title: Gene expression analyses in IRF8-induced monocyte differentiation

status: Public on Jan 24 2013

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

institute: Yokohama City University

summary: To understand the differentiation program in monocyte/macrophage differentiation, we performed ChIP-seq for IRF8 and H3K4me1 together with gene expression profiling during IRF8-induced monocyte differentiation. Both promoter-proximal and -distal binding of IRF8 associated with induction of the genes especially those related to monocytes/macrophages and immunity. DNA motif analysis for cis-regulatory elements of indirect IRF8 target genes predicted KLF4, essential for Ly6C+ monocyte development, to be a downstream transcription factor regulating the indirect target gene expression. Introduction of KLF4 into an Irf8-/- myeloid progenitor cell line induced a subset of IRF8 target genes and partially induced monocyte/macrophage differentiation. Together, this study revealed the genome-wide behavior of IRF8 and the IRF8-KLF4 axis during monocyte differentiation.

overall_design: Gene expressions in monocyte-like cells differentiated by IRF8 or KLF4 were measured at day 4 after retroviral transductions to myeloid progenitor cell line, Tot2. Two independent experiments were performed.

first: Akira

last: Nishiyama


title: Role of CDK8 in interferon-gamma-induced gene expression

status: Public on Feb 28 2013

city: Vienna

first: Pavel

last: Kovarik

address: Dr. Bohr-Gasse 9

department: Max F. Perutz Laboratories

country: Austria

institute: University of Vienna

summary: Gene regulation by cytokine-activated STAT transcription factors requires serine phosphorylation within the transactivation domain (TAD). STAT1 and STAT3 TAD phosphorylation was reported to occur upon promoter binding by an unknown kinase. Here we show that the Mediator CDK8 module phosphorylates S727 of the STAT1 TAD in the interferon (IFN) signaling pathway as well as the TADs of other STATs. Microarray analysis reveals that CDK8-mediated STAT1 TAD phosphorylation positively or negatively regulates over 40% of IFN-gamma-responsive genes, and RNA polymerase II occupancy correlates with gene expression changes. This selective regulation occurs despite CDK8 occupancy and STAT1 S727 phosphorylation at both S727 phosphorylation-dependent and -independent IFN-gamma target genes. Independently of its role as STAT1 S727 kinase CDK8 acts as a positive regulator of IFN-gamma responses. These data reveal a dual input of CDK8 in STAT1-controlled transcription and propose a key role for CDK8 in TAD phosphorylation of other STATs during cytokine responses.

overall_design:
STAT1 WT and STAT1 S727A mouse fibroblasts were treated with siRNA to CDK8 (siCdk8 smart pool, On Target Plus, Dharmacon) and control siRNA (siCtrl) and stimulated with IFN-gamma for 4 h or left untreated. Total RNA from three independent experiments for each treatment and each genotype was isolated from cells using Trizol reagent (Invitrogen) following the manufactures protocol and used for expression analysis using Agilent Whole Mouse Genome Microarrays, 8x60K. Standard protocols for labeling and hybridization were followed. In brief, fluorescent cRNA was generated using Low Input Quick Amp Labeling Kit (Agilent). The amplified cyanine 3-labeled cRNA samples were then purified using SV Total RNA Isolation System (Promega) and hybridized to microarray slides. Microarray slides were washed and scanned with an Agilent Scanner.
Note: The outlier array #10 [SA.CDK.gamma.R3] was removed from subsequent analysis and its processed data was not provided. However, its raw data file has been linked as a supplementary file at the foot of the Series record.

first: Joanna

last: Bancerek


title: Gene expression profiling of monocyte-derived dendritic cells (DCs) from peripheral blood mononuclear cells (PBMCs)

status: Public on Jan 28 2013

city: kunming

last: Zhao

address: Eastern Jiaochang road,32#

country: China

institute: Kunming institute of zoology.CAS

summary: In order to detect the gene expression profile of in vitro generated dendritic cells , purified monocytes from PBMCs were used as dendritic cell (DCs) precursors and were cultured in medium with cocktail for differentiation and maturation to immature dendritic cells (iDCs) and mature dendritic cells (mDCs). Total RNA samples were isolated from precursor, iDCs and mDCs and used for microarray-based gene expression profiles.

overall_design: To generate enough amount of immature DC (iDCs) and mature DCs (mDCs), monocytes were differentiated with GM-CSF and rhIL-4 for 2 days and maturated in the presence of TNF-α, IL-1β, IL-6 and PGE2 for another 2 days. With the anticipation to insight developmental-stage-specific genes with potential functions related to monocyte derived DCs, global gene expression profiling was set using microarray technology.gene expression profiles were performed in triplicate independent experiments starting for 3 groups of precursor, iDC and mDC generated from different blood donors.

first: Fengchao

last: Lang

first: Yan

last: Guo

first: Huatang

last: Zhang


title: Searching for human genes whose expression is controlled by nuclear paraspeckle

status: Public on Mar 15 2013

city: Tokyo

first: Tetsuro

last: Hirose

address: 2-4-7 Aomi, Koutou

department: Biomedical Research Institute

country: Japan

institute: AIST

summary: To identify  human genes whose expression is controled by nuclear paraspeckle, the microarray was carried out using the RNA samples prepared from the control and NEAT1 lncRNA knockdown HeLa cells where the nucelar paraspckels were disintegrated. NEAT1 lncRNA was eliminated by administration of antisense oligogapmer.

overall_design: Either NEAT1 ASO (#12) or control ASO (GFP) was ademnistered into HeLa cells to knockdown NEAT1 lncRNA. Total RNAs were prepared after 6, 12 and 24 hours after ASO administration.

first: Takahide

last: Yokoi


title: Transcriptome analysis of primary human CD4+ T-cell activation

status: Public on Jan 23 2013

city: Dresden

first: Zoltan

last: Maliga

address: Pfotenhauer Str 108

country: Germany

institute: MPI-CBG

summary: In order investigate the control of genes encoding cytoskeletal motor proteins and their interaction partners in primary T-cells, we performed whole transcriptome microarray profiling of cell activation for memory and naïve T-cells isolated from three anonymous blood donors.

overall_design: CD4+CD25- naïve or memory T-cells were cultured in medium alone or stimulated ex vivo and harvested for total RNA isolation and whole transcriptome microarray analysis.

first: Maliga

last: Zoltan


title: Microarray analysis of the leukocyte global gene expression profile following lithium treatment

status: Public on Mar 09 2013

city: Toon

first: Junichi

last: Iga

state: Ehime

address: Shitsukawa 454

department: Neuropsychiatry

institute: Ehime University

summary: To further development of our gene expression approach to lithium pharmacodynamics, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish lithium pharmacodynamics across an exposure range relevant for medical decision-making in lithium therapy. 8 healthy male subjects participated in this study. Lithium was prescribed for 2 weeks, enough to reach a therapeutic serum concentration (0.6-1.0mM). Leukocyte counts and serum lithium concentrations were determined at baseline (before medication), after 1 week and 2 weeks medication and post-2-weeks (2 weeks after stopping medication). Gene expression profiling was performed at each time point using Agilent G4112F Whole Human Genome arrays containing approximately 44,000 probe sets. Some of the candidate gene expressions were also determined by real-time PCR.

overall_design: Lithium-induced gene expression in human blood was measured at baseline, after 1 week and 2 weeks of treatment, and after 2 weeks after stopping medication. 4 independent experiments were performed (baseline, 1wk, 2wk, after 2wk) using mixed samples from each donor.

first: Shinya

last: Watanabe

last: Nishi

first: Shusuke

last: Numata

first: Makoto

last: Kinoshita

first: Kumiko

last: Kikuchi

first: Masahito

last: Nakataki

last: Ohmori


title: Characterization of monocyte-derived dendritic cells (DCs) from peripheral blood mononuclear cells (PBMCs)

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

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

overall_design: Refer to individual Series


title: Gene expression profiling of normal prostates and prostate cancer metastases

status: Public on Feb 04 2013

city: Charlestown

first: Martin

last: Aryee

state: MA

address: 149 13th Street

department: Pathology

country: USA

institute: Massachusetts General Hospital

summary: Gene expression profiling of normal prostates from organ donors and prostate cancer metastases from a rapid autopsy cohort of lethal metastatic prostate cancer

overall_design: Multiple anatomically distinct metastases (18) from each of five patients. 21 normal prostate samples from organ donors

middle: J

first: Srinivasan

last: Yegnasubramanian


title: The differentiation stage of p53- and Rb-deficient bone marrow mesenchymal stem cells imposes the phenotype of in vivo sarcoma development

city: Armilla

first: Alberto

last: Labarga

state: Granada

address: Av. Innovacion 1

country: Spain

institute: Experimental Serendipity S.L.


title: Expression of motor proteins in transgenic HeLa cell lines

summary: We employed whole transcriptome microarray profiling to measure the expression of myosin and kinesin genes in multiple HeLa cell lines and confirm the expression of recombinantly-tagged BAC transgenes encoding motor genes.

overall_design: Normal and transfected HeLa cells grown to confluence were harvested for extraction of total RNA and microarray analysis


title: mRNA changes induced by acute exercise

status: Public on Jan 01 2013

city: Tucson

first: Dawn

middle: K

last: Coletta

state: AZ

address: 1501 N. Campbell Ave

department: Medicine

institute: UNIVERSITY OF ARIZONA

summary: The purpose of this experiment was to determine what gene expression changes are induced by acute exercise in humans, and how those changes relate to insulin sensitivity

overall_design: 14 subjects had muscle biopsies at rest and 30 minutes after a single exercise bout for measurement of mRNA changes. Glucose clamps were used to assess insulin sensitivity.

first: Carrie

last: McLean

first: Clinton

last: Mielke

first: Jeanine

middle: M

last: Cordova

first: Paul

middle: R

last: Langlais

first: Benjamin

last: Bowen

first: Danielle

last: Miranda

first: Lawrence

last: Mandarino


title: Expression of M-CSF from cryopreserved teeth-derived human periodontal ligament cells with different freezing protocols

status: Public on Jan 19 2013

city: Seoul

first: Sang Hyuk

last: Park

address: Dongdaemungu, Hoegidong 1

country: South Korea

institute: Kyung Hee University

summary:
This study investigated which genes regarding root resorption are upregulated by cryopreservation and whether cryopreservation affects the expression of Macrophage –colony stimulating factor.
We manufactured the customized template which was made of genes selected regarding root resorption including osteoprotegerin (OPG), receptor activator of nuclear factor-kappa B ligand (RANKL), RANKL’s cognate receptor (RANK), macrophage colony-stimulating factor (M-CSF), interleukin-1β (IL-1β), and tumor necrosis factor-alpha (TNF-α), and bone morphogenetic proteins (BMP) and analyzed gene expression.

overall_design: cultured human periodontal ligament cells (control) VS cryopreserved and cultured periodontal ligament cells(cryopreserved group): 3 control replicates, 3 cryopreserved replicates

first: Eun-Mi

last: Rhim

first: Su-Jin

last: Ahn

first: Eun-Cheol

last: Kim

first: Ji-Yeon

first: Kyung-Hee

first: Hyeon-Woo

last: Lee

first: Sang-Hyuck


title: Comparison of gene expression signature between nascent Lhx6-GFP+ cells from mouse embryonic brain and differentiated Lhx6-GFP+ cells from ES cells (as well as comparing those of Lhx6-GFP+ and Lhx6-GFP- cells from ES cells)

status: Public on Jan 16 2013

city: San Francisco

first: Joshua

last: Pollack

state: CA

address: 2 Tower Pl.  Ste 800

institute: Pionyr Immunotherapeutics

summary: There was a remarkable similarity in the molecular properties of the MGE-GFP+ and ES-GFP+ cells. In particular, genes that are important for medial ganglionic eminence (MGE) and cortical interneurons development are both high in expression in both MGE-Lhx6-GFP+ and ES-Lhx6-GFP+ cells (compared to ES-Lhx6-GFP- cells).

overall_design: To investigate how closely ES cells-derived Lhx6-GFP+ cells resembled authentic Lhx6+ MGE cells, and  to define the molecular properties of the Lhx6-GFP+ and Lhx6-GFP- cells from differentiated ES cells, we compared their gene expression profiles. We used FACS to purify GFP+ cells from the E12.5 MGE of Lhx6-GFP transgenic mice. ES-Lhx6-GFP+ cells and ES-Lhx6-GFP- cells (both from D12 EB aggregates) were also isolated by fluorescent activated cell sorting (FACS) and all of the RNA samples were subjected to RNA expression microarray analyses.

first: John

last: Rubenstein

first: Jasmine

last: Chen


title: Developing a gene expression model for predicting ventilator-associated pneumonia in trauma patients: a pilot study.

city: Memphis

first: Joseph

last: Swanson

state: TN

address: 910 Madison Ave., Suite 308

department: Clinical Pharmacy

institute: University of Tennessee

summary:
Objective: Identify genes that are differentially expressed between critically ill trauma patients who go on to develop ventilator-associated pneumonia (VAP) compared to similar patients who do not develop VAP
Using gene expression differences, develop a model that predicts which patients are at greater risk of developing VAP.

overall_design: Prospective observational study, analysis of gene expression in 20 patient samples, 10 that developed ventilator-associated pneumonia, 10 that did not

first: G

middle: C

last: Wood

first: Lijing

last: Xu

first: Lisa

middle: E

last: Tang

first: Bernd

last: Meibohm

first: Ramin

last: Homayouni

first: Martin

middle: A

last: Croce

first: Timothy

last: Fabian


title: Identifying microRNA-mRNA regulatory networks in colorectal cancer by a combination of expression profile and bioinformatics analysis

status: Public on Jan 03 2013

city: shanghai

first: Jihong

last: Fu

state: shanghai

address: Kongjiang Road 1665, Shanghai, 200092, China

department: colorectal surgery department

institute: Xinhua Hospital

summary: A multi-step approach combining microarray profile and bioinformatics analysis was adopted to identify the CRC specific miRNA-mRNA regulatory network. First, differentially expressed miRNAs and mRNAs were found out in CRC samples compared with normal epithelial tissues by miRNA and mRNA microarray respectively. Secondly the target mRNAs of dysregualted miRNA were identified by a combination of Pearson correlation coefficient between the expression level of miRNAs and mRNAs and online miRNA target predicting databases. Thirdly, the biological pathways which the miRNA-mRNA pairs involved in were identified by DAVID. Finally, some of the dysregualted miRNAs and mRNAs were validated by qRT-PCR

overall_design: RNA isolated from 8 colorectal cancer tissues and their corresponding adjacent normal tissues were analyzed.

first: Wentao

first: Peng

last: Du

first: Guanghui

last: Wang

first: Wei

first: Jingming

last: Li

first: Yunxiang

last: Zhu

first: Jun

last: Gao

first: Long

last: Cui


title: Gene expression profiles of MCF7 with with the following NR ligands: estradiol/E2 (ERα agonist), AM580 (RARA agonist), CD437 (RARG agonist), ATRA (RARA/RARG agonist), GW0742 (PPARD agonist), R5020 (PGR agonist), and dexamethasone (GR/NR3C1 agonist).

city: Chicago

first: Jie

last: Zhou

state: ILLINOIS

address: 900 East 57th Street, KCBD 10100

institute: University of Chicago IGSB

summary: Altered gene expression patterns in human diseases reflect perturbations in the transcriptional networks that regulate cellular state. In breast cancer, Nuclear Receptors (NRs) play a prominent role in governing gene expression. NRs have prognostic utility and are therapeutically important targets. In order to understand the function of nuclear receptors in breast cancer, we treated MCF7 cells with 6 nuclear receptor agonist, and performed expression arrrays with three biological replicates each.

overall_design: MCF-7 cells were cultured for 48 hours in medium with 10% charcoal-stripped FBS, and then were treated with 6 diffferent NR ligand (E2, AM580, CD437, ATRA, R5020, DEX) separately  for 24h before collection and processing for microarrays. Three biological replicates were collected and processed for both control and treatment.   with the 100nM GW0742 (PPARD specific ligand) and 100nM ATRA (RARs ligand), then collected after 24h for microarray processing. Controls were non-treated MCF7 cells. Both treatments and controls have three biological replicates.

first: Ralf

last: Kittler

first: Sujun

last: Hua

first: Lijia

last: Ma

first: Yuwen

last: Liu

first: Chao

last: Cheng

first: Mark

last: Gerstein

first: Kevin

last: White


title: Endothelial Cells Provide an Instructive Niche for the Differentiation and Functional Polarization of M2-like Macrophages

status: Public on Dec 31 2012

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Endothelial cells and macrophages are known to engage in tight and specific interactions that contribute to the modulation of vascular function. Here we show that adult endothelial cells provide critical signals for the selective growth and differentiation of macrophages from several types of hematopoietic progenitor cells. The process features the formation of well-organized colonies that exhibit progressive differentiation from the center to the periphery and towards an M2-like phenotype, characterized by enhanced expression of Tie2 and CD206/Mrc1. These colonies are long-lived as long as the contact with the endothelium is maintained; removal of the endothelial monolayer results in rapid dissolution of the macrophage colonies. Not only the maintenance but also the formation of the colonies is strictly dependent on endothelial contact. We further found that M-CSF produced by the endothelium is critical for the expansion of the macrophage colonies and that blockade of M-CSF receptor impairs colony growth. Functional analyses indicate that these macrophages are capable of accelerating angiogenesis, promoting tumor growth and effectively engaging in tight associations with endothelial cells in vivo. These findings uncover a critical role of endothelial cells in the induction of macrophage differentiation and their ability to promote further polarization towards a proangiogenic phenotype.

overall_design: 8 samples were sequenced: bone marrow derived macrophages (BMDM) were stimulated with LPS, IL4, or none. Colony cells induced by endothelial cells for 7 days. Each was duplicated.

first: Huanhuan

last: He

first: Xinmin

first: Luisa

last: Iruela-Arispe


title: Gene expression profiling after S1004A induction

city: Sendai

first: yuriko

last: saiki

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Molecular Pathology

institute: Tohoku University School of Medicine

summary: We performed microarray analyses before and after induction of S100A4 using PCI-35 and PCI-43, and identified 72 and 18 genes that were two fold or more commonly upregulated or downregulated, respectively, in these two cell lines.

overall_design: Using two cell lines, PCI-35 and PCI-43, transfected with S1004A expression construct, we studied mRNA transcription levels by microarray analysis to see if there are any of the key molecules for malignant phenotype.

first: Yuriko

last: Saiki

first: Hitoshi

last: Sekine

first: Keisuke

last: Sato

first: Akira

last: Horii


title: Caco-2 cells: cultured in conventional vs apical anaerobic conditions

status: Public on Dec 21 2012

city: Puddle Alley

first: Alan

middle: Francis

last: McCulloch

state: Mosgiel

address: Invermay

country: New Zealand

institute: AgResearch NZ

summary: Transcriptional profiling of Caco-2 cells comparing Caco-2 monolayers cultured in a custom built co-culture chamber, either inside a 5% CO₂ incubator (conventional cell culture environment) or an anaerobic workstation (apical anaerobic environment) for 12 hours.

overall_design: Two-condition experiment with dye swap, A vs B, 6 biological replicates

first: Dulantha

last: Ulluwishewa

first: Wayne

last: Young


title: Transcriptome analysis of primary human monocyte differentiation

first: Zoltan

last: Maliga

summary: In order investigate the control of genes encoding cytoskeletal motor proteins and their interaction partners in the activation program of primary monocytes, we performed whole transcriptome microarray profiling of ex vivo monocyte differentiation to activated macrophages or dendritic cells in monocytes isolated from three anonymous blood donors.

overall_design: Monocytes were isolated from the buffy coats of three anonymous blood donors and differentiated into activated macrophages or activated dendritic cells (DCs) ex vivo. Total RNA from monocytes, activated macrophages or DCs was isolated and submitted for whole transcriptome microarray analysis.

first: Maliga

last: Zoltan


title: Comparison of the MC-LR and MC-RR effects on Caco-2 cells

city: Fougères

first: Perrine

last: Zeller

address: la haute marche-javené

department: UTC

country: France

institute: ANSES

summary:
Microcystins (MCs) are cyclic hepatotoxins produced worldwide by various species of cyanobacteria. Their structure includes two variable amino acids (AAs) and most of the studies focused on the most toxic variant: the microcystin LR (MC-LR). However, more than 80 MC variants have been described to date. Despite ingestion being the major pathway of human exposure, few in vivo studies have demonstrated macroscopic effects on the gastro-intestinal tract, but no data are available on the affected pathways by several variants on intestinal cells. Here, using a non-selective method, we investigated for the first time the effect of MC-RR and MC-LR on the human intestinal cell line Caco-2 and compared their response at the pangenomic scale. The cells were incubated for 4 hrs or 24 hrs with the same range of sub-lethal concentrations of MC-RR or MC-LR.

Low effects were observed for both variants after a short-term exposure. On the contrary, dose-dependent modulations of the genes transcription levels were noticed with MC-RR and MC-LR after 24 hrs. Furthermore, the genomic profiles induced by both variants were similar suggesting a common toxicity mechanism but with higher modulation following MC-LR than MC-RR exposure. However, the functional annotation revealed major differences between the variants effects. Indeed, the well-known MC-LR affected mainly two pathways, the oxidative stress response and the cell cycle regulation, which did not elicit significant alteration following MC-RR exposure.

This work is the first comparative description of the MC-LR and MC-RR effects on a human intestinal cell model. It allowed us to suggest differences in the mechanism of toxicity for MC-RR and MC-LR. These results illustrate that the toxicity of MC variants remains a key point for risk assessment.

overall_design: Differentiated Caco-2 cells were exposed to microcystins in free FCS culture medium for either 4 or 24 hours. Sub-lethal concentrations of 10, 50 and 100 µM of MC-LR or MC-RR were chosen for 4 hours, while 1, 5 and 10 µM were selected for 24 hours. For each condition (including the controls), the solvent concentration was fixed to 2% EtOH for MC-LR and 1.5% of 80% MeOH for MC-RR. Four to five culture replicates per condition were done.

first: Hélène

last: Felix

first: Yannick

last: Blanchard

first: Edouard

last: Hirchaud


title: Identifying CHIR99021 and AICAR-regulated genes in the J1 mESCs

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

summary: It has been demonstrated that CHIR99021 promotes self-renewal of mouse embryonic stem cells, however, the target genes of CHIR99021 is not fully understood. AICAR is the activator of AMP-activated protein kinase. It is reported that AICAR plays important role in mouse embryonic stem cells, however the moleculor mechanism of this phenomenon is unknown. To better understand the downstream target genes of CHIR99021 and AICAR, we performed Microarray analyses to identify their downstream targets. The data show the genes regulated by CHIR99021 or AICAR.

overall_design: J1 mESCs maintained in  medium containing 1000 U/mL LIF and supplemented without or with CHIR99021 or AICAR for 24 hours, then total RNA was extracted for analysis.

first: Xiaoyan

last: Shi

first: Zhiying

last: Ai

first: Zekun

last: Guo


title: Gene expression profiling of glioblastoma cell lines transfected with FGFR3-TACC3

status: Public on Dec 01 2012

city: Tampere

first: Matti

last: Annala

address: Korkeakoulunkatu 1

country: Finland

institute: Tampere University of Technology

summary: Gene expression profiling of SNB19 and U251 glioblastoma cell lines transfected with the FGFR3-TACC3 fusion, FGFR3 wildtype and TACC3 wildtype constructs.

overall_design: SNB19 and U251 cells were transfected with different clones of the FGFR3-TACC3 fusion and with wildtype FGFR3 and TACC3 constructs. Total RNA was extracted and hybridized onto Agilent dual channel gene expression microarrays. In each hybridization, empty vector transfected SNB19 or U251 cells were hybridized into the reference channel.

first: Brittany

last: Parker

first: David

last: Cogdell

first: Kirsi

last: Granberg

first: Yan

last: Sun

first: Ping

last: Ji

first: Xia

last: Li

first: Joy

last: Gumin

first: Hong

last: Zheng

first: Limei

last: Hu

first: Olli

last: Yli-Harja

first: Hannu

last: Haapasalo

first: Tapio

last: Visakorpi

first: Xiuping

last: Liu

first: Chang-gong

first: Raymond

last: Sawaya

first: Gregory

middle: N

last: Fuller

first: Kexin

last: Chen

first: Frederick

middle: L

last: Lang

last: Nykter

first: Wei

last: Zhang


title: Gene expression profiling of triple negative breast cancer, normal ductal cells, and normal tissues

city: Tokushima

first: Masato

last: Komatsu

address: Kuramoto-cho 3-18-15

institute: Genome Medicine

summary: To identify novel molecular targets for triple negative breast cancer (TNBC), we have employed whole genome microarray expression profiling.   We purified 30 surgically resected breast cancer tissue diagnosed triple negative by means of immunohistochemical staining and 13 normal mammary ductal cells with lasermicrobeam microdissection system (PALM MicroBeam, Carl Zeiss MicroImaging Co., Ltd), performed whole human genome microarray, and compared gene expression levels of TNBC, normal mammary ductal cells, and normal vital organs to develop molecular targets with a minimum risk.

overall_design: Gene expression levels of 30 TNBC, 13 normal mammary ductal cells, and 4 normal vital tissues were evaluated.  to clarify the molecular mechanism involved in TNBC, we analyzed gene expression profiles of 30 TNBC as well as 13 normal epithelial ductal cells purified by laser microbeam microdissection, and identified 301 transcripts that were significantly up-regulated and 321 transcripts that were significantly down-regulated in TNBC. In addition, gene-expression profiles analysis of normal human vital organs including heart, lung, liver, and kidney allowed us to identify 90 cancer-specific genes involved in breast carcinogenesis such as NEK2, PBK, DTL, MELK and GPSM2.  Among them, we focused on cell cycle regulators, asp (abnormal spindle) homolog, microcephaly associated (Drosophila) (ASPM) and centromere protein K (CENPK) as novel therapeutic targets for TNBC.

first: Toyomasa

last: Katagiri


title: PC-3 cells: siControl vs. siRNA ARHGAP21

city: Campinas

first: Mariana

last: Lazarini

state: São Paulo

address: Rua Carlos Chagas, num 480

department: Hematology and Hemotherapy Center

country: Brazil

institute: University of Campinas

summary: Transcriptional profiling of the prostate adenocarcinoma cell line PC-3 comparing control cells transfected with a pool of oligonucleotides control (siControl) with cells transfected a pool of oligonucleotides specific to inhibit ARHGAP21 expression (siARHGAP21). The efficiency of the transfection was checked with quantitative PCR and western blotting. Goal was to determine the effects of ARHGAP21 silencing on global PC-3 gene expression.

overall_design: Two-condition experiment, siControl vs. siARHGAP21 PC-3 cells with three biological samples of PC3 cells transfected with a pool of oligonucleotides control (siControl 1, 2 and 3) and three biological samples of PC3 cells transfected with a pool of oligonucleotides specific to inhibit ARHGAP21 (siARHGAP21 1, 2 and 3). For each sample (three siControl and three siARHGAP21), two technical replicates were performed (labelled with Cy3 or Cy5).

first: Fabiola

last: Traina

first: Joao

last: Machado-Neto

first: Karin

middle: S

last: Barcellos

first: Yuri

last: Moreira

first: Marcelo

last: Brandão

first: Sergio

last: Verjovski-Almeida

first: Anne

last: Ridley

first: Sara

middle: T

last: Olalla Saad


title: Nucleosome driven transcription factor binding and gene regulation [microarray]

city: Barcelona

first: Miguel

last: Beato

address: Aiguader 88

institute: CRG

summary:
Elucidating the global function of a transcription factor implies the identification of its target genes and genomic binding sites. The role of chromatin in this context is unclear, but the dominant view is that factors bind preferentially to nucleosome-depleted regions, identified as DNaseI-hypersensitive sites (DHS). Here we show by chromatin-IP, MNase and DNaseI assays followed by deep sequencing that the progesterone receptor (PR) requires nucleosomes for optimal binding and function. In breast cancer cells treated with progestins we identified 25,000 PR binding sites (PRbs), the majority encompassing several copies of the hexanucleotide TGTYCY, highly abundant in the genome. We found that functional PRbs accumulate around progesterone-induced genes mainly in enhancers, are enriched in DHS but exhibit high nucleosome occupancy. Progestin stimulation results in remodeling of these nucleosomes with displacement of histones H1 and H2A/H2B dimers. Our results strongly suggest that nucleosomes are crucial for PR binding and hormonal gene regulation.
Keywords: time course

overall_design: Whole genome expression microarrays were performed in T47D-MTVL cells stimulated 0, 1 and 6 hr with 10 nM of progestin R5020. 3 biological replicas were performed for T0 and 6 hr treatments and 4 for the one of 1hr.

first: Cecilia

last: Ballare


title: Design and use of multiplexed chemostat arrays

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

type:
Expression profiling by array
Genome variation profiling by array

summary: We developed and validated a small-footprint array of miniature chemostats built from readily available parts for low cost. Physiological and experimental evolution results were similar to larger volume chemostats. The ministat array provides a compact, inexpensive, and accessible platform for traditional chemostat experiments, functional genomics, and chemical screening applications.

overall_design: Three experiments are gene expression comparisons between three ministat cultures and a single Sixfors sample.  The four CGH arrays are individual clones evolved in four sulfate limitation ministats compared to a wt ancestor strain.

first: Aaron

middle: W

last: Miller

first: Corrie

last: Befort

first: Emily

middle: O

last: Kerr


title: Gene expression compare between liver cancer associated mesenchymal stem cells (LC8-MSC) and liver normal mesenchymal stem cells (LN8-MSC)

status: Public on Nov 17 2012

city: beijing

first: yan

last: xin long

address: 27 Taiping Road

institute: Beijing Institute of Transfusion Medicine

summary:
Transcriptional profiling of liver cancer associated mesenchymal stem cells comparing normal mesenchymal stem cells from adjacent tumor-free tissues of the same patient 8, Goal was to determine to detect the paracrine trophic factors from liver cancer mesenchymal stem cells.
8 represents liver cancer associated MSCs, N8 represents liver normal MSCs

overall_design: Two-condition experiment, 8 vs. N8 cells. Biological replicates: 1 replicate from the same patient.

first: X

last: Yan

first: W

last: Yue

last: Pei


title: Differentiating factors of cumulus cells related to quality of the human oocyte

status: Public on Dec 10 2012

city: Nantes

first: Raluca

last: TEUSAN

address: 1, rue gaston veil

institute: INSERM U915

summary:
Single embryo transfer (SET) is the most successful way to reduce the frequency of multiple pregnancies during in vitro fertilisation. However, selecting the embryo with the highest chances of pregnancy for SET remains a difficult challenge, since morphological and kinetics criteria provide poor prediction of both developmental and implantation ability. Partly through the expression of specific genes, the oocyte-cumulus interaction helps the oocyte to acquire its developmental competence. Our aim was therefore to identify at the level of cumulus cells (CCs) any genes related to oocyte developmental competence.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Rotating wall vessel (RWV) grown A549s compared to monolayer grown A549s infected with F. tularensis SchuS4 over a 22 hour time-course (2, 6 and 22 h post infection)

city: Salisbury

first: Jonathan

last: David

address: Porton Down

department: Biomedical Sciences

country: United Kingdom

institute: Dstl

summary: A549 epithelial cells grown under two different conditions were compared.  A549s grown in rotating wall vessel cultures display a more in-vivo like phenotype. The data here describe the transcriptional differences between the two culture methods when infected with Francisella tularensis SchuS4 over a 22 hour time-course

overall_design: 1 colour; Cy3 labelled, 6 biological replicates for each culture condition and time-point, A549s grown in RWVs (RWV) compared to A549 grown in monolayers (mono), Infected vs. Naïve


title: Gene expression analysis of U251 human glioblastoma cell line

city: Hamburg

first: Genrich

last: Tolstonog

department: Department of Tumor Virology

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

summary: The human TP53 gene is frequently mutated in tumors and cell lines. Unlike other tumor suppressors that are commonly inactivated by deletions or nonsense mutations, the majority of p53-mutations are missense point mutations that result in the expression of a full-length protein with an altered amino acid that has lost sequence specific DNA-binding. Expression of mutant p53 (mutp53) confers advantages to tumor cells and transcriptional regulation of several genes mediating the beneficial effects has been shown to play a role. However, molecular mechanisms of transcriptional regulation by mutp53 are still poorly understood. We used the glioblastoma-derived U-251 MG human cell line endogenously expressing mutp53 protein (R273H mutation) to analyze gene expression profiles on Agilent Whole Human Genome Microarray after transient and stable depletion of mutp53 expression. Gene expression data was correlated with a ChIP study on a custom tiling array to understand the contribution of endogenously expressed mutp53 to transcriptional regulation.

overall_design: This series of microarray experiments contains the gene expression profiles of glioblastoma-derived U-251 MG human cell lines engineered to constitutively express a p53-specific shRNA or scrambled control shRNA. To reverse the effect of mutp53 depletion, stable clones were modified by stable integration of a mutp53-R273H expression construct or empty pCDNA3 vector as a control. In addition, we performed gene expression analysis of U-251 MG cells transiently transfected with p53-specific siRNA or control siRNA (3 biological replicates each).

first: Timo

last: Quante

first: Benjamin

last: Otto

first: Wolfgang

last: Deppert


title: Identification of Novel Cholesteatoma-related Gene Expression Signatures Using Full-genome Microarrays

status: Public on Nov 14 2012

city: Bielefeld

first: Jörn

last: Kalinowski

address: Universitätsstr. 27

department: Centrum für Biotechnologie

institute: Universität Bielefeld

summary:
In this study, we investigated differentially expressed genes in human cholesteatomas  in comparison to regular auditory canal skin using Whole Human Genome Microarrays that contain 19,596 human genes. In addition to already described up-regulated mRNAs in cholesteatoma, such as MMP9, DEFB2 and KRT19, we identified 3558 new cholesteatoma-related transcripts. 811 genes appear to be significantly differentially up-regulated in cholesteatoma. 334 genes were down-regulated more than 2-fold.
Significantly regulated genes with protein metabolism activity include matrix metalloproteinases as well as PI3, SERPINB3 and SERPINB4. Genes like SPP1, KRT6B, PRPH, SPRR1B and LAMC2 are known as genes with cell growth and/or maintenance activity. Transport activity genes and signal transduction genes are LCN2, GJB2 and CEACAM6. The three cell communication genes are CDH19 and genes belonging to the S100 family.

overall_design: Two samples from each patient (cholesteatoma vs. normal auditory canal skin) for each two-colour hybridisation experiment

first: Christin

last: Klenke

first: Holger

last: Sudhoff


title: Gene expression profiling of mesial temporal lobe epilepsy

city: Bangalore

first: Akhilesh

last: Pandey

email: pandey@jhmi.edu, arivusudar@ibioinformatics.org, sameerkumar.iob@gmail.com, microarray@ibioinformatics.org

state: Karnataka

address: UnitI, Discoverer building, ITPL

country: India

institute: Institute of Bioinformatics

summary: The epilepsies represent one of the most common neurological disorders. Mesial temporal lobe epilepsies (MTLE) are the most frequent form of partial epilepsies and display frequent resistance to anti-epileptic drugs thus representing a major health care problem. In TLE, the origin of seizure activity typically involves the hippocampal formation, which displays major neuropathological features, described with the term hippocampal sclerosis (HS). HS is the most frequent pathological substrate of refractory mesial temporal lobe epilepsy. Complex partial seizures (CPS) are the predominant seizure type associated with medial temporal lobe epilepsy. MTLE is commonly due to mesial temporal sclerosis (MTS). The biology underlying the epilepstic seizures and the transcriptome associated to the seizure in intractable medial temporal lobe epilepsy is ill understood. The aim of the study was to identify potential biomarkers that could identify epileptic seizure. Thus we performed transcriptome profiling of ten medial temporal lobe epilepsy cases which are resistant to the drug and underwent temporal lobectomy. The cases constitutes of patients with intractable complex partial seizure, treated medically and have undergone detailed presurgical evaluation and subjected to surgery for standard temporal lobectomy and amygdalo-hippocampectomy. The spiking areas identified after the electrocorticography will form the test tissues, which compared with the nonspiking areas removed during the surgery, from the same patient. This could probably form one of the appropriate controls, as test and control are from same patient, which eliminates the genome variations that could incur due to the comparison with the tissues from the another patient. Also this could get rid of expression changes due to the treatments undergone by the patient.  We performed two color microarray wherein we labled seizure focus (spiking area) with Cy5 and non-seizure region tissues (non-spiking) with Cy3. As a strategy to test the possibility of potential diagnostic biomarkers we are intended to test the differentially regulated molecules in an independent set of epilepsy samples.

overall_design: Two color experiment


title: Differentiating factors of cumulus cells related to quality of the human oocyte [CadoretPart3]

summary: Our  aim  was  to  identify  at  the  level  of cumulus cells any genes related to oocyte developmental competence

overall_design: 2-condition experiment: blastocyst (B) AND embryo of poor quality (E).

first: D

last: Royère

first: P

last: Feuerstein


title: Spp1, a member of Set1 complex, promotes meiotic DSB formation by tethering histone H3K4 methylation sites to chromosome axes

status: Public on Dec 13 2012

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

institute: Institut Curie

type: Genome binding/occupancy profiling by genome tiling array

summary: Meiotic DSB, catalyzed by the Spo11 transesterase protein and accessory DSB proteins, form in the nucleosome depleted regions (NDR) at promoters, preferentially those located on the chromosome loops that shape meiotic chromosomes, whereas the DSB proteins are located on chromosome axes at the basis of these loops. Mechanisms bridging these two chromosomal regions for DSB formation have remained elusive. Here we show that Spp1, a conserved member of the histone H3K4 methyltransferase Set1 complex, is required for normal levels of DSB formation and is associated with chromosome axes in the DSB-rich domains during meiosis. Moreover, Spp1 physically interacts with the Mer2 axis-associated DSB protein, and uses its PHD finger as a magnet to read H3K4 trimethylation close to promoters, tether these regions to chromosome axes and activate cleavage in the nearby promoter by the DSB proteins. We further show that in the absence of Spp1 or the Set1 complex, DSB are introduced at a few new sites, located in promoters of transcriptionally induced genes, suggesting another selection mechanism of preferred DSB sequences. This paper provides the molecular mechanism linking H3K4me3 to the DSB forming machinery, by the meiosis-specific specialization of Spp1 as an active member of the DSB complex and a reader of H3K4me3, and opens perspectives for the study of DSB formation at mammalian recombination hotspots that are also enriched in H3K4me3.

overall_design: ChIP-chip experiment in vegetative or meiotic diploid SK1 yeast cells - two biological replicates

first: Valérie

last: BORDE


title: Role of Aldoketoreductases and Other Doxorubicin Pharmacokinetic Genes in Doxorubicin Resistance, DNA binding, and Subcellular Localization

status: Public on Nov 22 2012

city: Sudbury

first: Baoqing

last: Guo

state: ON

address: 41 Ramsey Lake Road

department: Tumor Biology

country: Canada

institute: Advanced Medical Research Institute of Canada

summary: Objective: To assess the role of aldoketoreductases and other doxorubicin pharmacokinetic or pharmacogenomic genes in doxorubicin cytotoxicity, resistance, DNA binding activity, and subcellular localization,      Methods: We conducted a whole genome microarray study to identify differences in between doxorubicin-sensitive MCF-7cc cells and doxorubicin-resistant MCF-7Dox2-12 cells in terms of their expression of genes related to doxorubicin pharmacokinetics or pharmacodynamics. Targets were then validated by pharmacologic inhibition in conjunction with drug metabolite profiling, drug localization, drug cytotoxicity, and drug DNA binding studies. Results: 2063 differentially expressed transcripts were identified, including 17% and 43% of genes or gene families associated with doxorubicin pharmacokinetics or pharmacodynamics (p values of significance of 0.05 and <0.0001, respectively).  The largest changes in the expression of genes associated with doxorubicin pharmacokinetics and pharmacodynamics were chiefly among the aldo-keto reductases (AKRs) Akr1c2, Akr1c3 and Akr1b10 which convert doxorubicin to doxorubicinol.  We observed that doxorubicinol exhibits dramatically reduced drug toxicity, reduced drug DNA-binding activity, and altered drug subcellular localization to lysosomes. Pharmacologic inhibition of these AKRs in MCF-7Dox2-12 cells restored drug cytotoxicity, and drug localization to the nucleus.  Conclusion: These findings demonstrate the utility of using curated pharmacokinetic and pharmacodynamic knowledgebases to identify highly relevant genes associated with doxorubicin resistance.  The products of one or more of these genes could effectively be shown to alter the drug’s properties, while inhibiting them restored drug DNA binding, cytotoxicity, and subcellular localization.

overall_design: Doxorubicin resistant cell lines of breast MCF-7 cells were  generated for gene expression profilling. Two colour microarray of Agilent whole human genome nucleotide arrays was conducted with four labelling replicates of both forward and reverse labellings plus another set of 8 arrays with forward labelling. Sixteen arrays were used for this experiments. The co-cultured control cells MCF-7cc12 was generated by parallel selection process in the absence of drug.

first: Allan

middle: D

last: Heibein

first: Jason

last: Sprowl

first: David

last: MacLean

first: Amadeo

last: Parissenti


title: Characterization of the EZH2-MMSET histone methyltransferase regulatory axis in cancer [expression]

status: Public on Nov 15 2012

city: Atlanta

first: Meng

last: Zhao

state: GA

address: 1518 Clifton Rd, #369

department: BIOS

institute: Emory University

summary: Histone methyltransferases (HMTases), as chromatin modifiers, regulate the transcriptomic landscape in normal development as well in diseases such as cancer.  Here, we molecularly order two HMTases, EZH2 and MMSET that have established genetic links to oncogenesis. EZH2, which mediates histone H3K27 trimethylation and is associated with gene silencing, was shown to be coordinately expressed and function upstream of MMSET, which mediates H3K36 dimethylation and is associated with active transcription. We found that the EZH2-MMSET HMTase axis is coordinated by a microRNA network and that the oncogenic functions of EZH2 require MMSET activity. Together, these results suggest that the EZH2-MMSET HMTase axis coordinately functions as a master regulator of transcriptional repression, activation, and oncogenesis and may represent an attractive therapeutic target in cancer.

overall_design: LacZ control vs MMSET overexpression or MMSET DeltaSET overexpression in replicates

first: Xiaojung

last: Jing

first: Irfan

last: Asangani


title: The tumorigenic fusion FGFR3-TACC3 escapes miR-99a regulation in glioblastoma

first: Matti

last: Annala

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series

first: Brittany

last: Parker

last: Cogdell

first: Kirsi

last: Granberg

first: Yan

last: Sun

first: Ping

last: Ji

first: Xia

last: Li

first: Joy

last: Gumin

first: Hong

last: Zheng

first: Limei

last: Hu

first: Olli

last: Yli-Harja

first: Hannu

last: Haapasalo

first: Tapio

last: Visakorpi

first: Xiuping

last: Liu

first: Chang-gong

first: Raymond

last: Sawaya

first: Gregory

last: Fuller

first: Kexin

last: Chen

first: Frederick

last: Lang

last: Nykter

first: Wei

last: Zhang


title: Differentiating factors of cumulus cells related to quality of the human oocyte [CadoretPart2]

first: Raluca

last: TEUSAN

overall_design: 2-condition experiment: blastocyst (B) ans embryo of poor quality (E).

first: D

last: Royère

first: P

last: Feuerstein


title: Gene expression and ChIP-chip analysis of U251 human glioblastoma cell line

first: Genrich

last: Tolstonog

summary:
Using human U251 glioblastoma cells with endogenous mutp53 expression as a model, we performed a ChIP-chip analysis of mutp53 binding sites on a custom tiling array, coupled with global expression profiling and an analysis of the epigenetic status of mutp53 regulated promoters. Mutp53 binds preferentially, and independent of other transcription factors (e.g. ETS1 and SP1), to G/C-rich DNA stretches around transcriptional start sites (TSS) of many genes. Mutp53-bound regions are frequently located in CpG islands and are highly prone to adopt non-B DNA conformation(s). Analysis of the transcriptional status of mutp53-regulated genes demonstrated that mutp53 generally modulates transcription from active promoters marked by H3K4me3. Based on our data we propose a dual mode model of mutp53 GOF, which includes both stochastic and deterministic components. On a local scale, mutp53 acts as a basal transcriptional co-factor that has the potential to bind autonomously and selectively to non-B DNA structures around TSSs of active genes and to modulate transcription rates of many genes in a context and stimulus-dependent fashion. Resulting stochastic alterations generate transcriptional plasticity and enhance transcriptional competence on a global scale.

This SuperSeries is composed of the SubSeries listed below.

first: Timo

last: Quante

first: Benjamin

last: Otto

first: Wolfgang

last: Deppert


title: Comparative analysis from hESC from different developmental sources of derivation

status: Public on Nov 27 2012

city: Valencia

first: David

last: Montaner

address: C/ Eduardo Primo Yufera, 3

department: Bioinformatics

institute: CIPF

summary: Whole genome expression analysis reveals that single blastomeres from day-3 human embryos and blastocysts show unique gene signature, thus hESC derived from these two developmental sources might show differential gene expression profile.  Comparative gene expression analysis has revealed that no significant differences exist between hESCs derived from blastomeres versus those obtained from ICMs, suggesting that pluripotent hESCs involve a new developmental progression.

overall_design: hESC derived from single blastomeres (VAL-10B and VAL-11B) and from ICM (VAL-5, -7, and -8) were compared by global gene expression

first: A

last: Galán

first: C

last: Simón

first: J

last: Dopazo


title: Differentiating factors of cumulus cells related to quality of the human oocyte [CadoretPart1]

overall_design: three-condition experiment: blastocyst (B), embryo of poor quality (E) AND immature oocytes (VG).


title: COLO320 cells: siCDX2 vs. non-targeting control

status: Public on Nov 02 2012

city: Boston

first: Keyan

last: Salari

address: Gray/Bigelow Rm 1102, 55 Fruit Street

institute: Massachusetts General Hospital

summary: Somatic DNA alteration underlies tumor development and progression, and gives rise to tumors with diverse genetic contexts. Here, we identify in a collection of 29 colorectal cancer cell lines and 226 primary colorectal tumors recurrent amplification of chromosome 13, an alteration highly restricted to colorectal-derived cancers. A minimal region of amplification on 13q12.2 pinpoints caudal type homeobox transcription factor CDX2, a master regulator of anterior-posterior patterning, midgut development, and intestinal epithelial cell differentiation and maintenance. In contrast to its described role as a colorectal tumor suppressor, we show that in the context of genomic amplification, CDX2 is required for proliferation and anchorage-independent growth of colorectal cancer cells. By genome-wide expression and location analysis, we reveal that CDX2 directly promotes expression of Wnt pathway genes. Further results suggest that CDX2 induces expression of intestinal differentiation markers and modulates b-catenin transcriptional activity. These data characterize CDX2 as a novel lineage-survival oncogene deregulated in colorectal cancer.

overall_design: Two-condition experiment, CDX2 siRNA knockdown vs. control, using two independent siRNAs against CDX2

first: Jonathan

last: Pollack


title: Murine HIV-gagP24 CD8 T cells: bone marrow vs Lymph node

status: Public on Oct 23 2012

city: Paris

first: Helene

last: Perrin

address: 91 boulevard de l'hopital

institute: INSERM

summary:
Transcriptional profiling to examine differences resulting from priming of virus-specific CD8 T cells in draining lymph node and in bone marrow, following intradermal injection of modified virus Ankara (MVA)-HIV gag.
Transcriptional profiling of mouse pentamer H2kD-AMQMLKETI (HIV-gagP24) CD8 T cells from draining lymph nodes(LN) and bone marrow (BM ) 5 days following intradermal injection of MVA-HIV gag, and compared to naive (CD62L Hi CD44 int) CD8+ T cells from lymph node of naive mice (NTc).

overall_design: Three-condition experiment, BM, LN and NTc. Experimental replicates: 5 BM, 5 LN, 5 NTc, RNA pooled from 3 independant experiments of 5 mice each.

first: Darragh

last: Duffy

first: Hélène

first: Valérie

last: Abadie

first: Nora

last: Benhabiles

first: Alexandre

last: Boissonnas

first: Christelle

last: Liard

last: Descours

first: Damien

last: Reboulleau

first: Olivia

last: Bonduelle

first: Bernard

last: Verrier

first: Nico

last: Van Rooijen

first: Christophe

last: Combadière

first: Béhazine


title: Screening for potential markers of metastases between low versus highly metastatic derived cell lines of same parental origin

status: Public on Oct 01 2012

city: Houston

first: Mark

last: Truty

address: 1515 Holcombe Blvd.

department: Surgical Oncology

institute: University of Texas, MD Anderson Cancer Center

summary: The objective of this study is to identify metastatic candidates via initial screening by gene expression profiling between subcloned cell lines of low (C5 and FG) and high (C5LM2 and L3.6) metastatic potential from their parental primary human pancreatic adenocarcinoma cell lines (Panc1 and COLO357). Agilent arrays were utilized for this experiment and there are 3 replicates for each cell line.

overall_design: Two-condition experiment, C5 vs. C5LM2 cell lysates with 3 replicates per cell line and FG vs. L3.6 cell lysates.

first: Xavier

last: Chopin-Laly


title: Rotating wall vessel (RWV) grown A549s compared to monolayer grown A549s

last: David

summary: A549 epithelial cells grown under two different conditions were compared.  A549s grown in rotating wall vessel cultures disp[lay a more in-vivo like phenotype. The data here describe the transcriptional differences between the two culture methods

overall_design: 1 colour; Cy3 labelled, 5 biological replicates for each culture condition, A549s grown in RWVs (RWV) compared to A549 grown in monolayers (mono)

first: Natalie

last: Sayer

first: Mitali

last: Sarkar-Tyson


title: Gene expression profile of peripheral blood leukocytes of 60Co gamma-ray accidently-irradiated persons

status: Public on Nov 01 2012

city: Taiyuan City

first: Cuiping

last: CHI

state: Shan Xi Province

address: Xue Fu Street No. 102

department: Radiation Medicine

institute: China Institute for Radiation Protection

summary:
In order to identified as candidate biomarkers for early  diagonosis or as therapeutic targets in late damages of ionizing radiation, gene expression profile was analyzed in the peripheral blood of three 60Co γ-ray accidently-exposed persons. The results showed that there were 285 up-regulated and 446 down-regulated genes in irradiated samples compared with control samples.
The large majority of those differentially expressed genes encode proteins that are associated with immune response, inflammation, cell structure, oxidative stress, neuro-hormone regulation, reproduction, susceptibility of psychiatric disorders, and transcriptional regulators.
The expressions of IL3, KDR, CEACAM8 and OSM were validated by real-time RT-PCR method. The findings of our study should help us understanding the molecular mechanisms underlying the late effects of ionizing radiation and to develop better diagonostic and therapeutic strategies for those damages.

overall_design: Fresh blood samples were collected from three 60Coγ-Ray accidentally-exposed persons(3 years post irradiation) and three non-irradiated healthy donors. Leucocytes cells were isolated and total RNA was extracted. Four RNA samples, from three accidently-exposed persons and a RNA mixture extracted from a combination of three healthy donors` leucocytes (ratio 1:1:1, each 3.3×106 cells) in EL buffer, were subjected to Agilent gene expression microarray assay.

last: Chi

first: Jinping

last: Wei

first: Jianping

last: Guo

first: Shufang

last: Li


title: Host cell tropism of Propionibacterium acnes: infection scenarios differ on skin and prostate epithelia

status: Public on Nov 21 2012

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Proprionibacterium acnes is a Gram positive bacterium found ubiquitously on human skin, where it is typically considered to assume a commensal relationship with its host. However, it is also closely associated with the skin condition acne vulgaris. More controversially, it has a postulated involvement in infections of implanted prosthetic devices and has been isolated from malignant prostate tissues. The role of P. acnes in these pathologies remains undetermined, although both bacterial and host factors are implicated. By microarray analysis, we have identified fundamental differences in the global transcriptional profiles of keratinocyte and prostate cells to P. acnes infection. Notably, P. acnes infection of the keratinocyte cell line, HaCaT, elicited a robust, but acute inflammatory response. By contrast, the inflammatory response of the prostate cell line, RWPE1, was delayed and persisted for longer times. Immunofluorescence and electron microscopy revealed higher numbers of internalized P. acnes bacteria in RWPE1 cells, which could still be detected intracellularly three weeks post infection. This contrasted with HaCaT cells, which P. acnes largely failed to invade. Moreover, P. acnes induced a delayed, sustained activation of NFκB in RWPE1 cells, which was absent in HaCaT cells. Further characterization of the host-cell response to infection revealed that the intermediate filament protein, vimentin, was a key determinant of P. acnes invasion, persistence and inflammatory profile in RWPE1 cells. siRNA mediated knock down of vimentin in RWPE1 cells attenuated bacterial invasion and the inflammatory response to infection; similarly, overexpression of vimentin in HaCaT cells increased bacterial invasion. We conclude that vimentin-dependent host-tissue tropism, in part, determines P. acnes invasion and inflammatory capacity. This could contribute to P. acnes pathology at non-skin infection sites.

overall_design: Microarray experiments were performed as dual-color hybridizations. In order to compensate specific effects of the dyes and to ensure statistically relevant data analysis, a color-swap dye-reversal was performed.

first: Tim

last: Mak

last: Fischer

first: Britta

last: Laube

first: Matteo

last: Metruccio

first: Thomas

middle: F

last: Meyer

first: Holger

last: Brüggemann


title: Expression profiling shows differential functions and provides potential new diagnostic biomarkers for colorectal serrated adenocarcinoma

status: Public on Oct 31 2012

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

summary: Our microarray study validates characteristic functions of serrated adenocarcinoma (SAC) reported in the only previous study which was performed on patients from a dissimilar environmental and genetic background and using a different microarray platform. In our study, fascin1 and hippocalcin were validated at the mRNA and protein level as the best biomarkers reported so far for the distinction of SAC from conventional carcinoma and from colorectal carcinoma showing molecular and histological features of high-level microsatellite instability.

overall_design: In this study, we used gene expression arrays  to investigate differences between two experimental classes: serrated and conventional carcinomas

first: Pablo

last: Conesa-Zamora

first: Jose

last: Garcia-Solano

last: Garcia-Garcia

last: Turpin

first: Javier

last: Trujillo-Santos

first: Daniel

last: Torres-Moreno

first: Isabel

last: Oviedo-Ramirez

first: Rosa

last: Carbonell-Muñoz

first: Encarnacion

last: Muñoz-Delgado

first: Edith

last: Rodriguez-Braun

first: Ana

last: Conesa

first: Miguel

last: Perez-Guillermo


title: Study of the consistency, comparability and identity of different Dendritic cells productions for clinical use

status: Public on Nov 16 2012

city: Bethesda

first: Luciano

last: Castiello

state: Maryland

address: 10 Center Drive

department: DTM

institute: NIH/CC

summary:
Gene expression profiling of monocyte-derived Dendritic cells manufactured several times from one healthy donor and one single time from 8 different healthy donors to test the sources of variability
Sources tested: Assay-related variability (8 samples), Manufacture-related variability (5 samples), Intra-donor-related variability (5 samples), inter-donor-related variability (9 samples)

overall_design: 4 different levels of variability were accounted: Assay, manufacture, intradonor, and interdonor

first: Marianna

last: Sabatino


title: Essential role of MALT1 protease activity in activated B cell-like diffuse large B-cell lymphoma

status: Public on Sep 20 2012

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: A key element for the development of suitable anti-cancer drugs is the identification of cancer-specific enzymatic activities that can be therapeutically targeted. Mucosa-associated lymphoid tissue transformation protein 1 (MALT1) is a proto-oncogene that contributes to tumorigenesis in diffuse large B-cell lymphoma (DLBCL) of the activated B-cell (ABC) subtype, the least curable subtype of DLBCL. Recent data suggest that MALT1 has proteolytic activity, but it is unknown whether this activity is relevant for tumor growth. Here we report that MALT1 is constitutively active in DLBCL lines of the ABC but not the GCB subtype. Inhibition of the MALT1 proteolytic activity led to reduced expression of growth factors and apoptosis inhibitors, and specifically affected the growth and survival of ABC DLBCL lines. These results demonstrate a key role for the proteolytic activity of MALT1 in DLBCL of the ABC subtype, and provide a rationale for the development of pharmacological inhibitors of MALT1 in DLBCL therapy.

overall_design: HBL-1 cells (n=8) were treated with IkB kinase beta inhibitor MLN120B (25 micromolar; Calbiochem) for 2h, 3h, 4h, 6h, 8h, 12h, 16h, and 24h (Cy5) and their gene expression compared to vehicle-treated cells (DMSO, Cy3). HBL-1 cells (n=4) and OCI-Ly3 cells (n=4) were treated with MALT1 inhibitor z-VRPR-fmk (50 micromolar; Alexis Biochemicals) for 6h, 12h, 24h, and 30h (Cy5) and their gene expression compared to vehicle-treated cells (DMSO, Cy3).


title: Factors regulated by interferon gamma and hypoxia-inducible factor 1A contribute to responses that protect mice from Coccidioides immitis infection.

status: Public on Sep 10 2012

city: London

first: Akul

last: Singhania

address: 1 Midland Road

institute: The Francis Crick Institute

summary:
Mouse strains have been identified that are resistant (i.e. DBA/2) or susceptible (i.e. C57BL/6) to infection from pathogenic fungus Coccidioides immitis.  However, the genetic and immunological basis for this difference has not been fully characterized.
Microarray technology was used to identify genes that were differentially expressed in lung tissue between resistant DBA/2 and sensitive C57BL/6 mice after infection with C. immitis.

overall_design: C57BL/6 and DBA/2 mice were infected with arthoconidia of C. immitis and RNA was extracted at different days post-infection and hybridized to Affymetrix microarrays (MGU74Av2), in order to identify differentially expressed genes between the two strains.

first: Christopher

middle: H

last: Woelk

first: Jin

middle: X

last: Zhang

first: Lorraine

last: Walls

first: Suganya

last: Viriyakosol

first: Theo

last: Kirkland

first: Joshua

last: Fierer


title: HEK293 cells with control or NFIL3 shRNA treatment

status: Public on Sep 02 2012

city: New York

first: Megan

middle: Erin

last: Keniry

state: New York

address: 1130 St. Nicholas Ave., room 407

department: Institute for Cancer Genetics

institute: Columbia University

summary: Transcriptional profiling with samples from HEK293 cells that were infected with control or NFIL3 shRNA

overall_design: Two condition experiment: control (scr) shRNA (six replicates) and NFIL3 shRNA (four replicates)

first: Maira

middle: M

last: Pires

first: Ying-Ka

middle: I

last: Lau

first: Ashley

last: Calahan

first: Ben

last: Hopkins

first: Sarah

last: Mense

first: Cindy

last: Hodakoski

first: Matt

last: Maurer

first: Ramon

last: Parsons


title: Gene expression of the pigmented and non-pigmented epithelia of the ciliary body of human healthy eyes

status: Public on Sep 18 2012

city: Amsterdam

last: Janssen

address: Meibergdreef 47

department: Ophthalmogenetics

country: Netherlands

institute: Netherlands Institute for Neuroscience

summary: The ciliary body (CB) of the human eye consists of the non-pigmented (NPE) and pigmented (PE) neuro-epithelia. We investigated the gene expression of the NPE and PE, to shed light on the molecular mechanisms underlying the most important functions of the CB. Therefore we isolated NPE and PE cells from seven healthy human donor eyes using laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays.

overall_design: We performed the microarrays against a common reference sample, namely human RPE/choroid RNA. We performed 7 replicates of PE samples from 7 different donors and 7 NPE replicates  from the same 7 different donors.

first: Arthur

middle: A

last: Bergen


title: Diminishment of NFIL3 by shRNA in HEK293 and BT549 cells


title: BT549 cells with control or NFIL3 shRNA treatment

summary: Transcriptional profiling with samples from BT549 cells that were infected with control or NFIL3 shRNA

overall_design: Two condition experiment: control (scr) shRNA (two replicates) and NFIL3 shRNA (two replicates)


title: Gene expression analysis of head and neck squamous cell carcinoma cell lines and a control normal oral epithelial cell line

status: Public on Aug 28 2012

city: Toronto

first: Lusia

last: Sepiashvili

state: ONtario

address: 101 College street TMDT unit 9-807

department: Medical Biophysics

institute: UHN/OCI

summary: Microarrays were used to examine gene expression differences between human head and neck squamous cell carcinoma cell lines (FaDu, UTSCC8, UTSCC42a) grown in culture in comparison to a normal oral epithelial cell line. Gene expression data was integrated with global protein expression of head and neck squamous cell carcinoma cell lines and conditioned media to identify secreted protein markers up-regulated at the mRNA level in cancer cells versus the normal cell line.

overall_design: Total RNA obtained from head and neck squamous cell carcinoma cell lines and a normal oral epithelial cell line

first: Angela

last: Hui

first: Fei-Fei

last: Liu

first: Thomas

last: Kislinger


title: Gene expression profile of H1 human embryonic stem cells, IMR90 lung fibroblasts, calcium induced keratinocytes, and primary hepatocytes

city: Los Angeles

first: Jing-Yu

last: Li

address: 615 Charles E. Young Dr. South BSRB 357

institute: University of California, Los Angeles

summary: In humans, there are eleven subtypes of linker histones that exhibit cell- and tissue-specific expression. Linker histone H1 proteins bind to both the core histones and linker DNA of chromatin fibers; and not only participate in control of gene activity but also serve to stabilize higher order chromatin structure. To determine the potential roles of linker histones in differentiation, we examined the global distribution of linker histone subtype H1.5 in human IMR90 fibroblasts and H1 embryonic stem cells (hESCs). Surprisingly, H1.5 binds to and represses a large fraction of gene family clusters in fully differentiated cell types representing all three embryonic germ layers. Little or no H1.5 enrichment at gene family clusters was detected in undifferentiated hESCs or partially differentiated somatic cells. We also found that SIRT1 histone deacetylase and H3K9me2, a repressive histone modification, are also enriched at gene family cluster in IMR90 cells, likely generating a stably repressive chromatin domain. To find out the mechanism of H1.5 targeting, H1.5 or SIRT1 was depleted in IMR90 cells by siRNA, and the binding patterns of SIRT1 and H1.5 were examined. In H1.5 knockdown cells, SIRT1 binding pattern was changed dramatically, and this changed pattern highly correlates to SIRT1 distribution in hESC. However, depletion of SIRT1 could not change the global binding pattern of H1.5. Depletion of H1.5 or SIRT1 leads to up-regulation of ~50% gene family clusters. However, the sets of gene family clusters that are affected by these two factors are different, suggesting H1.5 and SIRT1 may regulate gene transcription via different pathways.

overall_design: One-color array. Two replicates for each sample.

first: Michaela

last: Patterson

first: Hanna

middle: K

last: Mikkola

first: William

middle: E

last: Lowry

first: Siavash

last: Kurdistani


title: Gene expression profile of H1.5 knockdown and SIRT1 knockdown IMR90 cells versus control cells

overall_design: Two-color microarrays. Two replicates for each sample.


title: Gene Expression Profiling of Human Pediatric Astrocytomas

status: Public on Aug 24 2012

city: San Francisco

first: Jane

last: Engler

state: CA

address: 1450 3rd Street

institute: UCSF

summary: Analysis of grades II, II and iV pediatric astrocytomas. Results used to straify tumors into molecular subclasses representative of adult tumors. The mesenchymal subtype is associated with high expression of immune response-related genes.

overall_design: Gene expression of grade II, III and IV pediatric astrocytomas, 24 individual tumor samples were profiled

middle: R

first: Aaron

last: Robinson

first: Ivan

last: Smirnov

first: J

middle: G

last: Hodgson

first: Mitchel

middle: S

last: Berger

first: Nalin

last: Gupta

first: C

last: James

first: Annette

last: Molinaro

first: Joanna

middle: J

last: Phillips


title: Synergistic, context-dependent and hierarchical functions of hematopoietic progenitor niche components.

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

institute: Miltenyi Biotec GmbH

summary: Specialized niche environments specify and maintain stem and progenitor cells, but little is known about the identities and functional interactions of niche components in vivo. Here, we describe a modular system for the generation of artificial hematopoietic niches in the mouse embryo. A circumscribed tissue that lacks niche function but is physiologically accessible for hematopoietic progenitor cells is functionalized by individual and combinatorial expression of four factors, the chemokines Ccl25 and Cxcl12, the cytokine Scf and the Notch ligand DLL4. The distinct phenotypes and variable numbers of hematopoietic cells in the resulting niches reveal synergistic, context-dependent and hierarchical interactions among niche effector molecules. The surprisingly simple rules determining niche outcomes enable the in vivo engineering of artificial niches conducive to the presence of distinct myeloid or T or B lymphoid lineage precursors.

overall_design: The dataset comprises 24 samples divided into eight sample groups each representing a different lymphoid progenitor cell type isolated from wild-type (+/-) or transgenic (-/-) thymic niches. -/-, Foxn1-deficient genotype; +/-, Foxn1 heterozygous phenotype; DP, CD4/CD8 double-poisztive thymocytes; DN3, CD4/CD8-negative stage 3 thymocytes; SP4, CD4 single-positive thymocytes; SP8, CD8 single-positive thymocytes; B IgM-, IgM surface negative B cells; B IgM+, IgM surface positive B cells; B IgM- -/-, IgM surface negative B cells from Foxn1-deficient genotype.

last: Boehm

first: Lesly

last: Calderon


title: Genes Predictive of G1 arrest in Melanoma Cell Lines

status: Public on Aug 14 2012

city: Chapel Hill

first: Craig

last: Carson

state: North Carolina

address: 413 Mary Ellen Jones Bldg

department: DERMATOLOGY

institute: UNC-CH

summary: Transcriptional profiling of human melanoma cell lines to identify a G1 arrest signature

overall_design: Percentage of cells that arrest in G1 after irradiation was used to identify genes predictive of response

first: W

last: Kaufmann


title: Exploiting Synthetic Lethality for the Therapy of ABC Diffuse Large B Cell Lymphoma

status: Public on Aug 16 2012

first: Louis

last: Staudt

summary: Knowledge of essential oncogenic mutations can inspire therapeutic strategies that are synthetically lethal, affecting cancer cells bearing an oncogenic mutation while sparing normal cells. Lenalidomide is emerging as an active agent in diffuse large B cell lymphoma (DLBCL), especially for the activated B cell-like (ABC) subtype, but the mechanism of its action is unknown. Here we show that lenalidomide kills ABC DLBCL cells by augmenting the production of interferon 3/4, which these cells are predisposed to produce by their oncogenic MYD88 mutations. Lenalidomide stimulates the type I interferon pathway by suppressing IRF4, a repressor of IRF7. IRF4 is required for ABC DLBCL viability and is both a target and an amplifier of NF-kB signaling in this lymphoma subtype. Blockade of B cell receptor (BCR) signaling synergized with lenalidomide to reduce IRF4 levels, increase interferon 3/4 secretion, decrease NF-kB, and kill ABC DLBCL cells, suggesting therapeutic combinations that exploit the oncogenic signaling pathways in this cancer.

overall_design: For the OCILY10 cell line treated with 10 uM lenalidamide, a four point time course of 3, 6, 24, and 48 hours was analyzed (n=4). For the TMD8 cell line treated with 10 uM lenalidamide, a four point time course of 3, 6, 24, and 48 hours was analyzed (n=4).


title: Burkitt Lymphoma Pathogenesis and Therapeutic Targets from Structural and Functional Genomics

summary: Burkitt lymphoma (BL) can often be cured by intensive chemotherapy, but the toxicity of such therapy precludes its use in the elderly and in patients with endemic BL (eBL) in developing countries, necessitating new strategies. The normal germinal center B cell is the presumed cell of origin for both BL and diffuse large B cell lymphoma (DLBCL), yet gene expression analysis suggests that these malignancies may utilize different oncogenic pathways. BL is subdivided into a sporadic subtype (sBL) that is diagnosed in developed countries, the EBV-associated eBL subtype, and an HIV-associated subtype (hivBL), but it is unclear whether these subtypes employ similar or divergent oncogenic mechanisms. Here we used high throughput RNA sequencing and RNA interference screening to discover essential regulatory pathways that cooperate with MYC, the defining oncogene of this cancer. In 70% of sBL cases, mutations affecting the transcription factor TCF3 (E2A) or its negative regulator ID3 fostered TCF3 dependency. TCF3 activated the pro-survival PI(3) kinase pathway in BL, in part by augmenting tonic B cell receptor signaling. In 38% of sBL cases, oncogenic CCND3 mutations produced highly stable cyclin D3 isoforms that drive cell cycle progression. These findings suggest opportunities to improve therapy for patients with BL.

overall_design: Gene expression was analyzed using Agilent human 4X44K oligo gene expression arrays. Cell lines (Namalwa, BL41, Daudi, Defauw, and THOMAS) were infected with control (empty vector, Cy3) paired with ID3 (Cy5) or control (shControl, Cy3) paired with shTCF3 (Cy5) constructs, and changes in gene expression were monitored over time after induction of the constructs with doxycyclin. In Namalwa (n=8) and THOMAS (n=4) cell lines, a four timepoint series (24, 48, 72, 96 hours) of construct induction was analyzed, for a total of 12 arrays. In BL41 (n=4), Daudi (n=4) and Defauw (n=4) cell lines, a two timepoint series (24 and 48 hours) of construct induction was analyzed, for a total of 12 arrays. In addition, two cell lines (Daudi and THOMAS) were treated with Rapamycin (100 pM) and paired with a DMSO control in a four timepoint series (3, 6, 12 and 24 hours) for a total of 8 arrays.


title: Difference expression analyses before and after human fucosyltransferase gene 1 transfection into ovarian  cancer clear cell line

status: Public on Aug 02 2012

city: Shenyang

first: Ziwei

last: Feng

address: Sanhao street

institute: China Medical University

summary: 75% ovarian epithelial tumor overexpresses Lewis y antigen, which notably strenthen such malignant biological behaviors as metastasis, drug resistance and proliferation. The key enzyme of Lewis y synthesis is human fucosyltransferase gene 1(hfut1).  Through transfecting hfut1 into Lewis y low expressing cell line RMG-I, we got a pair of cell lines. We hypothesized that Lewis y antigen plays a major role in ovarian canceration . Using gene arrays, we comprehensively profiled mRNA differential expression between fut1-pretransfected and posttransfected clear cell of human epithelial OvCa. We expected that over-expression of lewis y antigen would lead to higher expression of genes associated with growth, metastasis,proliferation and so on.

overall_design: we established ovarian tumor cell line RMG-I-H by stably transfecting  human fucosyltransferase gene 1 into cell line RMG-I. RMG-I-H overexpresses Lewis y antigen, which is known as a cancer-related tetrasaccharide antigen. We profiled for gene expression both cells pretransfected and posttransfected.

first: Z

last: Liu

first: L

last: Bei


title: Co-addiction to IRF4 and SPIB in ABC-DLBCL

summary: RNA interference screens identified the transcription factor IRF4 as essential for the survival of the activated B-cell-like subtype of diffuse large B-cell lymphoma (ABC-DLBCL). Analysis of IRF4 genomic targets in ABC-DLBCL and Multiple Myeloma (MM) revealed that IRF4 regulates distinct networks in these cancers. IRF4 peaks in ABC-DLBCL, but not MM, were enriched for a composite ETS-IRF DNA motif that can be bound by heterodimers of IRF4 and the ETS-family transcription factor SPIB, whose expression is also essential for ABC-DLBCL survival. Gene expression and ChIP-Seq analysis identified essential genes co-regulated by IRF4 and SPIB. Together, these factors regulate a critical oncogenic loop by activating CARD11, which controls ABC-DLBCL survival via the NF-kB pathway. The interaction between IRF4 and SPIB presents an attractive therapeutic target in this aggressive lymphoma.

overall_design: Gene expression was analyzed using Agilent human 4X44K oligo gene expression arrays. Cell lines (HBL1, OCILY3, TMD8-ABC-DLBCL; KMS12-MM) were infected with control (shControl, Cy3), shIRF4_3'UTR (Cy5), shspiB_2_3'UTR (Cy5), shspib_2 (Cy5), chimeric repressor (Cy5) constructs, and changes in gene expression were monitored over time after induction of the shRNA with doxycyclin. For each of the three ABC-DLBCL cell line a four timepoint series (24, 48, 72, 96 hrs) of shRNA induction was analyzed, for a total of 12 arrays. In HBL-1 a second shRNA targeting the IRF4 cds (shIRF4_cds) was used in a similar time course of shRNA induction (4 arrays). Also in HBL-1 a shRNA targeting wild type SPIB (shspiB_2) was used in a similar time course of shRNA induction (4 arrays). Also in HBL-1 a shRNA targeting mutant SPIB (shspib_2) was used in a similar time course of shRNA induction (4 arrays). Also in HBL-1 an IRF4:SPIB chimeric repressor was used in a similar time course (4, 8, 24, 48 hrs) (4 arrays). For the KMS12 MM cell line a three point time course was analyzed using the shIRF4_3'UTR with one technical (using the same RNA sample) duplicate time point measurement (4 arrays).


title: Gene expression profiles of effector T cells induced by mTOR inhibition

status: Public on Sep 05 2012

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

institute: Tampere University

summary: To further develop our gene expression approach to treatment of autoimmunity, we have employed whole genome microarray expression profiling as a discovery platform to identify genes differentially expressed upon immunosuppressor treatment responsible for inhibition of T cell effector functions. Human CD4+CD25- cells from healthy donors were pretreated or not with rapamycin and stimulated with anti-CD3 and anti-CD28 for 12h.

overall_design: mTOR (Mammalian Target of Rapamycin) inhibition-induced gene expression was evaluated in human effector T cells after 1 hour rapamycin pretreatment and compared to vehicle-pretreated cells. Three independent experiments were performed for each of the two different experimental conditions using different donors for each experiment.

first: Claudio

last: Procaccini

first: Giuseppe

last: Matarese


title: Gene Expression Profiling in T-ALL and B-ALL of Childhood Acute Lymphoblastic Leukemia

status: Public on Aug 03 2012

city: Kuala Lumpur

first: Zubaidah

last: Zakaria

address: Jalan Pahang

department: Haematology Unit

country: Malaysia

institute: Institute for Medical Research

summary: Gene expression profiling in leukemia cases may predict the clinical outcome of the patients and may improve the treatment for specific leukemia subtypes. The goal is to compare the differences in gene expression pattern between T-ALL and B-ALL subtypes in Malaysian childhood acute lymphoblastic leukemia patients.

overall_design: Microarray study was carried out on 29 cases of acute lymphoblastic leukemia which include T-ALL and B-ALL subtype based on immunophenotyping and molecular result. Data on gene expression level was later confirmed using qRT-PCR.

first: Nor

last: Kamaluddin

first: Norodiyah

last: Othman

first: Mohd

last: Fadly


title: Identification of Murine Uterine Genes Regulated in a Ligand-Dependent Manner by the Progesterone Receptor.

status: Public on Aug 07 2012

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Progesterone (P4) acting through its cognate receptor, the progesterone receptor (PR), plays an important role in uterine physiology. The PR knockout (PRKO) mouse has demonstrated the importance of the P4-PR axis in the regulation of uterine function. To define the molecular pathways regulated by P4-PR in the mouse uterus, Affymetrix MG U74Av2 oligonucleotide arrays were used to identify alterations in gene expression after acute and chronic P4 treatments. In the analysis, retinoic acid metabolic genes, cytochrome P 450 26a1 (Cyp26a1), alcohol dehydrogenase 5, and aldehyde dehydrogenase 1a1 (Aldh1a1); kallikrein genes, Klk5 and Klk6; and specific transcription factors, GATA-2 and Cited2 [cAMP-corticosterone-binding protein/p300-interacting transactivator with glutamic acid (E) and aspartic acid (D)-rich tail], were validated as regulated by the P4-PR axis. Identification and analysis of these responsive genes will help define the role of PR in regulating uterine biology.

overall_design: Ovariectomized wild-type and progesterone receptor knockout mice were injected with either vehicle or 1 mg/mouse progesterone. The injections were repeated every 12 h, and groups of mice were killed 4 h after the first injection (acute P4 treatment) or 4 h after the fourth injection (chronic P4 treatment).

first: Jae-Wook

last: Jeong

first: Kevin

middle: Y

last: Lee

first: Inseok

last: Kwak

first: Lisa

last: White

first: Susan

last: Hilsenbeck

first: John

middle: P

last: Lydon

first: Francesco

last: DeMayo


title: Expression signature in peripheral blood cells for molecular diagnosis of head and neck squamous cell carcinoma

status: Public on Sep 03 2012

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: Patients with head and neck squamous cell carcinoma (HNSCC) have a poor prognosis due to the development of locoregional recurrences, distant metastases and second primary tumors. There is an urgent need for biomarkers that enable detection and monitoring of the disease to provide adequate therapeutic strategies. In this study we have investigated markers in peripheral blood cells (PBC) of  28 HNSCC patients who underwent surgery by means of expression profiling. Our hypothesis is that nucleated blood cells circulate continuously, also passing the tumor, and might change their expression profiles in response to tumor cell factors. For comparison, we enrolled a control group of 11 patients who underwent surgery in the head and neck region for non-HNSCC reasons. A set of 2,349 genes was found to be statistically different between the groups (p<0.05, false discovery rate-corrected) and the most prominently different pathways were EIF2 and mTOR signaling. These preliminary results are promising and warrant further studies on the definitive role of PBC gene expression as a biomarker for HNSCC detection and monitoring.

overall_design: Two-color experiment with each individual sample in a single channel. RNA of nucleated blood cells of humans was analysed. Case-control analysis, with 28 cases, patients with head and neck squamous cell carcinoma and 11 controls, without squamous cell carcinoma

first: Boudewijn

last: Braakhuis

first: A

last: Graveland

first: Frederike

last: Dijk

first: Bauke

last: Ylstra

first: Wessel

last: van Wieringen

first: C

last: Leemans

first: Ruud

last: Brakenhoff


title: Polycyclic aromatic hydrocarbons as skin carcinogens: Comparison of benzo[a]pyrene, dibenzo[def,p]chrysene and three environmental mixtures in the FVB/N mouse

status: Public on Aug 01 2012

city: Corvallis

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

summary: The polycyclic aromatic hydrocarbon (PAH), benzo[a]pyrene (BaP), was compared to dibenzo[def,p]chrysene (DBC) and combinations of three environmental PAH mixtures (coal tar, diesel particulate and cigarette smoke condensate) using a two stage, FVB/N  mouse  skin tumor model.  DBC (4 nmol) was most potent, reaching 100% tumor incidence with a shorter latency to tumor  formation,  less than 20 weeks of 12-O-tetradecanoylphorbol-13-acetate (TPA) promotion compared to all other treatments. Multiplicity was 4 times greater than BaP (400 nmol).  Both PAHs produced primarily papillomas followed by squamous cell carcinoma and carcinoma in situ.  Diesel particulate extract (1 mg SRM 1650b; mix 1 ) did not differ from toluene controls and failed to elicit a carcinogenic response. Addition of coal tar extract (1 mg SRM 1597a; mix 2) produced a response similar to BaP.  Further addition of 2 mg of cigarette smoke condensate (mix 3) did not alter the response of mix 2. PAH-DNA adducts measured in epidermis 12 h post initiation and analyzed by 32P post- labeling, did not correlate with tumor incidence. PAH dependent alteration in transcriptome of skin 12 h post initiation was assessed by microarray.  Principal component analysis (sum of all treatments) of the 922 significantly altered genes (p<0.05), showed DBC and BaP to cluster distinct from PAH mixtures and each other.  BaP and mixtures up-regulated phase 1 and 2 metabolizing enzymes while DBC did not.  The carcinogenicity with DBC and two of the mixtures was much greater than would be predicted based on published Relative Potency Factors (RPFs).

overall_design: Gene expression was measured in mouse skin 12 hours after initiation with PAH carcinogens.  The following initiation treatments were applied to mice (N=4 or 5 per biological replicates treatment); toluene vehicle control (200 μl), BaP 400 nmol (100 μg), DBC 4 nmol (1.2 μg), or to mixtures of environmental PAH mixtures containing diesel particulate extract, coal tar extract, or cigarette smoke condensate.

middle: C

first: David

last: Williams


title: Development of gene expression signature for defining the cell potency of muscle derived stem cells (MDSC) from mice of diffferent genotypes

city: Singapore

first: Bipasha

last: Bose

address: 60, Nanyang Drive

country: Singapore

institute: Nanyang Technological University

summary: In order to determine the cell potency, by identification of genes responsible for pluri/multi potency, we performed a global gene expression profiling of MDSC isolated from five week old male wild type(WT), C57Bl6J  and  another hypertrophied musculature mouse genotype called myostatin null (Mstn-/-) mice using microarray analysis and compared this gene expression to that of a standard mouse ES cell line W4. Muscle derived stem cells (MDSC) were isolated from WT and Mstn null mice using an established preplate technique and compared with  the gene expression signature of standard mouse ES cell line W4

overall_design: Entire hindlimb muscles of five week old WT and Mstn null male mice were subjected to primary cultures using the well established preplate technique based on adhesion properties of cells for sequential isolation of preplate6(PP6) cells on day4. The PP6 cells are called so because they are slowest adhering and attach to the matrigel coated dishes on day4. PP6 have stem cell like qualities as established by previous workers and are hence also known as MDSC. We expanded the MDSCs from the our isolation sources mentioned above for a fortnight in media containing 10% fetal bovine serum, 10% horse serum,1% chcken embryo extract,1% Penstep and 0.1µM βmercaptoethanol.RNA was extracted by RNeasy minit kit from Qiagen as per manufacturer's instructions and subjected to RNA integreity check by RIN score followed by microarray analysis for global gene expression using Agilent platform. Also, in parallel we cultured a standard mouse ES cell line from the company Taconic named W4 on feeder free conditions, extraced RNA and performed microarray analysis.

first: Ravi

last: Kambadur


title: The NS1 protein of influenza A virus suppresses interferon-regulated activation of antigen-presentation and immune-proteasome pathways

status: Public on Jul 10 2012

city: Seattle

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: The NS1 protein of influenza virus counters host antiviral defences primarily by antagonizing the type I interferon (IFN) response. Both the N-terminal dsRNA-binding domain and the C-terminal effector domain are required for optimal suppression of host responses during infection. To better understand the regulatory role of the NS1 effector domain, we used an NS1-truncated mutant virus derived from human H1N1 influenza isolate A/Texas/36/91 (Tx/91) and assessed global transcriptional profiles from two independent human lung cell-culture models.

overall_design: Primary human tracheobronchial epithelial (HTBE) cells were washed and infected with 4×10^6 p.f.u. Tx/91 or Tx/91 NS1 : 1–126 viruses per filter (m.o.i. of 20) for 1 h at 37 °C. Three replicate wells were infected for each condition per time point. Allantoic fluid was used for mock treatments. At 9.5 and 25 h p.i., cells were collected and resuspended in TRIzol reagent (Invitrogen) for total RNA extraction. A549 cells were infected with Tx/91 or Tx/91 NS1 : 1–126 viruses at an m.o.i. of 2 for 1 h at 4 °C. Three replicate wells were infected for each condition per time point. Allantoic fluid was used for mock treatments. A549 cells were collected and lysed in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5 % sarcosyl, 0.1 M β-mercaptoethanol) at 12 and 24 h p.i. for total RNA extraction.

first: Jennifer

last: Tisoncik

first: Rosalind

last: Billharz

first: Svetlana

last: Burmakina

first: Sarah

last: Belisle

first: Sean

last: Proll

first: Marcus

last: Korth

first: Adolfo

last: Garcia-Sastre


title: NS1 protein of influenza A virus and interferon

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

overall_design: Refer to individual Series


title: Gene Expression Response to Interferon Treatment at 12h and 24 in A549 cells

summary: The goal of this experiment was to use global gene expression profiling to understand human lung epithelial cellular responses to interferon treatment.

overall_design: A549 cells were treated individually with IFN-α (10 ng ml−1; Sigma I4276), IFN-β (500 U ml−1; Sigma I4151) and IFN-γ (10 ng ml−1; Sigma I32265) or mock-treated. At 12 and 24 h post-treatment, cells were harvested (n = 3 wells per condition) and total RNA was extracted and analysed by microarray. Individual well replicates were pooled for each array by combining equal masses of total RNA (n=1 array per time point for each treatment and control).


title: Female human induced pluripotent stem cells (hiPSCs)

status: Public on Jul 06 2012

first: Kiichiro

last: Tomoda

address: 1650 Owens Street

institute: The Gladstone Institutes, UCSF

summary: Female human induced pluripotent stem cell (hiPSC) lines exhibit considerable variability in X-inactivation status. Some lines maintain one transcriptionally active X chromosome (Xa) and one inactive X (Xi) from donor cells. However, hiPSC lines that have two Xas are infrequently produced. We show here Xinactivation status in female hiPSC lines depends on derivation conditions. hiPSC lines generated using the Kyoto method, which employs leukemia inhibitory factor (LIF)-expressing SNL feeders, frequently had two Xas. Lines derived on other feeders maintained an Xi. In addition, there appears to be a window in which SNL feeders promote Xi-reactivation. Upon differentiation, Xa/Xa hiPSCs silenced one X. The efficient production of Xa/Xa hiPSC lines provides unprecedented opportunities to understand human X-reactivation and inactivation.

overall_design: Gene expression patterns were compared between several human embryonic stem cell (hESC) and hiPSC lines. Gene expression ratios between genes on X and those on autosomes were calculated from each cell lines.

first: Shinya

last: Yamanaka

first: Barbara

last: Panning

first: Kazutoshi

last: Takahashi

first: Megumi

last: Narita


title: Transcriptional profiles of transgenic ALK^F1174L/MYCN vs. MYCN tumors

status: Public on Jul 05 2012

city: Sutton

first: Teeara

last: Berry

state: Surrey

address: 15 Cotswold Road

department: Paediatric Oncology

institute: The Institute of Cancer Research

summary: The ALK^F1174L mutation is associated with intrinsic and acquired resistance to crizotinib and cosegregates with MYCN in neuroblastoma. In this study, we generated a mouse model overexpressing ALK^F1174L in the neural crest. Comapred to mice expressing ALK^F1174L or MYCN alone, combined expression of the two aberrations led to development of neuroblastoma with a shorter latency and higher penetrance. Here, we evaluated the transcriptional profiles of MYCN-driven neuroblastomas with or without the expression of ALK^F1174L to determine the pathogenic consequences of the ALK^F1174L/MYCN interaction in neuroblastoma.

overall_design: 10 mice were analysed in this study. Five ALK^F1174L/MYCN tumors were compared with five MYCN tumors. Total RNA was extracted, samples were labeled and processed using the Agilent Low Input Quick Amp two color Cy3(sample) and Cy5 (mouse reference) labeling kit and hybridized to Agilent SurePrint G3 Mouse Gene Expression arrays.


title: Gene expression data of Ms4a8a transfected Raw 264.7 macrophage-like cells

status: Public on Jul 01 2012

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
The CD20-homolog Ms4a8a was identified as a novel molecule of tumor-associated macrophages directly enhancing tumor growth. In addition, Ms4a8a is expressed in typical M2-dominated pathologies as late stage Trypanosoma congolense and Taenia crassiceps infections. For its induction a complex stimulation with pro- and antiinflammatory mediators is necessary. In this study we analysed how forced over-expression of Ms4a8a modulates the TLR4 response of RAW264.7 macrophages.
We used microarrays to assess gene regulatory functions of Ms4a8a in Raw264.7 macrophages

overall_design: A recombinant Ms4a8a cDNA was amplified by PCR (primer: Ms4a8a-SpeI-fw 5’ATCGAATTCACTAGTAGCAAAGAGTTGGGAACCGGAGCAAGA3’ and Ms4a8a-NotI-rv: 5’ATATGCGGCCGCTAGAGCATCTTTAT3’) from Ms4a8a cDNA RZPDp981B0530D (IMAGE ID 905005), purified on agarose gel and subcloned after digestion with SpeI and NotI restriction enzymes into the expression vector pEF6/V5-His Topo (Invitrogen) according to standard molecular biology protocols. After confirming sequence identity, we transfected RAW264.7 cells with Ms4a8a vector DNA using Lipofectamine 2000 (Invitrogen) transfection reagent. Transfectants were selected by resistance to blasticidin (Invitrogen). Raw264.7Ms4a8a clone K8 with recombinant Ms4a4a expression were propagated. As a negative control, a vector-transfected RAW264.7mock (clone K3) was selected under parallel culture conditions.

first: Astrid

last: Schmieder

first: Kai

last: Schledzewski


title: Development of gene expression signatures for mesenchymal stem cells from neuroblastoma patients

city: Majadahonda

first: Javier

last: Garcia-Castro

state: Madrid

address: Ctra. Majadahonda-Pozuelo km 2,2

department: Centro Nacional de Microbiología

institute: Instituto de Salud Carlos III

summary: To obtain genetic evidence about the interaction between MSCs and metastatic NB cancer cells in bone marrow (BM), we isolated bone marrow-derived MSCs from children with NB and compared their global expression patterns with MSCs obtained from normal pediatric donors using the Agilent 44K microarrays.

overall_design: A total of eight different donors (four NB patients and four healthy donors) were analyzed and three independent microarrays hybridizations were performed for each donor.

last: García Castro

first: Miguel

last: Rodríguez Milla