title: Isolation and Characterization of a Novel Population of Pluripotent Stem Cells Derived from Human Adipose Tissue

status: Public on Apr 24 2013

city: Washington

first: Saleh

middle: Gamal

last: Heneidi

state: DC

address: 3900 Reservoir Rd, NW, SE404 Med-Dent Building

department: Department of Pharmacology and Physiology

institute: Georgetown University Medical Center

summary: Transcriptional comparison of two subpopulations of stem cells isolated from lipoaspirated human adipose tissue, profiling Adipose Stem Cells (ASCs) and Multilineage Differentiating Stress-Enduring Adipose Tissue cells (MUSE-ATs). Experiments focused in the isolation and characterization of a new population of adipose tissue (AT) derived pluripotent stem cells, termed MUSE-ATs, which are isolated using severe cellular stress conditions, including long-term exposure to the proteolytic enzyme collagenase, serum deprivation, low temperatures and hypoxia. Under these conditions, a homogenous, highly purified population of Muse-AT cells is isolated without the utilization of cell sorting methods. The goal of this experiment was to characterize MUSE-ATs, as well as compare them to the endogenous subpopulation of ASCs for reference.

overall_design: Single condition experiment, MUSE-ATs vs. ASCs. Biological replicates: 3 MUSE-ATs replicates, 3 ASCs replicates for reference.

first: Ariel

last: Simerman

first: Erica

last: Keller

first: Prapti

last: Singh

first: XinMin

last: Le

first: Gregorio

last: Chazenbalk


title: Profiling of human CD4+ T subsets identifies a Th2-specific non-coding RNA GATA3-AS1

status: Public on Jun 01 2013

city: Xuzhou

first: Hui

last: Wang

state: Jiangsu

address: 209 Tongshan Rd

country: China

institute: Xuzhou Medical University

summary: Host defense against diverse pathogens involves the recruitment and differentiation of CD4+ T effector subsets including T helper 1 (Th1), Th2, Th17 and induced regulatory T (Treg) cells. Surface phenotype studies have revealed subset-specific surface markers for the identification and purification of human primary CD4+ T effector subsets. In the present study, we aimed to characterize the mRNA and large intergenic non-coding RNA (lincRNA) expression differences between human primary CD4+ T effector subsets and identify potential subset-specific genes. To achieve this goal, mRNA and lincRNA microarray profiling of flow cytometry-sorted human primary Th1, Th2, Th17 and Treg cells was performed. Principal component and pathway analyses revealed subset-specific gene expression patterns. A Th2-specific lincRNA, GATA3-AS1, also termed FLJ45983, was identified in primary immune cells and tissues, as well as in in vitro polarized CD4+ T effector subsets. Further analysis showed that GATA3-AS1 was a potential diagnostic marker in allergy, a Th2-associated disease. This first systematic genome-wide analysis of gene expression differences between primary CD4+ T effector subsets may help to identify novel regulatory protein-coding genes and lincRNAs regulating CD4+ T cell subset differentiation, as well as potential diagnostic markers. As an example, we identified a GATA3-associated Th2-specific marker lincRNA GATA3-AS1.

overall_design: Gene expression microarray analysis of flow-cytometry sorted human primary naïve CD4+ T cells, CD4+ T central memory cells, Th1, Th2, Th17 and Treg cells from buffy coat of four healthy controls  Gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8X60K microarray.

first: Huan

last: Zhang

first: Colm

middle: E

last: Nestor

first: Shuli

last: Zhao

first: Antonio

last: Lentini

first: Barbara

last: Bohle

first: Mikael

last: Benson


title: Gene-expression comparison of human iPS cells

status: Public on Mar 22 2013

city: Kyoto

first: Haruhisa

last: Inoue

state: Kyoto

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

country: Japan

institute: Kyoto University

summary:
We generated 10 human iPS-cell clones.
We used microarray to evaluate global gene expression pattern, comparing with human ES cell and fibroblast

overall_design: Fibroblast, human ES cell, 10 clones of iPS cells

first: Takayuki

last: Kondo


title: Low- and High-Grade Mucoepidermoid Carcinomas have different genomic profiles and CRTC1-MAML2 Fusion Gene Status

status: Public on Dec 31 2012

city: Gotenburg

first: Marta

last: Persson

address: Box 425

country: Sweden

institute: Sahlgrenska Cancer Center

summary: Using high-resolution oligonucleotide arrayCGH, FISH, and RT-PCR we have performed a comprehensive analysis of genomic imbalances, and CRTC1-MAML2 gene fusion status in a series of 28 well characterized mucoepidermoid carcinomas (MECs) with the aims to identify distinct differences in genomic profiles and CRTC1-MAML2 gene fusion status between low- and high-grade MECs.

overall_design: High-resolution aCGH (44K/244K) on fresh frozen and paraffin embedded tissue from 28 well-characterized MECs.

first: Kowan

middle: J

last: Jee

first: Kristiina

last: Heikinheimo

first: Fabricio

last: Passador-Santos

first: Katri

last: Aro

first: Sakari

last: Knuutila

first: Edward

middle: W

last: Odell

first: Antti

last: Mäkitie

first: Kaarina

last: Sundelin

first: Göran

last: Stenman

first: Ilmo

last: Leivo


title: Folate and vitamin B12 imbalance induces endoplasmic reticulum stress and cholesterol biosynthesis gene expression in human adipocytes

status: Public on Dec 30 2012

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

country: United Kingdom

institute: The Genome Analysis Centre

summary:
Rationale: Low B12 has been shown to play an important role in the prediction of metabolic risk, but its significance and mechanism in the development of adiposity and adipose tissue dysfunction is largely unknown.

Objective: To investigate the role of B12 and folic acid in the development of adipocyte dysfunction.

Methods and Results: Microarray analysis of human adipocytes (CHUB-S7 cell line) cultured and differentiated in customised media with varying concentrations of B12 and folic acid led to the identification of two important pathways: cholesterol synthesis and unfolded protein response (UPR). Adipocytes cultured in media with low B12 (150 pmol/L) or no B12 had increased intracellular total cholesterol, higher secreted homocysteine levels, induced UPR and reduced glucose uptake capacity compared to adipocytes cultured in normal media with higher B12. The folate concentrations had either no or little effect on the measured functions. Further analysis of these adipocytes for overall DNA methylation showed that the promoter regions of sterol regulatory element-binding transcription factor 1 (SREBF1) and low density lipoprotein receptor (LDLR) were hypomethylated in the low and no B12 conditions. The SREB proteins (SREBP1 and 2) and mRNA expressions (SREBF1 and LDLR) were also increased in the same conditions.

Conclusion: The data suggest that low B12 can lead to adipocyte dysfunction by inducing excess cholesterol biosynthesis, homocysteine production and induction of UPR and overall adipocyte dysfunction. Both of these pathways and adipocyte dysfunction play a significant role in the development of cardiovascular diseases.

overall_design: Independent replicate samples of the human adipocyte cell line CHUB-S7 were treated with four different concentrations of B12 and folate.

first: Antonysunil

last: Adaikalakoteswari

first: Ciara

middle: M

last: McCarthy

middle: D

first: Philip

last: Voyias

first: Alison

middle: L

last: Harte

middle: G

last: McTernan

first: Sudhesh

last: Kumar

first: Ponnusamy

last: Saravanan

first: Gyanendra

last: Tripathi


title: Human hepatic stellate cell line LX-2 activated under acidic culture condition

status: Public on Jul 29 2013

city: Shanghai

first: Wenxin

last: Qin

address: No. 25/Ln 2200 Xie-Tu Road

institute: Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine

summary:
We found that the number of tumor-infiltrating myofibroblasts was positively correlated to tumor acidification status in hepatocellular carcinoma (HCC). Hepatic stellate cells (HSCs), the predominant precursors of liver myofibroblasts, were activated and transdifferentiated into myofibroblasts under acidic culture condition.
To identify the molecular phenotype of LX-2 cells in acidic culture conditions, we further conducted a gene expression profile analysis.

overall_design: LX-2 cells cultured in pH 7.2 or pH 6.2 medium separately for six days was used in gene expression microarray analysis.

first: Jin

last: Song


title: Transcription profile of adipose-resident macrophages and mesenchymal stem cells.

city: Tsukuba

first: Hisako

last: Ishimine

state: Japan Ibaraki

address: higashi1-1-1 Tsukuba central 4

department: Research Center for Stem Cell Engineering

institute: National Institute of Advanced Industrial Science and Technology

summary: It is commonly-recognized that hematopoietic cells residing in adipose tissue (AT) exhibit a broad range of physiological functions for maintenance of homeostasis and remodeling and repair of tissues aside from the involvement in inflammation. We evaluated the cell composition of hematopoietic cells in human non-obese AT and analyzed AT-resident macrophages in detail.

overall_design: Liposuction aspirates were obtained from healthy donors undergoing liposuction of the abdomen and thighs. CD34-positive AT resident macrophages (ATMs), CD34-negative ATMs and adipose stromal cells were sorted from aspirated AT by a multiparameter fluorescent-activated cell sorter. Circulating monocytes were also sorted from peripheral blood.These 4 condition were analysed transcription profile.

first: Hitomi

last: Eto

first: Akira

last: Kurisaki

first: Noriyuki

last: Aoi

first: Harunosuke

last: Kato

first: Kentaro

last: Doi

first: Shinichiro

last: Kuno

first: Hiromu

last: Sugino

first: Kotaro

last: Yoshimura


title: Therapeutic effect of γ-secretase inhibition in KrasG12V-driven non-small cell lung carcinoma through derepression of DUSP1 phosphatase and inhibition of ERK

status: Public on Dec 01 2012

city: Madrid

first: Antonio

last: Maraver

state: Madrid

address: Calle Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas

summary: We have investigated the role of the Notch pathway in the generation and maintenance of KrasG12V-driven non-small cell lung carcinomas (NSCLCs). We demonstrate by genetic means that γ-secretase and Rbpj activities are both essential in the formation of NSCLCs. Interestingly, pharmacologic treatment of mice carrying endogenous NSCLCs with a γ-secretase inhibitor (GSI) blocks cancer growth and induces partial regression. Treated cancers show a reduction in Hes1 levels, reduced phosphorylated Erk, decreased proliferation and higher apoptosis. We demonstrate that HES1 directly binds and represses the promoter of DUSP1, a dual phosphatase with activity against phospho-ERK, and this repression is relieved by GSI treatment both in mouse and human NSCLCs. Our data provide proof for the in vivo therapeutic potential of γ-secretase inhibitors in primary NSCLCs and provide a mechanistic explanation for its therapeutical effect.

overall_design: We have included 6 samples. 3 with vehicle and 3 with the gamma-secretase inhibitor DAPT and we compare both groups.

first: Pablo

last: Fernández-Marcos

first: Daniel

last: Herranz

first: Maribel

last: Muñoz-Martin

first: Gonzalo

last: Gomez-Lopez

first: Marta

last: Cañamero

first: Francisca

last: Mulero

first: Diego

last: Megías

last: Sanchez-Carbayo

first: Jie

last: Shen

first: Montserrat

last: Sanchez-Cespedes

first: Teresa

last: Palomero

first: Adolfo

last: Ferrando

first: Manuel

last: Serrano


title: Gene expression profiling of FUT8 knockdown CL1-5 cells

status: Public on Dec 07 2012

city: Taipei

first: Chi-Huey

last: Wong

address: 128, Academia Road, Section 2,

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary: Overexpression of fucosyltransferase 8 (FUT8) is found in many cancers including liver, ovarian, thyroid, colorectal and non-small cell lung cancers. Unlike other FUTs which are functionally redundant, FUT8 is the only enzyme responsible for the alpha1,6-linked fucosylation (core fucosylation) by adding fucose to the innermost GlcNAc residue of an N-linked glycan. A growing body of evidence indicates that core fucosylation is important for regulating protein functions, such as EGFR, TGF beta receptor and integrins. To understand the downstream molecular events in response to the global alteration of core fucosylation during cancer progression, microarray analysis was employed to profile the changes in gene expression following FUT8 silencing. The genes significantly (2-fold, P<0.01) changed in CL1-5/shFUT8 cells were selected for functional annotations using a Gene Ontology database. The result revealed that many genes involved in cell adhesion, motility, growth, angiogenesis, and inflammation were under the control of core fucosylation.

overall_design: In this experiment, the gene expression profile of two stable FUT8 knockdown clones of CL1-5 cells, CL1-5/shFUT8-1 and CL1-5/shFUT8-2, were compare with CL1-5/Control cells. A total of eight samples were analyzed, including four CL1-5/Control vs. CL1-5/shFUT8-1 and four CL1-5/Control vs. C1-5/shFUT8-2. The biological replicates for each cell lines were four.

first: Chien-Yu

last: Chen

first: Tsui-Ling

last: Hsu


title: The NIH Human Pluripotent Stem Cell Database (Agilent, cgh)

status: Public on Oct 31 2012

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

country: USA

institute: NINDS/NIH

type: Genome variation profiling by genome tiling array

summary: Array comparative genomic hybridization was performed on DNA samples matched to the RNA samples included in the NIH Human Pluripotent Stem Cell Database (Series GSE32923). Twenty two undifferentiated human embryonic stem cell lines were analyzed. Expanded descriptions of methods used are available at: http://stemcelldb.nih.gov.

overall_design: 22 hybridizations: 10 human male ESC (UNDIFFerentiated) lines vs human male reference, 12 human female ESC (UNDIFFerentiated) lines vs human female reference.

first: Barbara

middle: S

last: Mallon

first: Josh

last: Chenoweth

first: Rebecca

last: Hamilton

first: Paul

last: Tesar

first: Amarendra

last: Yavatkar

first: Leonard

last: Tyson

first: Yang

middle: C

last: Fann

first: Kye

middle: Y

last: Park

first: Kevin

first: Ronald

last: McKay


title: Genomic imbalances in BCL1/JH t(11;14)(q13;q32) positive multiple myeloma

city: Kuala Lumpur

first: Ivyna

middle: PN

last: Bong

state: Kuala Lumpur

address: Jalan Pahang

department: Cancer Research Centre

country: Malaysia

institute: Institute for Medical Research

summary: The aim of this study is to determine copy number variations in the multiple myeloma patients, which were positive for BCL1/JH t(11;14)(q13;q32) translocation. Identification of common chromosomal aberrations representing the t(11;14)(q13;q32) subtype is possible by comparing the microarray data across all the samples under studied.

overall_design: Eight multiple myeloma samples were analyzed. Each sample was compared against normal control (match with patient's race and gender), which was pooled from ten healthy individuals.

first: P

middle: N

first: K

last: Chang

first: Z

last: Zakaria


title: The HER2 amplicon includes several genes required for the growth and survival of HER2 positive breast cancer cells

city: Helsinki

first: Henrik

last: Edgren

address: Tukholmankatu 8

country: Finland

institute: Institute for Molecular Medicine, University of Helsinki

summary: Array-CGH experiments of HER2+ breast cancer cell lines grown under standard conditions.

overall_design: All hybridizations performed using pooled normal female DNA as reference. 11 cell lines profiled in total, 10 HER2+, 1 HER2-. Each was hybridized once on an Agilent 244k aCGH microarray.

first: Kristine

middle: K

last: Sahlberg

first: Vesa

last: Hongisto


title: Transcriptional profiling of hypoxic cells and identification of HEXIM1-dependent genes.

status: Public on Sep 21 2012

city: Tokyo

first: Olga

middle: Sergeevna

last: Safronova

address: Bunkyo-ku, Yushima, 1-5-45

department: Cellular Physiological Chemistry

institute: Tokyo Medical and Dental University

summary:
To identify primary response genes (PRGs) that were differently expressed within 1 hr of hypoxia exposure, we performed global transcriptional profiling using the Agilent Technologies SurePrint G3 Human GE Microarray .
To identify Hexim1-dependent genes, we compare profiles of hypoxia PRGs in cells transfected with control or Hexim1 targeting double-strand siRNA

overall_design: HeLa cells were transfected with control and HEXIM1-targeted double-strand siRNA and 48 hr after treated with IL-1beta in combination with normoxia or hypoxia (5% CO2, 0.5% O2, balanced with N2)  O for 1 hr.

first: Ikuo

last: Morita


title: Interplay between AP-1 and ERalpha in regulating gene expression and proliferation networks in breast cancer cells

status: Public on Aug 06 2012

city: Stockholm

first: Chunyan

last: Zhao

address: Hälsovägen 7-9

department: Biosciences and Nutrition

institute: Karolinska Institute

summary: Estrogen receptor alpha (ERalpha) is a ligand-dependent transcription factor that plays an important role in breast cancer. Estrogen-dependent gene regulation by ERalpha can be mediated by interaction with other DNA-binding proteins, such as activator protein-1 (AP-1). The nature of such interactions in mediating the estrogen response in breast cancer cells remains unclear. Here we show that knockdown of c-Fos, a component of the transcription factor AP-1, attenuates the expression of 37% of all estrogen-regulated genes, suggesting that AP-1 is a fundamental factor for ERalpha-mediated transcription. Additionally, knockdown of c-Fos affected the expression of a number of genes that were not regulated by estrogen. Pathway analysis reveals that silencing of c-Fos downregulates an E2F1-dependent pro-proliferative gene network. Thus, modulation of the E2F1 pathway by c-Fos represents a novel mechanism by which c-Fos enhances breast cancer cell proliferation. Furthermore, we show that c-Fos and ERalpha can cooperate in regulating E2F1 gene expression by binding to regulatory elements in the E2F1 promoter. To start to dissect the molecular details of the cross-talk between AP-1 and estrogen signaling, we identify a novel ERalpha/AP-1 target, PKIB (cAMP-dependent protein kinase inhibitor-beta), which is overexpressed in ERalpha-positive breast cancer tissues. Knockdown of PKIB by siRNA results in drastic growth suppression of breast cancer cells. Collectively, our findings support AP-1 as a critical factor that governs estrogen-dependent gene expression and breast cancer proliferation programs.

overall_design: MCF-7 cells were transfected with a control siRNA or with the pool of siRNAs targeting c-Fos for 72 h and were then treated with vehicle or E2 for 24 h, and global gene expression profiles were assessed. Three or four biological replicates were used for each group.

first: Karin

last: Dahlman-Wright

first: Yichun

last: Qiao

first: Philip

last: Jonsson

first: Cecilia

last: Williams

first: Jan-Åke

last: Gustafsson


title: Effects of DNA methyltransferase inhibitors (DNMTIs) on MDS-derived cell lines

status: Public on Sep 01 2012

first: Akira

last: Yokoi

state: Ibaraki

address: Tokodai 5-1-3

department: Oncology PCU

institute: Eisai Co., Ltd

summary: To further investigate the action mechanisms of decitabine (DAC), the molecular pathways regulated by DAC were explored using the gene expression profile of MDS-L cells treated with 4 nM DAC or DMSO for 7 days. Genes whose expression changed by more than 2.0-fold following drug treatment were defined as regulated genes. 956 genes were up-regulated and 461 genes down-regulated in MDS-L cells treated with DAC (4 nM) as compared with the control. Gene expression profiling suggested that DAC significantly affects various gene biogroups, including cellular movement, inflammatory response, hematological system development and function, hematopoiesis, and cell death.

overall_design: Decitabine-induced gene expression in MDS-L cells was measured after 7 days exposure at dose of 4 nM. Three independent samples.

first: Mai

last: Uesugi

first: Takayuki

last: Tsujioka


title: Evidence for a Crucial Role of a Host Non-coding RNA in Influenza A Virus Replication

status: Public on Jan 29 2014

city: Berlin

first: Carla

last: Winterling

address: Charitéplatz 1

country: Germany

institute: Max Planck Institute for Infection Biology

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

overall_design: Refer to individual Series

first: Fernando

last: Garcia

first: Manuel

last: Koch

first: Alexander

last: Karlas

first: Max

last: Köppel

first: Thomas

middle: F

last: Meyer


title: Genomic and phenotypic alterations of  the neuronal-like cells derived from the human embryonal carcinoma stem cells (NT2) caused by exposure to the organophosphorus compounds paraoxon and mipafox

status: Public on Oct 18 2012

city: Varese (VA)

first: Marco

last: Fabbri

address: via dunant 5

country: Italy

institute: Università dell'Insubria

summary:
hNT2 under neurodifferentiation were exposed during 4 days to 1 µM of the non-neuropathic organophosphorus compound paraoxon and 5 µM of the neuropathic organophosphorus compound and afterwards transcriptomics were analysed and compared regarding control non-exposed cells
Exposure to paraoxon caused alteration of 137 genes while only a single gene was altered after exposure to mipafox

overall_design: Comparing two experimental conditions: control versus paraoxon or mipafox exposed cells. Three biological replicates.

first: David

last: Pamies

first: Miguel

middle: A

last: Sogorb

first: Laura

last: Gribaldo

first: Angelo

last: Collotta

first: Bibiana

last: Scelfo

first: Eugenio

last: Vilanova

first: Georgina

last: Harris

first: Anna

last: Bal-Price


title: Expression data from Disulfiram or 5-FU treated tumor-initiating hepatocellular carcinoma (HCC) cells.

status: Public on Nov 16 2012

city: Chiba

first: Tetsuhiro

last: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Gastroenterology and Nephrology

institute: Graduate School of Medicine, Chiba University

summary: Cancer stem cells (CSCs) or tumor-initiating cells (TICs) organize a cellular hierarchy in a similar fashion to normal stem cell systems and exhibit high tumorigenic activity in xenograft transplantation assay. Disulfiram (DSF) could preferentially eradicate TICs, but the molecular machinery of its effect against TICs still remains largely unknown. We found that flow cytometric analyses showed that DSF but not 5-FU drastically reduces the number of tumor-initiating HCC cells. We conducted microarray analyses to examine gene expression profiling in DSF-treated tumor-initiating HCC cells.

overall_design: Purified EpCAM-positive HCC cells treated with Disulfiram or 5-FU were subjected to RNA extraction and hybridization on Agilent microarrays. Data were obtained for tripricate samples from three independent experiments.

first: Atsushi

last: Iwama

first: Osamu

last: Yokosuka


title: Human ALL Cell line RS4;11: Control vs. VE-465 treated

status: Public on Nov 30 2012

city: Tainan

first: Ya-Ping

last: Chen

address: No. 138, Sheng-Li Road

department: Internal Medicine

institute: National Cheng Kung University

summary: Transcriptional profiling of human acute lymphoblastic leukemia cell lines RS4;11: compare untreated RS4;11 with RS4;11 treated with VE-465. The goal was to determine the effects of VE-465 on global gene expression in RS4;11.

overall_design: VE-465 induced gene expression in RS4;11 was measured at 48 hours after exposure to doses of 0 and 200 nM VE-465. Three independent experiments were performed.

first: Liang-Yi

last: Hung

first: Tsai-Yun


title: Analysis of impact of a novel RNA gene named Papillary Thyroid Carcinoma Susceptibility 3 (PTCSC3) on gene expression in papillary thyroid carcinoma cell line cells (TPC-1)

status: Public on May 01 2012

city: Columbus

first: Jaroslaw

middle: Piotr

last: Jendrzejewski

state: Ohio

address: 460W. 12th Avenue

department: Comprehensive Cancer Center

institute: The Ohio State University

summary: Genome-wide gene expression analysis in TPC-1 cells transfected with and without expression construct for PTCSC3 .

overall_design: TPC-1 cells were transiently transfected in quadruplicate with an empty vector (pcDNA3) and with the expression vector harboring cDNA for PTCSC3. After 24 hours from transfection total RNA was extracted and used for microarray expreiment.

first: Huiling

last: He

first: Hanna

last: Radomska

first: Wei

last: Li

first: Jerneja

last: Tomsic

first: Sandya

last: Liyanarachchi

first: Ramana

middle: V

last: Davuluri

first: Rebecca

last: Nagy

first: Albert

last: de la Chapelle


title: AGS cells infected with Epstein Barr Virus

status: Public on May 08 2012

city: Chapel Hill

first: Aron

last: Marquitz

state: NC

address: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Gene expression profile of AGS gastric carcinoma cell line infected in vitro with Epstein-Barr Virus.  Some samples also contain are stably transfected with a dominant negative LMP1 construct.

overall_design: 8 total samples.  4 biological replicates of EBV infected cells, 2 biological replicates with EBV infected cells with LMP1DN construct, and 2 biological replicates with EBV infected cells with control vector.

first: N

last: Raab-Traub


title: Transcriptome changes affecting hedgehog and cytokine signalling in the umbilical cord in late pregnancy: implications for disease risk

status: Public on Sep 24 2012

city: Singapore

first: Joanna

middle: Dawn

last: Holbrook

address: 30 Medical Drive

department: Growth Development and Metabolism

country: Singapore

institute: Singapore Institute of Clinical Sciences

summary:
BACKGROUND: Babies born at lower gestational ages or smaller birthweights have a greater risk of poorer health in later life.   Both the causes of these sub-optimal birth outcomes and the mechanism by which the effects are transmitted over decades are the subject of extensive study.  We investigated whether a transcriptomic signature of either birthweight or gestational age could be detected in umbilical cord RNA.
METHODS: The gene expression patterns of 32 umbilical cords from Singaporean babies of Chinese ethnicity across a range of birthweights (BW, 1698-4151g) and gestational ages (GA, 35-41 weeks) were determined.  We confirmed the differential expression pattern by gestational age for 12 genes in a series of 127 umbilical cords of Chinese, Malay and Indian ethnicity.
RESULTS: We found that the transcriptome is substantially influenced by gestational age; but less so by birthweight.  We show that some of the expression changes dependent on gestational age are enriched in signal transduction pathways, such as Hedgehog and in genes with roles in cytokine signalling and angiogenesis. We show that some of the gene expression changes we report are reflected in the epigenome.
CONCLUSIONS: We studied the umbilical cord which is peripheral to disease susceptible tissues.  The results suggest that soma-wide transcriptome changes, preserved at the epigenetic level, may be a mechanism whereby birth outcomes are linked to the risk of adult metabolic and arthritic disease and suggest that greater attention be given to the association between premature birth and later disease risk.

overall_design:
8 umbilical cords form low birth weight babies, 8 umbilical cords from high birth weight babies, 14 umbilical cords from normal birth weigth babies, 7 matching the gestational ages of the low birth weigth group (norm1) and 7 matching the getsational ages of the high birth weight group (norm2).  Replicates for array, cRNA and slide spotting

REPLICATES:
biological replicate: LBW_1, LBW_2, LBW_3A, LBW_3B, LBW_3C, LBW_4, LBW_5, LBW_6, LBW_7, LBW_8A, LBW_8B
biological replicate: HBW_1, HBW_2A, HBW_2B, HBW_2C, HBW3, HBW4, HBW5, HBW6, HBW7, HBW8
biological replicate: norm1_1, norm1_2, norm1_3, norm1_4, norm1_5, norm1_7A, norm1_7B, norm1_7C, norm1_7D
biological replicate: norm2_1, norm2_2, norm2_3, norm2_4, norm2_5, norm2_6A, norm2_6B, norm2_7
technical replicate: HBW_2A, HBW_2B, HBW_2C
technical replicate: LBW_3A, LBW_3B, LBW_3C
technical replicate: LBW_8A, LBW_8B
techical replicate: norm1_7A, norm1_7B, norm1_7C, norm1_7D
technical repliacte: norm2_6A, norm2_6B


title: The gene expression pattern of bone marrow mesenchymal stem cells from patients with psoriasis

status: Public on Aug 11 2012

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

summary: Object: To study the difference of gene expression pattern of bone marrow mesenchymal stem cells (BMMSCs) between psoriatic patients, normal adults and aborted fetuses, and then to explore the influence of bone marrow mesenchymal stem cells to immune system. Methods: Bone marrow mononuclear cells (BMMNC) of 7 psoriatic patients, 4 healthy volunteers and 3 aborted fetuses were isolated and the BMMSCs were cultured using the adherent method. Gene expression of 14 samples was detected by gene microarray and the different expressed genes were analysised by SAM software. Results: 654 differentially expressed genes (66 up regulated, 588 down regulated) were detected between the psoriatic patients and normal adults, which were enriched in immune response, chemotaxis and cell adhesion etc. 2020 differentially expressed genes (888 up regulated, 1132 down regulated) were detected between the aborted fetuses and normal adults. These genes were enriched in cell cycle, cell division, immune response and MHC class II antigen etc. Conclusion: The gene expression pattern such as immune response, chemotaxis was aberrant in psoriatic BMMNCs, which was consistent with aborted fetuses in some immune related genes.

overall_design: Bone marrow mononuclear cells (BMMNC) of 7 psoriatic patients, 4 healthy volunteers and 3 aborted fetuses were isolated and the BMMSCs were cultured using the adherent method. Gene expression of 14 samples was detected by gene microarray and the different expressed genes were analyzed by SAM software.

first: Ruixia

last: Hou

first: Chong

last: Shen

first: Xin

last: Yan

first: Junqin

first: Ruifeng

last: Liu

first: Yanru

last: Jia

first: Feng

last: Dong

first: Xinhua

first: Yuanwen

last: Yang

first: Kaimin

last: Zhang


title: EGI-1 cell line treated with Saracatinib vs EGI-1 cell line untreated; EGI-1 xenograft treated with Saracatinib vs EGI-1 untreated

status: Public on Aug 03 2012

city: Biella

first: caterina

last: Peraldo Neia

state: Biella

address: via Malta 3

department: Laboratory of  Cancer Genomics

institute: Fondazione Edo ed Elvo Tempia

summary: Biliary tract carcinoma (BTC) has a poor prognosis due to limited treatment options. There is therefore urgent need to identify new targets and to design innovative therapeutic approaches. Among potential candidate molecules, we evaluated the non-receptor tyrosine kinase Src, observing promising antitumor effects of its small molecule inhibitor Saracatinib in BTC preclinical models. The presence of an active Src protein was investigated by immunohistochemistry in 19 surgical samples from BTC patients. Upon Saracatinib treatment, the phosphorylation of Src and of its downstream transducers was evaluated in the BTC cell lines TFK-1, EGI-1, HuH28 and TGBC1-TKB. The effect of Saracatinib on proliferation and migration was analyzed in these same cell lines, and its antitumor activity was essayed in EGI-1 mouse xenografts. Saracatinib-modulated transcriptome was profiled in EGI-1 cells and in tumor samples of the xenograft model. Src was activated in about 80% of the human BTC samples. In cultured BTC cell lines, low-dose Saracatinib counteracted the activation of Src and of its downstream effectors, increased the fraction of cells in G0/G1 phase, and inhibited cell migration. At high concentrations (median dose from 2.26 to 6.99 µM), Saracatinib was also capable of inhibiting BTC cell proliferation. In vivo, Saracatinib treatment resulted in delayed tumor growth, associated with an impaired vascular network. We here provide a demonstration that the targeted inhibition of Src kinase by Saracatinib is of therapeutic benefit in preclinical models of BTC. We propose our results as a basis for the design of Saracatinib-based clinical applications.

overall_design:
EGI-1 cell line treated with Saracatinib at the dose of 10 µM vs EGI-1 cell line untreated; EGI-1 xenograft treated with Saracatinib at the dose of 25 mg/Kg/die vs EGI-1 xenograft untreated
Transcriptional alteration mediated by Saracatinib in vitro and in vivo

first: Giuliana

last: Cavalloni

first: Caterina

last: Peraldo-Neia

first: Ivana

last: Sarotto

first: Loretta

last: Gammaitoni

first: Giorgia

last: Migliardi

first: Marco

last: Soster

first: Serena

last: Marchio

first: Massimo

last: Aglietta

first: Francesco

last: Leone


title: Modeling lethal prostate cancer variant with small cell carcinoma features [genomic profile]

status: Public on Jan 01 2012

city: Houston

first: Jiexin

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

summary:
Purpose: Small-cell prostate carcinoma (SCPC) morphology predicts for a distinct clinical behavior, resistance to androgen ablation, and frequent but short responses to chemotherapy. The model systems we report reflect the biology of the human disease and can be used to improve our understanding of SCPC and to develop new therapeutic strategies for it.
Experimental Design: We developed a set of CRPC xenografts and examined their fidelity to their human tumors of origin. We compared the expression and genomic profiles of SCPC and large cell neuroendocrine carcinoma (LCNEC) xenografts to those of typical prostate adenocarcinoma xenografts and used a panel of 60 human tumors to validate our findings using immunohistochemistry.
Results: We show that SCPC and LCNEC xenograft models retain high fidelity to their human tumors of origin and are characterized by a marked upregulation of UBE2C and other M-phase cell cycle genes in the absence of AR, retinoblastoma (RB1) and cyclin D1 (CCND1) expression and confirm these findings in a panel of CRPC patients’ samples. In addition, array comparative genomic hybridization of the xenografts showed that the SCPC/LCNEC tumors display more copy number variations than the adenocarcinoma counterparts and that there is amplification of the UBE2C locus and microdeletions of RB1 in a subset of these, but no AR nor CCND1 deletions. Moreover, the AR, RB1, and CCND1 promoters showed no CpG methylation in the SCPC xenografts.
Conclusion: Modeling human prostate cancer with xenografts allows in-depth and detailed studies of its underlying biology. The detailed clinical annotation of the donor tumors enables associations of anticipated relevance to be made. Futures studies in the xenografts will address the functional significance of the findings.

overall_design: Total of 6 samples

first: Ana

last: Aparicio

first: Maity

last: Sankar

first: Vassiliki

last: Tzelepi

first: Lu

last: Jing-Fang

first: Brittany

last: Kleb

first: Shoudan

last: Liang


title: Donor-dependent hepatic differentiation propensity among hiPSC lines.

status: Public on Jul 16 2012

city: Kyoto

first: Shinya

last: Yamanaka

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

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


summary: Hepatocytes generated from human induced pluripotent stem cells (hiPSCs) are unprecedented resources for pharmaceuticals and cell therapy. However, little attention has so far been paid to variations among hiPSC lines in terms of their hepatic differentiation. We developed an improved hepatic differentiation protocol and compared multiple hiPSC lines. This comparison indicated that the hepatic differentiation propensity varies among sibling hiPSC clones derived from the same adult human dermal fibroblasts (aHDFs). In addition, hiPSC clones derived from peripheral blood cells (PB-iPSCs) consistently showed good hepatic differentiation efficiency, whereas many hiPSC clones from adult dermal fibroblasts (aHDF-iPSCs) showed poor hepatic differentiation. However, when we compared hiPSCs from blood and dermal fibroblasts from the same individuals, we found that variations in hepatic differentiation were largely attributable to donor differences, rather than to the types of the original cells. In order to understand the molecular mechanisms underlying the observed variations in hepatic differentiation, we performed microarray analyses of sibling aHDF-iPSC clones, and aHDF- and PB-iPSC clones from the same individuals.

overall_design: Undifferentiated aHDF- and PB-iPSCs from the same individuals (two Parkinson’s disease patients (PD #1 and PD #2) and one adult healthy donor (donor91))

first: M

last: Kajiwara

last: Narita


title: Array Comparative Genomic Hybridization of Pancreatic Xenografts and Cell Lines

status: Public on Dec 15 2011

city: San Francisco

first: Alan

middle: Hunter

last: Shain

state: CA

address: 555 MISSION BAY SOUTH BLVD RM 282 # 3118

department: Pathology and Dermatology

institute: University of California San Francisco

summary: Array Comparative Genomic Hybridization (aCGH) of 70 pancreatic ductal adenocarcinoma (PDAC) samples was performed on Agilent 244K CGH arrays in order to find common genomic aberrations for cancer gene discovery. Additionally, matched expression profiling on Agilent 44K arrays was performed. Common copy number aberrations were identified in order to identify a list of putative cancer genes. Expression profiling data was used to further enrich this list of putative cancer genes for more likely candidates. Last, the most promising candidates were functionally interrogated using RNA interference-mediated knockdown to mimic loss. Well-known PDAC cancer genes were observed as amplified (KRAS and MYC) and deleted (CDKN2A, TGFBR2, SMAD4, and MAP2K4).

overall_design:
70 tumor samples (48 xenografts, 22 cell lines). 2-color arrays hybridized against a common reference pool of genomic DNA from 8 normal individuals.

This dataset represents the aCGH component of the study.

middle: H


title: Gene expressions in normal breast duct vs lobule

status: Public on Jun 30 2012

first: wang

last: liang

summary: Gene expressions were measured in 8 normal breast duct samples and 8 normal breast lobule samples from premenopausal patients using Agilent-028004 SurePrint G3 Human GE 8x60K Microarray. A total of 426 transcripts were identified as being significantly differentially expressed. Supervised hierarchical clustering based on the 426 differentially expressed genes showed distinct clustering of the duct and lobule samples.The significant enrichment analysis of GO terms for the differentially expressed genes using the R language package software demonstrated that these 426 differentially expressed genes were involved in many important biological processes, including negative regulation of low-density lipoprotein receptor biosynthetic process, response to steroid hormone stimulus and oxidation reduction. 17 differential expressed genes identified by microarray were randomly chosen for further validation using quantitative RT-PCR. As results, fold changes measured by quantitative RT-PCR were closely correlated with those measured by microarray.

overall_design: 8 normal breast duct samples vs 8 normal breast lobule samples from premenopausal patients, unpaired

first: Jian-min

last: Yang

first: Hai-jing

last: Yu

first: Qi

last: Wang

first: Wen-ping

last: LI

first: Hong-yi

last: Gao


title: Molecular crosstalk between hepatocytes and hepatic stellate cells.

status: Public on Jun 01 2012

city: Rennes

first: Cedric

last: Coulouarn

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

country: France

institute: INSERM

summary:
Aim of the study was to characterize at a molecular level (changes in transcriptomes) the crosstalk between tumor hepatocytes and activated hepatic stellate cells (HSC) in liver cancer.
This was adressed by using a coculture model system of HepaRG cell line (tumor hepatocytes, human), and LX2 cell line (HSC, human). By using genome-wide expression profiling, we demonstrated that hepatocyte-HSC crosstalk is bidirectional and results in the deregulation of functionally relevant gene networks.

overall_design: HepaRG and LX2 cells were cultured alone in serum- and DMSO-free William's E medium or together using 1 µm pore size transwell inserts which allow diffusion of media components but prevent cell migration (BD Biosciences, San Jose, CA). Triplicate experiments were performed: HepaRG (culture versus coculture), LX2 (culture versus coculture).

first: Cédric

first: Bruno

last: Clément


title: The effect on gene expression by the knockdown of lincRNAs

status: Public on Aug 02 2012

city: Sapporo

first: Masashi

last: Idogawa

institute: Sapporo Medical University

summary: To evaluate the effect on gene expression by lincRNAs, we knocked down three lincRNAs and evaluated the gene expression by microarray analysis.

overall_design: Gene expression was measured in Hep3B cells transfected with siRNAs targeting the indicated lincRNAs or negative control siRNA and infected with adenovirus expressing p53 (Ad-p53) or LacZ (Ad-LacZ).


title: DNA hypermethylation and gene expression in breast cancer: breast cancer tissues vs. normal breast tissues

status: Public on Nov 11 2011

type:
Methylation profiling by array
Expression profiling by array


title: sibling aHDF-iPSC clones derived from the same fibroblasts

overall_design: sibling aHDF-iPSC clones (201B6 and 201B7; derived from the same aHDFs)  (1) undifferentiated state (n=4, biological replicate #1-#4)  (2) CXCR4-positive cell populations sorted by flowcytometry after 7 days of endodermal differentiation (n=4, biological replicate #1-#4)  (3) CXCR4-negative cell populations sorted by flowcytometry after 7 days of endodermal differentiation (n=4, biological replicate #1-#4)


title: Glioblastoma Xenograft Comparative Genomic Hybridization Arrays

status: Public on Jul 11 2012

city: Phoenix

first: Brock

last: Armstrong

state: AZ

address: 445 N. 5th Street

department: Cancer and Cell Biology

institute: TGen

summary: DNA copy number profiling of 32 glioblastoma orthotopic xenografts

overall_design: Descriptive experiment, comparison of 39 glioblastoma tumors as orthotopic xenografts flow sorted for anueploidy

first: Mike

last: Berens


title: Comparison of expression microarray data and somatic mutation signature in primary HCC

status: Public on Mar 10 2012

city: Tokyo

first: Tatsuhiro

last: Shibata

address: 5-1-1, Tsukiji, Chuo-ku

institute: National Cancer Center

summary: Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. We sequenced and analyzed the whole genomes of primary HCCs. To examine the influence of transcription-coupled repair (TCR) on somatic substitution patterns in HCC, we performed expression microarrays analysis and compared gene expression levels and the number of substitutions in 7 HCCs.

overall_design: Seven primary HCC were analyzed and compared with somatic substituion numbers.


title: Deletion of UTX, a histone demethylase interacting with MLL2, in three patients with Kabuki syndrome.

city: Gosselies (Charleroi)

first: Bernard

last: Grisart

address: Avenue Georges Lemaitre,25

department: Centre de génétique humaine

country: Belgium

institute: Institut de pathologie et de génétique

summary: Kabuki syndrome (KS) is a rare multiple congenital anomalies/mental retardation (MCA/MR) syndrome described in 19811,2.  In 2010, exome sequencing identified MLL2 mutations in patients with KS3.  Since then, 5 studies identified a mutation in MLL2 in 56-75,6% of KS patients3-7.  Here, we describe 2 KS and 1 KS-like patient with a de novo partial or complete deletion of UTX, a histone demethylase interacting with MLL2 in gene regulation.  UTX locates on the X chromosome and we showed that the X chromosome with the deleted copy of UTX is preferentially inactivated despite the fact that UTX escapes X-inactivation.  This study unveiled deletion of UTX as a second cause of KS and highlights the growing role of histone methylase/demethylase in MCA/MR syndrome.

overall_design:
Two patients were analysed by Agilent array CGH 244K (AMADID: 014693)

Three patients DNA were analyzed by CGH on custom targeted array 44K (AMADID: 032482).  Two of them were initially analyzed using 244K Whole genome Arrays (AMADID: 014693).  One third patient was selected given suspicion of deletion in one of the targeted gene (KDM6A) as amplification of some exons performed in our lab to sequence this gene failed.

first: Damien

last: Lederer

first: Maria

last: Digilio

first: Valérie

last: Benoit

first: Marianne

last: Crespin

first: Sophie

last: Ghariani

first: Isabelle

last: Maystadt

last: Dallapiccola

first: Christine

last: Verellen-Dumoulin


title: Comparing gene expression profiles in the mammary glands of high- and low-milk-yield Holstein Friesian cows

status: Public on Nov 16 2011

city: Berlin

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

summary: Analysis of key genes and gene networks determining milk productivity of the dairy HF cows

overall_design: Transcriptomes were compared of in the mammary glands of the healthy lactating Holstein Friesian cows of the high- (average 11097 kg milk/lactation) and low- (average 6956 kg milk/lactation) milk yield.

first: Michal

last: Miller

first: Joanna

last: Goscik

first: Ewa

middle: M

last: Kosciuczuk

first: Rafal

last: Olbromski

first: Emilia

last: Bagnicka

first: Lech

last: Zwierzchowski


title: Molecular characterization of a series of 22 NF1-associated plexiform neurofibromas

status: Public on Sep 30 2011

city: Paris

first: Eric

last: Pasmant

address: Faculté de Pharmacie de Paris, 4 avenue de l’Observatoire

institute: Paris Descartes University

summary: 22 plexiform neurofibromas from 18 unrelated neurofibromatosis-type 1 patients were screened with a high resolution array-CGH. Each PNF DNA (somatic tumor DNA) was individually hybridized on Agilent whole human genome 244K microarrays (Platform GPL4091) using the matched genomic constitutional DNA (lymphocytes DNA) from the corresponding patient as reference, in order to detect tumor-specific aberrations.

overall_design: NF1-associated plexiform neurofibromas DNA vs. constitutional DNA

first: Julien

last: Masliah-Planchon

first: Ingrid

last: Laurendeau

first: Pierre

last: Wolkenstein

first: Ivan

last: Bièche

first: Béatrice

last: Parfait

first: Michel

last: Vidaud

first: Dominique


title: Whole Genome Methylation Analysis of Metastatic Castration Resistant Prostate Cancer

status: Public on Dec 06 2011

first: Terence

last: Friedlander

address: 1450 3rd Street

department: Hemotology-Oncology

institute: UCSF

summary: Relatively little is known about how changes in gene copy number (CN) and gene CpG methylation interact to affect specific pathways in metastatic castration-resistant prostate cancer (CRPC). Oligonucleotide array comparative genomic hybridization (aCGH) was performed on DNA isolated from 15 metastatic CRPC samples. Commonly aberrant genes were evaluated in a confirmatory fashion using PCR, aCGH data from primary tumors, and existing CRPC expression data. Array-based comprehensive CpG methylation was assessed on the same sample set. A total of 495 genes (79 gained, 416 deleted) were CN aberrant in ≥66% of the samples by aCGH, and 77 (9 amplified, 68 deleted) had statistically concordant expression including gain of AR and loss of PTEN and RB1. Significant CN differences were seen between the genomes of patients with AR-amplified and AR-unamplified tumors, including common loss of AR repressors in AR-unamplified tumors. The majority of CRPC samples were hypermethylated compared to benign prostate tissue. Simultaneous methylation and heterozygous gene deletion occurred in the tumor suppressor RB1 and in HSD17B2, responsible for testosterone metabolism. Establishment of a comprehensive methylation signature and coupling of epigenomic and structural analyses sheds light on the alterations that allow CRPC to circumvent hormonal therapy and may provide new drug targets for what is currently an incurable disease state.

overall_design: 15 tumor samples taken from 14 men with metastatic castration resistant prostate cancer were analyzed, including two samples from the same patient. No control samples were used for this experiment.

middle: W

first: Pamela

middle: L

last: Paris

first: Vy

last: Ngo


title: Augmented hematopoiesis in induced pluripotent stem cells derived from patients with Down syndrome.

status: Public on Nov 29 2011

city: Minato-ku

first: Yasuhiro

last: Ebihara

state: Tokyo

address: 4-6-1, Shirokanedai

institute: The Institute of Medical Science, The University of Tokyo

summary: To identify the genes, which led to the augmented hematopoiesis in DS-iPS cells, we performed gene expression profiling of D12-DS-iPS cells (DS-iPS-T32, DS-iPS-T33 and DS-iPS-T31) and control hiPS cells (253G1, 253G4 and A31) generated by 3 factors.  In the comparison of gene expression levels in each DS-iPS cell clone with the average of these in control iPS cell clones, 972 genes showed more than 2-fold increased expression, and 1118 genes showed decreased expression in all DS-iPS cell clones. Among these upregulated genes, 61 genes including GATA1 were involved in hematopoiesis-related genes according to Ingenuity Pathways Analysis (IPA). Among the above 2-fold more upregulated genes in DS-iPS cells, 18 genes were on Hsa21. The expression of RUNX1 on Hsa21, a hematopoiesis-related gene, was significantly upregulated in DS-iPS cells. The high expressions of GATA1 and RUNX1 were also identified in 4-factor DS-iPS cells.

overall_design: Gene expression in blood cells differentiated from human induced pluripotent stem cells derived from patients with Down syndrome and healthy donor was measured in 12 days after induction of differentiation. Eight cell lines were used.

first: Natsumi

last: Nishihama

first: Kiyoshi

last: Yamaguchi

first: Emiko

last: Matsuzaka


title: Primary Central Nervous System Lymphomas. A validation study of array-based Comparative Genomic Hybridization in Formalin-Fixed Paraffin-Embedded Tumor Specimens

status: Public on Apr 30 2012

city: Scottsdale

first: Esteban

last: Braggio

address: 13400 E. Shea Blvd, MCCRB-300

institute: Mayo Clinic Arizona

summary: Purpose: Only a limited number of genetic studies have been performed in primary central nervous system lymphomas (PCNSL), partly due to the rarity of the tumors and the very limited amount of available tissue.  In this report, we present the first molecular characterization of copy-number abnormalities (CNA) of newly diagnosed PCNSL by array-based comparative genomic hybridization in formalin fixed paraffin embedded (FFPE) specimens and compare the results with matched frozen tumor specimens.  Experimental design: We performed array-based comparative genomic hybridization (aCGH) in FFPE tissues from PCNSL.  Results were compared with matched paired frozen tumors.  Results: Our analysis confirmed the good to fair quality and reliability of the data generated from limited amounts of tumoral FFPE tissue.  Overall, all PCNSL cases were characterized by highly complex karyotypes with a median of 23 copy-number abnormalities (CNA) per patient (range 17-47).  Overall, 20 chromosomal regions were recurrently found in more than 40% of cases.  Deletions of 6p21, 6q, 9p21.3 and gain of 12q12-q24.33 were the commonest CNA.  Other minimal affected regions were defined, and novel recurrent CNAs affecting single genes were identified in 3q26.32 (TBL1XR1) and 8q12.1 (TOX).    Conclusions: The results obtained are encouraging.  Larger archival tissue collections can now be analyzed in order to complement the still fragmented knowledge we have of the genetic basis of the PCNSL.

overall_design: We included samples from 7 PCNSL patients. In 6 out of these 7 PCNSL patients (cases B – G), aCGH experiments were performed in DNA samples obtained from both snap-frozen and FFPE tissues for assay quality comparative purposes.  In the remaining sample (case A), only frozen sample was analyzed.

first: Rafael

last: Fonseca

first: Brian

middle: P

last: O'Neill


title: Clonal competition with alternating dominance in multiple myeloma [244kCGH]

status: Public on Mar 28 2012

first: Jonathan

middle: J

last: Keats

state: Arizona

address: 445 N. Fifth Street

department: Integrated Cancer Genomics

institute: Translational Genomics Research Institute (TGen)

summary:
Copy number and Gene expression profiling multiple myeloma patients at multiple stages of their individual clinical course
Identification of evolutionary paterns in multiple myeloma

overall_design: Copy number differences between individual CD138 purified tumor populations from multiple myeloma patients and control female using the Agilent 244A Human CGH microarray

first: P

last: Bergsagel


title: Gene expression of human skin fibroblast cells derived from hypospadias patients in response to low-dose bisphenol A exposure

status: Public on Jan 13 2012

city: tsukuba

first: Sone

last: Hideko

state: ibaraki

department: Center for Environmental Risk Research

institute: National Institute for Environmental Studies

summary: To better understand the molecular basis of the reproductive health effects of bisphenol A (BPA) on humans, a genome-wide screening was applied to identify novel targets of low-dose bisphenol A exposure in huamn skin fibroblast cells (hSFCs) derived from hypospadias patient children. Three hSFCs were collected at National Research Institute for Child Health and Development, Japan. Gene expression profiles of hSFCs were measured at 24 hours after exposure to 10nM BPA, 0.01nM 17β-estradiol (E2) and 1nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Differentially expressed genes following chemical treatments were identified by unpaired Student’s t test with P values cut off by 0.05 and fold change of more than 1.2 and selected for the network generation and pathway analysis using Ingenuity Pathways Analysis (IPA) program. As the result, 71 genes (42 downregulated and 29 upregulated), 814 genes (371 downregulated and 443 upregulated), and 824 genes (344 downregulated and 480 upregulated) were identified significantly differently expressed in response to BPA, E2, and TCDD, respectively. The network analysis indicated that the most associated network fuctions of genes genes with altered expression profile derived from microarray analysis were “Endocrine System Disorders, Gastrointestinal Disease, Genetic Disorder”, “Cellular Growth and Proliferation, Skeletal and Muscular System Development and Function, Cell Cycle”, and “Post-Translational Modification, Genetic Disorder, Hematological Disease” in response to BPA, E2, and TCDD, respectively.

overall_design: Gene expression profiles of 3 hSFCs derived from hypospadias patient children were measured at 24 hours after exposure to  10nM BPA, 0.01nM E2 and 1nM TCDD.

first: Hideko

last: Sone

first: Xian-Yang

last: Qin

first: Hiromi

last: Akanuma


title: Profile of gene expression in K562 cells exposed to  2 mM sodium valproate for 12 hours using Agilent SurePrint G3 Human GE 8x60K Microarray.

first: wang

last: liang

institute: BioChainBJ

summary: To explore the mechanism underlying anti-leukaemia effect of sodium valproate, the growth and survival of the K562 cell line were investigated using the Annexin V/PI dual staining method. Global profiles of gene expression in K562 cells exposed to sodium valproate were assessed using gene expression microarray and validated by qRT-PCR. Gene ontology analysis was performed to establish the function of differentially expressed genes. The differentially expressed genes identified by using gene expression array were further used to query the CMAP database to retrieve a ranked list of compounds that act on the same intracellular targets as sodium valproate. A significant increase in cell apoptosis was observed in valproate exposed K562 cells using flow cytometry. A total of 706 transcripts were identified as being significantly differentially expressed. Eight differentially expressed genes that might be involved in apoptosis were verified by qRT-PCR. The significant enrichment analysis of gene ontology terms for the differentially expressed genes revealed that these genes are involved in many important biological processes such as apoptosis. The connectivity map analysis showed gene expression profile in K562 cells exposed to sodium valproate observed in this study was most similar to that of HDACi and PI3K inhibitor in the connectivity map database, suggesting that sodium valproate might exert anti-leukaemic action by inhibiting HDAC as well as inhibiting PI3K pathway. In conclusion, the data obtained in this study might provide the ground for further studies to elucidate the molecular and therapeutic potential of VPA in leukaemia treatment.

overall_design: Gene expression in K562 cell line were measured after exposure to  2 mM valproate for 12 hours or left untreated as a control using Agilent SurePrint G3 Human GE 8x60K Microarray.

first: Xiang-Zhong

last: Zhang

first: Ai-Hua

last: Yin

first: Xiao-Yu

last: Zhu

first: Qian

last: Ding

first: Chun-Huai

last: Wang

first: Yun-Xian

last: Chen


title: Gene expression profiles in breast cancer: breast cancer tissues vs. normal breast tissues

summary: To screen candidate methylation markers for early detection of breast cancer, we performed methylated-CpG island recovery assay combined with CpG island array on 61982 CpG sites across 4162 genes in 10 breast tumor tissues and 10 non-tumor breast tissues. We detected 70 significantly hypermethylated genes in breast tumor tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. Direct bisulfite sequencing showed widespread methylations occurred in intragenic regions of WT1, PAX6 and ITGA4 genes and promoter region of OTX2 in breast cancer tissue. COBRA assay in independent tumor and non-tumor samples confirmed that WT1, OTX2 and PAX6 genes were hypermethylated in breast cancer tissues. To explore the relationship between methylation and gene expression, gene expression profiling analysis was performed in 8 breast tumor tissues and 8 non-tumor breast tissues. We found that some hypermethylated genes in breast cancer were not expressed in breast tissues. RT-PCR assay showed that WT1 and PITX2 were only weakly expressed in the breast tumor tissues and weren’t expressed in most non-tumor breast tissues. OTX2 and PAX6 weren’t expressed in both breast tumor tissues and non-tumor tissues.

overall_design: Unpaired experiments, breast tumor tissues vs. breast non-tumor tissues. Biological replicates: 8 breast cancer tissue replicates, 8 breast non-tumor tissue replicates.

first: Zhen-qiang

last: Lian

first: Qi

first: Wen-ping

last: Li

first: An-qin

first: Ling

last: Wu


title: Cereblon expression is required for the anti-myeloma activity of lenalidomide and pomalidomide [aCGH]

status: Public on Oct 01 2011

first: Esteban

last: Braggio

address: 13208 East Shea Boulevard, MCRB 3-024

department: Biochemistry

institute: Mayo Clinic

summary: The precise molecular mechanism of action and targets through which thalidomide and related immunomodulatory drugs (IMiDs) exert their anti-tumor effects remains unclear.  We investigated the role of cereblon (CRBN), a primary teratogenic target of thalidomide, in the anti-myeloma activity of IMiDs.  CRBN depletion is initially cytotoxic to human myeloma cells but surviving cells with stable CRBN depletion become highly resistant to both lenalidomide and pomalidomide, but not to the unrelated drugs bortezomib, dexamethasone and melphalan.  Acquired deletion of CRBN was found to be the primary genetic event differentiating isogenic MM1.S cell lines cultured to be sensitive or resistant to lenalidomide and pomalidomide.  Gene expression changes induced by lenalidomide were dramatically suppressed in the presence of CRBN depletion further demonstrating that CRBN is required for lenalidomide activity.  Downstream targets of CRBN include interferon regulatory factor 4 (IRF4) previously reported to also be a target of lenalidomide.  Patients exposed to and putatively resistant to lenalidomide had lower CRBN levels in paired samples before and after therapy.  In summary, CRBN is an essential requirement for IMiD activity, and a possible biomarker for the clinical assessment of anti-myeloma efficacy.

overall_design: We included two isogenic MM1.S cell lines, which differ in the sensibiligy to lenalidomide. We included MM1.S and MM1.S res, which were sensitive and resistant to lenalidomide, respectively.

first: Braggio

last: Esteban

first: Zhu

middle: Y

last: Xiao

first: Stewart

last: Keith


title: High-throughput sequencing of small RNAs in Nicotiana tabacum

status: Public on May 10 2011

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

institute: University of Udine

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Nicotiana tabacum tissues (including leaves, flowers and pods). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from  leaves,  flowers and pods of Nicotiana tabacum. Total RNA was isolated using the TriReagent (Molecular Research Center) for leaves and flowers, and the Plant RNA Purification Reagent (Invitrogen) for pods, and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank  Barbara Baker for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

first: Monica

last: Accerbi

first: Pamela

last: Green

first: Blake

middle: C

last: Meyers


title: Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Agilent 244K)

status: Public on Feb 17 2011

city: Vancouver

first: Tracy

last: Tucker

address: Box 153 4480 Oak Street

country: Canada

institute: University of British Columbia

summary: Clinical laboratories are adopting array comparative genomic hybridization (AGH) as a standard clinical test. A number of whole genome AGH systems are available, but little is known about the comparative performance in a clinical context.  We prospectively studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500K GeneChip SNP arrays, Agilent Human Genome 244K oligonucleotide arrays and NimbleGen 385K Whole-Genome oligonucleotide arrays. We determined whether CNVs called on these platforms were detected by Illumina Hap550 beadchips or SMRT 32K BAC whole genome tiling arrays and tested 15 of the 30 trios on Affymetrix 6.0 SNP array.  The Affymetrix 500K, Agilent and NimbleGen platforms identified 3061 autosomal and 117 X chromosome CNVs in 30 trios. 147 of these CNVs were de novo, but only 33 (22%) of the de novo CNVs were found on more than one platform. Performing genotype-phenotype correlations, we identified 7 pathogenic and 4 possibly pathogenic CNVs for MR. All 11 of these CNVs were detected by both the Agilent and NimbleGen arrays, 9 by the Affymetrix 500K and Illumina beadchips, and 5 by the SMRT BAC array. Two of the 4 pathogenic or possibly pathogenic CNVs present in the trios tested with the Affymetrix 6.0 array were identified.   Our findings demonstrate that different results are obtained with different AGH platforms and illustrate the trade-off that exists between sensitivity and specificity. The large number of apparently false positive CNV calls supports the need for validating clinically important findings with a different methodology.

overall_design: 30 trios were analysed consisting of child (proband) and both normal parents.

first: Alexandre

last: Montpetit

first: David

last: Chai

first: Susanna

last: Chan

first: Sébastien

last: Chénier

first: Bradley

last: Coe

first: Allen

last: Delaney

first: Patrice

last: Eydoux

first: Wan

last: Lam

first: Sylvie

last: Langlois

first: Emmanuelle

last: Lemyre

first: Marco

last: Marra

first: Hong

last: Qian

first: Guy

last: Rouleau

last: Vincent

first: Jacques

last: Lmichaud

first: Jan

last: Friedman


title: Human mesenchymal stem cells at 24 hours and 0.5% O2, gene expression and exon array, three independent biological replicates

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

summary: Multipotent bone marrow-derived mesenchymal stem cells (MSCs) represent a promising cell source for autologous transplantation in many human diseases. To better realize their in vivo therapeutic potential, hypoxia preconditioning has become a novel strategy to improve the survival, migration, and angiogenic capability of MSCs. To elucidate the molecular mechanisms underlying the beneficial effect of hypoxia preconditioning on MSCs, we respectively used standard expression microarray and exon microarray to investigate the global profiling of gene expression and alternative splicing in hypoxia preconditioned-MSCs, and the detection sensitivity of differential gene expression using exon microarray and standard expression microarray was compared. A total of 414 genes were identified as significantly differentially expressed using standard expression microarray, while only 72 genes were identified as significantly differentially expressed using exon microarray, suggesting that standard expression microarray should be preferred if exclusively to detect changes in gene level. Our finding generated a global profiling of gene expression and alternative splicing which may be responsible for enhanced therapeutic effect of the hypoxia preconditioned-hMSCs. Our work provides a general framework for the systematic study of stem cell biology under clinically relevant pathophysiologic conditions

overall_design: Gene expression/alternative splicing in human mesenchymal stem cells (hMSCs) isolated from human bone marrow were measured after exposure to 0.5% O2 or 21% O2 for 24 hours using  gene expression array/exon array. Three independent experiments were performed using different donors for each experiment for both gene expression array analysis and exon array analysis.

first: Xinyang

last: Hu

first: Rongrong

last: Wu

first: Feng

last: Gao

first: Xin

last: Huang

first: Zhi

last: Jiang

first: Jian'an

last: Wang


title: Advancing a Clinically Relevant Perspective of the Clonal Nature of Cancer

status: Public on Jul 04 2011

first: Michael

middle: Thomas

last: Barrett

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

summary: We used DNA content-based flow cytometry to distinguish and isolate nuclei from clonal populations in primary tissues from three disparate cancers with variable clinical histories. We then developed a methodology to adapt flow cytometrically purified nuclei samples for use with whole genome technologies including aCGH and next generation sequencing (NGS). Our results demonstrate that selected aberrations in the genomes of distinct clonal populations in each patient create clinically relevant contexts at least with respect to the cancer types profiled in this study.

overall_design: We applied DNA content based flow sorting to isolate the nuclei of clonal populations from tumor biopsies. Genomic DNA from each sorted population was amplified with phi29 polymerase. A 1ug aliquot of each amplified sample was digested with DNAse 1 then labeled with Cy5 using a Klenow-based commercial kit (Invitrogen). Each sample was hybridized with a pooled normal (46,XX) reference (Promega) to Agilent 244k CGH arrays. The use of highly purified objectively defined flow sorted populations provides high definition genomic profiles of clonal populations from pancreatic adenocarcinomas (PA), adrenal cortical carcinomas (ACC), and prostate adenocarcinomas (PC).

first: Christian

last: Ruiz

first: Alex

last: Robeson

last: Demeure

first: Jeffrey

last: Kiefer

last: Shen

first: Donna

last: Prunkard

first: Peter

middle: S

last: Rabinovitch

first: Tobias

last: Zellweger

last: Trent

first: John

last: Carpten

first: Spyro

last: Mousses

first: Lukas

last: Bubendorf

first: Daniel

last: VonHoff

middle: T


title: A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (244A)

status: Public on Jun 30 2011

city: Toronto

first: Stephen

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

institute: The Hospital for Sick Children

summary: Systematic evaluation of eleven array platforms commonly used for CNV detection to address parameters of quality and CNV calling.

overall_design: 18 Samples

first: Dalila

last: Pinto

middle: R

last: MacDonald


title: LSD1/KDM1 regulates the balance between self-renewal and differentiation in human embryonic stem cells.

status: Public on May 27 2011

city: Barcelona

first: Stephanie

last: Boue

address: Dr Aiguader 88

institute: CMRB

type: Genome binding/occupancy profiling by array

summary: Embryonic stem (ES) cells have the ability to differentiate into all the cell types of the adult organism. This unusual property has been proposed to emanate from a particular chromatin environment that simultaneously contains both H3K4 and H3K27 trimethylation marks at the regulatory regions of the developmental genes, which are thus poised for activation during differentiation following resolution of these “bivalent domains.” Our work identifies Lysine Specific Demethylase 1 (LSD1/AOF2/KDM1A) as a key histone modifier in the maintenance of  pluripotency. We show that the knock-down of LSD1 causes the differentiation of human ES cells and the induction of key endo- and mesodermal genes marked with bivalent domains. This induction correlates with an increase in the levels of H3K4 methylation at the regulatory regions of these genes. ChIP on chip analysis reveals that in human ES cells LSD1 preferentially occupies the promoters of a subset of developmental genes that contain bivalent domains that are also occupied by OCT4 and NANOG. We conclude that LSD1 contributes to maintain a subset of developmental genes in human ES in a silenced state by maintaining the critical balance between H3K4 and H3K27 methylation at the regulatory regions of these genes.

overall_design: Lsd1 binding sites in human embryonic stem cells have been determined by ChIP on chip, and gene expression changes upon Lsd1 knock down have been tracked by microarray profiling.

first: Antonio

last: Adamo

first: Stéphanie

last: Boué

first: Borja

last: Sesé

first: Julio

last: Castaño

first: Maria

last: Barrero

first: Juan-Carlos

last: Izpisúa-Belmonte


title: Amplification and overexpression of vinculin are associated with increased tumor cell proliferation and progression in advanced prostate cancer

status: Public on Feb 08 2011

city: Basel

first: Christian

last: Ruiz

address: Schoenbeinstrasse 40

department: Institute for Pathology

country: Switzerland

institute: University Hospital Basel

summary: We analyzed the 10q22 amplification in advanced prostate cancer and subjected the genes located in the common amplified region to an RNAi screen. We found vinculin as the most promising candidate gene and analyzed its protein expression on more than 400 prostate cancers by using the tissue micrarray (TMA) technology. We discovered a strong correlation between amplification of the vinculin gene and increased protein expression. Further, vinculin protein expression was strongly associated with increased tumor cell proliferation.

overall_design: We isolated DNA from four 10q22 amplified cell lines (PC-3, MFM-223, SK-BR-3, ME-180). Genomic DNA was digested with the restriction enzymes RSA I / ALU I and then labeled with Cy5 using a Klenow-based commercial kit (Invitrogen). Each sample was hybridized with a pooled normal (46,XX) reference (Promega) to Agilent 244k CGH arrays. This experiment allowed us to define the common amplified region of the 10q22 amplification.

first: David

last: Holz

first: Martin

last: Oeggerli

first: Sandra

last: Schneider

first: Irma

last: Gonzales

first: Jeffrey

last: Kiefer

first: Alexander

last: Bachmann

first: Pasi

middle: A

last: Koivisto

first: Heikki

last: Helin

first: Michael

last: Barrett

middle: O

last: Azorsa


title: Genomic analysis of marginal zone and lymphoplasmacytic lymphomas identified common and disease-specific abnormalities

status: Public on Jan 24 2012

first: Esteban

last: Braggio

summary: Lymphoplasmacytic lymphomas and marginal zone lymphomas of nodal, extra-nodal and splenic types account for 10% of non-Hodgkin lymphomas.  They are similar at the cell differentiation level, sometimes making difficult to distinguish them from other indolent non-Hodgkin lymphomas.  To better characterize their genetic basis, we performed array-based comparative genomic hybridization in 101 marginal zone lymphomas (46 MALT, 35 splenic and 20 nodal marginal zone lymphomas) and 13 lymphoplasmacytic lymphomas.  Overall, 90.1% exhibited copy-number abnormalities.  Lymphoplasmacytic lymphomas demonstrated the most complex karyotype (median=7 copy-number abnormalities), followed by MALT (4), nodal (3.5) and splenic marginal zone lymphomas (3).  A comparative analysis exposed a group of copy-number abnormalities shared by several or all the entities with few disease-specific abnormalities.  Gain of chromosomes 3, 12 and 18 and loss of 6q23-q24 (TNFAIP3) were identified in all entities.  Losses of 13q14.3 (MIRN15A-MIRN16-1) and 17p13.3-p12 (TP53) were found in lymphoplasmacytic and splenic marginal zone lymphomas; loss of 11q21-q22 (ATM) in nodal, splenic marginal zone and lymphoplasmacytic lymphomas; loss of 7q32.1-q33 in MALT, splenic and lymphoplasmacytic lymphomas.  Abnormalities affecting the NF-kB pathway were observed in 70% of MALT and lymphoplasmacytic lymphomas and 30% of splenic and nodal marginal zone lymphomas, suggesting distinct roles of this pathway in the pathogenesis/progression of these subtypes.  Elucidation of the genetic alterations contributing to the pathogenesis of these lymphomas may guide to design specific therapeutic approaches.

overall_design: One hundred fourteen patients were included in this study: 46 MALT lymphomas (22 pulmonary, 11 salivary glands, 7 lacrimal glands and 6 gastrointestinal), 35 splenic marginal zone lymphomas, 20 nodal marginal zone lymphomas and 13 non-Waldenström’s Macroglobulinemia lymphoplasmacytic lymphomas.  All cases were reviewed prior to study on paraffin sections with immunohistochemistry.  Sections of each frozen tissue used for study were also reviewed by histological examination and immunohistochemistry before was submitted for the study.

first: Rafael

last: Fonseca

first: Ahmet

last: Dogan


title: Heat shock: genomic run-on (GRO) analysis

status: Public on Apr 19 2011

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

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

overall_design: Refer to individual Series


title: RA heat-shock

summary: Within a GRO experiment, samples for mRNA amount (RA) were taken at 0, 4, 11, 16, 26 and 40 minutes after heat stress (from 25ºC to 37ºC). Analysis was done in filters also used for Transcription rate (TR) analysis of aliquots from the same cultures.

overall_design: The analysis includes 3 repeats of stress treatment of the W3030-1a strain. The same times were used for sampling in each repeat of the experiment. A single genomic DNA hybridization on every one of the filters is used for normalization between gene probes.

middle: E


title: High-resolution, genome-wide analysis of human medulloblastoma samples by array-Comparative Genomic Hybridization (aCGH)

status: Public on Jan 01 2011

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

institute: IRCCS Ospedale Policlinico San Martino

summary: Medulloblastoma (MB) is the most common pediatric brain tumor and is an aggressive neoplasia arising in the cerebellum. MB includes four major histological subsets commonly subdivided in: classic, desmoplastic, anaplastic or large-cell, and nodular. The current patients risk stratification is based on the age at diagnosis (> or < 3 years at diagnosis), the extent of residual tumor mass post-operative, and disease dissemination. An average risk is assigned to patients older than 3 years of age with minimal or no tumor residual. These patients are more than 60% of overall MBs and have an overall survival between 50-70% at 5 years. It is widely accepted that tumor aggressiveness and progression depend on genetic abnormalities.   We performed the genome-wide study, focused on classic MB belonging to pediatric patients at standard risk. We analyzed 31 MB samples using high resolution oligonucleotide Human Genome CGH 244K (Agilent Technologies). The present study may help to identify novel molecular prognostic markers useful to refining current criteria of patients´ relapse risk estimation in this subgroup of patients.

overall_design: We analyzed 31 samples of classic medulloblastoma from patients older than 3 years of age at diagnosis

first: Simona

last: Coco

first: Francesca

last: Valdora

first: Paola

last: Scaruffi

first: Sara

last: Stigliani

first: GianPaolo

last: Tonini


title: Array CGH of breast cancer cells with distinct metastatic properties

status: Public on Dec 12 2010

city: Houston

first: Xiang

last: Zhang

address: One Baylor Plaza, BCM600

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

summary: Xenograft metastases from MDA-MB-231 cells and CN34 cells at different organs were collected and yielded sub-populations that exhibited increased metastagenicity to the lung or brain. Genomic aberrations of these subpopulations were profiled and compared to the parental populations.


title: Comprehensive array CGH of normal karyotype Myelodysplastic syndrome reveals hidden recurrent and individual genomic copy number aberrations with prognostic relevance

status: Public on Jan 30 2011

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

summary: About 40% of patients with myelodysplastic syndromes (MDS) present with a normal karyotype and they are facing different courses of disease. To advance the biological understanding and find molecular prognostic markers we performed a high resolution oligonucleotide array study of 107 MDS patients (FAB) with a normal karyotype. Recurrent hidden deletions overlapping with known cytogenetic aberrations or sites of known tumor associated genes were identified in 4q24 (TET2, 2x), 5q31.2 (2x), 7q22.1 (3x) and 21q22.12 (RUNX1, 2x). One patient with a 7q22.1 had an additional 5q31.2 deletion of the AML/MDS region; the smallest deletion identified so far and includes the putative tumor suppressor (ts) genes EGR1 and CTNNA1. One TET2 deletion was homozygous and one heterozygous, with a missense mutation in the remaining allele, further supporting its role as ts gene. Besides these recurrent alterations, additional individual imbalances were found in 34 cases; in total 42/107 (39%) cases had genomic imbalances, deletions were more frequent than gains. These patients had an inferior survival as compared with the rest of the patients (P=0.002). This study emphasizes the heterogeneity of MDS but points to interesting genes which may have diagnostic and prognostic impact.

overall_design: Array CGH experiment, MDS tumor cells vs. control DNA. Total of 107 tumors.

first: Anne

last: Thiel

first: Manfred

last: Beier

first: Deborah

last: Ingenhag

first: Kati

last: Servan

first: Markus

last: Hein

first: Vera

last: Moeller

first: Beate

last: Betz

first: Barbara

last: Hildebrandt

first: Christina

last: Evers

first: Ulrich

last: Germing


title: aCGH of Pancreatic Ductal Adenocarcinoma (PDAC) Cell Line and Xenografts

status: Public on Jan 11 2011

city: San Francisco

first: Alan

middle: Hunter

last: Shain

address: 555 MISSION BAY SOUTH BLVD RM 282 # 3118

institute: University of California San Francisco

summary: PDAC tumor DNA hybridized against pooled normal genomic DNA

overall_design: DNA was extracted from tumor samples and hybridized against normal DNA in order to query copy number aberrations.


title: Recurrent 17q23.2 microdeletion flanked by segmental duplications associated with heart defects and limb abnormalities

status: Public on Dec 31 2010

city: Spokane

first: Blake

middle: C.

last: Ballif

state: WA

address: 2820 North Astor Street

department: Research & Development

institute: Signature Genomic Laboratories

summary:
[original title] Identification of recurrent microdeletion on 17q23.2 flanked by segmental duplications associated with heart defects and limb abnormalities.

Segmental duplications, are known to mediate non-allelic homologous recombination and have been suggested to be hotspots in chromosome evolution and human genomic instability. We report the identification by microarray-based comparative genomic hybridization (aCGH) of seven individuals with microdeletions of 17q23.1q23.2. The clinical information obtained from six individuals for whom medical records were available showed common features including mild to moderate developmental delay, postnatal growth retardation, eye anomalies, heart defects and hand/foot/limb abnormalities. The presence in the deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome.

overall_design:
aCGH control vs. patient, total of 7 patients
Lowest normalized log2 ratio = patient 1: -1.99; patient 2: -1.87; patient 3: -2.16; patient 4: -2.11; patient 5: -1.974802452; patient 6: -2.23; patient 7: -1.36.

first: Aaron

last: Theisen

first: Jill

last: Rosenfeld

first: Ryan

middle: N

last: Traylor

first: Julie

last: Gastier-Foster

first: Devon

last: Lamb

first: Kim

last: McBride

first: Wendy

last: Smith

first: Valerie

last: Banks

first: William

middle: B

last: Gallentine

first: Gordon

last: Gowans

first: Pamela

last: Brock

first: M

middle: K

last: Rudd

first: Margaret

last: Adam

first: Julia

last: Keene

first: Sue

last: Kang

first: Pawel

last: Stankiewicz

first: Bassem

last: Bejjani

first: Lisa

middle: G

last: Shaffer


title: CGH microarray analysis of human prostate adenocarcinoma and normal samples

status: Public on Sep 23 2010

city: South San Francisco

first: Thomas

middle: D.

last: Wu

address: 1 DNA Way

institute: Genentech, Inc.

summary: Prostate adenocarcinoma and matched adjacent normal samples were profiled for copy number with the Agilent 244A CGH Array to support a study of deep transcriptional sequencing on these samples.

overall_design: Two-condition experiment: Prostate adenocarcinoma versus matched normal from three separate patients.

middle: D

first: Somasekar

last: Seshagiri

first: Zora

last: Modrusan

first: Celina

last: Rivers


title: Genome-wide array comparative genomic hybridization (aCGH) profiling of endothelial progenitor cells, and their comparison to tumor plasma cells, in multiple myeloma

status: Public on Apr 02 2011

city: Brooklyn

first: Olcay

last: Batuman

state: NY

address: 450 Clarkson Ave, Box 20

institute: SUNY Downstate Medical Center

summary: In multiple myeloma (MM), endothelial progenitor cells (EPCs) regulate tumor angiogenesis and disease progression. EPCs from 16 newly diagnosed patients with advanced MM were examined for genomic instability by aCGH to assess chromosomal gains and losses. Data were compared to aCGH results from corresponding CD138+ tumor plasma cells from these patients.

overall_design: EPCs and tumor cells were derived from single-cell suspensions of bone marrow (BM) aspirates from newly diagnosed MM patients, and total genomic DNA was extracted for aCGH. DNA from healthy male peripheral blood mononuclear cells (PBMCs; Promega, Madison, WI) was used as the normal control DNA.

first: Marc

last: Braunstein


title: aCGH hybridization of breast cancer cell line T47D

status: Public on Jun 25 2010

city: Helsinki

first: Henrik

last: Edgren

address: Tukholmankatu 8

institute: Institute for Molecular Medicine, University of Helsinki

summary: An array CGH hybridization of breast cancer cell line T47D compared against a normal human female reference.

overall_design: One hybridization of T47D genomic DNA against a normal human female reference was performed. T47D was labeled with Cy5 and reference with Cy3.

first: Maija

last: Wolf


title: CGH analysis of triple synchronous mantle cell lymphoma, clear cell renal cell carcinoma and gastrointestinal stromal tumor

status: Public on Aug 02 2010

city: Duarte

first: Robin

last: Guo

address: 1500 E. Duarte Rd.

department: Molecular Pharmacology

institute: City of Hope

summary:
Synchronous tumors are a rare disease and the underlying mechanism is seldom discussed. Here we present a case study of synchronous primary neoplasms detected in three distinct tissues: mantle cell lymphoma (MCL), clear cell renal cell carcinoma (ccRCC) and gastrointestinal stromal tumor (GIST). MCL is one form of B-cell non-Hodgkin’s lymphoma (NHL) that affects approximately 6% of NHL patients. GIST is thought to be derived from the Interstitial Cells of Cajal, a group of mesenchymal cells in the gastrointestinal tract involved in peristaltic motor activity. ccRCC tumor cells are the most common malignancy of kidney cancer and are characterized by enlarged cytoplasms.

Genomic DNA from FFPE tumor sections and control DNA extracted from saliva were heat-fragmentated, labeled, hybridized and scanned following manufacturer’s recommendation for 244K arrays (Agilent). Raw data were background corrected and normalized in R. Nexus v4.1 (Biodiscovery) software was then used to call aberrant regions using Rank Segmentation algorithm from the processed data. Genes within aberrant regions can be indicated as copy number gain or loss accordingly.

To identify significantly enriched canonical pathways, upstream and downstream genes for several cancer-related pathways were explored in Ingenuity knowledge base (Ingenuity Systems) and Genespring GX-10 (Agilent) with their copy number change status checked in Nexus. The analysis revealed high copy-number amplifications in gene regions related to an anti-apoptotic and cell-growth promoting pathway in all three cancers.

overall_design: Genomic DNA was isolated from mantle cell lymphoma (MCL), clear cell renal cell carcinoma (ccRCC) and gastrointestinal stromal tumor (GIST) FFPE tumor sections using the WaxFreeTM DNA Extraction Kit (TrimGen). Control DNA extracted from saliva was collected using a saliva self-collecting kit (Oragene). Heat-fragmentation, one-cycle target labeling, hybridization and scanning of the DNA were performed following manufacturer’s recommendation for 244K arrays (Agilent). The arrays were scanned by using the Agilent Scanner G2505B and Agilent Feature Extraction software v10.5 to produce raw data files. Raw data were background corrected and normalized in R. Nexus v4.1 (Biodiscovery) software was then used to call aberrant regions using Rank Segmentation algorithm from the processed data. Genes within aberrant regions can be indicated as copy number gain or loss accordingly.

first: Lufen

last: Chang

first: Zheng

last: Liu

first: Arthur

last: Li

first: Qin

last: Huang

first: David

last: Ann

first: Hao-Chien

last: Wang

first: Chung-Wu

last: Lin

first: Xiwei

first: Yate-Ching

last: Yuan

first: Yun

last: Yen


title: Array comparative genomic hybridization data from RCC cell lines to study metastasis progression

status: Public on Aug 17 2010

city: New York

first: Venkata

middle: J

last: Thodima

department: Cell Biology

institute: Memorial Sloan-Kettering Cancer Center

summary: This study investigates the molecular signatures that drive Renal Cell Carcinoma (RCC) metastatic conversion using the metastatic (LM2) and non-metastatic (SN12C) RCC cell lines.

overall_design: Two-condition experiment, RCC Cell lines vs. Reference human genome DNA from normal male.

first: Miguel

last: Lopez-Lago


title: Agilent 244K aCGH data for human primary and metastatic prostate cancer samples

status: Public on Jun 24 2010

first: Barry

middle: Stephen

last: Taylor

address: 1275 York Avenue, Box #460

summary: Current knowledge of prostate cancer genomes is largely based on relatively small patient cohorts using single modality analysis platforms. Here we report concordant assessment of DNA copy number, mRNA and microRNA expression and focused exon resequencing in prostate tumors from 218 patients with primary or metastatic prostate cancer with a median of 5 years clinical follow-up, now made available as a public resource. Mutations in known, commonly mutated oncogenes and tumor suppressor genes such as PIK3CA, KRAS, BRAF and TP53 are present but generally rare. However, integrative analysis of mutations with copy number alterations (CNAs) and expression changes reveal alterations in the PI3K, RAS/RAF and androgen receptor (AR) pathways in nearly all metastatic samples and in a higher frequency of primary samples than previously suspected based on single-gene studies. Other new findings include evidence that the nuclear receptor coactivator NCOA2 functions as a driver oncogene in ~20 percent of primaries. Tumors with the androgen-driven TMPRSS2-ERG fusion were significantly associated with a small, previously unrecognized, prostate-specific 3p14 deletion that, through mRNA expression and resequencing analysis, implicates FOXP1, RYBP and SHQ1 as candidate cooperative tumor suppressors. Comparison of transcriptome and DNA copy number data from primary tumors for prognostic impact revealed that CNAs robustly define clusters of low- and high-risk disease beyond that achieved by Gleason score. In sum, this integrative genomic analysis of a substantial cohort of tumors clarifies the role of several known cancer pathways in prostate cancer, implicates several new ones, reveals a previously unappreciated role for CNAs in prognosis and provides a blueprint for clinical development of pathway inhibitors.

overall_design: Human prostate samples were profiled on Agilent 244K aCGH arrays per manufacturer's instructions. Either matched normal DNA or a pooled reference normal DNA was used as the reference.

first: Nikolaus

last: Schultz

first: Haley

last: Hieronymus

first: Charles

middle: L

last: Sawyers


title: Chromosomal aberrations of human bladder cancer cell lines

status: Public on Jan 05 2010

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

summary: In order to identify putative targets in human bladder cancer (BC) cell lines, a survey of parallel chromosomal alterations and gene expression studies in 5 BC cell lines were performed using array-CGH and microarray techniques. Predominantly gained loci were observed at 1q21.3, 8q24.2, 8q24.3, 11q13.3, and 20q13.33 in four or more of the cell lines. The focus was on the typical gain locus of 8q24.3, which has not been studied in detail for BC.

overall_design: Genomic DNAs from 5 cell lines and normal diploid cells were subjected to array CGH analysis to identify genomic alterations in the each cell lines. These DNAs were labeled with Cy5 and Cy3, respectively.


title: PAIS experiment

status: Public on May 20 2010

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

institute: KULeuven

summary:
Intimal sarcoma (IS) is a rare, malignant and aggressive tumor that shows a relentless course with a concomitant low survival rate, for which no effective treatment is available.  In this study, 21 cases of large arterial blood vessel IS were analyzed by immunohistochemistry and fluorescent in situ hydridisation (FISH), and selectively by karyotyping, array-CGH, sequencing, phospho-kinase antibody arrays and Western immunoblotting, in search for the novel diagnostic markers and potential molecular targets.  Ex vivo immunoassays were applied to test the sensitivity of IS primary tumor cells to the receptor tyrosine kinase (RTK) inhibitors imatinib and dasatinib.We demonstrated that amplification of the platelet-derived growth factor receptor alpha  (PDGFRA) is a common finding in IS,  and might be considered as a cytogenetic hallmark of this entity.  This amplification is consistently associated with PDGFRA activation.  Furthermore, the tumors reveal persistent activation of the epidermal growth factor receptor (EGFR), concurrent to PDGFRA activation.  Activated PDGFRA and EGFR frequently co-exist with amplification and overexpression of MDM2.  Ex vivo immunoassays on primary cells showed the potency of dasatinib to inhibit PDGFRA and downstream effectors in IS.  Our findings provide a rationale for investigating therapies that target PDGFRA, EGFR or MDM2 in IS.  Given the molecular heterogeneity of this tumor type and the potential crosstalk between PDGFRA and EGFR signaling pathways, targeting multiple RTKs and aberrant downstream effectors might be required to improve therapeutic outcome for patients with this disease.

Key words: intimal sarcoma, PDGFRA, EGFR, MDM2, targeted therapy, amplification

overall_design:
Genomic profiling of 8 PAIS cases for detection of chormosomal aberrations
Individual sample Against a normal control


title: Copy number variation analysis of nasopharyngeal carcinoma cell lines

status: Public on Mar 09 2010

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

institute: Taiwan National Health Research Institute

summary:
To analyze the global copy number aberrations of two nasopharyngeal carcinoma cell lines, TW01 and HONE1.
Global copy number aberrations were analyzed by using high-resolution oligoarray CGH on two NPC cell lines, TW01 and HONE1. The overviews of array CGH profiles reveal high similarity between both NPC cell lines, but the degree of copy-number alterations were more severe in TW01 than in HONE1. There were 1204 and 1513 genes with copy-number gain (CNVs with aberration score > 0.5 and number of contiguous probes ≥ 3) in TW01 and HONE1, respectively. Among them, 850 were commonly amplified in both cell lines (Gain-TH). There were 3525 genes and 926 genes with copy-number loss (CNVs with aberration score < 0.5 and number of contiguous probe ≥ 3) in TW01 and HONE1, respectively. Among them, 582 were commonly deleted in both cell lines (Loss-TH). The most prominent CNVs observed including gain on 3q26.2-q26.31, loss on 3p21.2-q12.1, 9p24.3-p21.3, and nearly the whole Y chromosome.

overall_design: Comparison experiment, genome of NPC cells vs. normal male genome (NM). Biological replicates: TW01-1 vs. NM; TW01-2 vs. NM; HONE1-1 vs. NM; HONE1-2 vs. NM.

first: C

middle: H

last: Chen