin

last: Zhao

first: Andrea

last: Krönke

first: Birte

last: Sönnichse

first: Nadine

last: Dulyaninova

first: Anne

last: Bresnick

first: Jörg

last: Klingelhöfer

first: Zou

last: Xiang


title: Effect of excessive c-MYC expression on self-replication and apoptosis of iPS cell-derived megakaryocyte progenitor cell lines

status: Public on Jan 17 2014

first: Akira

last: Watanabe

state: Kyoto

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

institute: CyberomiX Inc

summary: To further address the mechanism by which excessive c-MYC represses self-replication and induces apoptosis, microarray analysis of iPSC-derived megakaryocyte progenitor cell lines(MKCLs) with high or low level of c-MYC expression were examined.

overall_design: We established iPS cell lines integrated with DD-tagged c-MYC genes whose protein expression level could be controlled by the concentration of Shield-1. Gene expressions of iPSC-derived MKCLs with high or low levels of ectopic c-MYC were analyzed by microarray.

first: Sou

last: Nakamura

first: Naoya

last: Takayama

first: Naoki

last: Amano

first: Koji

last: Eto


title: Gene expression analysis of lymphoblast cells in patients with genetic defects in comparison with normal control samples: Profile and characterization of gene pathway expression

status: Public on Jan 02 2014

city: Madrid

first: Pablo

last: Lapunzina

state: Madrid

address: Pª de la Castellana, 261

department: Endocrinology

institute: INGEMM

summary: To underestand the possible effect of different genetic mutation in the transcriptome of the human lymphoblast cells.

overall_design: RNA were extracted from peripheral blood from 3 patients and also for 3 controls age and sex matched.

first: Jair

middle: A

last: Tenorio

first: Victor

last: Glez


title: Physical and functional interactions between the histone H3K4 demethylase JARID1A and the NuRD complex

status: Public on Feb 21 2014

city: Nagoya

first: Jun-ichi

last: Nakayama

state: Aichi

address: 1 Yamanohata, Mizuho

department: Graduate School of Natural Sciences

institute: Nagoya city University

summary: Histone H3K4 methylation has been linked to transcriptional activation. JARID1A (also known as RBP2 or KDM5A), a member of the JARID1 protein family, is an H3K4 demethylase, previously implicated in the regulation of transcription and differentiation. Here we show that JARID1A is physically and functionally associated with two histone deacetylase complexes. Immunoaffinity purification of JARID1A confirmed a previously described association with the SIN3B-containing HDAC complex, and revealed an association with the nucleosome remodeling and deacetylase (NuRD) complex. Sucrose density gradient and sequential immunoprecipitation analyses further confirmed the stable association of JARID1A with these two HDAC complexes.  JARID1A depletion led to changes in the expression of hundreds of genes, two-thirds of which were also controlled by CHD4, the NuRD catalytic subunit. Gene ontology analysis confirmed that the genes commonly regulated by both JARID1A and CHD4 were categorized as developmentally regulated genes. ChIP analyses suggested that CHD4 controls chromatin association with JARID1A and modulates H3K4 levels at the promoter and coding regions of target genes. We further demonstrated that the C. elegans homologues of JARID1 and CHD4 function in the same pathway during vulva development. Taken together, these results suggest that JARID1A and the NuRD complex cooperatively function to control developmentally regulated genes.

overall_design: Genome-wide transcriptomic analysis of HeLa cells transfected with JARID1A complex component siRNA

first: G

last: Nishibuchi

first: J


title: Comparison of gene expression profilings between SFEBq differentiation-defective clones and good clones

status: Public on Dec 03 2013

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

summary: It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine.

overall_design: We extracted total RNA from 10 hESCs and 40 hiPSCs, and hybridized them to Agilent gene expression microarrays.

first: M

last: Koyanagi-Aoi

last: Narita


title: Gene expression signatures of C-terminal shorter RUNX1 protein hematopoietic models

status: Public on Jan 01 2014

first: Sandra

last: Rodriguez-Perales

address: Melchor Fernandez Almagro,3

institute: CNIO

summary: RUNX1 gene chromosomal translocations and mutations are frequent in acute myeloid leukaemia, sometimes resulting in the aberrant expression of C-terminal-truncated RUNX1 proteins lacking the transactivation domain (TAD). Some AML patients anomalously over-express a RUNX1a splice variant with the same TAD deficit. We performed an in-depth in vitro study of the role of TAD-defective RUNX1 proteins in AML development in human hematopoietic/progenitor stem cells. Transformation ability, maturation phenotype and differentiation/proliferation effects were assessed. Short RUNX1 protein expression seemed to increase both proliferation and self-renewal capacity, disrupting the differentiation program and interfering with wild-type RUNX1b protein, in a dominant-negative, dose-dependent manner. Expression microarray analysis showed short RUNX1 and RUNX1/ETO models had similar aberrant expression patterns. Genes known to be broadly involved in self-renewal and leukemogenesis were found to be altered; specifically observed were overexpression of homeobox genes, downregulation of primitive erythroid genes and alterations in leukemogenic transcription factors. The Wnt/b-catenin and RhoA pathways were also observed to be altered, whereas short RUNX1 proteins appeared not to affect the Notch1 pathway, which is altered in the RUNX1/ETO model. Therefore, we propose that TAD-defective RUNX1 proteins may contribute to leukemogenesis and could form the basis of a new genetic category of AML.

overall_design: Comparative experiment: Human CD34+ hematopoietic cells gene expression was measured after TAD defective RUNX1 cDNA transfection vs empty vector transfection. Two independent experiments were performed for each protein model, using different cord blood donors for each experiment.

first: Juan

last: Cigudosa


title: GATA2 as a potential prostate cancer metastasis-driving gene

status: Public on Jan 20 2014

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

summary: Metastatic prostate cancer (PCa) is a terminal disease and establishment of novel therapeutic strategy specifically targeting metastasis is critically required for its management. This study was aimed at identifying metastasis-driving genes which could potentially be therapeutic targets for metastatic prostate cancer. Integrative analysis of gene expression profiles from a pair of metastatic and non-metastatic prostate cancer tissue xenografts was used to identify potential prostate cancer metastasis-driving genes. Among the candidate genes found, GATA2, a master regulator gene in the development of hematopoietic system, was particularly interesting since it is an important pioneer factor in the regulation of AR-target gene in prostate cancer. In consistent with our finding, elevated expression of the GATA2 gene in metastatic prostate cancers was found and its expression was significantly correlated with poor prognosis in prostate cancer patients. Furthermore, indication of the GATA2 gene maybe the metastasis-driving gene was evidenced in decreased of cell migration, tissue invasion and focal adhesion disassembly in GATA2-down-regulated LNCaP cells. Global gene expression analysis after silencing of the GATA2 gene revealed a significant changed in cell transcriptomes with ~ 2500 genes with > 2 fold mRNA level changed and FDR <0.05, indicates that GATA2 plays a critical role in cell reprogramming as pioneer factor in the development of prostate cancer metastasis.

overall_design: LNCaP human prostate cancer cells transiently knockdown with siRNA that specifically targeting GATA2 (siGATA2) or scrambled siRNA (sicontrol). RNAs were isolated from cells after 72 hours of incubation. Gene expression profiles of four biological replicates from each sample group were analyzed to identify differentially regulated downstream genes after knockdown of GATA2.

first: Y

last: Chiang

first: Kendric

last: Wang

first: Colin

last: Collins

first: Yuzhuo

middle: Y


title: Recurrent 11q aberrations in MYC-neg mature aggressive B-cell lymphomas resembling BL

status: Public on Jan 10 2014

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

institute: Hospital Clínic

summary: Copy number analysis using Agilent 244k or 180k (Case9) arrays was performed for 8 MYC-negative B-cell lymphomas, with sex-matched control DNAs

overall_design: Agilent 244k (cases 4-7 and 10-12) and 180k (Case9) arrays

first: Reiner

last: Siebert


title: Effects of EDAG knockdown on gene expression profiles in human erythroid cells

status: Public on Nov 06 2013

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

summary: To investigate the effects of EDAG knockdown on gene exrpession profile in human cord blood CD34+ cells with EPO treatment with microarray assay. Freshly isolated human cord blood CD34+ cells were pre-activated for 24 hours and then infected with EDAG RNAi lentivirus or control lentivirus for 3 times within 24 hours. Then the cells were cultured in the presence of EPO to induce erythroid differentiation. Four days later, the cells were harvested for microarray test. The microarray showed that 3149 differentially expressed genes in siEDAG group compared to control group.The altered genes were associated with gene exrpression, cell cycle and hematopoietic differentiation. These data show that EDAG knckdown led to down-regulation of erythroid genes which are activated by GATA1.

overall_design: Human CD34+ cells infected with EDAG RNAi or control lentivirus were treated with EPO (5U/ml) for 4 days and gene expression were measured using Agilent human whole Genome 8*60K array. Two replicates.

first: Wei-Wei

last: Zheng

first: Mei-Jiang

last: Zhang

first: Rong-Hua

last: Yin

first: Xiao-Ming

last: Dong

first: Jun-Jie

last: Bi

first: Chang-Yan

last: Li

last: Yang


title: Gene expression profile of TCR Vdelta1 positive gammadelta T cells expressed CD161

status: Public on Jan 09 2014

city: Tsukuba

first: Seiji

last: Segawa

address: 1-1-1, Tennoudai

department: Faculty of Medicine

institute: University of Tsukuba

summary: To elucidate the difference between CD161-negative TCR Vdelta1 and CD161-positive TCR Vdelta1 cells, we performed GeneChip analysis of these two types of cells in peripheral blood mononuclear cells from healthy donors.   Such analysis identified 192 genes that were expressed at two-fold or higher levels on CD161-positive TCR Vdelta1 cells than on CD161-negative TCR Vdelta1 cells. Expression of three genes (CCL3, CCL4 and CD161) from this signature was quantified in the same RNA samples by real-time PCR.

overall_design: CD161-negative and CD161-positive TCR Vdelta1cells of three healthy volunteers were isolated from freshly peripheral blood mononuclear cells.

first: Takayuki

last: Sumida


title: Comparison of gene expression profilings between hESCs and hiPSCs

first: Shinya

last: Yamanaka

overall_design: We extracted total RNA from 10 hESCs, 49 hiPSCs, 2 hECCs, 6 somatic cells and 3 cancer cell lines and hybridized them to Agilent gene expression microarrays.

first: M

last: Koyanagi-Aoi

last: Narita


title: Comparison of gene expression at day 11 of iPSC reprogramming with different reprogramming cocktails

status: Public on Nov 20 2013

city: San Francisco

first: Kathleen

last: Worringer

state: CA

address: 1650 Owens St.

country: USA

institute: Gladstone Institutes

summary: To identify genes altered upon LIN-41 expression during reprogramming to induced pluripotent stem cells, human dermal fibroblasts were infected with combinations of GFP alone, OSK, OSKM, OSK+LIN-41, or OSK+let-7 inhibitor (transfected on days 1 and 6). After 11 days, TRA-1-60+ reprogramming cells were isolated as described in Tanabe et al 2013 or in the case of GFP-infected fibroblasts, GFP+ cells were collected. Total RNA was used for gene expression analysis.

overall_design: After 11 days of reprogramming with OSK, OSK+let-7inh, OSKM, or OSK+LIN-41, TRA-1-60+ cells were isolated and total RNA was isolated.


title: Monitoring response and resistance to the novel arsenical darinaparsin in an AML patient

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

summary: A patient diagnosed with AML with inversion of chromosome 3 inv(3)(q21q26.2) was treated with the organic arsenical darinaparsin on an experimental protocol. The patient underwent two treatment cycles. During the first, a stabilization of WBC counts was noted along with a marked improvement in subjective well-being. During the second cycle, the patient's WBC counts continued to increase suggesting the emergence of resistance. RNA was isolated from PBMCs before each cycle and after 48 hours of darinaparsin treatment in each cycle. Gene expression changes were determined by Agilent 8x60K array.

overall_design: For cycle 1, one pre-treatment sample and one 48hr treatment sample was analyzed. Likewise for cycle 2, one pre-treatment sample and one 48hr treatment sample was analyzed.

first: Torsten

middle: H

last: Nielsen

first: Koren

last: Mann


title: Transcriptome Analysis of Cbx7 Knockdown Effects in Ovarian Clear Cell Adenocarcinoma Cell Lines

status: Public on Nov 01 2013

first: Yoriko

last: Yamashita

address: 65 Tsurumai-cho, Showa-ku

department: Department of Pathology and Biological Resoponses

institute: Nagoya University Graduate School of Medicine

summary: Cbx7 knockdown resulted in increase of genes related with apoptosis and  inflammation.

overall_design: Expression microarray was performed using RNA extracted from 2 ovarian clear cell adenocarcinoma cell lines, namely, KOC-7C and TOV21G, either trancduced by Cbx7 siRNA or control.

first: Yamashita

last: Yoriko

first: Shinjo

last: Kanako

first: Toyokuni

last: Shinya

first: Akatsuka


title: The effect on gene expression by p53 family members and the knockdown of AKR1B10

status: Public on Oct 31 2013

city: Sapporo

first: Masashi

last: Idogawa

institute: Sapporo Medical University

summary: To evaluate the effect on gene expression by p53 family members and AKR1B10, we overexpressed p53 family members in H1299 cells or knocked down AKR1B10 in HCT116 cells and evaluated the gene expression by microarray analysis.

overall_design: Gene expression was measured in H1299 cells infected with adenovirus expressing p53, p63g and p73b, and in HCT116 cells transfected with siRNAs targeting AKR1B10 and then treated with adriamycin.


title: BAI3, CDX2 and VIL1: a panel of three antibodies to distinguish small cell from large cell neuroendocrine lung carcinomas

city: Karachi

first: Muhammad

middle: Furqan

last: Bari

state: Sindh

address: Suparco Road, Ojha campus

department: Department of Pathology

country: Pakistan

institute: Dow University of Health Sciences

summary: To identify potential markers for distinction of Small cell (SCLC) from large cell neuroendocrine (LCNEC) carcinoma, we have conducted the gene expression profiling on precisely isolated cancer cells and bronchial epithelial cells from these tumours and normal background lung. After statistical analysis and finding highly differentially expressed genes between these tumour groups, we performed qRT-PCR to delineate markers to test at protein level using immunohistochemistry. Markers showing statistical significance at qRT-PCR level were taken forward to stain tissue microarray sections of SCLC and LCNEC to further delineate markers. This resulted in identification of BAI3, CDX2, VIL1 and CD99 as potential candidates. These markers were then taken forward to stain whole sections of tumour sample available in house (University Hospitals Coventry and Warwickshire) which resulted in elimination of CD99. Thus, BAI3, CDX2 and VIL1 were taken further forward to stain tumour samples acquired externally in UK.

overall_design: Four Small cell lung carcinoma, four large cell neuroendocrine carcinoma and seven background lungs were laser microdissected and profiled on Agilent SurePrint G3 human gene expression 8x60K single channel array to identify potential markers for their classification and validated using qRT-PCR and immunohistochemistry.

first: Keith

last: Kerr

first: Andrew

middle: G

last: Nicholson

first: Helen

last: Brown

first: Lesley

last: Ward

first: Jonathan

last: Moore

first: Manu

last: Vatish

first: David

last: Snead


title: Genome-wide profiling of DNA methylation and expression identifies CIMP in myelodysplastic syndrome [Agilent]

status: Public on Oct 29 2013

city: Shanghai

first: xiaoqin

last: wang

address: 12 wulumuqi road central

institute: Huashan  hospital

summary: To identify genes hypermethylated and transcriptionally downregulated, we have employed the Illumina Infinium HumanMethylation450 BeadChip and Agilent SurePrint G3 Human Gene Expression 8x60K.And we validated selected genes in cases and controls. eventually we estalished CIMP of MDS.

overall_design: The gene expressions of four cases and four controls were measured.

first: Xiaoqin

last: Wang

first: Xiaodong

last: Jia

first: Xiaoli

last: Zhao

first: Feng

last: Yang

first: Shuang

last: Li

first: Meixia

last: Liu

first: Shaoxu

last: Ying

first: Rong

last: Fan


title: Generation of functional cholangiocytes from human pluripotent stem cells and HepaRG cells

status: Public on Oct 28 2013

city: Rennes

first: Hélène

last: Dubois-Pot-Schneider

address: Hopital Pontchaillou, rue Henri Le Guilloux

institute: INSERM UMR 991

summary: Gene expression profile analysis allowed to identify a panel of genes and pathways characteristic of hESC-and HepaRG-derived cholangiocytes.

overall_design: Microarrays were conducted at day 23 and day 10 of differentiation for hESC-Chol and HepaRG-Chol respectively and compared to hESC-HB and HepaRG-HB.  Five, four or three independent experiments were performed depending the experimental sample

first: Anne

last: Corlu


title: Gene expression analysis of human adipose-derived stem cells.

status: Public on Sep 21 2013

city: Philadelphia

first: Olga

last: Igoucheva

state: PA

address: 233 South 10th street

institute: Thomas Jefferson University

summary:
Transcriptional activity was identified in all categories of genes expressed by ADSC, including collagens, ECM and basement membrane constituents, adhesion molecules involved in cell-cell and cell-matrix interactions, and proteases involved in degradation of the ECM and their inhibitors.
Importantly, it was observed that ADSC synthesize and secrete all three collagen VI chains, suggesting suitability of ADSC for collagen VI congenital muscular dytrophy treatment.

overall_design: We developed a procedure for isolation of human stem cells from adipose layer of neonatal foreskin skin. The adipose-derived stem cells (ADSC) were examined for expression of extracellular matrix (ECM) and related genes using gene expression array analysis.

first: Sankar

last: Addya

first: Vitali

last: Alexeev


title: Long-term androgen withdrawal and treatment (R1881) of LNCaP-FGC prostate cancer cells

status: Public on Oct 22 2013

city: Copenhagen

first: Charlotte

last: Svensson

state: Please select one

address: Blegdamsvej 3

department: Novo Nordisk foundation center for protein research

country: Denmark

institute: University of copenhagen

summary:
LNCaP cells were cultures in steroid depleted medium for 5 days before treatment with synthetic androgen (R1881, 10nM) for 16h.
Transcriptomics analysis was performed to compare gene expression changes induced by androgen withdrawal or androgen treatment.

overall_design: Genome-wide transcriptomic analysis of LNCaP cells grown in steroid depleted medium, normal (steroid-containing) medium and R1881 treated cells was performed using the Agilent platform

first: Amilcar

last: Flores-Morales

first: Colin

last: Collins


title: Gene expression profiling in whole blood in patients for Klinefelter’s Syndrome

status: Public on Sep 01 2013

first: wang

last: liang

summary: To study the difference of gene expression pattern of whole blood between klinefelter’s syndrome and normal individuals and discovered the disease-related genes and biological pathway. 717 differentially expressed genes (480 up regulated, 237 down regulated) were identified between whole blood samples of the klinefelter’s patients and normal volunteers. Function enrichment analysis identified a number of genes involved in immune response, metabolism etc. Three genes with significant down-regulation in Klinefelter’s patients were also confirmed by qRT-PCR.Using the whole blood as material in patients with klinefelter’s syndrome, the differentially expressed genes was identified. It is noticed that genes involved in metabolism pathways were significantly decreased. These observations may suggest aberrant of metabolism may be important for developing the klinefelter’s syndrome. In addition, our results also show that no X-linked genes are overexpression in the peripheral blood cells of KS patients.

overall_design: In the present study, we examined gene expression in whole blood of 5 klinefelter’s patients and 5 healthy control volunteers. The RNA of 10 samples was isolated and Gene expression was detected by gene microarray. The different expressed genes were analyzed by SAM software.

first: HUANG

last: Jin

first: ZHANG

last: Liang

first: CHANG

first: LIU

last: Qinli

last: Ping


title: REST knockdown in LNCaP prostate cancer cells

summary:
LNCaP cells were transfected with 3 different REST siRNAs
Transcriptomics analysis was performed to compare gene expression changes induced by REST knockdown

overall_design: Genome-wide transcriptomic analysis of LNCaP cells transfected with REST siRNA


title: LNCaP

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

overall_design: Refer to individual Series


title: Breast cancer cell lines treated with EZH2 inhibitor compounds

status: Public on Aug 27 2013

city: London

first: Ed

last: Curry

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: Imperial College London

summary: Loss of H3K27me3 repressive chromatin histone marks, maintained by the histone methyltransferase (HKMT) EZH2, may lead to reversal of epigenetic silencing in tumor cells and have therapeutic potential.  Using a cell-based assay, we have identified three compounds from a HKMT inhibitor chemical library which re-express H3K27me3 mediated, silenced genes. Chromatin immunoprecipitation verified a decrease in silencing marks (H3K27me3, H3K9me3) and importantly an increase in active marks (H3K4me2/3, H3K27ac) at the promoter of re-expressed genes. Compound treated breast tumor cells induced enrichment for genome-wide changes in expression of known target genes for EZH2 and induced cell growth inhibition: with most sensitive breast tumor cell lines having low EZH2 protein expression, while a normal epithelial breast line was least sensitive.

overall_design: Agilent SurePrint G3 Human 8x60k two-colour microarrays were used to profile gene expression changes induced by treatment with drug compounds in MDA MB-231 cells, both at 24h and 48h. 4 replicates were used for each drug, time combination. A separate untreated control sample was used for comparison with each replicate.

first: Robert

last: Brown


title: Angiosarcoma gene expression

status: Public on Oct 21 2013

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: A comparison of gene expression in OCT frozen human angiosarcoma compared with OCT frozen normal mesenchymal tissues

overall_design: RNA was isolated from 18 AS and normal human. RNA was isolated from 3 kidney and 2 skeletal muscle OCT frozen sections and 3 samples of frozen whole blood. Twenty-five nanograms of total RNA from each sample was used for amplification, and then was fluorescently labeled using Cy3 and hybridized onto Agilent whole human genome 8x60k gene expression microarrays (Agilent Technologies, Santa Clara, CA) according to Agilent standard procedures.  After hybridization for 17 h at 65 oC and 10 rpm, the arrays were washed and scanned with the Agilent G3 high-resolution scanner.  Probe features were extracted from the microarray scan data using Feature Extraction software v.10.7.3.1 (Agilent Technologies). Microarray data was read and processed with R/Bioconductor (version 2.15.1/2.16) statistical software environment using the limma package (version 3.12.1).  The raw data was within array quantile normalized and probes that mapped to the same gene were combined by averaging.

first: Nicholas

last: Duesbery

last: Andersen


title: Analysis of differentially expressed genes in placental tissues of Pre-eclampsia Using microarray combined with Connectivity Map database

status: Public on Oct 01 2013

summary: Preeclampsia (PE), which affects 2-7% of human pregnancies, causes significant maternal and neonatal morbidity and mortality. To better understand the pathophysiology of PE, gene expression profiling of placental tissue from 5 controls and 5 PEs were assessed using microarray. A total of 224 transcripts were identified as being significantly differentially expressed (fold change > 2 and q value < 0.05 in the SAM software), GO enrichment analysis indicated that genes involved hypoxia, oxidative and reductive processes were significantly changed. Ten differentially expressed genes (DEGs) involved in these biological process were further verified by quantitative real-time PCR. Finally, the potential therapeutic agents for PE were explored via Connectivity Map database . In conclusion, the data obtained in this study might provide clues to better understand the pathophysiology of PE and found potential therapeutic agents for PE patients.

first: Yingna

last: Song

first: Juntao

last: Liu

first: Saiqiong

last: Huang

first: Liang

last: Zhang


title: Deletion of DMD exon 52 in the pig results in fulminant muscular dystrophy

status: Public on Aug 06 2013

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

summary: Duchenne muscular dystrophy (DMD) is caused by mutations in the X-linked dystrophin (DMD) gene. The absence of dystrophin protein leads to progressive muscle weakness and wasting, disability and death. To establish a tailored large animal model of DMD, we deleted DMD exon 52 in male pig cells by gene targeting and generated offspring by nuclear transfer. DMD pigs exhibit absence of dystrophin in skeletal muscles, increased serum creatine kinase levels, progressive dystrophic changes of skeletal muscles, impaired mobility, muscle weakness, and a maximum life span of 3 months due to respiratory impairment. To address the accelerated development of muscular dystrophy in DMD pigs as compared to human patients, we performed a genome-wide transcriptome study of M. biceps femoris samples from 2-day-old and 3-month-old DMD and age-matched wild-type pigs. The transcriptome changes in 3-month-old DMD pigs were in good accordance with the findings of gene expression profiles in human DMD, reflecting the processes of degeneration, regeneration, inflammation, fibrosis, and impaired metabolic activity. The transcriptome profile of 2-day-old DMD pigs pointed towards increased protein and DNA catabolism, reduced extracellular matrix formation and cell proliferation and showed similarities with transcriptome changes induced by exercise injury in muscle. Our transcriptome studies provide new insights into congenital changes associated with dystrophin deficiency and secondary complications arising during postnatal development. Thus the DMD pig is a useful model to determine the hierarchy of physiological derangements in dystrophin-deficient muscle.

overall_design: 13 samples, two conditions, two age-groups, 3-4 biological replicates

first: Nikolai

last: Klymiuk

first: Andreas

last: Blutke

first: Alexander

last: Graf

first: Sabine

last: Krause

first: Katinka

last: Burkhardt

first: Annegret

last: Wuensch

first: Barbara

last: Kessler

first: Valeri

last: Zakhartchenko

first: Mayuko

last: Kurome

first: Elisabeth

last: Kemter

first: Hiroshi

last: Nagashima

first: Benedikt

last: Schoser

first: Nadja

last: Herbach

first: Helmut

last: Blum

first: Rüdiger

last: Wanke

first: Christian

last: Thirion

first: Hanns

last: Lochmüller

first: Maggie

middle: C

last: Walter

first: Eckhard

last: Wolf


title: HSC-3 cells (control) vs. HSC-3-5 cells

status: Public on Aug 13 2013

city: Tainan

first: Yi-Ting

last: Chen

address: No. 1 University Road

department: Department of Medical Laboratory Science and Biotecnology

country: Taiwan

institute: National Cheng Kung University


title: Gene expression profiling of chronic myeloid leukemia with variant t(9;22) reveals a different signature from cases with classic translocation.

city: Bari

first: Francesco

last: Albano

address: P.zza G. Cesare, 11

country: Italy

institute: University of Bari

summary: The t(9;22)(q34;q11) generating the Philadelphia chromosome and the BCR/ABL1 fusion gene represents the cytogenetic hallmark of chronic myeloid leukemia (CML). About 5–10% of CML cases show variant translocations with the involvement of other chromosomes in addition to chromosomes 9 and 22. The molecular bases of differences between CML patients with classic and variant t(9;22) have never been elucidated. In this study, we performed gene expression microarrays analysis  to compare CML patients bearing variant rearrangements and those with classic t(9;22)(q34;q11). We identified a list of 59 differentially expressed genes  significantly associated with the two analyzed groups. These genes are mostly involved in the intracellular protein kinase cascade and their upregulation enhances cellular processes already known to sustain the CML pathogenesis.

overall_design: According to conventional and molecular cytogenetics (FISH) data, 12 CML cases with classic t(9;22) and of 8 cases with variant translocations were selected and analyzed by GEP.

first: Antonella

last: Zagaria

first: Luisa

last: Anelli

first: Giorgina

last: Specchia


title: Expression profiling of HCC

status: Public on Sep 05 2013

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: 61 human HCCs were analyzed for genome-wide gene expression. Samples were collected at two sites in Germany, Heidelberg (HD) and Hannover (N). The Heidelberg Collection include 40 independent HCC: 19 liver resections and 17 explant liver specimen (4 not determined); median age at surgery was 57 years (range, 16-78), and the male/female ratio was 3:1. All diagnoses were confirmed by histological reevaluation, and use of the samples was approved by the local ethics committee.  From 3 patients, two HCC nodules were included that previously showed different aCGH, indicating independent tumor development (tagged by _2). The underlying etiologies were HBV (n=8), HCV (n=9), alcohol (n=14), cryptogenic (n=11), genetic hemochromatosis (n=3), and Alpha-1 antitrypsin deficiency (n=2). The Hannover Collection include 21 HCC (HCC-Grad: G1-G3). Technical replicates were tagged with _B or _C

overall_design: differential genes expression in HCC liver (n=61) compared to control group (cell lines, n=3; normal liver tissue(NL), n=7). Technical replicates are indicated by _2.

first: R

first: T

last: Longerich


title: Resistant starch induces catabolic but suppresses immune and cell division pathways and changes the microbiome in proximal colon of male pigs

status: Public on Oct 18 2013

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Consumption of resistant starch (RS) has been associated with various intestinal health benefits, but knowledge on its effects on global gene expression in the colon is limited. The main objective of the current study was to identify genes affected by RS in the proximal colon to infer which biologic pathways were modulated. Ten 17-wk-old male pigs, fitted with a cannula in the proximal colon for repeated collection of tissue biopsy samples and luminal content, were fed a digestible starch (DS) diet or a diet high in RS (34%) for 2 consecutive periods of 14 d in a crossover design. Analysis of the colonic transcriptome profiles revealed that, upon RS feeding, oxidative metabolic pathways, such as the tricarboxylic acid cycle and β-oxidation, were induced, whereas many immune response pathways, including adaptive and innate immune system, as well as cell division were suppressed. The nuclear receptor peroxisome proliferator-activated receptor γ (PPARG) was identified as a potential key upstream regulator. RS significantly (P < 0.05) increased the relative abundance of several butyrate-producing microbial groups, including the butyrate producers Faecalibacterium prausnitzii and Megasphaera elsdenii, and reduced the abundance of potentially pathogenic members of the genus Leptospira and the phylum Proteobacteria. Concentrations in carotid plasma of the 3 main short-chain fatty acids acetate, propionate, and butyrate were significantly higher with RS consumption compared with DS consumption. Overall, this study provides novel insights on effects of RS in proximal colon and contributes to our understanding of a healthy diet.

overall_design: Ten pigs were fitted with a cannula in the proximal colon for repeated collection of tissue biopsies, and were fed a digestible starch or a resistant starch diet for two consecutive periods of 14 days in a crossover design. After each intervention period a colonic biopsy was taken and subjected to gene expression profiling.

first: Danielle

last: Haenen

first: Michael

last: Müller

middle: J


title: PINT lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb Repressive Complex 2 (tissue)

status: Public on Aug 09 2013

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada

summary: It has been recently shown that the transcription factor p53 induces the expression of multiple lincRNAs. However, relatively little is known about the role that lincRNAs play in this pathway. Here we characterize a lincRNA named PINT (p53 Induced Noncoding Transcript). We show that PINT is a ubiquitously expressed lincRNA that is finely regulated by p53. In mouse cells, PINT promotes cell proliferation and survival by regulating the expression of genes of TGF-beta, MAPK and p53 pathways. PINT is a nuclear lincRNA that directly interacts with Polycomb Repressive Complex 2 (PRC2), being required for PRC2 targeting of specific genes for repression. Furthermore, PINT functional activity is dependent on PRC2 expression, representing a connection between the p53 pathway and epigenetic regulation by PRC2. We have also identified PINT human ortholog (hPINT), which presents suggestive analogies with the mouse lincRNA. hPINT is similarly regulated by p53, and its expression correlates significantly with the same cellular pathways as the mouse ortholog, including the p53 pathway. Interestingly, hPINT is significantly downregulated in colon cancer, representing a novel tumor suppressor candidate. Our results not only help our understanding of the role of p53 and lincRNAs in cancer, but also contribute to the open debate regarding the utility of mouse models for the study of lincRNAs.

overall_design: Normal tissue located at least 20 cm away from a tumor was obtained through surgical resection from patients of colorectal cancer. Total RNA was extracted and subjected to microarray analysis.

first: Oskar

last: Marín-Béjar

first: Alejandro

last: Athie


title: Global gene expresion profile of phenotypically distinct human mammary epithelial subpopulations of various developmental age

status: Public on Jul 26 2013

city: Vancouver

first: Connie

last: Eaves

address: 675 W 10th Ave

department: Terry Fox Laboratory

institute: BC Cancer Agency

summary: To get molecular insight into age- and compartment-specific changes in telomere maintenance and associated properties in human mammary gland, we analyzed distinct subsets of normal human mammary epithelial cells.  The cells were isolated by fluorescent activated cell sorting (FACS) directly from mammary tissue obtained from normal women undergoing reduction mammoplasties with concomitant removal of hematopoietic and endothelial cells by depletion of CD45pos and CD31pos cells.  The three epithelial cell populations then isolated were: (i) CD49fhiEPCAMneg/low cells, (ii) CD49fposEPCAMpos cells and (iii) CD49fnegEPCAMpos cells.  The CD49fhiEPCAM-/low cells are selectively enriched in mammary stem cells with functional mammary gland regenerating activity in suitably transplanted immunodeficient mice, bipotent progenitors that form colonies of adherent myoepithelial and luminal cells in vitro, myoepithelial-restricted progenitors that form colonies of exclusively adherent myoepithelial cells in vitro, and mature myoepithelial cells that are not clonogenic (collectively referred to as basal cells, BCs).  The CD49fposEPCAMpos cells are selectively enriched in luminal progenitors (referred to as luminal progenitors, LPs); and the CD49fnegEPCAMpos cells are selectively enriched in mature luminal cells (referred to as luminal cells, LCs).  Differences in gene expression in general and telomere associated genes in particular were elucidated by analyzing mammary epithelial subpopulations.

overall_design: Total RNA was isolated from 24 samples obtained from FACS purification of mammary epithelial subpopulations from 9 reduction mammoplasty breast tissues. Global gene expression profiling was performed by array.

first: Nagarajan

last: Kannan

first: Nazmul

last: Huda

first: LiRen

last: Tu

first: Radina

last: Droumeva

first: Ryan

last: Brinkman

first: Joanne

last: Emerman

first: Satoshi

last: Abe

first: David

last: Gilley


title: Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells [PB]

status: Public on May 12 2015

city: Ottawa

first: Julie

last: Buick

address: 50 Colombine Driveway

department: Mechanistic Studies Division

institute: Health Canada

summary: The use of integrated approaches in genetic toxicology, including the incorporation of gene expression data to determine the molecular pathways involved in the response, is becoming more common. In a companion paper, a genomic biomarker was developed in human TK6 cells to classify chemicals as genotoxic or non-genotoxic. Because TK6 cells are not metabolically competent, we set out to broaden the utility of the biomarker for use with chemicals requiring metabolic activation. Specifically, chemical exposures were conducted in the presence of rat liver S9. The ability of the biomarker to classify genotoxic (benzo[a]pyrene, BaP; aflatoxin B1, AFB1) and non-genotoxic (dexamethasone, DEX; phenobarbital, PB) agents correctly was evaluated. Cells were exposed to increasing chemical concentrations for 4h and collected 0h, 4h and 20h post-exposure. Relative survival, apoptosis, and micronucleus frequency were measured at 24h. Transcriptome profiles were measured with Agilent microarrays. Statistical modeling and bioinformatics tools were applied to classify each chemical using the genomic biomarker. BaP and AFB1 were correctly classified as genotoxic at the mid- and high concentrations at all three time points, whereas DEX was correctly classified as non-genotoxic at all concentrations and time points. The high concentration of PB was misclassified at 24h, suggesting that cytotoxicity at later time points may cause misclassification. The data suggest that the use of S9 does not impair the ability of the biomarker to classify genotoxicity in TK6 cells. Finally, we demonstrate that the classifier is also able to accurately classify genotoxicity using a publicly available dataset derived from human HepaRG cells.

overall_design: This experiment examined the whole genome transcriptional response of TK6 cells exposed to phenobarbital for 4 hours followed by recovery times of 4h and 20h in fresh media (8h and 24h time points, respectively) at 3 different concentrations, including a low (1 mM), a medium (3.2 mM), and a high (10 mM) concentration, in addition to a vehicle control (+S9). Each concentration and time point had 3 biological replicates, which were pooled for gene expression analysis. There were a total of 6 samples (12 arrays) included in the final analysis using a two-colour dye swap design.

first: Ivy

last: Moffat

first: Andrew

last: Williams

first: Carol

last: Swartz

first: Leslie

last: Recio

first: Daniel

last: Hyduke

first: Heng

last: Li

first: Albert

last: Fornace Jr.

first: Jiri

last: Aubrecht

first: Carole

middle: L

last: Yauk


title: HSC-3 cells (control) vs. HSC-3-5 cells [subcutaneous tumor]

first: Yi-Ting

last: Chen

summary: HSC-3-5 cells, which drived from human HSC-3 cells via transwell invasion assay was high invasive.Tumor cells were injected into the flank of SCID mice. After 6 weeks, transcriptional profiling of human HSC-3 tumor comparing with high invasive HSC-3-5 tumor.  Goal was to determine the effects of invasion on global HSC-3-5 gene expression during tumor metastasis.

overall_design: HSC-3 and HSC-3-5 oral cancer cells were respectively injected into the flank and tongue of SCID mice. After 1 and 6 weeks, total RNA was respectively extracted from the tumor tissue on tongue and flank of SCID mice for gene expression profiling during metastasis. Briefly, two-condition experiment,HSC-3 vs. HSC-3-5 cells.

first: Chuan-Fa

last: Chang


title: HSC-3 cells (control) vs. HSC-3-5 cells [tongue]

summary: HSC-3-5 cells, which drived from human HSC-3 cells via transwell invasion assay was high invasive.Tumor cells were injected into the tongue of SCID mice. After 1 week, transcriptional profiling of human HSC-3 tumor comparing with high invasive HSC-3-5 tumor.  Goal was to determine the effects of invasion on global HSC-3-5 gene expression during tumor metastasis.

overall_design: HSC-3 and HSC-3-5 oral cancer cells were respectively injected into the tongue of SCID mice. After 1 weeks, total RNA was respectively extracted from the tumor tissue on tongue of SCID mice for gene expression profiling during metastasis. Briefly, two-condition experiment,HSC-3 vs. HSC-3-5 cells.


title: HSC-3 cells (control) vs. HSC-3-5 cells [cell line]

summary: HSC-3-5 cells were derived from human HSC-3 cells via transwell invasion assay. Transcriptional profiling of human HSC-3 cells comparing with high invasive HSC-3-5 cells.  Goal was to determine the effects of invasion on global HSC-3-5 gene expression during tumor metastasis.

overall_design: Two-condition experiment, HSC-3 vs. HSC-3-5 cells.


title: Gene expression data in Meg-01 cells following transfection with platelet-enriched microRNA-1225-3p

status: Public on Jun 20 2013

city: Pittsburgh

first: Shilpa

last: Jain

address: 200 Lothrop Street

institute: Uinversity of Pittsburgh

summary: Platelets from sickle cell disease patients have differentially expressed microRNAs as compared to platelets from healthy control subjects. The objective of this study is to overexpress an upregulated miRNA,miR-1225-3p, in MEG01 cells to identify putative targets.

overall_design: MEG-01 cells were transfected with microRNA-1225-3p mimic for overexpression. Simultaneously, a negative control (scrambled) RNA was transfected for comparison. Gene expression was measured at 24 hours after transfection.  Five independent experiments were performed at the same time in each group: microRNA-1225-3p transfected and scrambled.

first: Mark

middle: T

last: Gladwin

first: Naftali

last: Kaminski


title: Gene expression profiling of tumor stroma in human intrahepatic cholangiocarcinoma

status: Public on Jun 21 2013

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

summary: Intrahepatic cholangiocarcinoma (ICC) is the second most common type of primary cancer in the liver. ICC is an aggressive cancer with poor prognosis and limited therapeutic strategies. The identification of new drug targets and prognostic biomarkers is an important clinical challenge for ICC. The presence of an abundant stroma is a histological hallmark of ICC. Given the well established role of the stromal compartment in the progression of cancer diseases, we hypothesized that relevant biomarkers could be identified by analyzing the stroma of ICC. By combining laser capture microdissection and gene expression profiling we demonstrated that ICC stromal cells exhibit dramatic genomic changes. We identified a signature of 1,073 non-redundant genes that significantly discriminate the tumor stroma from non tumor fibrous tissue. Functional analysis of differentially expressed genes demonstrated that up-regulated genes in the stroma of ICC were related to cell cycle, extracellular matrix and Transforming Growth Factor beta (TGFβ) pathways. Tissue microarray analysis using an independent cohort of 40 ICC patients validated at a protein level the increase expression of Collagen 4, Laminin, Osteopontin/SPP1, KIAA0101 and TGFβ2 genes in the stroma of ICC. Statistical analysis of clinical and pathological features demonstrated that the expression of Osteopontin, TGFβ2 and Laminin in the stroma of ICC was significantly correlated with patient overall survival. More importantly, multivariate analysis demonstrated that the stromal expression of Osteopontin was an independent prognostic marker for overall and disease-free survival. Conclusion: The study identifies clinically relevant genomic alterations in the stroma of ICC, including candidates biomarkers for prognosis, supporting the idea that tumor stroma is an important factor for ICC onset and progression.

overall_design: 20 RNA samples were analyzed, from 10 patients with ICC. For each patient, RNA were isolated from laser capture microdissected (LCM) stroma from tumor and non tumor areas.


title: Maturation,not initiation, is major roadblock during reprogramming toward pluripotency from human fibrobalsts

status: Public on Jul 01 2013

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

summary: Reprogrammed cells are reverted to non reprogrammed cell fate in a maturation step of reprogramming.

overall_design: Cell fate changes during reprogramming from fibroblasts to iPSC , N=60  fibrobalst lines, N=13  Undifferentiated pluripotent stem cells, N=16  Nascent reprogrammed cells, N=31

first: Koji

last: Tanabe

first: M

last: Narita


title: Role of platelet micrornas in sickle cell disease

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


title: linc-UBC1 physically associates with polycomb repressive complex 2 (PRC2) and acts as a negative prognostic factor for lymph node metastasis and survival in bladder cancer

status: Public on Mar 15 2013

city: Guangzhou

first: Wang

last: He

state: Guangdong

address: 107th, Yanjiangxi Road

department: Urology

country: China

institute: Sun Yat-sen Memorial Hospital

summary: To identify aberrantly expressed long intergenic noncoding RNAs (lincRNAs) in bladder cancer tissues compared with normal adjacent tissues, we have employed microarray expression profiling as a discovery platform to identify lincRNAs that may play important roles in bladder cancer origin and progression. Samples of fresh frozen cancer tissues, together with normal adjacent tissues (3 cm away from the tumor), were obtained during surgical resection, and total RNA was extracted for microarray analysis. Expression of six mRNAs and lincRNAs (E2F1, CCNE2, CCNB1, lincRNA:chr1:205404014-205407007, lincRNA:chr7:130723313-130727663, lincRNA:chr4:15669186-15683175) from this signature was quantified in the same RNA samples by real-time PCR, confirming good quality of the microarray analysis. Data in the matrix are log2 transformed.

overall_design:
Gene expression signatures for bladder cancer tissues and normal adjacent tissues.
Three pairs of fresh frozen bladder cancer tissues and corresponding normal adjacent tissues were used in the microarray analysis.

first: Qingqing

last: Cai

first: Fenyong

last: Sun

first: Guangzheng

last: Zhong

first: Pei

last: Wang

first: Hongyan

last: Liu

first: Junhua

last: Luo

first: Hao

last: Yu

first: Jian

last: Huang

first: Tianxin

last: Lin


title: Influence of plasma from normal and preeclamptic women on HUVEC cells

status: Public on Jun 30 2013

city: Paris

first: Daniel

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

country: France

summary: Plasma from normal and preeclamptic pregnancies was collected and added in the culture medium of HUVEC cells. The aims are double: identifying putative biomarkers that could be modified recurrently in the endothelium under preeclampsia and understand at term the molecular bases of the increased risk of cardiovascular and kidney diseases in woman that have had a preeclampsia.

overall_design: 2 pools of 3 control plasmas and 2 pools of 4 preeclamptic plasma were organized and added at a concentration of 1/10 on HUVEC cells, during 24 hours before transcriptomic analysis


title: Comparative study of deoxynivalenol and 15-acetyldeoxynivalenol on gene expression in the human cell line Caco-2

status: Public on Feb 27 2013

city: Yokohama

first: Tomoyuki

last: Kadota

state: Kanagawa

address: 1-13-5, Fukuura Kanazawa-ku

department: Research & Development Division

institute: Kirin Company, Limited

summary:
To screen cellular effects on Caco-2 cells by deoxynivalenol (DON) and 15-acetyldeoxynivalenol (15ADON), toxin-treated Caco-2 cells were analyzed by DNA microarray. Exposure to either toxin induced up- or downregulation of genes in Caco-2 cells. Upregulation of 1290 and 3238 genes was observed for the DON- and 15ADON-treated groups, respectively, after a 60-min incubation period. This represented a greater than 1.5-fold change relative to the 0-min exposure (control) group. Five hundred and sixty-one genes showed a 1.5-fold upregulation in the both the DON- and 15ADON-treated groups. Similarly, 13 genes and 105 genes were upregulated with a log2 ratio > 2 (4-fold change) in the DON- and 15ADON-treated groups, respectively.
The most remarkable gene upregulation corresponded to the inflammatory chemokine, IL-8, which showed a greater than 4-fold upregulation in response to both treatments.

overall_design: Deoxynivalenol and 15-acetyldeoxynivalenol at concentrations of 1 ug/mL were added separately to the AP chamber, and cells were harvested with 0.5% trypsin-EDTA after incubation for 0, 5, 30, and 60 min. Toxin-treated Caco-2 cells were analyzed by DNA microarray to screen for changes in gene expression in response to deoxynivalenol or 15-acetyldeoxynivalenol.

first: Yoshiko

last: Sugita-Konishi


title: Expression of FUS-CHOP fusion protein in immortalized/transformed human Mesenchymal Stem Cells drives mixoid liposarcoma formation

status: Public on Jun 18 2013

city: Oviedo

first: Rene

last: Rodriguez

state: Asturias

address: Av. Hospital Universitario s/n

country: Spain

institute: Health Research Institute of Asturias (ISPA)

summary: Although different sarcomas have been modeled in mice upon expression of fusion oncogenes in MSCs, sarcomagenesis has not been successfully modeled in human MSCs (hMSCs). We report that FUS-CHOP, a hallmark fusion gene in mixoid liposarcoma (MLS), has an instructive role in lineage commitment, and its expression in hMSC sequentially immortalized/transformed with up to 5 oncogenic hits (p53 and Rb deficiency, hTERT over-expression, c-myc stabilization and H-RASv12 mutation) drives the formation of serially transplantable MLS. This is the first model of sarcoma based on the expression of a sarcoma-associated fusion protein in hMSC, and allowed us to unravel the differentiation processes and signaling pathways altered in the MLS-initiating cells. This study will contribute to test novel therapeutic approaches, and constitutes a proof-of-concept to employ hMSCs as target cell for modeling other fusion gene-associated human sarcomas.

overall_design: Wild type (MSC-0H) or transformed (MSC-5H) BM-hMSCs were transduced with concentrated viral particles expressing either pRRL-EF1α-PGK-GFP (empty vector; GFP) or pRRL-EF1α-FUS-CHOP-PGK-GFP (FUSCHOP expressing vector; FC) in order to generate MSC-0H-GFP, MSC-0H-FC, MSC-5H-GFP and MSC-5H-FC cell lines. MSC-0H-GFP and MSC-0H-FC cells did not develop tumors, meanwhile MSC-5H-GFP cells gave rise to undifferentiated sarcomas and MSC-5H-FC originated mixoid liposarcoma tumors when inoculated into immunedeficient mice. Several cell lines were derived from tumors developed from MSC-5H-GFP (T-5H-GFP-1 to -3 cell lines) and MSC-5H-FC (T-5H-FC-1 to -3 cell lines) cells. Gene expression analysis was performed using MSC-0H, MSC-5H and T-5H cell lines and lists of differentially expressed genes were created by comparing the gene expression profiles of MSC-0H-FC, MSC-5H-FC and T-5H-FC cell types to the control MSC-0H-GFP cells.

first: Pablo

last: Menendez


title: Patient specific orthotopic glioblastoma xenograft models recapitulate the histopathology and biology of human glioblastomas in situ (CGH)

status: Public on Jan 18 2013

city: Seoul

first: Jinkuk

last: Kim

address: 50 Irwon-dong, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

summary: Frequent discrepancies between preclinical and clinical results of anti-cancer agents demand a reliable translational platform that can precisely recapitulate the biology of human cancers. Another critical unmet need is the ability to predict therapeutic responses for individual patients. Toward this goal, we have established a library of orthotopic glioblastoma (GBM) xenograft models using surgical samples of GBM patients. These patient-specific GBM xenograft tumors recapitulate histopathological properties and maintain genomic characteristics of parental GBMs in situ. Furthermore, in vivo irradiation, chemotherapy, and targeted therapy of these xenograft tumors mimic the treatment response of parental GBMs. We also found that establishment of orthotopic xenograft models portends poor prognosis of GBM patients and identified the gene signatures and pathways signatures associated with the clinical aggressiveness of GBMs. Together, the patient-specific orthotopic GBM xenograft library represent the preclinically and clinically valuable “patient tumor’s phenocopy” that represents molecular and functional heterogeneity of GBMs.

overall_design: aCGH experiments were performed for a human glioblastoma tissue (sample ID: PC-NS08-559) and the matching xenograft tumor tissue using the Agilent Human Whole Genome CGH 244K microarray according to manufacturer's protocol (2-color).

first: Kyeung-Min

last: Joo

first: Juyoun

last: Jin

first: Misuk

first: Ho-Jun

last: Seol

first: Do-Hyun

last: Nam